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1524 variant records found

By default, variants are sorted chronologically by year of publication, to provide a historical perspective. Readers can re-sort on any column by clicking on the column header. Click it again to sort in a descending order. To create a multiple-field sort, hold down Shift while clicking on the second, third etc relevant column headers.

WARNING! Inclusion of a variant in this table does not automatically mean that it should be used for DNA testing. Anyone contemplating the use of any of these variants for DNA testing should examine critically the relevant evidence (especially in breeds other than the breed in which the variant was first described). If it is decided to proceed, the location and orientation of the variant sequence should be checked very carefully.

Since October 2021, OMIA includes a semiautomated lift-over pipeline to facilitate updates of genomic positions to a recent reference genome position. These changes to genomic positions are not always reflected in the ‘acknowledgements’ or ‘verbal description’ fields in this table.

OMIA Variant ID	OMIA Phene-Species ID(s)	Species Name	Breed(s)	Variant Phenotype	Gene	Allele	Type of Variant	Source of Genetic Variant	Deleterious?	Reference Sequence	Chr.	g. or m.	c. or n.	p.	Verbal Description	EVA ID	Inferred EVA rsID	Year Published	PubMed ID(s)	Acknowledgements
2	OMIA:000042-9031	chicken	Wisconsin hypoalpha mutant (WHAM), United States of America (Chicken)	Analphalipoproteinaemia	ABCA1		missense	Naturally occurring variant	yes	GRCg6a	Z	g.54877918C>T	c.265G>A	p.(E89K)				2002	12364545	Variant coordinates obtained from or confirmed by EBI's Variant Effect Predictor (VEP) tool
1126	OMIA:002238-9913	cattle	Shorthorn (Cattle)	Ichthyosis, ABCA12-related	ABCA12		missense	Naturally occurring variant	yes	ARS-UCD1.2	2	g.103016791A>G	c.6776T>C	p.(L2259P)	NM_001191294.2:c.6776T>C; NP_001178223.2:p.(Leu2259Pro)		rs5334475100	2019	31568573
195	OMIA:002238-9913	cattle	Chianina (Cattle)	Ichthyosis, ABCA12-related	ABCA12		missense	Naturally occurring variant	yes	ARS-UCD1.2	2	g.103025585T>C	c.5804A>G	p.(H1935R)			rs5334474994	2008	18344998	Variant coordinates obtained from or confirmed by EBI's Some Effect Predictor (VEP) tool
1220	OMIA:002238-9913	cattle	Polled Hereford (Cattle)	Ichthyosis, ABCA12-related	ABCA12		insertion, small (<=20)	Naturally occurring variant	yes	ARS-UCD1.2	2	g.103043495_103043496insG	c.5689_5690insC	p.(S1784Ifs*33)	BTA 2:103043495–103043496insG; ENSBTAT00000004518.6:c.5689‐5690insC; ENSBTAP00000004518.6:p.(Ser1784Ilefs*33) (Eager et al., 2020)	rs3423092881	rs3423092881	2020	32567073
1379	OMIA:002238-9823	pig	Bama Xiang Zhu, China (Pig)	Ichthyosis	ABCA12		splicing	Chemical mutagenesis (ENU)	unknown	Sscrofa11.1	15	g.117250799T>C			Intronic mutation IVS49-727 A>G results in splicing alteration resulting in a 132-nt insertion and a premature stop codon (Wang et al., 2019)			2019	30925591
1050	OMIA:002179-9615	dog	Labrador Retriever	Stargardt disease 1	ABCA4		insertion, small (<=20)	Naturally occurring variant	yes	CanFam3.1	6	g.55146556dup	c.4176dup	p.(F1393Lfs*3)	Mäkeläinen et al. (2019): "ENSCAFT00000005367 exon28 4170dupC* V1390fs" Importantly, the same authors also explain in Table S3 that "The insertion is found in a cytosine mononucleotide-repeat region [55,146,550–55,146,556] and it is arbitrary at what position the actual insertion occurs. In the text we have denoted the insertion as c.4176insC, p.F1393Lfs1395)." Variant information changed to reflect HGVS nomenclature			2019	30889179
607	OMIA:001402-9615	dog	Border Collie	Adverse reaction to certain drugs	ABCB1		insertion, small (<=20)	Naturally occurring variant	yes	CanFam3.1	14	CanFam3.1			published as c.73insAAT - allele is reflected by the reference sequence CanFam3.1 and NM_001003215.2 as reference: g.13737172_13737174; c.73_75, p.N25			2010	21113104
469	OMIA:001402-9615	dog	Australian Shepherd Border Collie Collie German Shepherd Dog Longhaired whippet Miniature Australian shepherd Old English Sheepdog Shetland Sheepdog Silken windhound Waller White Swiss shepherd	Adverse reaction to certain drugs	ABCB1		deletion, small (<=20)	Naturally occurring variant	yes	CanFam3.1	14	g.13726596_13726599del	c.228_231del	p.(D77Afs*16)	NM_001003215.2; NP_001003215.2			2001	11692082	Variant information gleaned from or confirmed by Donner et al. (2016) PLoS One 11:e0161005
442	OMIA:001402-9615	dog	Border Collie	Adverse reaction to certain drugs	ABCB1		regulatory	Naturally occurring variant	no	CanFam3.1	14	g.13742402A>C			published as Canfam2 chr14:16692274T>G, c.-6-180T>G, possible regulatory variant associated with resistance to phenobarbital treatment in epileptic Border Collies	rs852787132	rs852787132	2011	21488961	Genomic coordinates in CanFam3.1 and EVA ID provided by Zoe Shmidt and Robert Kuhn.
1322	OMIA:001402-9685	domestic cat		Adverse reaction to certain drugs	ABCB1		deletion, small (<=20)	Naturally occurring variant	yes	Felis_catus_9.0	A2	g.93144355_93144356del	c.1930_1931del		NM_001171064.2; published as ABCB1:1930_1931delTC; resuling in a frameshift generating a series of stop codons immediately downstream from the deletion. The protein product is predicted to be severely truncated (~50%) and non functional. (Mealey and Burke, 2015)			2015	25660379	Genomic position in Felis_catus_9.0 provided by Leslie Lyons and Reuben Buckley.
572	OMIA:001524-9615	dog	Shetland Sheepdog	Gallbladder mucoceles	ABCB4		insertion, small (<=20)	Naturally occurring variant	yes	CanFam3.1	14	g.13584928_13584929insC	c.1660_1661insG	p.(L554Rfs)	XM_539403.6; XP_539403.3; published as c.1583_1584G, the association between this variant and disease was later disproven and this variant should not be used as a diagnostic marker for GBM (Cullen et al. 2014)			2010	20598156
1574	OMIA:002710-9615	dog	Manchester Terrier	Cardiomyopathy, dilated, ABCC9-related	ABCC9	SCDY/DCM	missense	Naturally occurring variant	unknown	Dog10K_Boxer_Tasha	27	g.21042635C>T	c.3557G>A	p.(R1186Q)	XM_022410972.2; XP_022266680.2			2023	37239348
1499	OMIA:002589-8839	Mallard		Blue eggshell	ABCG2		regulatory	Naturally occurring variant	no	BGI_duck1.0	NW_004676534.1	g.[3573054A>G;3573085A>G]			The BGI_duck1.0 reference genome represents the blue eggshell genotype.			2020	33186356
1477	OMIA:002561-9913	cattle	Deutsche Holstein Schwarzbunt, Germany (Cattle)	Infertility	ABHD16B		nonsense (stop-gain)	Naturally occurring variant	yes	ARS-UCD1.2	13	g.53957903G>A	c.652C>T	p.(Q218*)	ENSBTAT00000045249.4; ENSBTAP00000055253.1	rs468948776	rs468948776	2020	31963602
1388	OMIA:002368-9615	dog	Golden Retriever	Ichthyosis, ABHD5-related	ABHD5	ICH2	deletion, small (<=20)	Naturally occurring variant	yes	CanFam3.1	23	g.2587000_2587013del	c.1006_1019del	p.(D336Sfs*6)	XM_542689.5; XP_542689.2			2022	34791225
1504	OMIA:002594-9823	pig		N-acetyl-galactosamine intestinal concentration	ABO		deletion, gross (>20)	Naturally occurring variant	unknown		1				2.3kb deletion encompassing exon 8			2022	35477154
1177	OMIA:001089-9542	Japanese macaque		Antigen B	ABO		haplotype	Naturally occurring variant	no						Allele B reflects the peptide haplotype p.266Met + p.268Ala			2000	10984838
20	OMIA:001089-9541	crab-eating macaque		A antigen	ABO		haplotype	Naturally occurring variant	no					p.266L + p.268G	Allele A is reflected in the peptide haplotype p.266Leu + p.268Gly			1998	9583803
21	OMIA:001089-9544	Rhesus monkey		Antigen A	ABO		haplotype	Naturally occurring variant	no					p.266L + p.268G	Allele A is reflected in the peptide haplotype p.266Leu + p.268Gly			1998	9583803
1174	OMIA:001089-9544	Rhesus monkey		Antigen B	ABO		haplotype	Naturally occurring variant	no					p.266M + p.268A	Allele B is a reflection of the peptide haplotype p.266Met + p.268Ala			1998	9583803
1175	OMIA:001089-9541	crab-eating macaque		B antigen	ABO		haplotype	Naturally occurring variant	unknown					p.266M + p.268A	Allele B is a reflection of the peptide haplotype p.266Met + p.268Ala			1998	9583803
22	OMIA:001089-9579	agile gibbon		Alleles A and B	ABO		missense	Naturally occurring variant	no				c.2178C>A and c.2185G>C		Haplotype c.2178C + c.2185G is allele A; haplotype c.2178A + c.2185C is allele B			2009	19298858
23	OMIA:001089-9580	common gibbon		Blood group system ABO	ABO		missense	Naturally occurring variant	no				c.2178C>A and c.2185G>C					2009	19298858
532	OMIA:001089-9598	chimpanzee		O (lack of antigen)	ABO	O^del	deletion, small (<=20)	Naturally occurring variant	no				c.514_522delGTGCTGGAG	p.(V172-E174del)				1999	10380696
24	OMIA:001089-9598	chimpanzee		O (lack of antigen)	ABO	O^x	missense	Naturally occurring variant	no				c.791A>C	p.(Y264C)				1999	10380696
1497	OMIA:002585-9615	dog	Cavalier King Charles Spaniel	medium-chain acyl-CoA dehydrogenase	ACADM		delins, gross (>20)	Naturally occurring variant	yes	UU_Cfam_GSD_1.0	6	g.71401388_71401389delinsCATAATTCTTAGACAATATTGAGAATTAAC	c.444_445delinsGTTAATTCTCAATATTGTCTAAGAATTATG	p.(T150Ifs*6)	XM_038541645.1; XP_038397573.1			2022	36292732
972	OMIA:002140-9615	dog	German Hunting Terrier	Exercise induced metabolic myopathy	ACADVL		nonsense (stop-gain)	Naturally occurring variant	yes	CanFam3.1	5	g.32193689C>A	c.1728C>A	p.(Y576*)	XM_546581.5; XP_546581.3			2018	29491033
429	OMIA:001271-9913	cattle	Dexter (Cattle)	Bulldog calf	ACAN	BD2	regulatory	Naturally occurring variant	yes	ARS-UCD1.2	21	g.20377856C>T	c.-198C>T				rs3423095877	2007	17952705	Variant information kindly provided or confirmed by Matt McClure and Jennifer McClure from "Understanding Genetics and Complete Genetic Disease and Trait Definition (Expanded 2016 Edition)" (https://www.icbf.com/wp/?page_id=2170)
590	OMIA:001271-9913	cattle	Dexter (Cattle) Highland (Cattle)	Bulldog calf	ACAN	BD1	insertion, small (<=20)	Naturally occurring variant	yes	ARS-UCD1.2	21	g.20422104_20422105insGGCA	c.2266_2267insGGCA					2007	17952705	Variant information kindly provided or confirmed by Matt McClure and Jennifer McClure from "Understanding Genetics and Complete Genetic Disease and Trait Definition (Expanded 2016 Edition)" (https://www.icbf.com/wp/?page_id=2170)
1060	OMIA:001271-9913	cattle	Miniature Zebu, United Kingdom of Great Britain and Northern Ireland (Cattle)	Bulldog calf	ACAN		insertion, small (<=20)	Naturally occurring variant	yes	ARS-UCD1.2	21	g.20428539_20428540insC	c.5688_5689insC	p.(V1897fs*9)	cDNA position based on transcript NM_173981.2			2018	30305023
1001	OMIA:001271-9796	horse	Miniature Horse (Horse)	Dwarfism, ACAN-related	ACAN	D4	deletion, small (<=20)	Naturally occurring variant	yes	EquCab3.0	1	g.95257480_95257500del	c.7633_7653del	p.(F2545_D2551del)	220110: corrected genomic position from g.95257458_95257500del to 95257480_95257500 and updated cDNA and published protein coordinates (p.(F2017_D2023del)) based on the following transcripts: ENSECAT00000040213.1:c.7633_7653del ENSECAP00000032890.1:p.Phe2545_Cys2551del	rs1095048839		2018	30058072
788	OMIA:001271-9796	horse	Miniature Horse (Horse) Shetland Pony (Horse)	Dwarfism, ACAN-related	ACAN	D3*	missense	Naturally occurring variant	yes	EquCab3.0	1	g.95282140C>G	c.1513G>C	p.(A505P)	ENSECAT00000040213.1:c.1513G>C ENSECAP00000032890.1:p.Ala505Pro This variant was named D3* by Eberth et al. (2018)	rs1095048823	rs1095048823	2017	27942904	Variant coordinates obtained from Eberth et al. (2018) and EVA_ID link
1000	OMIA:001271-9796	horse	Miniature Horse (Horse)	Dwarfism, ACAN-related	ACAN	D2	missense	Naturally occurring variant	yes	EquCab3.0	1	g.95284530C>T		p.(V424M)			rs3091781465	2018	30058072
999	OMIA:001271-9796	horse	Miniature Horse (Horse)	Dwarfism, ACAN-related	ACAN	D1	deletion, small (<=20)	Naturally occurring variant	yes	EquCab3.0	1	g.95291271del	c.245del	p.(K82Rfs*54)	220110: changed g.95291270del to g.95291271del based on HGVS 3'rule. ENSECAT00000040213.1:c.245del ENSECAP00000032890.1:p.Lys82ArgfsTer54	rs1095048841	rs1095048841	2018	30058072
323	OMIA:000702-9031	chicken		Nanomelia	ACAN		nonsense (stop-gain)	Naturally occurring variant	yes	GRCg6a	10	g.13502829C>A	c.4537G>T	p.(E1513*)				1994	7827752	Variant coordinates obtained from or confirmed by EBI's Some Effect Predictor (VEP) tool
1045	OMIA:002177-9615	dog	Akita American Akita	Amelogenesis imperfecta, ACP4-related	ACPT		insertion, small (<=20)	Naturally occurring variant	yes	CanFam3.1	1	g.106051997dupC	c.1189dupG	p.(A397Gfs)	XM_541473.2; XP_541473.2; ACPT is a synonym of ACP4			2019	30877375
1419	OMIA:002226-9913	cattle	Brown Swiss (Cattle)	Haplotype with homozygous deficiency BH34	ACSL5	BH34	missense	Naturally occurring variant	yes	ARS-UCD1.2	26	g.32940521C>G	c.528C>G	p.(N176K)	NM_001075650.1		rs5357452907	2021	34915862
1259	OMIA:002226-9615	dog	Australian Kelpie	Intestinal lipid malabsorption	ACSL5		deletion, gross (>20)	Naturally occurring variant	yes	CanFam3.1	28	g.23380074_23483377del			NC_006610.3CFA28:g.23380074_23483377del (O/Brien et al., 2020)			2020	33106515
1073	OMIA:000388-9685	domestic cat	Domestic Shorthair	Fibrodysplasia ossificans progressiva	ACVR1		missense	Naturally occurring variant	yes	Felis_catus_9.0	C1	g.150014354C>T	c.617G>A	p.(R206H)	XM_023259334.1; XP_023115102.1			2019	31007133	Genomic position in Felis_catus_9.0 provided by Leslie Lyons and Reuben Buckley.
633	OMIA:001520-9615	dog	Glen of Imaal Terrier	Cone-rod dystrophy 3	ADAM9		deletion, gross (>20)	Naturally occurring variant	yes		16				"a deletion of exons 15 and 16 which alters the reading frame leading to a premature stop codon" in the ADAM9 gene			2010	20691256
43	OMIA:001870-9615	dog	Beagle	Glaucoma, primary open angle	ADAMTS10		missense	Naturally occurring variant	yes	CanFam3.1	20	g.53096339C>T	c.1981G>A	p.(G661R)	XM_849227.3; XP_854320.1			2011	21379321
101	OMIA:001870-9615	dog	Norwegian Elkhound	Glaucoma, primary open angle	ADAMTS10		missense	Naturally occurring variant	yes	CanFam3.1	20	g.53101896C>T	c.1159G>A	p.(A387T)	XM_849227.3; XP_854320.1			2014	25372548	Variant coordinates obtained from or confirmed by EBI's Some Effect Predictor (VEP) tool
685	OMIA:001976-9615	dog	Basset Hound	Glaucoma, primary open angle, ADAMTS17-related	ADAMTS17		deletion, small (<=20)	Naturally occurring variant	yes	CanFam3.1	3	g.40614853_40614872del	c.194_213del	p.(L68Gfs*)	XM_022416850.1; XP_022272558.1			2015	26474315
365	OMIA:000588-9615	dog	Chinese Crested Dog German Hunting Terrier Jack Russell Terrier Lancashire heeler Miniature Bull Terrier Parson Russell Terrier Patterdale Terrier Rat Terrier Sealyham Terrier Tenterfield Terrier Tibetan Terrier Toy Fox Terrier Volpino Italiano Welsh Terrier Wirehaired Fox Terrier Yorkshire Terrier	Lens luxation	ADAMTS17		splicing	Naturally occurring variant	yes	CanFam3.1	3	g.40782144G>A	c.1473+1G>A		XM_022416850.1; additional breeds reported by Gould et al. (2011)	rs1152388408	rs1152388408	2010	20375329	Variant coordinates obtained from or confirmed by EBI's Some Effect Predictor (VEP) tool
96	OMIA:001976-9615	dog	Basset Fauve de Bretagne	Glaucoma, primary open angle, ADAMTS17-related	ADAMTS17		missense	Naturally occurring variant	yes	CanFam3.1	3	g.40808345G>A	c.1552G>A	p.(G518S)	XM_022416851.1; XP_022272559.1			2015	26474315	Variant coordinates obtained from or confirmed by EBI's Some Effect Predictor (VEP) tool
1086	OMIA:001976-9615	dog	Petit Basset Griffon Vendéen	Glaucoma, primary open angle, ADAMTS17-related	ADAMTS17		inversion	Naturally occurring variant	yes	CanFam3.1	3	g.40812274_45768123inv	c.1721+2668_*4831255inv		XM_545825.4; Forman et al. (2015): "a 4.96 Mb inversion . . . with breakpoints in intron 12 of ADAMTS17 (chr3:40,812,274) and a downstream intergenic region (chr3:45,768,123) [Canfam3.1]… Analysis of RNAseq data revealed novel exon expression for ADAMTS17 due to cryptic splicing occurring 3’ of the exons located immediately upstream of the inversion event."			2015	26683476
942	OMIA:000588-9615 OMIA:001976-9615	dog	Chinese Shar-Pei	Primary open-angle glaucoma (POAG), primary lens luxation (PLL), or both	ADAMTS17		deletion, small (<=20)	Naturally occurring variant	yes	CanFam3.1	3	g.40935387_40935392del	c.3069_3074del	p.(V1024_V1025del)	XM_014112382.2; XP_013967857.1; published as c.3070_3075delCGTGGT; p.(V1025_V1026del)			2018	29287154
486	OMIA:000328-9913	cattle	Belgian Blue (Cattle)	Ehlers-Danlos syndrome, type VII (Dermatosparaxis)	ADAMTS2		delins, small (<=20)	Naturally occurring variant	yes	ARS-UCD1.2	7	g.2017035_2017051delinsAGC	c.464_480delinsAGC					1999	10417273	Variant information kindly provided or confirmed by Hubert Pausch, including information from Additional Table 6 of Jansen et al. (2013) BMC Genomics201314:446 https://doi.org/10.1186/1471-2164-14-446
1513	OMIA:000328-9615	dog	Alapaha Blue Blood Bulldog Pit Bull Terrier	Ehlers-Danlos syndrome, type VII (Dermatosparaxis)	ADAMTS2		deletion, small (<=20)	Naturally occurring variant	yes	CanFam3.1	11	g.2280117delC	c.10delC	p.(P4Rfs*175)				2022	36421833
1117	OMIA:000328-9615	dog	Doberman Pinscher	Ehlers-Danlos syndrome, type VII (Dermatosparaxis)	ADAMTS2		nonsense (stop-gain)	Naturally occurring variant	yes	CanFam3.1	11	g.2408978C>T	c.769C>T	p.(R257*)				2019	31294848
1514	OMIA:000328-9615	dog	Catahoula leopard dogs	Ehlers-Danlos syndrome, type VII (Dermatosparaxis)	ADAMTS2		missense	Genome-editing (CRISPR-Cas9)	yes	CanFam3.1	11	g.2491238G>A	c.2897G>A	p.(R966H)				2022	36421833
318	OMIA:000328-9940	sheep	Dorper (Sheep)	Ehlers-Danlos syndrome, type VII (Dermatosparaxis)	ADAMTS2		nonsense (stop-gain)	Naturally occurring variant	yes	Oar_rambouillet_v1.0	5	g.1938399G>T	c.424G>T	p.(E142*)	XM_012156230:c.424G>T, XP_012011620:p.Glu142* (Joller et al., 2017)			2012	22497338	The genomic location on Oar_rambouillet_v1.0 was determined by Katie Eager, EMAI, NSW Department of Primary Industries.
857	OMIA:000328-9940	sheep	Dorper (Sheep)	Ehlers-Danlos syndrome, type VII (Dermatosparaxis)	ADAMTS2		nonsense (stop-gain)	Naturally occurring variant	yes	Oar_rambouillet_v1.0	5	g.2088231G>A	c.805G>A	p.(V269M)	XM_012156230:c.805G>A, XP_012011620:p.Val269Met (Joller et al., 2017)			2015	25354687	The genomic location on Oar_rambouillet_v1.0 was determined by Katie Eager, EMAI, NSW Department of Primary Industries.
537	OMIA:001140-9615	dog	Nova Scotia Duck Tolling retriever	Cleft lip with or without cleft palate	ADAMTS20		deletion, small (<=20)	Naturally occurring variant	yes	CanFam3.1	27	g.10553479_10553480del	c.1358_1359del	p.(K453Ifs*4)	XM_022410988.1; XP_022266696.1; published as c.1360_1361delAA and p.(K453Ifs*3); coordinates in the table have been updated to a recent reference genome and / or transcript and HGVS nomenclature			2015	25798845	Genomic position in CanFam3.1 provided by Mateo Etcheveste and Robert Kuhn.
1163	OMIA:001562-9913	cattle	Cikasto govedo, Slovenia (Cattle)	Pulmonary hypoplasia and anasarca syndrome	ADAMTS3		missense	Naturally occurring variant	yes	ARS-UCD1.2	6	g.87462016G>A	c.1222C>T	p.(H408T)	NM_001192797.1: c.1222C>T; NP_001179726.1: p.(His408Tyr) (Häfliger et al., 2020)		rs5334475098	2020	32069517
1084	OMIA:001893-9615	dog	Norwich Terrier	Upper airway syndrome	ADAMTS3		missense	Naturally occurring variant	yes	CanFam3.1	13	g.61287796G>A	c.2786G>A	p.(R929H)				2019	31095560
60	OMIA:001509-9615	dog	Beagle	Musladin-Lueke syndrome	ADAMTSL2		missense	Naturally occurring variant	yes	CanFam3.1	9	g.49931561C>T	c.661C>T	p.(R221C)				2010	20862248	Variant coordinates obtained from or confirmed by EBI's Some Effect Predictor (VEP) tool
935	OMIA:001511-9913	cattle	Angus (Cattle)	Contractual arachnodactyly (Fawn calf syndrome)	ADAMTSL3		deletion, gross (>20)	Naturally occurring variant	yes		21				"a large (~58 kilobase pair) deletion affecting the ADAMTSL3 gene"			2014	Reference not in PubMed; see OMIA 001511-9913 for reference details
1435	OMIA:002535-9913	cattle	Brown Swiss (Cattle)	Congenital cataract	ADAMTSL4		missense	Naturally occurring variant	yes	ARS-UCD1.2	3	g.20146737C>T	c.2327G>A	p.(R776H)	NM_001101061.1; NP_001094531.1		rs5353205567	2022	35233794
466	OMIA:001577-9615	dog	Curly-coated retriever	Glycogen storage disease IIIa	AGL		deletion, small (<=20)	Naturally occurring variant	yes	CanFam3.1	6	g.50050457del	c.4223del	p.(K1408Sfs*6)	NM_001048096.1; NP_001041561.1; published as c.4223delA; genomic position adjusted to HGVS 3' rule			2007	17338148	Genomic and protein coordinates in CanFam3.1 provided by Robert Kuhn
934	OMIA:002135-9913	cattle	Angus (Cattle)	Arthrogryposis multiplex congenita, AGRN-related	AGRN		deletion, gross (>20)	Naturally occurring variant	yes		16				A 23,363 bp deletion "encompasses the entirety of the ISG15 ubiquitin-like modifier (ISG15) gene . . . one or both of the 5' regulatory region of the hairy and enhancer split 4 (HES4) and of the agrin (AGRN) gene and of the first two exons of the AGRN gene" (Beever and Marron, 2011)			2011	Reference not in PubMed; see OMIA 002135-9913 for reference details
233	OMIA:000662-9940	sheep	Romney Marsh (Sheep)	Motor neuron disease, lower	AGTPBP1		missense	Naturally occurring variant	yes	Oar_rambouillet_v1.0	2	g.35795594G>C	c.2909G>C	p.(R970P)	protein and cDNA positions are based on XP_014948529.2 and XM_015093043.2, respectively			2012	22588130	The genomic location on Oar_rambouillet_v1.0 was determined by Katie Eager, EMAI, NSW Department of Primary Industries.
75	OMIA:001672-9615	dog	Coton de Tulear	Primary hyperoxaluria type I (Oxalosis I)	AGXT		missense	Naturally occurring variant	yes	CanFam3.1	25	g.50968854G>A	c.304G>A	p.(G102S)	XP_003639939.1:p.Gly102Ser	rs397510072	rs397510072	2012	22486513	Variant coordinates obtained from or confirmed by EBI's Some Effect Predictor (VEP) tool
1252	OMIA:001672-9940	sheep	Zwartbles (Sheep)	Type 1 Primary Hyperoxaluria	AGXT		missense	Naturally occurring variant	yes	Oar_rambouillet_v1.0	1	g.801189C>T	c.584G>A	p.(C195Y)	NC_040252.1: g.801189C>T; XM_027966918.1: c.584G>A; XP_027822719.1: p.Cys195Tyr (Letko et al., 2020)			2020	33003365
1214	OMIA:001222-9685	domestic cat	Persian (Cat)	Leber congenital amaurosis	AIPL1		nonsense (stop-gain)	Naturally occurring variant	yes	Felis_catus_9.0	E1	g.940445C>T	c.577C>T	p.(R193*)	XM_023243858.1:c.577C>T			2016	27030474	The genomic location on Felis_catus_9.0 and transcript information is based on Rodney et al. 2021 (PMID: 33785770)
1094	OMIA:002205-9615	dog	Rough Collie	Recurrent inflammatory pulmonary disease	AKNA		deletion, small (<=20)	Naturally occurring variant	yes	CanFam3.1	11	g.68576241_68576244del	c.2717_2720delACAG	p.(D906Afs*173)	XM_014117950.2: c.2717_2720delACAG; XP_013973425.1:p.(Asp906Alafs*173)			2019	31357536
1240	OMIA:002250-9615	dog	Saluki	Succinic Semialdehyde Dehydrogenase Deficiency	ALDH5A1		missense	Naturally occurring variant	yes	CanFam3.1	35	g.22572768G>A	c.866G>A	p.(G288D)	XM_014110599.2: c.866G>A; XP_013966074.2: p.(Gly288Asp) (Vernau et al., 2020)			2020	32887425
1292	OMIA:002316-9685	domestic cat	American Shorthair (Cat) Exotic Shorthair (Cat) Munchkin (Cat) Scottish Fold (Cat) Sphynx (Cat)	Cardiomyopathy, hypertrophic	ALMS1		missense	Naturally occurring variant	unknown	Felis_catus_9.0	A3	g.92439157G>C	c.7384G>C	p.(G2462R)	cDNA and protein positions have been predicted using Ensemble VEP based on transcript ENSFCAT00000077013.1; variant initially reported in Sphynx cats and in a later study (Akiyama et al., 2023) identified in other breeds.			2021	33639992
1021	OMIA:002162-9615	dog	Karelian bear dog	Hypophosphatasia	ALPL		missense	Naturally occurring variant	yes	CanFam3.1	2	g.77561953A>C	c.1301T>G	p.(V434G)	XM_005617214.3; XP_005617271.1			2019	30700765
1486	OMIA:002162-9940	sheep		Hypophosphatasia	ALPL		missense	Genome-editing (CRISPR-Cas9)	yes	Oar_rambouillet_v1.0	2	g.260716094G>C	c.1077C>G	p.(I359M)	XM_027965561.1; XP_027821362.1			2018	30446691
550	OMIA:001551-9685	domestic cat	Burmese (Cat)	Brachycephaly	ALX1		deletion, small (<=20)	Naturally occurring variant	yes	Felis_catus_9.0	B4	g.110088245_110088256del	c.497_508del	p.(A166_T169del)	XM_003989090.4; XP_003989139.1; published as c.496delCTCTCAGGACTG			2016	26610632	Genomic position in Felis_catus_9.0 provided by Leslie Lyons and Reuben Buckley.
764	OMIA:001009-9913	cattle	Shorthorn (Cattle)	Tibial hemimelia	ALX4		deletion, gross (>20)	Naturally occurring variant	yes		15				Deletion of 45,694 bp including exon 1 of ALX4			2012	Reference not in PubMed; see OMIA 001009-9913 for reference details
763	OMIA:001009-9913	cattle	Galloway (Cattle)	Tibial hemimelia	ALX4	ALX4dup-GAU	duplication	Naturally occurring variant	yes	ARS-UCD1.2	15	g.74384916_74384935dup			UMD3.1 position is g.75154399_75154418dup. Duplication of 20bp in exon 2 is predicted to result in a frameshift leading to a premature stop codon and truncated protein.			2015	26076463	The genomic location on ARS-UCD1.2 was determined by Katie Eager and Shernae Woolley, EMAI, NSW. Department of Primary Industries. The same ARS-UCD1.2 location in the reverse order was included in the paper by Buitkamp et al. (2022). The allele name ALX4dup-GAU was also given by Buitkamp et al. (2022).
1516	OMIA:001009-9913	cattle	Galloway (Cattle)	Tibial hemimelia	ALX4	ALX4dup-LfL	duplication	Naturally occurring variant	yes	ARS-UCD1.2	15	g.74384938_74384919dup			Buitkamp et al. (2022): "The ALX4dup-LfL duplication results in a frameshift (amino acid position 151) leading to a truncated protein of 248 nt in length, compared with 303 nt of the wild-type protein (XP_027418402.1)".			2023	36585373
1129	OMIA:001868-9615	dog	Siberian Husky	Blue eyes	ALX4		duplication	Naturally occurring variant	no	CanFam3.1	18	g.44791414_44890185dup			Deane-Coe et al. (2018): "a 98.6-kb duplication directly upstream of the Homeobox gene ALX4"			2018	30286082	g. coordinates kindly provided by Anna Letko and Cord Drögemüller (7th Oct 2019)
280	OMIA:000791-9615	dog	Miniature Schnauzer	Persistent Mullerian duct syndrome	AMHR2		nonsense (stop-gain)	Naturally occurring variant	yes	CanFam3.1	27	g.1794738G>A	c.262C>T	p.(R88*)	XM_543632.6; XP_543632.4; published as c.241C>T; coordinates in the table have been updated to a recent reference genome and / or transcript			2009	18723470
639	OMIA:000565-9615	dog	Giant Schnauzer	Intestinal cobalamin malabsorption, AMN-related	AMN		deletion, gross (>20)	Naturally occurring variant	yes	CanFam3.1	8	g.70807271_70807303del	c.1113_1145del	p.(G372_A382del)	NM_001002960.1; NP_001002960.1			2005	15845892	Genomic position in CanFam3.1 provided by Robert Kuhn and Mateo Etcheveste.
426	OMIA:000565-9615	dog	Australian Shepherd	Intestinal cobalamin malabsorption, AMN-related	AMN		start-lost	Naturally occurring variant	yes	ROS_Cfam_1.0	8	g.71077084G>A	c.3G>A	p.(M1?)	NM_001002960.1; NP_001002960.1			2005	15845892
353	OMIA:002539-9615	dog	Dalmatian	Respiratory distress syndrome	ANLN		nonsense (stop-gain)	Naturally occurring variant	yes	CanFam3.1	14	g.47812143C>T	c.31C>T	p.(R11*)				2017	28222102	Variant coordinates obtained from or confirmed by EBI's Some Effect Predictor (VEP) tool
422	OMIA:001353-9615	dog	German Shepherd Dog	Platelet receptor for factor X, deficiency of	ANO6		splicing	Naturally occurring variant	yes	CanFam3.1	27	g.8912219C>T	c.1934+1G>A		XM_005636953.1			2015	26414452	Variant coordinates obtained from or confirmed by EBI's Variant Effect Predictor (VEP) tool
927	OMIA:002083-9913	cattle	Japanese Black, Japan (Cattle)	Abortion (embryonic lethality), ANXA10-related	ANXA10		repeat variation	Naturally occurring variant	yes		8				"a "34-kb deleted-type" CNV "associated with embryonic mortality at 30-60 days after artificial insemination. The CNV harbors exon 2 to 6 of ANNEXIN A10 (ANXA10). . . . Western blot analysis showed that the CNV results in a null allele of ANXA10."			2016	27881083
580	OMIA:000248-9615	dog	Collie	Neutropenia, cyclic	AP3B1		insertion, small (<=20)	Naturally occurring variant	yes	CanFam3.1	3	g.28663129_28663130insA	c.2407_2408insA	p.(T803Nfs*5)	NM_001002974.2; NP_001002974.1; a single base pair (A) insertion in exon 20 of the AP3 beta gene (AP3B1)		rs1152388405	2003	12897784
286	OMIA:000001-9913	cattle	Holstein (black and white) (Cattle)	Abortion due to a nonsense mutation in APAF1 on haplotype HH1	APAF1		nonsense (stop-gain)	Naturally occurring variant	yes	ARS-UCD1.2	5	g.62810245C>T	c.1741C>T	p.(Q581*)		rs448942533	rs448942533	2016	27289157	Variant coordinates obtained from or confirmed by EBI's Some Effect Predictor (VEP) tool; Breed information kindly provided or confirmed by Matt McClure and Jennifer McClure from "Understanding Genetics and Complete Genetic Disease and Trait Definition (Expanded 2016 Edition)" (https://www.icbf.com/wp/?page_id=2170)
1206	OMIA:001916-9615	dog	Jack Russell Terrier	Familial Adenomatous Polyposis	APC		delins, small (<=20)	Naturally occurring variant	yes	CanFam3.1	3	g.312131_312132delinsAA	c.[462_463delinsTT]	p.(K155X)	XM_014111995.2; XP_013967470.1			2020	32445578	Reference assembly and genomic location kindly provided by Kyoko Yoshizaki, 17 Dec 2020
731	OMIA:001965-9913	cattle	Holstein (black and white) (Cattle)	Holstein cholesterol deficiency	APOB		insertion, gross (>20)	Naturally occurring variant	yes		11				"1.3kb insertion of a transposable LTR element (ERV2-1) in the coding sequence of the APOB gene, which leads to truncated transcripts and aberrant splicing [p.Gly135ValfsX10)]"			2016	26763170
436	OMIA:000991-9796	horse	Quarter Horse (Horse)	Androgen insensitivity syndrome (AIS)	AR		regulatory	Naturally occurring variant	yes	EquCab3.0	X	g.52728703A>G	c.1A>G		NM_001163891.1; NP_001157363.1; mutation in start codon			2012	22095250	The genomic position in EquCab3.0 was provided by Ceara Mulvey, working under the guidance of Professor Ernie Bailey in April 2022
1143	OMIA:000991-9796	horse	Tennessee Walking Horse (Horse)	Androgen insensitivity syndrome (AIS)	AR		deletion, small (<=20)	Naturally occurring variant	yes	EquCab3.0	X	g.52728885del	c.183del	p.(R63Gfs)	NM_001163891.1; NP_001157363.1; published as c.183delT and p.(Ser61fs); c. and p. information in the table has been updated to HGVS nomenclature			2020	31936796	The genomic position in EquCab3.0 was provided by Ceara Mulvey, working under the guidance of Professor Ernie Bailey in April 2022
783	OMIA:000991-9796	horse		Androgen insensitivity syndrome	AR		deletion, gross (>20)	Naturally occurring variant	yes	EquCab3.0	X	g.52808634_52808658del	c.1630_1654del		NM_001163891.1; NP_001157363.1; the deletion is predicted to create a frameshift: "resulting in altered amino acid composition from p.543Lys and a premature stop codon 44 amino acid residues downstream in exon 3"			2017	28192783
786	OMIA:000991-9796	horse	Thoroughbred (Horse)	Androgen insensitivity syndrome	AR		missense	Naturally occurring variant	yes	EquCab3.0	X	g.52872393G>C	c.2042G>C	p.(W681S)	NM_001163891.1; NP_001157363.1			2016	27073903	The genomic position in EquCab3.0 was provided by Ceara Mulvey, working under the guidance of Professor Ernie Bailey in April 2022; p. coordinates obtained from Villagomez et al. (2019)
1144	OMIA:000991-9796	horse	Thoroughbred (Horse)	Androgen insensitivity syndrome (AIS)	AR		missense	Naturally occurring variant	yes	EquCab3.0	X	g.52878093C>T	c.2132C>T	p.(A711V)	NM_001163891.1; NP_001157363.1			2020	31936796
960	OMIA:001917-9615	dog	Leonberger Saint Bernard	Polyneuropathy, ARHGEF10-related	ARHGEF10		deletion, small (<=20)	Naturally occurring variant	yes	CanFam3.1	16	g.54349199_54349208del	c.1955_1958+6del		XM_005630036.3; XP_005630093.1; published as c.1955_1958+6delCACGGTGAGC - eliminating the 3'-splice junction of exon 17 and creating an alternate splice site leading to a truncated protein			2014	25275565	Genomic coordinates in CanFam3.1 provided by Robert Kuhn
780	OMIA:001334-9913	cattle	Swedish Red (Cattle)	Sperm, short tail	ARMC3		deletion, small (<=20)	Naturally occurring variant	yes	ARS-UCD1.2	13	g.24024660del	c.1442del	p.(A451fs*26)		rs797454424		2016	26923438	Some variant information kindly provided or confirmed by Hubert Pausch, including information from Additional Table 6 of Jansen et al. (2013) BMC Genomics201314:446 https://doi.org/10.1186/1471-2164-14-446
56	OMIA:000666-9615	dog	Miniature Schnauzer	Mucopolysaccharidosis VI	ARSB		deletion, gross (>20)	Naturally occurring variant	yes	CanFam3.1	3	g.27870127_27870182del	c.-24_32del		NM_001048133.1			2020	32985704	g. coordinate kindly provided by Karthik Raj 29 Oct 2020
640	OMIA:000666-9615	dog	Miniature Poodle	Mucopolysaccharidosis VI	ARSB		deletion, gross (>20)	Naturally occurring variant	yes	CanFam3.1	3	g.27870253_27870274del	c.103_124del	p.(A35Gfs*108)	NM_001048133.1; NP_001041598.1			2012	22329490	Variant information initially provided byÂ Karthik Raj and Urs Giger
859	OMIA:000666-9615	dog	Great Dane	Mucopolysaccharidosis VI	ARSB		nonsense (stop-gain)	Naturally occurring variant	yes	CanFam3.1	3	g.27870445C>T	c.295C>T	p.(Q99*)	NM_001048133.1; NP_001041598.1			2018	29157190	Variant information initially provided byÂ Karthik Raj and Urs Giger, and confirmed by Ensembl's VEP
1258	OMIA:000666-9615	dog	Miniature Pinscher	Mucopolysaccharidosis VI	ARSB		missense	Naturally occurring variant	yes	CanFam3.1	3	g.27950471G>A	c.910G>A	p.(G304R)	NM_001048133.1; NP_001041598.1			2020	32985704	g. coordinate kindly provided by Karthik Raj 29 Oct 2020
1320	OMIA:000666-9685	domestic cat	Siamese (Cat)	Mucopolysaccharidosis VI, mild, in L476P/D520N cats	ARSB		missense	Naturally occurring variant	yes	Felis_catus_9.0	A1	g.145138738C>T	c.1558G>A	p.(D520N)	NM_001142259.1; NP_001135731.1; D520N/D520N and L476P/D520N cats have normal growth and appearance. L476P/D520N cats have a very mild MPS VI phenotype (increased incidence of degenerative joint disease).			1998	9421472	Genomic position in Felis_catus_9.0 provided by Leslie Lyons and Reuben Buckley.
132	OMIA:000666-9685	domestic cat	Domestic Shorthair Siamese (Cat)	Mucopolysaccharidosis VI	ARSB		missense	Naturally occurring variant	yes	Felis_catus_9.0	A1	g.145138869A>G	c.1427T>C	p.(L476P)	NM_001142259.1; NP_001135731.1			1996	8910299	Variant coordinates obtained from or confirmed by EBI's Some Effect Predictor (VEP) tool
67	OMIA:001503-9615	dog	American Staffordshire Terrier	Neuronal ceroid lipofuscinosis, 4A	ARSG		missense	Naturally occurring variant	yes	CanFam3.1	9	g.15071276G>A	c.296G>A	p.(R99H)				2010	20679209	Variant coordinates obtained from or confirmed by EBI's Some Effect Predictor (VEP) tool
665	OMIA:000201-10042	North American deer mouse	New Hampshire (Chicken)	Melanic (non-agouti)	ASIP		deletion, gross (>20)	Naturally occurring variant	no						"a 125-kb deletion, which includes the upstream regulatory region and exons 1 and 2 of Agouti, results in a loss of Agouti expression"			2009	19649329
712	OMIA:000201-9913	cattle	Normande (Cattle)	Brindle	ASIP	Abr	insertion, gross (>20)	Naturally occurring variant	no		13				"insertion of a full-length Bos taurus LINE element"			2006	16827753
1199	OMIA:000201-9925	goat	Peacock Goat (Goat) Valais Grüenochte	Peacock	ASIP	A^pc	repeat variation	Naturally occurring variant	no		13				"The ASIP allele in Peacock goats, which we propose to term “peacock” (A^pc), has a quadruplication of the same ~45 kb region having five copies in the A^b allele. It is additionally flanked by triplicated segments of 27,996 bp and 41,807 bp on the left and right side of the quadruplicated sequence (Fig 3, S4 Fig, S5 Table). The central part of the A^pc allele has exactly the same breakpoints as the A^b allele suggesting a common origin of A^b and A^pc." (Henkel et al., 2019) "63'158'171-63'203'851: 4 copies (corresponds to the CNV in the Ab allele)" (Table S5; Henkel et al., 2019) 200922: Marius picked this g. entry up as requiring attention: "g.63130175_63245658 (3 copies)". Because this will take time to sort out, I have removed it from the g. field for the time being.			2019	31841508
1075	OMIA:001602-93934	Japanese quail		Feather colour, fawn-2/beige	ASIP	Y^f2	duplication	Naturally occurring variant	no		20				Robic et al. (2019) concluded "that fawn-2 and beige are the same allele, and that it is caused by a 70,895-bp tandem duplication . . . [with breakpoints] (NC-029535 [1,371,395(or 98)–1,442,295 (or 98)]) . . . located downstream of the ITCH exon 1 and upstream of the ASIP exon e4 (5′ UTR). . . . The 70,895 bp of the duplicated region include the entire AHCY gene on one strand, and parts of the ASIP and ITCH genes on the other strand."			2019	30987584
1321	OMIA:002200-9915	zebu	Brahman (Cattle) Nellore, India (Sheep)	Darkness of hair coat	ASIP		delins, gross (>20)	Naturally occurring variant	unknown		13				1155-bp deletion followed by an insertion of a transposable element of more than 150 bp that may impact the recruitment of ASIP non-coding exons (Trigo et al.2021)			2021	33910501
1200	OMIA:000201-9925	goat	Bezoar (Goat) Valais Blackneck (Goat) Valais Copperneck	Wild type or Bezaur	ASIP	A^bz	reference sequence allele	Naturally occurring variant	no		13				"The goat genome reference sequence is derived from a San Clemente goat, which has a similar coat color pattern as bezoars. The genome reference therefore supposedly represents the wildtype allele at the ASIP locus, termed “bezoar” (Abz) [8]. Bezoars and all other Swiss goat breeds did not show any CNVs at the ASIP locus." (Henkel et al., 2019)			2019	31841508
251	OMIA:000201-61386	Kodkod		Melanism (black coat)	ASIP		missense	Naturally occurring variant	no					p.(C126Y)				2015	25695801
252	OMIA:000201-61406	Colocolo		Melanism (black coat)	ASIP		missense	Naturally occurring variant	no					p.(R120C)				2015	25695801
1119	OMIA:000201-10141	domestic guinea pig		Recessive black	Asip		deletion, small (<=20)	Naturally occurring variant	no				c.181_184delTTCA		MH026115: c.181_184delTTCA; the deletion leads to a truncated protein of 77 amino acids due to the premature stop codon.			2019	30746725
330	OMIA:000201-10042	North American deer mouse	Alaska, United States of America (North American deer mouse)	Melanic (non-agouti)	ASIP		nonsense (stop-gain)	Naturally occurring variant	no				c.193?>?	p.(Q65*)				2009	19649329
333	OMIA:000201-9691	leopard		Black panther	ASIP		nonsense (stop-gain)	Naturally occurring variant	no				c.333C>A	p.(C111*)				2012	23251368
1219	OMIA:000201-9858	Western roe deer		Melanistic (black)	ASIP		missense	Naturally occurring variant	no				c.33G>T	p.(L11F)				2020	32545389
149	OMIA:000201-9793	ass		No light points	ASIP	NLP	missense	Naturally occurring variant	no				c.349T>C	p.(C117R)				2015	25887951
504	OMIA:001602-93934	Japanese quail		Feather colour, recessive black	ASIP	rb	deletion, small (<=20)	Naturally occurring variant	no		20		c.373_380del		"A deletion of 8 bases was found in the ASIP gene"			2008	18287406
253	OMIA:000201-61455	Asiatic golden cat		Black	ASIP		missense	Naturally occurring variant	no				c.384C>G	p.(C128W)				2012	23251368
567	OMIA:000201-9986	rabbit	New Zealand White (Rabbit)	Black (non-agouti)	ASIP	a	insertion, small (<=20)	Naturally occurring variant	no		4		c.5_6insA		Letko et al. (2020): NM_001122939.1:c.5_6insA			2010	20004240
1010	OMIA:000201-9838	Arabian camel		Black and dark-brown coat colour	ASIP		haplotype	Naturally occurring variant	no				c.[23delT;c.25G>A]		KU179868; c.[23delT;c.25G>A]. As described by Almathen et al. (2018), this haplotype comprises "a 1-bp deletion (23delT/T) and a SNP (25G/A) in exon 2 of ASIP".			2018	29893870
654	OMIA:001602-93934	Japanese quail		Feather colour, lethal yellow	ASIP	Y	deletion, gross (>20)	Naturally occurring variant	yes		20	g.1463709_1604872del			Nadeau et al. (2008): "a >90-kb [141162bp] deletion upstream of ASIP"			2008	18287407	The g. coordinates were provided by Robic et al. (2019)
509	OMIA:000201-9796	horse		Coat colour, recessive black	ASIP	a	deletion, small (<=20)	Naturally occurring variant	no		22	g.2174_2184del	c.191_201del					2001	11353392
1196	OMIA:000201-9925	goat	Appenzell (Goat) Girgentana, Italy (Goat) Saanen (Goat)	White or tan	ASIP	A^Wt	repeat variation	Naturally occurring variant	no	ARS1	13				"CNV [copy number variation] affecting a region of less that 100 kb including the ASIP and AHCY genes" (Fontanesi et al., 2009)."spans 154,677 bp ofthe reference genome sequence and comprises the entire coding sequence ofthe ASIP, AHCYand ITCH genes. The individual copies are arranged in tandem in a head to tail orientation." (Henkel et al., 2019) 200922: moved the g. entry to here (g.63,226,824-63,381,501 (3 copies)) until it can be standardised			2009	20016133
1197	OMIA:000201-9925	goat	Grisons Striped (Goat) Toggenburg (Goat)	Swiss markings	ASIP	A^sm	repeat variation	Naturally occurring variant	no	ARS1	13				"8 tandem copies of a 13,433 bp sequence from the 5’-flanking region of ASIP" (Henkel et al., 2019) 200922: moved g. entry to here (g.63,129,198-63,142,631 (8 copies)) until it can be fixed			2019	31841508
1198	OMIA:000201-9925	goat	Chamois Coloured (Goat) St Gallen Booted Goat (Goat)	Badgerface	ASIP	A^b	repeat variation	Naturally occurring variant	no	ARS1	13				"a five-fold amplification of45,680 bp located ~61 kb downstream ofthe Asm amplification" (Henkel et al., 2019) 200922: move the g. entry to here (g.63,158,171-63,203,851 (5 copies)), until it can be fixed			2019	31841508
1382	OMIA:000201-9615	dog		Dominant yellow	ASIP	DY	reference sequence allele	Naturally occurring variant	no	CanFam3.1	24	CanFam3.1			The reference sequence CanFam3.1 represents the dominant yellow phenotype.			2021	34385618
1386	OMIA:000201-9615	dog		Black saddle	ASIP	BS	delins, gross (>20)	Naturally occurring variant	no	CanFam3.1	24	g.23378062_23379640delins[MT319116.1:424_663]			Likely causal regulatory promoter variant			2021	34385618
30	OMIA:000201-9615	dog	German Shepherd Dog	Recessive black	ASIP		missense	Naturally occurring variant	no	CanFam3.1	24	g.23393552C>T	c.286C>T	p.(R96C)		rs851336386	rs851336386	2004	15520882	Variant coordinates obtained from or confirmed by EBI's Some Effect Predictor (VEP) tool
1385	OMIA:000201-9615	dog		Black back 3	ASIP	BB3	haplotype	Naturally occurring variant	no	CanFam3.1	24	g.[23353288_23353472del;23354716_23354751A[4];23377890_23378086del;23378320_23378343del;g.23378858_2			Haplotype containing a likely causal regulatory promoter variant			2021	34385618
1380	OMIA:000201-9615	dog		Agouti	ASIP	AG	haplotype	Naturally occurring variant	no	CanFam3.1	24	g.[23353288_23353472del;23354716_23354751A[4];23377890_23378086del;23378320_23378343del]			Haplotype containing a likely causal regulatory promoter variant			2021	34385618
1383	OMIA:000201-9615	dog		Black back 1	ASIP	BB1	haplotype	Naturally occurring variant	no	CanFam3.1	24	g.[23353288_23353472del;23354716_23354751A[4];23378062_23378231delins[MT319115.1:424_674]			Haplotype containing a likely causal regulatory promoter variant			2021	34385618
1384	OMIA:000201-9615	dog		Black back 2	ASIP	BB2	haplotype	Naturally occurring variant	no	CanFam3.1	24	g.[23353288_23353472del;23354716_23354751A[4];23378062_23379640delins[MT319116.1:424_663]]			Haplotype containing a likely causal regulatory promoter variant			2021	34385618
1381	OMIA:000201-9615	dog		Shaded yellow	ASIP	SY	haplotype	Naturally occurring variant	no	CanFam3.1	24	g.[23353288_23353472del;23354716_23354751A[4]]			Haplotype containing a likely causal regulatory promoter variant			2021	34385618
1452	OMIA:002549-9685	domestic cat	Bengal (Cat)	Coat colour and pattern, charcoal	ASIP		missense	Naturally occurring variant	no	Felis_catus_9.0	A3		c.251A>G	p.(Q84R)	variant contributes to A^Pbe haplotype associated with charcoal colour/pattern (in exon 4, not present in Felis_catus_9.0)			2014	25143047
1453	OMIA:002549-9685	domestic cat	Bengal (Cat)	Coat colour and pattern, charcoal	ASIP		missense	Naturally occurring variant	no	Felis_catus_9.0	A3		c.302A>G	p.(D101G)	variant contributes to A^Pbe haplotype associated with charcoal colour/pattern (in exon 4, not present in Felis_catus_9.0)			2014	25143047
1450	OMIA:002549-9685	domestic cat	Bengal (Cat)	Coat colour and pattern, charcoal	ASIP		missense	Naturally occurring variant	no	Felis_catus_9.0	A3	g.25086548A>G	c.142T>C	p.(S48P)	NM_001009190.1; NP_001009190.1; variant contributes to A^Pbe haplotype associated with charcoal colour/pattern			2014	25143047
493	OMIA:000201-9685	domestic cat		Coat colour, non-agouti (black)	ASIP	a	deletion, small (<=20)	Naturally occurring variant	no	Felis_catus_9.0	A3	g.25086566_25086567del	c.123_124del	p.(M42Efs*59)	NM_001009190.1; NP_001009190.1; "a 2 bp deletion in the ASIP gene [at nucleotide positions 123-124]"			2003	12620197	The genomic location on Felis_catus_9.0 is based on Rodney et al. 2021 (PMID: 33785770
1451	OMIA:002549-9685	domestic cat	Bengal (Cat)	Coat colour and pattern, charcoal	ASIP		missense	Naturally occurring variant	no	Felis_catus_9.0	A3	g.25086649C>G	c.41G>C	p.(C14S)	NM_001009190.1; NP_001009190.1; variant contributes to A^Pbe haplotype associated with charcoal colour/pattern			2014	25143047
714	OMIA:000201-9940	sheep	Merino (Sheep)	White fleece	ASIP	Wt	insertion, gross (>20)	Naturally occurring variant	no	Oar_rambouillet_v1.0	13				a 190kb tandem duplication encompassing the ASIP gene, the neighbouring AHCY gene and the promoter for a third gene ITCH			2008	18493018
1112	OMIA:000201-9940	sheep		Recessive black	ASIP	a	missense	Naturally occurring variant	no	Oar_rambouillet_v1.0	13	g.66474980T>A	c.376T>A	p.(C126S)	Published as g.5172T>A (Norris et al. 2008). cDNA and protein positions based on NM_001134303.1 and NP_001127775.1			2008	18493018	The genomic location on Oar_rambouillet_v1.0 was determined by Katie Eager, EMAI, NSW Department of Primary Industries.
1111	OMIA:000201-9940	sheep		Recessive black	ASIP	a	deletion, small (<=20)	Naturally occurring variant	no	Oar_rambouillet_v1.0	13	g.66475132_66475136del			published as g.100_105del / D5 and predicted to result in a frame shift followed by a premature stop codon 63 amino acids downstream of the start site			2002	12354151	The genomic location on Oar_rambouillet_v1.0 was determined by Katie Eager, EMAI, NSW Department of Primary Industries.
1134	OMIA:000201-9986	rabbit		Black and tan	ASIP	a^t	deletion, gross (>20)	Naturally occurring variant	no	OryCun2.0	4	g.5455408_5466123del			Letko et al. (2020): NC_013672.1:g.5,455,408_5,466,123del			2020	31729778
1270	OMIA:000213-89462	water buffalo		White	ASIP		insertion, gross (>20)	Naturally occurring variant	no	UOA_WB_1	14				"2,809-bp-long LINE-1 insertion in the ASIP (agouti signaling protein) gene" (Liang et al. (2020)			2021	33212507
667	OMIA:000201-9627	red fox		Dark Standard Silver	ASIP		deletion, gross (>20)	Naturally occurring variant	no	VulVul2.2	NW_020356514.1				A 16.5-kb deletion resulting in "a 166-nt deletion in the Standard Silver fox cDNA, spanning the second exon ... .This deletion removes the start codon and entire signal peptide"			1997	9054949
1309	OMIA:002325-9685	domestic cat		Encephalopathy, spongy	ASPA		missense	Naturally occurring variant	yes	Felis_catus_9.0	E1	g.13585610C>G	c.859G>C	p.(A287P)	XM_006939957.4; XP_006940019.1			2021	33779415
111	OMIA:002099-9615	dog	German Shepherd Dog	Ichthyosis, ASPRV1-related	ASPRV1		missense	Naturally occurring variant	yes	CanFam3.1	10	g.68587027A>G	c.1052T>C	p.(L351P)	XM_014117456.1; XP_013972931.1			2017	28249031	Genomic position in CanFam3.1 provided by Robert Kuhn and Mateo Etcheveste.
289	OMIA:000194-9913	cattle	Holstein Friesian (Cattle)	Citrullinaemia	ASS1		nonsense (stop-gain)	Naturally occurring variant	yes	ARS-UCD1.2	11	g.100781668C>T	c.256C>T	p.(R86*)				1989	2813370	Variant coordinates obtained from or confirmed by EBI's Some Effect Predictor (VEP) tool; Breed information kindly provided or confirmed by Matt McClure and Jennifer McClure from "Understanding Genetics and Complete Genetic Disease and Trait Definition (Expanded 2016 Edition)" (https://www.icbf.com/wp/?page_id=2170)
65	OMIA:001471-9615	dog	Standard Poodle	Neonatal encephalopathy with seizures	ATF2		missense	Naturally occurring variant	yes	CanFam3.1	36	g.19078954A>C	c.152T>G	p.(M51R)				2008	18074159	Variant coordinates obtained from or confirmed by EBI's Some Effect Predictor (VEP) tool
94	OMIA:001954-9615	dog	Lagotto Romagnolo	Neurodegenerative vacuolar storage disease	ATG4D		missense	Naturally occurring variant	yes	CanFam3.1	20	g.50618958C>T	c.1288G>A	p.(A430T)				2015	25875846	Variant coordinates obtained from or confirmed by EBI's Some Effect Predictor (VEP) tool
1067	OMIA:001552-9615	dog	Australian Cattle Dog	Neuronal ceroid lipofuscinosis, 12	ATP13A2		missense	Naturally occurring variant	yes	CanFam3.1	2	g.81208162C>T	c.1118C>T	p.(T373I)	XM_005617949.3; XP_005618006.1			2019	30956123
400	OMIA:001552-9615	dog	Tibetan Terrier	Neuronal ceroid lipofuscinosis, 12	ATP13A2		splicing	Naturally occurring variant	yes	CanFam3.1	2	g.81210367del	c.1623del		XM_005617949.3; XP_005618006.1; variant was published as c.1623delG p.P541fs*597 by Farias et al. (2011); Wöhlke et al. (2011) provided an alternate transcript position c.1620delG and proposed that the variant causes exon 16 skipping in NCL-affected Tibetan terriers. The sequence information provided by Wöhlke et al. (2011) corresponds to XM_005617949.3:c.1623del			2011	21362476 22022275
734	OMIA:002110-9615	dog	Belgian Shepherd	Ataxia, cerebellar, ATP1B2-related	ATP1B2		insertion, gross (>20)	Naturally occurring variant	yes	CanFam3.1	5	g.32551064_32551065ins[LT796559.1:g.50_276]	c.130_131ins[LT796559.1:g.50_276]		XM_546597.5; "a 227 bp SINE insertion into exon 2 of the ATP1B2 gene"			2017	28620085
188	OMIA:001450-9913	cattle	Belgian Blue (Cattle) Maas-Rijn-Ijssel (Cattle)	Congenital muscular dystonia 1	ATP2A1		missense	Naturally occurring variant	yes	ARS-UCD1.2	25	g.25933247G>A	c.1675C>T	p.(R559C)				2008	18344998	Variant coordinates obtained from or confirmed by EBI's Some Effect Predictor (VEP) tool; Breed information kindly provided or confirmed by Matt McClure and Jennifer McClure from "Understanding Genetics and Complete Genetic Disease and Trait Definition (Expanded 2016 Edition)" (https://www.icbf.com/wp/?page_id=2170)
219	OMIA:001464-9913	cattle	Romagnola (Cattle)	Pseudomyotonia, congenital	ATP2A1		missense	Naturally occurring variant	yes	ARS-UCD1.2	25	g.25939141C>A	c.857G>T	p.(G286V)			rs3423529256	2012	23046865	Variant coordinates obtained from or confirmed by EBI's Some Effect Predictor (VEP) tool; Breed information kindly provided or confirmed by Matt McClure and Jennifer McClure from "Understanding Genetics and Complete Genetic Disease and Trait Definition (Expanded 2016 Edition)" (https://www.icbf.com/wp/?page_id=2170)
218	OMIA:001464-9913	cattle	Romagnola (Cattle)	Pseudomyotonia, congenital	ATP2A1		missense	Naturally occurring variant	yes	ARS-UCD1.2	25	g.25939366C>A	c.632G>T	p.(G211V)				2012	23046865	Variant coordinates obtained from or confirmed by EBI's Some Effect Predictor (VEP) tool; Breed information kindly provided or confirmed by Matt McClure and Jennifer McClure from "Understanding Genetics and Complete Genetic Disease and Trait Definition (Expanded 2016 Edition)" (https://www.icbf.com/wp/?page_id=2170)
205	OMIA:001464-9913	cattle	Chianina (Cattle)	Pseudomyotonia, congenital	ATP2A1		missense	Naturally occurring variant	yes	ARS-UCD1.2	25	g.25940510C>T	c.491G>A	p.(R164H)			rs3423529241	2008	18786632	Variant coordinates obtained from or confirmed by EBI's Some Effect Predictor (VEP) tool; Breed information kindly provided or confirmed by Matt McClure and Jennifer McClure from "Understanding Genetics and Complete Genetic Disease and Trait Definition (Expanded 2016 Edition)" (https://www.icbf.com/wp/?page_id=2170)
1192	OMIA:002265-9615	dog	Irish Terrier	Darier disease	ATP2A2		insertion, gross (>20)	Naturally occurring variant	yes	CanFam3.1	26	g.8200944_8200945insN[(205)]	c.2098-3_2098-2insN[(205)]	p.(T700Vfs*6)	NM_001003214.1; NP_001003214.1; Linek et al. (2020): "a heterozygous SINE insertion [~205bp] into the ATP2A2 gene, at the end of intron 14, close to the boundary of exon 15", giving rise to NP_001003214.1:p.(Thr700Valfs*6)			2020	32354065
1533	OMIA:002265-9615	dog	Shih-Tzu	Darier disease	ATP2A2		missense	Naturally occurring variant	yes	UU_Cfam_GSD_1.0	26	g.8434781A>C	c.2425A>C	p.(N809H)	NM_001003214.1; NP_001003214.1			2023	36883421
107	OMIA:002608-9615	dog	Labrador Retriever	Modifier of copper toxicosis	ATP7A		missense	Naturally occurring variant	yes	CanFam3.1	X	g.60279238C>T	c.980C>T	p.(T327I)		rs852523339	rs852523339	2016	26747866	Variant coordinates obtained from or confirmed by EBI's Some Effect Predictor (VEP) tool. The phenotype was renamed from 'Menkes disease' to 'Modifier of copper toxicosis' based on feedback from Tom Nagels [10/01/2023].
1347	OMIA:001071-9685	domestic cat		Wilson disease	ATP7B		missense	Naturally occurring variant	yes		A1			p.(P550L)				2020	31687873
106	OMIA:001071-9615	dog	Labrador Retriever	Wilson disease	ATP7B		missense	Naturally occurring variant	yes	CanFam3.1	22	g.225112G>A	c.4151G>A	p.(R1384Q)	XM_005633831.3; XP_005633888.1; variant published as c.4358G>A / p.(R1453Q) and the variant coordinates in this table have been changed to reflect recent transcript IDs	rs851958524	rs851958524	2016	26747866	30 Dec 2020: correct genomic location provided by Angelica K Kallenberg
1136	OMIA:001071-9685	domestic cat		Wilson disease	ATP7B		missense	Naturally occurring variant	yes	Felis_catus_9.0	A1	g.19611002C>G	c.3890C>G	p.(T1297R)	XM_023251176.1; XM_023251176.1			2019	30561139	Genomic position in Felis_catus_9.0 provided by Leslie Lyons and Reuben Buckley.
1076	OMIA:001645-10036	golden hamster		Black tremor	Atrn		insertion, gross (>20)	Naturally occurring variant	yes						Kuramoto et al. (2002): "an approximately 10-kb DNA fragment, which had 557-bp direct repeats in both ends and was flanked by the identical 6-bp target duplication sequences, [that] was inserted into exon 24"			2002	11773967
348	OMIA:000487-9796	horse	Belgian Draft (Horse) Friesian (Horse)	Hydrocephalus	B3GALNT2		nonsense (stop-gain)	Naturally occurring variant	yes	EquCab3.0	1	g.76887901C>T	c.1423C>T	p.(Q475*)	Ducro et al./ (2015): "The nomenclature for the mutation is c.1423C>T [GenBank:XM_001491545] corresponding to p.Gln475* [GenBank:XP_001491595]". As at 25 April 2019, Ensembl's Variant Effect Predictor (VEP) gives the EquCab3 c. and p. coordinates as having not changed from the EquCab2 coordinates reported by Ducro et al. (2015). The Ensembl ref is ENSECAT00000049072		rs3429464524	2015	26452345	c. and p. variant coordinates obtained from or confirmed by EBI's Some Effect Predictor (VEP) tool. EquCab3 g. coordinate provided by Meredith O’Connell, working under the supervision of Professor Ernie Bailey, 24 April 2019
439	OMIA:001885-9940	sheep	Lacaune (Sheep)	Fecundity, Lacaune, FecL	B4GALNT2		regulatory	Naturally occurring variant	no	Oar_v3.1	11	g.36938224T>A	c.766+2831A>T		ENSOART00000006875.1:c.766+2831A>T ENSOART00000006877.1:c.781+2831A>T	rs588626728		2013	24086150
440	OMIA:001885-9940	sheep	Lacaune (Sheep)	Fecundity, Lacaune, FecL	B4GALNT2		regulatory	Naturally occurring variant	no	Oar_v3.1	11	g.37034573A>G						2013	24086150
421	OMIA:002068-9796	horse	Friesian (Horse)	Dwarfism, Friesian	B4GALT7		splicing	Naturally occurring variant	yes	EquCab3.0	14	g.3772591C>T	c.50G>A	p.(R17K)			rs3447120064	2016	27793082	Variant coordinates obtained from or confirmed by EBI's Some Effect Predictor (VEP) tool. FN thanks Elizabeth Huffman, who updated the g. coordinates to EquCab3, working under the supervision of Professor Ernie Bailey; 23 April 2020.
1391	OMIA:002484-9615	dog	Shetland Sheepdog	Bardet-Biedl syndrome 2	BBS2		missense	Naturally occurring variant	yes	CanFam3.1	2	g.59693737G>C	c.1222G>C	p.(A408P)	ENSCAFT00000014523.5; ENSCAFP00000013435.4			2021	34828377
356	OMIA:002045-9615	dog	Hungarian Puli	Bardet-Biedl syndrome 4	BBS4		nonsense (stop-gain)	Naturally occurring variant	yes	CanFam3.1	30	g.36063748A>T	c.58A>T	p.(K20*)				2017	28533336
1131	OMIA:002216-9544	Rhesus monkey		Bardet-Biedl syndrome 7	BBS7		deletion, small (<=20)	Naturally occurring variant	yes	Mmul_8.0.1			c.160delG	p.(A54fs)				2019	31589838
1049	OMIA:002178-9823	pig	Large White (Pig)	Abortion, BBS9 and BMPER-related	BBS9		deletion, gross (>20)	Naturally occurring variant	yes	Sscrofa11.1	18	g.39817373_40029300del			Derks et al. (2018): "a large deletion in complete LD with the SSC18 haplotype of approximately 212kb (position 39,817,373 to 40,029,300), spanning a part of the BBS9 gene ... [and reducing] expression of the downstream BMPER gene"			2018	30231021
635	OMIA:001592-9615	dog	Cavalier King Charles Spaniel	Episodic falling	BCAN		deletion, gross (>20)	Naturally occurring variant	yes	CanFam3.1	7	g.41325010_41340731delinsAAGGCC	c.-13991_466+85delinsGGCCTT		XM_005622698.1; a 15.7kb deletion in the BCAN gene removing the first 3 exons			2012	21821125
298	OMIA:000627-9913	cattle	Polled Hereford (Cattle)	Maple syrup urine disease	BCKDHA		nonsense (stop-gain)	Naturally occurring variant	yes	ARS-UCD1.2	18	g.50551011C>T	c.148C>T	p.(Q50*)	cDNA position based on ENSBTAT00000021342.6			1990	2303405
200	OMIA:000627-9913	cattle	Shorthorn (Cattle)	Maple syrup urine disease	BCKDHA		missense	Naturally occurring variant	yes	ARS-UCD1.2	18	g.50560242C>T	c.1380C>T	p.(P372L)			rs3423447991	1999	10425233	Breed and variant information kindly provided or confirmed by Matt McClure and Jennifer McClure from "Understanding Genetics and Complete Genetic Disease and Trait Definition (Expanded 2016 Edition)" (https://www.icbf.com/wp/?page_id=2170)
1333	OMIA:001079-9940	sheep	Spælsau	yellow fat	BCO2		insertion, gross (>20)	Naturally occurring variant	yes		15				"insertion of a 7.9 kb endogenous Jaagsiekte Sheep Retrovirus (enJSRV) sequence in the first intron of the BCO2 gene" (Kent et al. 2021)			2021	34193038
549	OMIA:001079-9986	rabbit	Flemish Giant (Rabbit) New Zealand White (Rabbit)	Yellow fat	BCO2		deletion, small (<=20)	Naturally occurring variant	yes		1		delAAT					2015	26002694
1375	OMIA:002466-48883 OMIA:002466-48882 OMIA:002466-87173 OMIA:002466-48884 OMIA:002466-48885 OMIA:002466-48886 OMIA:002466-1553461	medium ground-finch		Beak colour, yellow	BCO2		synonymous	Naturally occurring variant	no		24	g.6166878G>A		p.(V?V)	synonymous change 32 bp into exon 4			2021	34687609
305	OMIA:001079-9913	cattle	Holstein (black and white) (Cattle)	Yellow fat	BCO2		nonsense (stop-gain)	Naturally occurring variant	yes	ARS-UCD1.2	15	g.22552375G>A	c.306G>A	p.(W102*)	UMD3.1 position is g.22877552G>A; cDNA position is based on XM_024975217.1	rs109226280	rs109226280	2009	19398771	Variant information kindly provided or confirmed by Hubert Pausch, including information from Additional Table 6 of Jansen et al. (2013) BMC Genomics201314:446 https://doi.org/10.1186/1471-2164-14-446. The genomic location on ARS-UCD1.2 was determined by Katie Eager and Shernae Woolley, EMAI, NSW. Department of Primary Industries.
1559	OMIA:002466-9135	common canary		Beak and leg colour, red	BCO2		missense	Naturally occurring variant	no	NW_022042652.1		g.75258192G>A		p.R413H				2020	31930402	XP_009096268.1, genomic position as reported by Bovo et al. (2023) PMID:37194440
320	OMIA:001079-9940	sheep	Gammelnorsk spaelsau, Norway (Sheep)	Yellow fat	BCO2		nonsense (stop-gain)	Naturally occurring variant	yes	Oar_rambouillet_v1.0	15	g.25024133C>T	c.196C>T	p.(Q66*)	Oar_v3.1 position is g.21947481C>T	rs1090867485		2010	20122251	Variant coordinates obtained from or confirmed by EBI's Some Effect Predictor (VEP) tool
737	OMIA:001554-9615	dog	Lapponian Herder	Multifocal retinopathy 3	BEST1	cmr3	deletion, small (<=20)	Naturally occurring variant	yes	CanFam3.1	18	g.54470590del	c.1388del	p.(P463Hfs)	NM_001097545.1; NP_001091014.1; published as c.1388delC	rs397509969		2010	21197113	Variant information and allele abbreviation gleaned from or confirmed by Donner et al. (2016) PLoS One 11:e0161005 and genomic position in CanFam3.1 and EVA ID provided by Mateo Etcheveste and Robert Kuhn.
59	OMIA:001553-9615	dog	Coton de Tulear	Multifocal retinopathy 2	BEST1	cmr2	missense	Naturally occurring variant	yes	CanFam3.1	18	g.54476143C>T	c.482G>A	p.(G161D)	NM_001097545.1; NP_001091014.1			2007	17460247	Genomic coordinates in CanFam3.1 provided by Zoe Shmidt and Robert Kuhn.
275	OMIA:001444-9615	dog	Boerboel Bull Mastiff English Mastiff Great Pyrenees	Multifocal retinopathy 1	BEST1	cmr1	nonsense (stop-gain)	Naturally occurring variant	yes	CanFam3.1	18	g.54478586G>A	c.73C>T	p.(R25*)	NM_001097545.1; NP_001091014.1			2007	17460247	Variant coordinates obtained from or confirmed by EBI's Some Effect Predictor (VEP) tool
398	OMIA:001660-9615	dog	Great Dane	Inherited myopathy of Great Danes	BIN1		splicing	Naturally occurring variant	yes	CanFam3.1	19	g.23522400A>G	c.786-2A>G	p.(R262_K263insASASRPFPQ)	XM_014121413.2; XP_013976888.1; published as IVS10-2A>G, updated in this table to HGVS nomenclature			2013	23754947
244	OMIA:002306-9940	sheep	Belclare (Sheep) Cambridge (Sheep)	Fecundity, Belclare	BMP15	FecX(B)	missense	Naturally occurring variant	no	Oar_rambouillet_v1.0	X	g.56594843C>A	c.1100G>T	p.(S367I)				2004	14627550	The genomic location on Oar_rambouillet_v1.0 was determined by Katie Eager, EMAI, NSW Department of Primary Industries.
238	OMIA:002306-9940	sheep	Olkuska (Sheep)	Fecundity, Olkuska	BMP15	FecX(O)	missense	Naturally occurring variant	no	Oar_rambouillet_v1.0	X	g.56594934T>G	c.1009A>C	p.(N337H)	Protein and cDNA positions based on NP_001108239.1 and NM_001114767.1, respectively.			2013	23637641	The genomic location on Oar_rambouillet_v1.0 was determined by Katie Eager, EMAI, NSW Department of Primary Industries.
236	OMIA:002306-9940	sheep	Lacaune (Sheep)	Fecundity, Lacaune	BMP15	FecX(L)	missense	Naturally occurring variant	no	Oar_rambouillet_v1.0	X	g.56594981C>T	c.962G>A	p.(C321Y)	cDNA position based on NP_001108239.1			2007	17038554	The genomic location on Oar_rambouillet_v1.0 was determined by Katie Eager, EMAI, NSW Department of Primary Industries.
237	OMIA:002306-9940	sheep	Grivette (Sheep)	Fecundity, Grivette	BMP15	FecX(Gr)	missense	Naturally occurring variant	no	Oar_rambouillet_v1.0	X	g.56594993G>A	c.950C>T	p.(T317I)	protein and cDNA positions based on NP_001108239.1 and NM_001114767.1, respectively			2013	23637641	The genomic location on Oar_rambouillet_v1.0 was determined by Katie Eager, EMAI, NSW Department of Primary Industries.
235	OMIA:002306-9940	sheep	Romney Marsh (Sheep)	Fecundity, Inverdale	BMP15	FecX(I)	missense	Naturally occurring variant	no	Oar_rambouillet_v1.0	X	g.56595047A>T	c.896T>A	p.(V299D)	protein and cDNA positions based on NP_001108239.1 and NM_001114767.1, respectively	rs398521635		2000	10888873	The genomic location on Oar_rambouillet_v1.0 was determined by Katie Eager, EMAI, NSW Department of Primary Industries.
335	OMIA:002306-9940	sheep	Romney Marsh (Sheep)	Fecundity, Hanna	BMP15	FecX(H)	nonsense (stop-gain)	Naturally occurring variant	no	Oar_rambouillet_v1.0	X	g.56595072G>A	c.871C>T	p.(Q291*)	previously listed as c.1184C>T; protein and cDNA position based on NP_001108239.1 and NM_001114767.1, respectively	rs413916687		2000	10888873
334	OMIA:002306-9940	sheep	Cambridge (Sheep)	Fecundity, Galway	BMP15	FecX(G)	nonsense (stop-gain)	Naturally occurring variant	no	Oar_rambouillet_v1.0	X	g.56595225G>A	c.718C>T	p.(Q239*)		rs425019156		2004	14627550
521	OMIA:002306-9940	sheep	Rasa Aragonesa, Spain (Sheep)	Fecundity, Rasa Aragonesa	BMP15	FecX(R)	deletion, small (<=20)	Naturally occurring variant	no	Oar_rambouillet_v1.0	X	g.56595467_56595483del	c.460_476del	p.(W154Nfs*55)	published as c.525_541delTGGGTCCAGAAAAGCCC based on AF236079, protein and cDNA position in table based on NP_001108239.1 and NM_001114767.1, respectively			2008	18355397	The genomic location on Oar_rambouillet_v1.0 was determined by Katie Eager, EMAI, NSW Department of Primary Industries.
755	OMIA:002306-9940	sheep	Tunisian Barbary (Sheep)	Fecundity, Barbarine	BMP15	FecX(Bar)	complex rearrangement	Naturally occurring variant	no	Oar_rambouillet_v1.0	X	g.[56600937insG;56600945_56600947del;56600948C>A]	c.[301G>T;302_304delCTA;310insC]	p.(A101Cfs*113)	"a composite polymorphism associating a single nucleotide substitution (c.301G > T), a 3 bp deletion (c.302_304delCTA) and a C insertion (c.310insC) in the ovine BMP15 cDNA leading to a frame shift at protein position 101" - cDNA positions based on NM_001114767			2017	28506298
1341	OMIA:002306-9940	sheep	Rasa Aragonesa, Spain (Sheep)	Fecundity	BMP15	FecX(RA)	missense	Naturally occurring variant	unknown	Oar_v3.1	X	g.50970948C>T	c.1172C>T	p.(T400I)	protein position based on ENSOART00000010201			2020	31927415
1345	OMIA:002306-9940	sheep	Blanc Du Massif Central (Sheep) Noir du Velay, France (Sheep)	Fecundity	BMP15	FecX(N)	regulatory	Naturally occurring variant	unknown	Oar_v3.1	X	g.50977717T>A						2020	32636872
1281	OMIA:002306-9823	pig	German Landrace (Pig)	Infertility and increased litter size	BMP15		nonsense (stop-gain)	Naturally occurring variant	yes	Sscrofa11.1	X	g.44618787C>T		p.(R212*)	"NP_001005155.2:p.R212X" (Flossmann et al., 2021)			2021	33413103
862	OMIA:001551-9615	dog		Brachycephaly	BMP3		missense	Naturally occurring variant	yes	CanFam3.1	32	g.5231894C>A	c.1344C>A	p.(F448L)		rs851217657	rs851217657	2012	22876193	Variant coordinates obtained from or confirmed by EBI's Some Effect Predictor (VEP) tool
241	OMIA:000383-9940	sheep	Booroola (Sheep) Small Tailed Han, China (Sheep)	Fecundity, Booroola	BMPR1B	FecB(B)	missense	Naturally occurring variant	no	Oar_rambouillet_v1.0	6	g.34010859T>C	c.914A>G	p.(Q305R)	Position on Oar_v3.1: g.29382188T>C	rs418841713		2001	11259271	Variant coordinates obtained from or confirmed by EBI's Some Effect Predictor (VEP) tool, the genomic location on Oar_rambouillet_v1.0 was determined by Katie Eager, EMAI, NSW Department of Primary Industries.
1254	OMIA:000576-9823	pig	Yorkshire (Pig)	Knobbed acrosome defect	BOLL		deletion, gross (>20)	Naturally occurring variant	yes	Sscrofa11.1	15	g.101549770_101604750del						2020	32975846
93	OMIA:001512-9615	dog		Invasive transitional cell carcinoma of the bladder	BRAF		missense	Naturally occurring variant	yes	CanFam3.1	16	g.8296284T>A	c.1643T>A	p.(V548E)	XM_005629551.3; XP_005629608.1; published as somatic mutation p.(V594E)			2015	25767210
851	OMIA:002132-9615	dog	German Shorthaired Pointer	Abortion (embryonic lethality), BTBD17-related	BTBD17		insertion, small (<=20)	Naturally occurring variant	yes	CanFam3.1	9	g.6048201_6048202insG	c.85+206_85+207insG		ROS_Cfam_1.0:g.6720627_6720628insG ENSCAFT00845033049.1:c.85+206_85+207insG	rs852549625		2017	29053721
981	OMIA:001991-9913	cattle	Nordic Red (Cattle)	Stillbirth	BTBD9		deletion, gross (>20)	Naturally occurring variant	yes		23				"∼525 KB deletion on Chr23:12,291,761-12,817,087 (overlapping BTBD9, GLO1 and DNAH8)"			2016	27091210
325	OMIA:001622-9031	chicken		Resistance to avian sarcoma and leukosis viruses, subgroup C	BTN1A1		nonsense (stop-gain)	Naturally occurring variant	no	GRCg6a	28	g.903289G>T	c.165C>A	p.(C55*)		rs735807319	rs735807319	2005	16051833	Variant coordinates obtained from or confirmed by EBI's Some Effect Predictor (VEP) tool
583	OMIA:001575-9615	dog	Gordon Setter Irish Setter Miniature Poodle Old Danish Pointing Dog (Dog) Polski Owczarek Nizinny Polski Owczarek Podhalanski Standard Poodle Tibetan Terrier	Rod-cone dysplasia 4	C17H2orf71		insertion, small (<=20)	Naturally occurring variant	yes	CanFam3.1	17	g.22907394_22907395insG	c.3149_3150insC	p.(C1051Vfs*90)	NM_001284459.1; NP_001271388.1; genomic position adjusted based on HGVS 3' rule; EVA variant with equivalent alleles: rs397510935	rs1152388416	rs1152388416	2013	22686255
1047	OMIA:000303-9031	chicken	White Leghorn (Chicken)	Dwarfism, autosomal	C1H12ORF23		nonsense (stop-gain)	Naturally occurring variant	yes	GRCg6a	1	g.53638233C>T	c.433G>A	p.(W59*)	Wu et al. (2018): "NM_001006244.1:c.433G > A . . . NP_001006244.1:p.(Trp59∗)"			2018	29930570
1085	OMIA:001040-9615	dog	Rhodesian Ridgeback	Ventricular arrhythmias and sudden death	C20H19orf70		missense	Naturally occurring variant	yes	CanFam3.1	20	g.54343438G>A	c.325G>A	p.(G109S)	ENSCAFG00000018796: g.54343438 G>A. ENSCAFT00000029838.4:c.325G>A ENSCAFP00000027731.3:p.G109S)	rs852200012	rs852200012	2019	30795627
455	OMIA:000155-9615	dog	Brittany Spaniel	C3 deficiency	C3		deletion, small (<=20)	Naturally occurring variant	yes	CanFam3.1	20	g.53573746del	c.2136del	p.(F712Lfs*11)	XM_038428862.1; XP_038284790.1 "a deletion of a cytosine at position 2136 (codon 712), leading to a frameshift that generates a stop codon 11 amino acids downstream"			1998	9510185
1087	OMIA:002201-9913	cattle	Normande (Cattle)	Abortion due to haplotype NH7	CAD		missense	Naturally occurring variant	yes	ARS-UCD1.2	11	g.72409143T>C		p.(Y452C)	published as CAD g.72399397T>C; p.Tyr452Cys			2019	31056337	The genomic location on ARS-UCD1.2 was determined by Katie Eager and Shernae Woolley, EMAI, NSW. Department of Primary Industries.
1490	OMIA:002573-151761	yellow-crowned parrot		Lewy body-like disease	CADPS2		missense	Naturally occurring variant	yes				c.1675G>C	p.(V559L)				2022	36086934
105	OMIA:001820-9615	dog	Parson Russell Terrier	Ataxia, spinocerebellar	CAPN1		missense	Naturally occurring variant	yes	CanFam3.1	18	g.52009339C>T	c.344G>A	p.(C115Y)	XM_540866.5; XP_540866.2			2013	23741357	Genomic coordinates in CanFam3.1 provided by Robert Kuhn
49	OMIA:001138-9615	dog	American Foxhound Beagle	Hypocatalasia	CAT		missense	Naturally occurring variant	yes	CanFam3.1	18	g.33397548C>T	c.979G>A	p.(A327T)				2000	11137458	Variant coordinates obtained from or confirmed by EBI's Some Effect Predictor (VEP) tool
516	OMIA:001416-9612	gray wolf		Coat colour, dominant black	CBD103	K^B	deletion, small (<=20)	Naturally occurring variant	no						3bp deletion of the CBD103 gene			2009	19197024
520	OMIA:001416-9614	coyote		Coat colour, dominant black	CBD103		deletion, small (<=20)	Naturally occurring variant	no						3bp deletion of the CBD103 gene			2009	19197024
458	OMIA:001416-9615	dog		Coat colour, dominant black	CBD103	ΔG23 = K^B	deletion, small (<=20)	Naturally occurring variant	no	CanFam3.1	16	g.58965449_58965451del	c.231_233del	p.(G78del)	"a 3-base pair (bp) deletion in the second exon of CBD103, the ortholog of human DEFB103, that predicts an in-frame glycine deletion (Î”G23)"	rs851502010	rs851502010	2007	17947548	Genomic location provided by Professor Claire Wade August 2018. Allele designations taken from Ollivier et al. (2013)
1032	OMIA:002167-9913	cattle	Nordic Red (Cattle)	Asthenospermia	CCDC189		splicing	Naturally occurring variant	yes	ARS-UCD1.2	25	g.26880841C>T			Touru et al. (2019): "a variant disrupting a canonical 5’ splice donor site (GCA_000003055.3:Chr25:g.27138357C>T) in CCDC189 (transcript - ID:ENSBTAT00000045037) encoding the coiled-coil domain containing protein 189."			2019	30975085
266	OMIA:001540-9615	dog	Old English Sheepdog	Ciliary dyskinesia, primary	CCDC39		nonsense (stop-gain)	Naturally occurring variant	yes	CanFam3.1	34	g.13952270G>A	c.286C>T	p.(R96*)				2011	21131972	Variant coordinates obtained from or confirmed by EBI's Some Effect Predictor (VEP) tool
1403	OMIA:002342-9940	sheep	Blanc Du Massif Central (Sheep) Lacaune (Sheep)	Ciliary dyskinesia, primary (respiratory failure)	CCDC65	LDHH6	nonsense (stop-gain)	Naturally occurring variant	yes	Oar_rambouillet_v1.0	3	g.147207999C>A	c.521G>T	p.(E111*)	XM_004006389.4; XP_004006438.1; published as NC_040254.1:g.147,207,999C>A	rs1085624756		2021	35052387
1274	OMIA:001521-9615	dog	Portugese water dog	Progressive retinal atrophy, early onset	CCDC66	EOPRA	insertion, small (<=20)	Naturally occurring variant	yes	CanFam3.1	20	g.33717704_33717705insT	c.2262_c.2263insA	p.(V747Sfs*8)				2020	33273526
574	OMIA:001521-9615	dog	Schapendoes	Generalized PRA	CCDC66		insertion, small (<=20)	Naturally occurring variant	yes	CanFam3.1	20	g.33745452_33745453insT	c.521_522insA	p.(N174Kfs*2)	NM_001168012.1; NP_001161484.1; genomic coordinates in accordance with HGVS 3'-rule			2010	19777273	Genomic coordinates in CanFam3.1 provided by Zoe Shmidt and Robert Kuhn.
1008	OMIA:001752-9823	pig		Resistance to PRRS virus	CD163		deletion, gross (>20)	Naturally occurring variant	no		5				Burkhard et al (2018): "the deletion of exon 7 of CD163 using CRISPR/Cas9 editing"			2018	29925651
538	OMIA:001299-9031	chicken		Resistance to avian sarcoma and leukosis viruses, subgroup A	CD320		deletion, small (<=20)	Naturally occurring variant	no		28		c.502_511delCGCTCACCCC					2015	25873518
539	OMIA:001299-9031	chicken		Resistance to avian sarcoma and leukosis viruses, subgroup A	CD320		deletion, small (<=20)	Naturally occurring variant	no		28		c.502_516delCGCTCACCCCGCCCC					2015	25873518
395	OMIA:001299-9031	chicken		Resistance to avian sarcoma and leukosis viruses, subgroup A	CD320		splicing	Naturally occurring variant	no		28		c.506-515del10					2012	22171251
396	OMIA:001299-9031	chicken		Resistance to avian sarcoma and leukosis viruses, subgroup A	CD320		splicing	Naturally occurring variant	no		28		c.507-511del5					2012	22171251
603	OMIA:001299-9031	chicken		Resistance to avian sarcoma and leukosis viruses, subgroup A	CD320	tva^r2	insertion, small (<=20)	Naturally occurring variant	no	GRCg6a	28	g.985659_985660insCTCG	c.48_49insCTCG	p.(P18Afs)	NM_001044645.1; NP_001038110.1			2004	15564460	Genomic position in GRCg6a provided by Joshua Khamis.
12	OMIA:001299-9031	chicken		Resistance to avian sarcoma and leukosis viruses, subgroup A	CD320	tva^r	missense	Naturally occurring variant	no	GRCg6a	28	g.985980C>G	c.185C>G	p.(C62W)	NM_001044645.1; NP_001038110.1; published as c.120C>G and p.(C40W); coordinates in the table have been updated to a recent reference genome and / or transcript			2004	15564460	Genomic position in GRCg6a provided by Joshua Khamis.
1340	OMIA:002386-9544	Rhesus monkey		OKT4 epitope deficiency	CD4		missense	Naturally occurring variant	unknown		11		c.C793T	p.(A265W)				2021	33893743
1528	OMIA:002626-9913	cattle	Japanese Black, Japan (Cattle)	Haplotype with homozygous deficiency JBH17, CDC45-related	CDC45		splicing	Naturally occurring variant	yes	UMD_3.1.1	17	g.74743512G>T			located in a splicing donor site at a distance of 5 bp, affecting pre-mRNA splicing			2021	33758295
1496	OMIA:002584-9615	dog	Beauceron	Deafness, CDH23-related	CDH23		missense	Naturally occurring variant	yes	CanFam 3.1	4	g:22340631C>T	c.700C>T	p.(P234S)	ON462053; XM_022417544.1; XP_022273252.1			2022	36308003	The UU_Cfam_GSD_1.0 genomic variant coordinate is: g.Chr4:23074925C>T
3	OMIA:000102-9031	chicken		Sex-linked extreme dilution	CDKN2A	B0	complex rearrangement	Naturally occurring variant	no		Z				The B0 allele is characterised by two non-coding variants:Â "The first, SNP1, is within the CDKN2A (ARF) promoter region, 265 bp upstream of the transcription start site (according to GenBank AY138245), and the second, SNP2, is located at nucleotide position 385 bp in CDKN2A intron 1"			2010	20374521
5	OMIA:000102-9031	chicken		Sex-linked dilution	CDKN2A	B2	missense	Naturally occurring variant	no	GRCg6a	Z	g.78856557G>A	c.28C>T	p.(R10C)			rs1059941965	2010	20374521	Variant coordinates obtained from or confirmed by EBI's Some Effect Predictor (VEP) tool
4	OMIA:000102-9031	chicken		Sex-linked barring	CDKN2A	B1	missense	Naturally occurring variant	no	GRCg6a	Z	g.78856559A>T	c.26T>A	p.(V9D)			rs3388417177	2010	20374521	Variant coordinates obtained from or confirmed by EBI's Some Effect Predictor (VEP) tool
863	OMIA:001890-198806	ruff		Male body size/courtship behaviour	CENPN		inversion	Naturally occurring variant	unknown						"a 4.5Mb inversion on the ruff orthologue of chicken chromosomr GGA11 which, due to the well-known lethality of recombinants within an inversion, has created a supergene determining male breeding behaviour, body size and plumage colour"			2016	26569123
991	OMIA:001830-9913	cattle	Holstein (black and white) (Cattle)	Abortion due to haplotype HH7	CENPU		deletion, small (<=20)	Naturally occurring variant	yes	ARS-UCD1.2	27	g.15123637_15123640del			Hozé et al. (2019): "Considering that CENPU is transcribed in the antisense orientation, this mutation is predicted to result in deletion of the nucleotides located at position +3 to + 6 bp after the splicing donor site of exon 11. Using cross-species nucleotide alignment, we observed that the nucleotide at position +3 is entirely conserved among vertebrates . . . , which suggests that it plays an important role in regulation of CENPU splicing. If modified after exon 11, the abnormal splicing of CENPU could cause mRNA decay or the production of a protein modified after residue 319 out of 409 AA. Based on these factors, we assumed that mutation g.14168130_14168133delTACT on chromosome 27 alters the splicing of CENPU and is embryonic lethal."			2020	31733857
964	OMIA:001502-9913	cattle	Montbéliarde (Cattle)	Caprine-like Generalized Hypoplasia Syndrome	CEP250		nonsense (stop-gain)	Naturally occurring variant	yes	ARS-UCD1.2	13	g.64710424C>T	c.493C>T	p.(Q165*)				2015	25902731	Coordinates obtained from and/or confirmed by EBI's VEP
384	OMIA:001244-9685	domestic cat	Abyssinian (Cat) American Curl (Cat) American Wirehair (Cat) Balinese (Cat) Bengal (Cat) Colorpoint Shorthair (Cat) Cornish Rex (Cat) Munchkin (Cat) Ocicat (Cat) Oriental Shorthair (Cat) Peterbald (Cat) Siamese (Cat) Singapura (Cat) Somali (Cat) Tonkinese (Cat)	Retinal degeneration II	CEP290		splicing	Naturally occurring variant	yes	Felis_catus_9.0	B4	g.112522818A>C	c.7584+9T>G		XM_023256243.1; published as IVS50 + 9T>G. The cat sequenced to generate the Felis_catus_9.0 reference genome is homozygous for the likely causal variant. The genomic and cDNA coordinates had therefore been previously listed in this table as g.112522818TC>A and c.7584+9G>T. The information has been updated based on feedback from 潘旭 to reflect that the likely causal variant is c.7584+9G and that the normal allele is c.7584+9T[6/4/2023].			2007	17507457	The genomic location on Felis_catus_9.0 and transcript information is based on Rodney et al. 2021 (PMID: 33785770). Variant was initially identified in the Abyssinian and Somali breeds but identified to be present in several other breeds (Menotti-Raymond et al., 2020; Pubmed:19747862)
177	OMIA:000636-9823	pig		Membranoproliferative glomerulonephritis type II	CFH		missense	Naturally occurring variant	yes	Sscrofa11.1	10		c.3610T>G	p.(I1166R)	CFH is located on Chr10 in Sscrofa10.2 g.2553907T>G, but recorded as 'unplaced/NW_018085100.1' in Sscrofa11.1.			2002	12466119	The genomic location on Sscrofa11.1 was determined by Stephanie Shields (27/05/2020)
1479	OMIA:001794-9940	sheep	Romney (Sheep)	Cystic fibrosis	CFTR		nonsense (stop-gain)	Genome-editing (CRISPR-Cas9)	yes	Oar_rambouillet_v1.0	4	g.57192317C>A	c.1621G>T	p.(G541*)	NM_001009781.1; NP_001009781.1; published as p.(G542X), coordinates in this table are updated to recent reference sequence			2021	34632318
1478	OMIA:001794-9940	sheep	Romney (Sheep)	Cystic fibrosis	CFTR		deletion, small (<=20)	Genome-editing (CRISPR-Cas9)	yes	Oar_rambouillet_v1.0	4	g.57218683_57218685del	c.1518_1520del	p.(F507del)	NM_001009781.1; NP_001009781.1; published as p.(F508del), coordinates are updated in this table to recent reference sequence			2021	34632318
61	OMIA:002072-9615	dog	Old Danish Pointing Dog (Dog)	Myasthenic syndrome, congenital	CHAT		missense	Naturally occurring variant	yes	CanFam3.1	28	g.1484906G>A	c.85G>A	p.(V29M)	XM_005637485.3; XP_005637542.1			2007	17586598	20181218 Thanks to Maarten de Groot for advising FN of the genomic location of this variant.
838	OMIA:002125-9913	cattle	Montbéliarde (Cattle)	Neurocristopathy	CHD7		deletion, small (<=20)	Naturally occurring variant	yes	ARS-UCD1.2	14	g.26402250_26402254del		p.(K594Afs*29)				2017	28904385
554	OMIA:002022-9913	cattle	Red Dane (Cattle)	Arthrogryposis multiplex congenita, CHRNB1-related	CHRNB1		deletion, small (<=20)	Naturally occurring variant	yes	ARS-UCD1.2	19	g.27122027del	c.55del	p.(A19Pfs47*)	Published as Chr19:27757270CG > C; CHRNB1 c.55delG; (p.Ala19Profs47*)			2016	27364156	The genomic location on ARS-UCD1.2 was determined by Katie Eager and Shernae Woolley, EMAI, NSW. Department of Primary Industries.
490	OMIA:000685-9913	cattle	Brahman (Cattle)	Myasthenic syndrome, congenital, CHRNE-related	CHRNE	470del20	deletion, small (<=20)	Naturally occurring variant	yes	ARS-UCD1.2	19	g.26485848_26485867del	c.470_489del		Kraner et al. (2002): "a loss of 20 bp within the coding sequence of exon 5 (Fig. 2), between nucleotide 469 and 490 (nucleotide numbering referring to the cDNA sequence published under accession number X02597". These authors (and subsequent authors) call this variant "470del20". The current (2020) HGVS nomenclature is c.470_489del 200922: g. information move here (g.27119615) until standardised			2002	12481987	Variant information kindly provided or confirmed by Hubert Pausch, including information from Additional Table 6 of Jansen et al. (2013) BMC Genomics201314:446 https://doi.org/10.1186/1471-2164-14-446. The genomic location on ARS-UCD1.2 was determined by Katie Eager and Shernae Woolley, EMAI, NSW. Department of Primary Industries.
614	OMIA:000685-9615	dog	Jack Russell Terrier	Myasthenic syndrome, congenital, due to CHRNE	CHRNE		insertion, small (<=20)	Naturally occurring variant	yes	CanFam3.1	5	g.31705136_31705137insC	c.636_637insC	p.(G212Rfs*274)	ENSCAFT00000083466.1; ENSCAFP00000057633.1; published as c.633_634insC, coordinates in the table updated in accordance to HGVS 3'-rule			2015	26429099
804	OMIA:000685-9615	dog	Heideterrier	Myasthenic syndrome, congenital, due to CHRNE	CHRNE		insertion, small (<=20)	Naturally occurring variant	yes	CanFam3.1	5	g.31707450_31707451insG	c.1436_1437insG	p.(S479Rfs*14)	XM_014113502.1; XP_013968977.1			2017	28508416
399	OMIA:000698-89462	water buffalo		Myotonia	CLCN1		splicing	Naturally occurring variant	yes				c.396C>T					2013	23339992
224	OMIA:000698-9925	goat		Myotonia	CLCN1		missense	Naturally occurring variant	yes	ARS1	4	g.13857007C>G	c.2590G>C	p.(P864A)	ENSEMBL Variant Effect Predictor: transcript ENSCHIT00000031898.1			1996	8855341
609	OMIA:000698-9615	dog	Australian Cattle Dog Border Collie	Myotonia	CLCN1		insertion, small (<=20)	Naturally occurring variant	yes	CanFam3.1	16	g.6344748_6344749insT	c.2647_2648insA	p.(R883Qfs*18)	NM_001003124.2; NP_001003124.1; published as c.2665insA; p.(R889fs); coordinates in the table have been updated to a recent reference genome and / or transcript			2007	17552451
1041	OMIA:000698-9615	dog	Labrador Retriever	Myotonia	CLCN1		nonsense (stop-gain)	Naturally occurring variant	yes	CanFam3.1	16	g.6348929T>A	c.2275A>T	p.(R759X)	Quitt et al. (2018): "Chr16:6348929 T A CLCN1 ENSCAFG00000003619.3 stopgain"			2018	29934119
62	OMIA:000698-9615	dog	Miniature Schnauzer	Myotonia	CLCN1		missense	Naturally occurring variant	yes	CanFam3.1	16	g.6366383G>A	c.803C>T	p.(T268M)				1999	10452529	Variant coordinates obtained from or confirmed by EBI's Some Effect Predictor (VEP) tool
1364	OMIA:000698-9615	dog	American Bulldog	Myotonia	CLCN1		insertion, small (<=20)	Naturally occurring variant	yes	CanFam3.1	16	g.6369245_6369246insAGAG	c.436_437insCTCT	p.(Y146Sfs*49)	cDNA and protein position based on NM_001003124.2 and NP_001003124.1			2020	33246886
1570	OMIA:000698-9615	dog	Mixed breed (dog)	Myotonia	CLCN1		deletion, gross (>20)	Naturally occurring variant	yes	CanFam3.1	16	g.[6367458_6367478del;6367482del;6367485A>C]	c.[703T>G;706del;710_730del]	p.[(F235V;V236fs)]	NM_001003124.2; NP_001003124.1; published as c.[705T>G; 708del; 712_732del], coordinates in the table have been updated to the CanFam3.1 reference genome.			2023	37212506
161	OMIA:000698-9796	horse	New Forest Pony (Horse)	Myotonia	CLCN1		missense	Naturally occurring variant	yes	EquCab3.0	4	g.96518592A>C	c.1775A>C	p.(D592A)	c.1775A>C, Genbank acc. XM_001915636); p.D592A, Genbank acc. XP_001915671 (Wijnberg et al., 2014)			2012	22197188	(FN thanks Izabela De Assis Rocha, who provided genomic location in EquCab3.0 and the Genbank acc IDs, working under the supervision of Professor Ernie Bailey; 15 April 2020) Revised genomic location kindly provided by Cord Drögemüller; 21 May 2021
1573	OMIA:000698-9685	domestic cat	Domestic Longhair	Myotonia	CLCN1		deletion, small (<=20)	Naturally occurring variant	yes	Felis_catus_9.0	A2	g.158967085_158967092del		p.(L143Qfs3*)	published as chrA2:15897085‐15 897 092, coordinates in this table have been verified in Felis_catus_9.0			2022	35815860	NP_001291956.1
408	OMIA:000698-9685	domestic cat		Myotonia	CLCN1		splicing	Naturally occurring variant	yes	Felis_catus_9.0	A2	g.158986498G>T	c.1930+1G>T		NM_001305027.1			2014	25356766	Variant coordinates obtained from or confirmed by EBI's Some Effect Predictor (VEP) tool
245	OMIA:000698-9940	sheep	Rasa Aragonesa, Spain (Sheep)	Myotonia	CLCN1		missense	Naturally occurring variant	yes	Oar_rambouillet_v1.0	4	g.115541101G>A	c.277G>A	p.(E93K)	Oar_v3.1 position is g.106140081G>A published as p.Gln93Lys. cDNA and protein position predicted using Variant Effect Predictor ENSOART00020002372.1	rs401726021		2015	25744800	The genomic location on Oar_rambouillet_v1.0 was determined by Katie Eager, EMAI, NSW Department of Primary Industries.
1365	OMIA:000698-9823	pig		Myotonia	CLCN1		deletion, gross (>20)	Naturally occurring variant	yes	Sscrofa11.1	18	g.6912538_6916702del						2019	31666547
210	OMIA:001887-9913	cattle	Belgian Blue (Cattle)	Osteopetrosis with gingival hamartomas	CLCN7		missense	Naturally occurring variant	yes	ARS-UCD1.2	25	g.[1139611G>T; 1139613A>G]	c.[2248T>C;2250C>A]	p.(Y750Q)				2014	24159188	The genomic location on ARS-UCD1.2 was determined by Katie Eager and Shernae Woolley, EMAI, NSW. Department of Primary Industries.
648	OMIA:001135-9913	cattle	Japanese Black, Japan (Cattle)	Renal dysplasia	CLDN16	Type 1	deletion, gross (>20)	Naturally occurring variant	yes		1				37kb deletion of exons 1-4			2000	10810088
781	OMIA:001135-9913	cattle	Japanese Black, Japan (Cattle)	Renal dysplasia	CLDN16	Type 2	deletion, gross (>20)	Naturally occurring variant	yes		1				"a 56-kb deletion that eliminates exons 1-4 and 21-bp of exon 5" 200922: g. info moved to here (g.77528017_?) until can be standardised			2002	12047224	Some variant information kindly provided or confirmed by Hubert Pausch, including information from Additional Table 6 of Jansen et al. (2013) BMC Genomics201314:446 https://doi.org/10.1186/1471-2164-14-446
593	OMIA:001482-9913	cattle	Devon (Cattle)	Neuronal ceroid lipofuscinosis, 5	CLN5		insertion, small (<=20)	Naturally occurring variant	yes	ARS-UCD1.2	12	g.52112732_52112733insG	c.662_663insG	p.(R221Gfs*6)				2006	16935476	Breed and variant information kindly provided or confirmed by Matt McClure and Jennifer McClure from "Understanding Genetics and Complete Genetic Disease and Trait Definition (Expanded 2016 Edition)" (https://www.icbf.com/wp/?page_id=2170) 210909: after checking the genome assembly sequence, FN changed g.52461241insG to g.52461241_52461242insG; and c.662insG to c.662_663insG
279	OMIA:001482-9615	dog	Australian Cattle Dog Border Collie	Neuronal ceroid lipofuscinosis, 5	CLN5		nonsense (stop-gain)	Naturally occurring variant	yes	CanFam3.1	22	g.30574637C>T	c.619C>T	p.(Q207*)		rs1152388418	rs1152388418	2005	16033706	Variant coordinates obtained from or confirmed by EBI's Some Effect Predictor (VEP) tool 30 Dec 2020: g. coordinate corrected, with thanks to Angelica K Kallenberg
541	OMIA:001482-9615	dog	Golden Retriever	Neuronal ceroid lipofuscinosis, 5	CLN5		deletion, small (<=20)	Naturally occurring variant	yes	CanFam3.1	22	g.30574953_30574954del	c.935_936del	p.(E312Vfs*6)	NM_001011556.1; NP_001011556.1,published as CLN5:c.934_935delAG; coordinates in the table have been updated to a recent reference genome and / or transcript			2015	25934231	Breed information obtained from Katz et al. (2017) Neurobiol Dis. doi: 10.1016/j.nbd.2017.08.017; Genomic coordinates in CanFam3.1 provided by Zoe Shmidt and Robert Kuhn.
389	OMIA:001482-9940	sheep	Borderdale, New Zealand (Sheep)	Neuronal ceroid lipofuscinosis, 5	CLN5		splicing	Naturally occurring variant	yes	Oar_rambouillet_v1.0	10	g.56313269G>A	c.571+1G>A			rs422165326		2008	17988881	The genomic location on Oar_rambouillet_v1.0 was determined by Katie Eager, EMAI, NSW Department of Primary Industries.
68	OMIA:001443-9615	dog	Australian Shepherd	Neuronal ceroid lipofuscinosis, 6	CLN6		missense	Naturally occurring variant	yes	CanFam3.1	30	g.32247875A>G	c.829T>C	p.(W277R)	ROS_Cfam_1.0:g.32443458A>G ENSCAFT00845033654.1:c.829T>C ENSCAFP00845026347.1:p.Trp277Arg	rs1152388420	rs1152388420	2011	21234413	Variant coordinates obtained from or confirmed by EBI's Variant Effect Predictor (VEP) tool
1213	OMIA:001443-9685	domestic cat	Domestic medium-haired	Neuronal ceroid lipofuscinosis, 6	CLN6		nonsense (stop-gain)	Naturally occurring variant	yes	Felis_catus_9.0	B3	g.39334330G>A	c.668G>A	p.(W223*)	ENSFCAT00000025909:c.668G>A; XM_003987007.5:c.668G>A (Katz et al. (2020)			2020	32518081
671	OMIA:001443-9940	sheep	South Hampshire, New Zealand (Sheep)	Neuronal ceroid lipofuscinosis	CLN6		deletion, gross (>20)	Naturally occurring variant	yes	Oar_rambouillet_v1.0	7				deletion of exon 1			2013	23338040
234	OMIA:001443-9940	sheep	Merino (Sheep)	Neuronal ceroid lipofuscinosis, 6	CLN6		missense	Naturally occurring variant	yes	Oar_rambouillet_v1.0	7	g.16039510G>A	c.184C>T	p.(R62C)	protein and cDNA position based on NP_001035379.1 and NM_001040289.1, respectively	rs399747319		2006	17046213	The genomic location on Oar_rambouillet_v1.0 was determined by Katie Eager, EMAI, NSW Department of Primary Industries.
1030	OMIA:001962-9542	Japanese macaque		Neuronal ceroid lipofuscinosis, 7	CLN7		deletion, small (<=20)	Naturally occurring variant	yes		4		c.769delA	p.(I257Lfs*36)				2018	30048804
690	OMIA:001506-9615	dog	Alpenländische Dachsbracke	Neuronal ceroid lipofuscinosis, 8	CLN8		deletion, gross (>20)	Naturally occurring variant	yes	CanFam3.1	37	g.30852988_30902901del	c.-14679_*18669del		NM_001012343.1; a homozygous deletion encompassing the entire CLN8 gene			2017	28024876	g. information obtained from Katz et al. (2017) Neurobiol Dis. doi: 10.1016/j.nbd.2017.08.017
971	OMIA:001506-9615	dog	Saluki	Neuronal ceroid lipofuscinosis, 8	CLN8		insertion, small (<=20)	Naturally occurring variant	yes	CanFam3.1	37	g.30874636dupT	c.349dupT	p.(E117*)	"an insertion of 1 bp (T) in the CLN8 gene (Fig. S2) in a short T repeat, thereby changing the stretch of 9 T's to a stretch consisting of 10 T's. The exact position of the inserted base could obviously not be verified, given that this was an insertion of a single base in a stretch of nine repeats of the same base (CFA37:g.30874628–30874636). According to the recommended nomenclature, the T insertion was noted as a T duplication in the T farthest in the 3′ direction (g.30874636dupT; c.349dupT)"			2018	29446145
69	OMIA:001506-9615	dog	English Setter	Neuronal ceroid lipofuscinosis, 8	CLN8		missense	Naturally occurring variant	yes	CanFam3.1	37	g.30874779T>C	c.491T>C	p.(L164P)				2005	15629147	Variant coordinates obtained from or confirmed by EBI's Some Effect Predictor (VEP) tool
338	OMIA:001506-9615	dog	Australian Shepherd German Shorthaired Pointer	Neuronal ceroid lipofuscinosis, 8	CLN8		nonsense (stop-gain)	Naturally occurring variant	yes	CanFam3.1	37	g.30883950G>A	c.585G>A	p.(W195*)	NM_001012343: c.585G>A (Guo et al., 2014)			2014	24953404	Variant coordinates obtained from or confirmed by EBI's Some Effect Predictor (VEP) tool; confirmed by Guo et al. (2019, pages 3, 4, 5 and 6), assuming that the g. coordinate (g.30,895,648) in the abstract of Guo et al. (2019) is a typo.
431	OMIA:000119-9685	domestic cat		Blood group system AB	CMAH		regulatory	Naturally occurring variant	no	Felis_catus_9.0	B2	g.4934641C>T			published as C-371T			2007	17553163
1432	OMIA:000119-9685	domestic cat		Blood group system AB	CMAH		regulatory	Naturally occurring variant	no	Felis_catus_9.0	B2	g.4934795G>A			published as G-217A			2007	17553163
430	OMIA:000119-9685	domestic cat		Blood group system AB	CMAH		insertion, small (<=20)	Naturally occurring variant	no	Felis_catus_9.0	B2	g.4934941_4934942insAACGAGCAACCGAAGCTG			published as "an indel in the exon 1 5' UTR"; Delta-53; Felis_catus_9.0 represents the deletion allele			2007	17553163	Genomic position in Felis_catus_9.0 provided by Leslie Lyons and Reuben Buckley.
1431	OMIA:000119-9685	domestic cat		Blood group system AB	CMAH		missense	Naturally occurring variant	no	Felis_catus_9.0	B2	g.4935345C>T	c.139C>T	p.(R47C)	NM_001244985.1; NP_001231914.1; published as c.136C>T			2014	24697343	Genomic position in Felis_catus_9.0 provided by Leslie Lyons and Reuben Buckley.
118	OMIA:000119-9685	domestic cat		Blood group system AB	CMAH		missense	Naturally occurring variant	no	Felis_catus_9.0	B2	g.4935348G>A	c.142G>A	p.(V48M)	NM_001244985.1; NP_001231914.1; initially reported as Felis_catus_6.2: B2:4587414G>A; c.139G>A; p.(V47M)			2007	17553163	The genomic location on Felis_catus_9.0 is based on Rodney et al. 2021 (PMID: 33785770)
800	OMIA:000119-9685	domestic cat		2019 TYPING PANEL	CMAH		missense	Naturally occurring variant	no	Felis_catus_9.0	B2	g.4935385G>T	c.179G>T	p.(G60V)	NM_001244985.1; NP_001231914.1			2016	27755584	The genomic location on Felis_catus_9.0 is based on Rodney et al. 2021 (PMID: 33785770)
801	OMIA:000119-9685	domestic cat		Blood group system AB	CMAH		missense	Naturally occurring variant	no	Felis_catus_9.0	B2	g.4935393A>G	c.187A>G	p.(I63V)	NM_001244985.1; NP_001231914.1			2016	27755584
119	OMIA:000119-9685	domestic cat		2019 TYPING PANEL	CMAH		missense	Naturally occurring variant	no	Felis_catus_9.0	B2	g.4938728T>A	c.268T>A	p.(Y90N)	NM_001244985.1; NP_001231914.1; published as c.265T>A (2007); revised designation of c.268T>A was reported by Kehl et al. (2019)			2007	17553163	The genomic location on Felis_catus_9.0 is based on Rodney et al. 2021 (PMID: 33785770)
1446	OMIA:000119-9685	domestic cat		Blood group system AB	CMAH		missense	Naturally occurring variant	no	Felis_catus_9.0	B2	g.4947482C>A	c.327A>C	p.(E109D)	NM_001244985.1; NP_001231914.1; published as c.327A>C; variant is reported to be not causal for blood type B, but may impact Neu5GC levels (Omi et al.,2016). The Felis_catus_9.0 reference genome represents the C allele, while transcript NM_001244985.1 represents the A allele.			2016	27171395
799	OMIA:000119-9685	domestic cat		2019 TYPING PANEL	CMAH		missense	Naturally occurring variant	no	Felis_catus_9.0	B2	g.4947519C>T	c.364C>T	p.(P122S)	NM_001244985.1; NP_001231914.1			2016	27171395	The genomic location on Felis_catus_9.0 is based on Rodney et al. 2021 (PMID: 33785770)
1413	OMIA:000119-9685	domestic cat		Blood group system AB	CMAH		missense	Naturally occurring variant	no	Felis_catus_9.0	B2	g.4953568G>A	c.773G>A	p.(R258Q)	NM_001244985.1; NP_001231914.1			2021	34589535
1430	OMIA:000119-9685	domestic cat		Blood group system AB	CMAH		deletion, small (<=20)	Naturally occurring variant	no	Felis_catus_9.0	B2	g.4955359del	c.933del	p.(A312Hfs*6)	NM_001244985.1; NP_001231914.1			2018	30235335	Genomic position in Felis_catus_9.0 provided by Leslie Lyons and Reuben Buckley.
1062	OMIA:000119-9685	domestic cat		2019 TYPING PANEL	CMAH		deletion, small (<=20)	Naturally occurring variant	no	Felis_catus_9.0	B2	g.4978934del	c.1322del	p.(L441*)	NM_001244985.1; NP_001231914.1; published as c.1322delT			2018	30235335	Genomic position in Felis_catus_9.0 provided by Leslie Lyons and Reuben Buckley.
120	OMIA:000119-9685	domestic cat		Blood group system AB	CMAH		missense	Naturally occurring variant	no	Felis_catus_9.0	B2	g.4985762G>A	c.1603G>A	p.(D535N)	NM_001244985.1; NP_001231914.1; also published as c.1600G>A; p.(D534N)			2007	17553163	The genomic location on Felis_catus_9.0 is based on Rodney et al. 2021 (PMID: 33785770)
547	OMIA:001977-9615	dog	Shetland Sheepdog	Progressive retinal atrophy, due to CNGA1 mutations	CNGA1		deletion, small (<=20)	Naturally occurring variant	yes	CanFam3.1	13	g.43831897_43831900del	c.1752_1755del	p.(T585Sfs*7)	NM_001003222.1; published as c.1752_1755delAACT			2015	26202106	Genomic and protein coordinates in CanFam3.1 provided by Robert Kuhn
548	OMIA:001481-9615	dog	Labrador Retriever	Achromatopsia-2	CNGA3		deletion, small (<=20)	Naturally occurring variant	yes	CanFam3.1	10	g.44234198_44234200del	c.1931_1933del	p.(V644del)	NM_001301112.1; published as c.1931_1933delTGG	rs852784090	rs852784090	2015	26407004	Genomic coordinates in CanFam3.1 and EVA ID provided by Robert Kuhn
97	OMIA:001481-9615	dog	German Shepherd Dog	Achromatopsia-2	CNGA3		missense	Naturally occurring variant	yes	CanFam3.1	10	g.44234861C>T	c.1270C>T	p.(R424W)	NM_001301112.1; NP_001288041.1			2015	26407004	Genomic position in CanFam3.1 provided by Mateo Etcheveste.
1016	OMIA:001481-9940	sheep	Awassi (Sheep)	Achromatopsia-2 (day blindness)	CNGA3		missense	Naturally occurring variant	yes	Oar_rambouillet_v1.0	3	g.108958871C>T	c.1618G>A	p.(G540S)				2017	28282490	Genomic coordinate on Oar_v4.0 (g.102602387G>A) kindly provided by Eyal Seroussi via Elisha Gootwine. The genomic location on Oar_rambouillet_v1.0 was determined by Katie Eager & Shernae Woolley, EMAI, NSW Department of Primary Industries.
317	OMIA:001481-9940	sheep	Awassi (Sheep)	Achromatopsia-2 (day blindness)	CNGA3		nonsense (stop-gain)	Naturally occurring variant	yes	Oori1 scaffold00739	3	g.263324C>T	c.706C>T	p.(R236*)	In a pers. comm. to FN via Elisha Gootwine, Eyal Seroussi advises that the Oar_v4.0 assembly has errors in the region of of this mutation, such that it cannot be mapped onto that assembly. It can, however, be mapped on to the Ovis aries musimon sequence: "Exon 8 mutation is at position 263,324 in Ovis aries musimon unplaced genomic scaffold, alternate assembly Oori1 scaffold00739 (Sequence ID: NW_011942977.1 Length: 1056687)"			2010	19874885
918	OMIA:000830-9615	dog	Papillon Phalène	Progressive retinal atrophy	CNGB1		delins, small (<=20)	Naturally occurring variant	yes	CanFam3.1	2	g.58622673_58622675delinsCTAGCTAC	c.2387_2389delinsCTAGCTAC	p.(Y796Sfs*7)	NM_001284462.1; NP_001271391.1; published as c.2685delA2687_2688insTAGCTA and p.(Y889Sfs*5); coordinates in the table have been updated to a recent reference genome and / or transcript and updated to HGVS recommendations		rs1152388403	2013	24015210
631	OMIA:001365-9615	dog	Alaskan Malamute Miniature Australian shepherd	Achromatopsia (cone degeneration, hemeralopia), AMAL	CNGB3	cd^AMAL	deletion, gross (>20)	Naturally occurring variant	yes		29				"deletion removing all exons of canine CNGB3"			2002	12140185
1400	OMIA:001365-9913	cattle	Brown Swiss (Cattle)	Achromatopsia	CNGB3	OH1	missense	Naturally occurring variant	yes	ARS-UCD1.2	14	g.76011964G>A	c.751G>A	p.(D251N)	XM_015474554.2: c.751G>A, XP_015330040.2: p.Asp251Asn ENSBTAT00000065296.2:c.751G>A ENSBTAP00000054173.2:p.Asp251Asn	rs716218235	rs716218235	2021	34830323
27	OMIA:001365-9615	dog	German Shorthaired Pointer	Achromatopsia (cone degeneration, hemeralopia), GSPT	CNGB3	cd^GSPT	missense	Naturally occurring variant	yes	CanFam3.1	29	g.32837065C>T	c.784G>A	p.(D262N)				2002	12140185	Variant coordinates obtained from or confirmed by EBI's Some Effect Predictor (VEP) tool 30 Dec 2020 Chromosome corrected, thanks to Angelica K Kallenberg
1502	OMIA:002591-9615	dog	Dalmatian	Lysosomal storage disease, CNP-related	CNP		deletion, small (<=20)	Naturally occurring variant	yes	Dog10K_Boxer_Tasha	9	g.20350240del	c.1107del	p.(K370Nfs*11)	ENSCAFT00000102206			2022	35447247
1273	OMIA:002301-9615	dog	Labrador Retriever Leonberger Saint Bernard	Laryngeal paralysis and polyneuropathy	CNTNAP1	LPPN3	missense	Naturally occurring variant	yes	CanFam3.1	9	g.20298261C>T	c.2810G>A	p.(G937E)	XM_548083.6:c.2810G>A; XP_548083.3:p.Gly937Glu	rs24587752	rs24587752	2020	33261176
172	OMIA:001718-9823	pig		Dwarfism, Schmid metaphyseal chondrodysplasia	COL10A1		missense	Naturally occurring variant	yes	Sscrofa11.1	1	g.81767089C>T	c.1768G>A	p.(G590R)				2000	11130976	The genomic and CDS position was determined by Stephanie Shields and the effect was confirmed with Ensembl VEP (27/05/2020)
78	OMIA:001772-9615	dog	Labrador Retriever	Skeletal dysplasia 2 (SD2)	COL11A2		missense	Naturally occurring variant	yes	CanFam3.1	12	g.2652874C>G	c.143G>C	p.(R48P)	ROS_Cfam_1.0:g.2983602C>G ENSCAFT00845034709.1:c.143G>C ENSCAFP00845027184.1:p.Arg48Pro	rs851399084	rs851399084	2013	23527306	Variant coordinates obtained from or confirmed by EBI's Some Effect Predictor (VEP) tool
1031	OMIA:002127-9913	cattle	Red Angus (Cattle)	Osteogenesis imperfecta, type II, COL1A1-related	COL1A1		missense	Naturally occurring variant	yes	ARS-UCD1.2	19	g.36463798G>A	c.1063G>A	p.(G355S)	Petersen et al. (2019): "PolyPhen-2 predicted the mutation to be “probably damaging” with a score of 1.000 (sensitivity 0.00; specificity 1.00). Similarly, PROVEAN prediction classified the variant as “Deleterious” with a score of − 4.615, exceeding both the default (− 2.5) and stringent (− 4.1) thresholds for this classification." The genomic coordinate in the UMD3.1 assembly is g.37094333G>A (Petersen et al., 2019). The coding sequence coordinates are c.1063G>A (ENSBTAT00000017420.4) (Petersen, pers. comm.)	rs3423092630	rs3423092630	2019	30788588
839	OMIA:002127-9913	cattle	Simmental (Cattle)	Osteogenesis imperfecta, type II, COL1A1-related	COL1A1		delins, small (<=20)	Naturally occurring variant	yes	ARS-UCD1.2	19	g.36470764_36470767delinsT	c.3145_3148delinsT	p.(A1049_P1050delinsS)	UMD3.1 position is g.37101299_37101302delinsT; cDNA position based on ENSBTAT00000017420.4	rs876049195	rs876049195	2017	28904385	The genomic location on ARS-UCD1.2 was determined by Katie Eager and Shernae Woolley, EMAI, NSW. Department of Primary Industries.
1289	OMIA:002127-9913	cattle	Holstein (black and white) (Cattle)	Osteogenesis imperfecta, type II, COL1A1-related	COL1A1		missense	Naturally occurring variant	yes	ARS-UCD1.2	19	g.36473359T>A	c.3917T>A	p.(V1306E)	NM_001034039.2: c.3917T>A; XP_024835395.1: p.Val1306Glu (Jacinto et al., 2021)			2021	33672767
959	OMIA:002126-9615	dog	Golden Retriever	Osteogenesis imperfecta, type III, COL1A1-related	COL1A1		missense	Naturally occurring variant	yes	CanFam3.1	9	g.26193593C>G	c.1145G>C	p.(G382A)	NM_001003090.1; NP_001003090.1; published as c.1276G>C, p.(G208A); coordinates in the table have been updated to a recent reference genome and / or transcript	rs1152388502	rs1152388502	2000	11147834
762	OMIA:002112-9615	dog	Beagle	Osteogenesis imperfecta, COL1A2-related	COL1A2		delins, small (<=20)	Naturally occurring variant	yes	CanFam3.1	14	g.(19918265_19918268delinsTGTCATTGG)	c.3656_3859delinsTGTCATTGG	p.(L1286Cfs*31)	NM_001003187.1; NP_001003187.1; "a mutation in which nucleotides 3991-3994 ("CTAG") were replaced with "TGTCATTGG." The first seven bases of the inserted sequence were identical to nucleotides 4002-4008 of the normal canine COL1A2 sequence. The resulting frameshift changed 30 amino acids and introduced a premature stop codon." The genomic information is presented in brackets as the variant was detected in cDNA and the genomic position is predicted. Coordinates in the table have been updated to a recent reference genome and or transcripts.			2001	11393792
1114	OMIA:002112-9615	dog	Lagotto Romagnolo	Osteogenesis imperfecta, COL1A2-related	COL1A2		duplication	Naturally occurring variant	yes	CanFam3.1	14	g.19898279_19898281dup	c.877_879dup	p.(P293dup)	NM_001003187.1; NP_001003187.1			2019	31468557
852	OMIA:002112-9615	dog	Chow Chow	Osteogenesis imperfecta, COL1A2-related	COL1A2		splicing	Naturally occurring variant	yes	CanFam3.1	14	g.19898487G>A	c.936+1G>A					2018	29036614
840	OMIA:001926-9913	cattle	Charolais (Cattle) Salers (Cattle)	Bulldog calf	COL2A1		missense	Naturally occurring variant	yes	ARS-UCD1.2	5	g.32301746G>A	c.1791G>A	p.(G600D)				2017	28904385	Variant coordinates obtained from or confirmed by EBI's Some Effect Predictor (VEP) tool
1275	OMIA:001926-9913	cattle	Holstein (black and white) (Cattle)	Bulldog calf	COL2A1		deletion, gross (>20)	Naturally occurring variant	yes	ARS-UCD1.2	5	g.32301911_32308589del			"Sanger sequencing revealed the precise breakpoints of the heterozygous deletion from position 32 301 911 located in intron 25 to 32 308 589 located within exon 45. The 6679 bp deletion includes the entire sequence of 18 exons (26–44) plus the first 36 nucleotides of exon 45" (Jacinto et al., 2020)			2021	33316082
1241	OMIA:001926-9913	cattle	Holstein (black and white) (Cattle)	Bulldog calf	COL2A1		delins, gross (>20)	Naturally occurring variant	yes	ARS-UCD1.2	5	g.32303127_32306640delinsTCTGGGGAGC						2020	32894162
842	OMIA:001926-9913	cattle	Holstein (black and white) (Cattle)	Bulldog calf	COL2A1		missense	Naturally occurring variant	yes	ARS-UCD1.2	5	g.32303739G>A	c.2158G>A	p.(G720S)				2017	28904385	Variant coordinates obtained from or confirmed by EBI's Some Effect Predictor (VEP) tool
414	OMIA:001926-9913	cattle	Danish Holstein (Cattle)	bulldog calf	COL2A1		splicing	Naturally occurring variant	yes	ARS-UCD1.2	5	g.32305226G>A	c.2463+1G>A					2016	27296271	Variant coordinates obtained from or confirmed by EBI's Some Effect Predictor (VEP) tool
223	OMIA:001926-9913	cattle	Holstein (black and white) (Cattle)	Bulldog calf	COL2A1		missense	Naturally occurring variant	yes	ARS-UCD1.2	5	g.32307658G>A		p.(G960R)			rs3423194986	2014	25017103
841	OMIA:001926-9913	cattle	Holstein (black and white) (Cattle)	Bulldog calf	COL2A1		missense	Naturally occurring variant	yes	ARS-UCD1.2	5	g.32308008G>A	c.2986G>A	p.(G996S)		rs876243579	rs876243579	2017	28904385	Variant coordinates obtained from or confirmed by EBI's Some Effect Predictor (VEP) tool
1026	OMIA:001926-9913	cattle	Holstein (black and white) (Cattle)	Bulldog calf	COL2A1		missense	Naturally occurring variant	yes	ARS-UCD1.2	5	g.32308734G>A	c.3166G>A	p.(G1056S)				2019	30378686
278	OMIA:002618-9615	dog	English Springer Spaniel	Nephropathy	COL4A4		nonsense (stop-gain)	Naturally occurring variant	yes	CanFam3.1	25	g.39893376G>A	c.2713C>T	p.(Q905*)	NM_001031818.1; NP_001026988.1; published as c.2806C>T and p.(Q904*)			2012	22369189
277	OMIA:002618-9615	dog	English Cocker Spaniel	Nephropathy	COL4A4		nonsense (stop-gain)	Naturally occurring variant	yes	CanFam3.1	25	g.39953906T>A	c.115A>T	p.(K39*)				2007	17552442	Variant coordinates obtained from or confirmed by EBI's Some Effect Predictor (VEP) tool
471	OMIA:001112-9615	dog	Navasota (mixed breed)	Nephritis, X-linked	COL4A5		deletion, small (<=20)	Naturally occurring variant	yes	CanFam3.1	X	g.82134508_82134517del	c.513_522del	p.(N172Ifs)	XM_005640969.3; XP_005641026.1; a 10 base pair (TAATCCAGGA) deletion in exon 9 of COL4A5			2003	12879362
276	OMIA:001112-9615	dog	Samoyed	Nephritis, X-linked	COL4A5		nonsense (stop-gain)	Naturally occurring variant	yes	CanFam3.1	X	g.82196868G>T	c.3079G>T	p.(G1027*)				1994	8171024	Variant coordinates obtained from or confirmed by EBI's Some Effect Predictor (VEP) tool
1124	OMIA:002165-9615	dog	Labrador Retriever	Ehlers-Danlos syndrome, classic type, 1	COL5A1		deletion, small (<=20)	Naturally occurring variant	yes	CanFam3.1	9	g.50806169del	c.3038del	p.(G1013Vfs*260)	XM_022423936.1; XP_022279644.1; published as c.3038delG - "variant arose by a de novo mutation event during the development of the mother." (Bauer et al., 2019)			2019	31546637
1125	OMIA:002165-9615	dog	Mixed breed (dog)	Ehlers-Danlos syndrome, classic type, 1	COL5A1		missense	Naturally occurring variant	yes	CanFam3.1	9	g.50832936G>A	c.4711G>A	p.(G1571R)	XM_022423936.1,c.4711G>A; XP_022279644.1,p.(Gly1571Arg)			2019	31546637
1465	OMIA:002165-9685	domestic cat	Bombay (Cat)	classical Ehlers-Danlos syndrome	COL5A1		nonsense (stop-gain)	Naturally occurring variant	yes	Felis_catus_9.0	D4	g.93209345T>A	c.3514A>T	p.(Lys1172*)	XM_023242950.1; XP_023098718.1			2022	35627182
1025	OMIA:002165-9685	domestic cat	Domestic Shorthair	Ehlers-Danlos syndrome, classic type, 1	COL5A1		deletion, small (<=20)	Naturally occurring variant	yes	Felis_catus_9.0	D4	g.93210344del	c.3420del	p.(L1141Sfs*134)	XM_023242951.1; XP_023098719.1; published as c.3420delG			2018	30246406
1466	OMIA:002165-9685	domestic cat	Domestic Shorthair	classical Ehlers-Danlos syndrome	COL5A1		deletion, small (<=20)	Naturally occurring variant	yes	Felis_catus_9.0	D4	g.93215496del	c.3066del	p.(Gly1023Valfs*50)	XM_023242950.1; XP_023098718.1			2022	35627182
1464	OMIA:002165-9685	domestic cat	Bengal (Cat)	classical Ehlers-Danlos syndrome	COL5A1		deletion, gross (>20)	Naturally occurring variant	yes	Felis_catus_9.0	D4	g.93331577_93331598del	c.112_118+15del	r.spl?	XM_023242950.1			2022	35627182
1263	OMIA:002295-9913	cattle	Holstein (black and white) (Cattle)	Ehlers-Danlos syndrome, classic type, 2	COL5A2		missense	Naturally occurring variant	yes	ARS-UCD1.2	2	g.7331916G>T	c.2366G>T	p.(G789V)	XM_024979774.1: c.2366G>T; XP_024835542.1: p.Gly789Val (Jacinto et al., 2020)			2020	33143196
1460	OMIA:002295-9615	dog	Chihuahua	Ehlers-Danlos syndrome, classic type, 2	COL5A2		deletion, gross (>20)	Naturally occurring variant	yes	CanFam3.1	36	g.30548697_30548723del	c.3388_3414del	p.(Lys1130_Asp1138del)	XM_005640393.3; XP_005640450.1			2022	35627319
340	OMIA:001967-9615	dog	Landseer	Muscular dystrophy, Ullrich type	COL6A1		nonsense (stop-gain)	Naturally occurring variant	yes	CanFam3.1	31	g.39303964G>T	c.289G>T	p.(E97*)	XM_003434001.5; XP_003434049.2; previously incorrectly listed in this table as c.289C>T; p.(Q97*) - corrected 8/2/2022			2015	26438297
1184	OMIA:002260-9913	cattle	Holstein (black and white) (Cattle)	de novo mutation in an AI sire	COL6A3		missense	Naturally occurring variant	yes	ARS-UCD1.2	3	g.116826597G>A		p.(T1894M)	Bourneuf et al. (2017) detected COL6A3 g.117453719G>A; p.T1894M as a de novo recessive potentially lethal mutation from an analysis of whole-genome-sequence of a Holstein AI bull. No information was provided on the descendants of this bull.			2017	28904385
1208	OMIA:002274-9615	dog	Labrador Retriever	Muscular dystrophy, COL6A3-related	COL6A3		splicing	Naturally occurring variant	yes	CanFam3.1	25	g.48007994C>T	c.6210+1G>A		CanFam3.1 chr25:48,007,994C > T; NM_001103215.1 c.6210 + 1G > A (Bolduc et al., 2020)			2020	32439203
1207	OMIA:002274-9615	dog	Labrador Retriever	Muscular dystrophy, COL6A3-related	COL6A3		nonsense (stop-gain)	Naturally occurring variant	yes	CanFam3.1	25	g.48014962G>A	c.4726C>T	p.(R1576*)	CanFam3.1 chr25:48,014,962G > A; NM_001103215.1 c.4726C > T, p.R1576* (Bolduc et al., 2020)			2020	32439203
292	OMIA:000341-9913	cattle	Rotes Höhenvieh, Germany (Cattle) Vorderwälder, Germany (Cattle)	Epidermolysis bullosa, dystrophic	COL7A1		nonsense (stop-gain)	Naturally occurring variant	yes	ARS-UCD1.2	22	g.51301158C>T	c.4762C>T	p.(R1588*)		rs876174537	rs876174537	2012	22715415	Variant coordinates obtained from or confirmed by EBI's Some Effect Predictor (VEP) tool; Breed and some variant information kindly provided or confirmed by Matt McClure and Jennifer McClure from "Understanding Genetics and Complete Genetic Disease and Trait Definition (Expanded 2016 Edition)" (https://www.icbf.com/wp/?page_id=2170)
357	OMIA:000341-9615	dog	Central Asian Shepherd	Epidermolysis bullosa, dystrophic	COL7A1		nonsense (stop-gain)	Naturally occurring variant	yes	CanFam3.1	20	g.40532043C>T	c.4579C>T	p.(R1527*)				2017	28493971	Variant coordinates obtained from or confirmed by EBI's Variant Effect Predictor (VEP) tool
38	OMIA:000341-9615	dog	Golden Retriever	Epidermolysis bullosa, dystrophic	COL7A1		missense	Naturally occurring variant	yes	CanFam3.1	20	g.40538034G>A	c.5716G>A	p.(G1906S)			rs1152388417	2003	12874109	Variant coordinates obtained from or confirmed by EBI's Some Effect Predictor (VEP) tool
1276	OMIA:000341-9615	dog	Basset Hound	Epidermolysis bullosa, dystrophic	COL7A1		complex rearrangement	Naturally occurring variant	yes	CanFam3.1	20	g.[40524302_40524308del;40524267_40524380dup]	c.[2028_2034del;1993_2050+56dup]	p.(V677Sfs*11)	NM_001002980.1; NP_001002980.1; complex duplication event spanning parts of exon 15 and intron 15 of the COL7A1 gene, starting at position 40,524,267 and ending at 40,524,380 on chromosome 20 (CanFam3.1 assembly) (Garcia et al., 2020).			2020	33291836
641	OMIA:001523-9615	dog	Samoyed	Oculoskeletal dysplasia 2	COL9A2		deletion, gross (>20)	Naturally occurring variant	yes		15				a 1,267 bp deletion that eliminates part of the 5â€™UTR, all of exon 1 and part of intron 1			2010	20686772
581	OMIA:001522-9615	dog	Labrador Retriever	Oculoskeletal dysplasia 1	COL9A3		insertion, small (<=20)	Naturally occurring variant	yes	CanFam3.1	24	g.46653422_46653423insG	c.10_11insG	p.(A4Gfs*46)	NM_001197171.1; NP_001184100.1; published as "a 1-base insertion (guanine) in exon 1 that changes a string of four guanines (CFA24: 49,699,847–49,699,850; CanFam2) to a string of five guanines (c.7–10insG). ... (p.A4GX46)" Goldstein et al. (2010). Information in this table has been changed in accordance to HGVS 3'rule and updated to the current reference genome.			2010	20686772
1092	OMIA:001522-9615	dog	Northern Inuit Dog	Oculoskeletal dysplasia 1	COL9A3		nonsense (stop-gain)	Naturally occurring variant	yes	CanFam3.1	24	g.46660067C>T	c.700C>T	p.(R234*)				2019	31415586
944	OMIA:001621-9685	domestic cat	Devon Rex (Cat) Sphynx (Cat)	Muscular dystrophy-dystroglycanopathy (limb-girdle)	COLQ		missense	Naturally occurring variant	yes	Felis_catus_9.0	C2	g.135068287C>T	c.1190G>A	p.(C397Y)		rs869320615	rs869320615	2015	26327126 26374066	Genomic location obtained via Ensembl's VEP
643	OMIA:001988-9615	dog	Bedlington Terrier	Wilson disease, COMMD1 type	COMMD1		deletion, gross (>20)	Naturally occurring variant	yes		10				deletion "breakpoints were positioned at 65.3091 and 65.3489 Mb of dog chromosome 10, in intron 1 and intron 2 of COMMD1 respectively, a deletion of 39.7 kb"			2005	16293123
1545	OMIA:002667-9031	chicken		Feather colour, Inhibitor of gold	COMTD1	IG	insertion, small (<=20)	Naturally occurring variant	no	GRCg6a	6	g.15675521_15675522insCT	c.747_748insCT	p.(Q250fs)	XM_015288295.1; XP_015143781.1			2023	37068079
215	OMIA:001529-9913	cattle	Holstein (black and white) (Cattle)	Dominant red	COPA	DR^DR	missense	Naturally occurring variant	no	ARS-UCD1.2	3	g.9361962C>T	c.478C>T	p.(R160C)			rs3423151160	2017	28904385	Variant coordinates obtained from or confirmed by EBI's Some Effect Predictor (VEP) tool
1506	OMIA:001274-452646	American mink		Coat colour, black crystal	COPA		missense	Naturally occurring variant	unknown	NNQGG.v01	FNWR01000261.1	g.4876673G>A	c.478C>T	p.(R160C)				2022	35729186
1012	OMIA:002159-9694	tiger		Golden tiger	CORIN		missense	Naturally occurring variant	no				c.1759C>T	p.(H587Y)				2017	28281538
1463	OMIA:002159-9685	domestic cat	British Shorthair (Cat)	Copper (British recessive wideband)	CORIN	wb^BSH	nonsense (stop-gain)	Naturally occurring variant	no	Felis_catus_9.0	B1		c.2425C>T	p.(R809*)	ON640807			2022	35703390
1456	OMIA:002159-9685	domestic cat	Siberian (Cat)	Extreme sunshine (Siberian recessive extreme wideband)	CORIN	wb^eSIB	missense	Naturally occurring variant	no	Felis_catus_9.0	B1	g.167737406G>A	c.839G>A	p.(C280Y)	XM_019829549.2; XP_019685108.1; reported as Genbank ID ON355336			2022	35574714
1313	OMIA:002159-9685	domestic cat	Siberian (Cat)	Sunshine (golden)	CORIN	wb^SIB	missense	Naturally occurring variant	no	Felis_catus_9.0	B1	g.167809720C>T	c.2383C>T	p.(R795C)	XM_019829551.2; XP_019685110.1			2021	33970502	Genomic position in Felis_catus_9.0 provided by Joshua Khamis.
358	OMIA:002111-9913	cattle	Holstein (red and white) (Cattle)	Cataract, recessive, CPAMD8-related	CPAMD8		nonsense (stop-gain)	Naturally occurring variant	yes	ARS-UCD1.2	7	g.6073556C>T	c.220C>T	p.(Q74*)				2017	28683140
1418	OMIA:002519-9913	cattle	Brown Swiss (Cattle)	Haplotype with homozygous deficiency BH24	CPT1C	BH24	missense	Naturally occurring variant	yes	ARS-UCD1.2	18	g.56098048G>A	c.158G>A	p.(G53D)	XM_002695120.5		rs719328437	2021	34915862
1428	OMIA:002533-9685	domestic cat	Domestic Shorthair	Osteogenesis imperfecta	CREB3L1		deletion, small (<=20)	Naturally occurring variant	yes	Felis_catus_9.0	D1	g.100436508_100436509del	c.370_371del	p.(C124Lfs)	XM_003993204.4; XP_003993253.1; published as c.370_371delTG			2022	35168412
916	OMIA:000881-9685	domestic cat	Abyssinian (Cat)	Rod-cone dysplasia	CRX	Rdy	deletion, small (<=20)	Naturally occurring variant	yes	F.catus_Fca126_mat1.0	E2	g.9492897del	c.546del	p.(P185Lfs*2)	XM_045045412.1; XP_044901347.1; published as CRX: n.546delC; in the Felis_catus_9.0 assembly the CRX gene is duplicated and genomic coordinates in this table are given for a more recent reference genome			2010	20053974
1491	OMIA:001643-10036	golden hamster		duper	Cry1		deletion, small (<=20)	Naturally occurring variant	unknown				c.578del	p.(P193fs)	published as c.578delC			2022	35471909
1176	OMIA:000168-10141	domestic guinea pig		Cataract	Cryz		splicing	Naturally occurring variant	yes						"a 102-bp deletion towards the 3' end of the coding region. This deletion does not interfere with the reading frame but results in a protein 34 amino acids shorter." (Rodriguez et al., 1992)			1992	1390943
692	OMIA:000852-9925	goat		Casein, alpha-S1, reduced concentration	CSN1S1		insertion, gross (>20)	Naturally occurring variant	no		6				"a 457-bp insertion within exon 19 (last untranslated exon). This insert is a truncated long interspersed repeated element (LINE) containing part of the ORF-2, the 3' UTR and the poly(A) tail of the original retroposon."			1994	7926797
907	OMIA:001623-9925	goat		Casein, alpha-S2, absence	CSN1S2		nonsense (stop-gain)	Naturally occurring variant	no	ARS1	6	g.86085134G>A	c.763G>A	p.(T110*)		rs268293093	rs268293093	2001	11419340	The genomic location on ARS1 was determined by Katie Eager, EMAI, NSW Department of Primary Industries
220	OMIA:002033-9913	cattle		A2 milk	CSN2	A2	missense	Naturally occurring variant	no	ARS-UCD1.2	6	g.85451298T>G	c.245A>C	p.(H82P)	Note that cattle cannot be genotyped for the A2 allele solely on the basis of the c.245A>C variant because this variant is common to 4 other alleles; see Table 2 of Caroli et al. (2009) J. Dairy Sci. 92, 5335-5352 (Matt McClure, pers. comm.)	rs43703011	rs43703011	2013	23102962	Variant coordinates obtained from or confirmed by EBI's Some Effect Predictor (VEP) tool
1312	OMIA:001424-9925	goat		Absence of β‐casein	CSN2	CSN2^0	deletion, small (<=20)	Naturally occurring variant	no	ARS1	6	g.86008404del	c.175del	p.I59Sfs*10	Changed from g.86008401del to g.86008404del to adhere to the HGVS 3’rule [220110] ENSCHIT00000032661.1:c.175del ENSCHIP00000024801.1:p.Ile59SerfsTer10 Persuy et al. (1999): "allele CSN2^O had a one-nucleotide deletion in the 5' end of exon 7, which introduces a premature stop codon. The open reading frame of allele CSN2^O encodes a shortened polypeptide of 72 amino acids, compared to 223 amino acids for caprine pre beta-casein A."	rs645737170	rs645737170	1999	10612234
1311	OMIA:001424-9925	goat		Absence of β‐casein	CSN2	CSN2^01	regulatory	Naturally occurring variant	no	ARS1	6	g.86015651A>G			Cosenza et al. (2016): "nucleotide C .... negatively affects the promoter activity of the CSN2 gene" Synonyms: dbSNP ss1245869815	rs654545998	rs654545998	2007	17931404	The genomic location on ARS1 was determined by Katie Eager, EMAI, NSW Department of Primary Industries
1186	OMIA:002262-9913	cattle	Montbéliarde (Cattle)	de novo mutation in an AI sire	CSNK1G2		missense	Naturally occurring variant	yes	ARS-UCD1.2	7	g.44265842G>C		p.(D164H)	Bourneuf et al. (2017) detected Chr7 CSNK1G2 g.45885860G>C; p.D164H as a de novo recessive potentially lethal mutation from an analysis of whole-genome-sequence of a Montbéliarde AI bull. No information was provided on the descendants of this bull.			2017	28904385
66	OMIA:001505-9615	dog	American Bulldog	Neuronal ceroid lipofuscinosis, 10	CTSD		missense	Naturally occurring variant	yes	CanFam3.1	18	g.46013354C>T	c.597G>A	p.(M199I)				2006	16386934	Variant coordinates obtained from or confirmed by EBI's Some Effect Predictor (VEP) tool
1517	OMIA:002607-9685	domestic cat	Domestic Longhair	Pyknodysostosis	CTSK		nonsense (stop-gain)	Naturally occurring variant	yes	Felis_catus_9.0	C1	g.105945826G>A	c.724C>T	p.(R242*)	ENSFCAT00000003643; variant is reported in a single affected cat			2022	36532681
529	OMIA:001786-9615	dog	Beagle	Intestinal cobalamin malabsorption due to CUBN mutation	CUBN		deletion, small (<=20)	Naturally occurring variant	yes	CanFam3.1	2	g.19796293del	c.786del	p.(D262Efs*47)	NM_001003148.1; NP_001003148.1; deletion C	rs1152388404	rs1152388404	2014	24164695
447	OMIA:001786-9615	dog	Border Collie	Intestinal cobalamin malabsorption due to CUBN mutation	CUBN		deletion, small (<=20)	Naturally occurring variant	yes	CanFam3.1	2	g.19974334del	c.8392del	p.(Q2798Rfs*3)	NM_001003148.1; NP_001003148.1; deletion C			2013	23613799
1036	OMIA:001786-9615	dog	Komondor	Intestinal cobalamin malabsorption, CUBN-related	CUBN		splicing	Naturally occurring variant	yes	CanFam3.1	2	g.19981457G>A	c.8746+1G>A		NM_001003148.1			2018	30591068
287	OMIA:001697-9913	cattle	Jersey (Cattle)	Abortion due to haplotype JH1	CWC15		nonsense (stop-gain)	Naturally occurring variant	yes	ARS-UCD1.2	15	g.15449431C>T	c.163C>T	p.(R55*)	UMD3.1 position is g.15707169C>T, cDNA and protein positions based on XM_005215764.2	rs1115118696	rs1115118696	2013	23349982	Variant coordinates obtained from or confirmed by EBI's Some Effect Predictor (VEP) tool; Breed information kindly provided or confirmed by Matt McClure and Jennifer McClure from "Understanding Genetics and Complete Genetic Disease and Trait Definition (Expanded 2016 Edition)" (https://www.icbf.com/wp/?page_id=2170). The genomic location on ARS-UCD1.2 was determined by Katie Eager and Shernae Woolley, EMAI, NSW. Department of Primary Industries.
850	OMIA:002131-9615	dog	Mixed breed (dog)	Methemoglobinaemia, CYB5R3-related	CYB5R3		missense	Naturally occurring variant	yes	CanFam3.1	10	g.22832963G>A	c.214G>A	p.(G72S)				2017	28963729	Variant coordinates obtained from or confirmed by EBI's Some Effect Predictor (VEP) tool
967	OMIA:002131-9615	dog	Pomeranian	Methemoglobinaemia, CYB5R3-related	CYB5R3		missense	Naturally occurring variant	yes	CanFam3.1	10	g.22836951A>C	c.580A>C	p.(I194L)	NM_001048084.1, NP_001041549.1			2018	29356095	Genomic coordinates in CanFam3.1 provided by Zoe Shmidt and Robert Kuhn.
1548	OMIA:002131-9685	domestic cat	Domestic Shorthair	Methaemoglobinaemia, CYB5R3-related	CYB5R3		splicing	Naturally occurring variant	yes	F.catus_Fca126_mat1.0	B4	g.135605715C>T	c.226+5G>A		XM_045062469.1; two transcripts were observed in the cat with the splice variant resulting in two predicted protein variants: XP_044918404.1:p.(G76_Q77insERSPDPARVEPG) and XP_044918404.1:p.(V52Afs*58),			2023	37048064
1155	OMIA:002131-9685	domestic cat	Domestic Shorthair	Methaemoglobinaemia, CYB5R3-related	CYB5R3		missense	Naturally occurring variant	yes	Felis_catus_9.0	B4	g.137967506C>T	c.625G>A	p.(G209S)	Jaffey e al. (2019): "p.Gly209Ser amino acid change in transcript CYB5R3-202 (ENSFCAT00000056925) at position B4:137967506"			2019	31650629
1156	OMIA:002131-9685	domestic cat	Domestic Shorthair	Methaemoglobinaemia, CYB5R3-related	CYB5R3		splicing	Naturally occurring variant	yes	Felis_catus_9.0	B4	g.137970815C>G	c.232-1G>C		Jaffey et al. (2019): "a putative loss of function splice acceptor variant at c.232-1G>C in the CYB5R3-202 transcript (ENSFCAT00000056925) at position B4:137970815 that is in the acceptor site for exon 4, which likely affects downstream translation of the protein."			2019	31650629
629	OMIA:000017-9986	rabbit		Adrenal hyperplasia, congenital	CYP11A1		deletion, gross (>20)	Naturally occurring variant	yes						"a large deletion mutation in the P450scc gene"			1993	7682938
117	OMIA:001661-9685	domestic cat		Adrenal hyperplasia, congenital, due to 11-beta hydroxylase deficiency	CYP11B1		missense	Naturally occurring variant	yes	Felis_catus_9.0	F2	g.84247412G>A	c.1151G>A	p.(R384Q)	XM_004000154.3; XP_004000203.1 published as "a guanosine-to-adenosine mutation in exon 7 that results in an arginine to glutamine amino acid substitution; this latter mutation results in 11β-hydroxylase deficiency-associated CAH in people [Parajes et al. (2010) J Clin Endocrinol Metab 95:779–788].			2012	22827537	Genomic position in Felis_catus_9.0 provided by Leslie Lyons and Reuben Buckley.
720	OMIA:000452-9031	chicken	Campine (Chicken) Sebright Bantams, United Kingdom of Great Britain and Northern Ireland (Chicken)	Henny feathering	CYP19A1		insertion, gross (>20)	Naturally occurring variant	no	GRCg6a	10	g.9683879_9683880insN[7524]			The insertion is 7524bp and "contains an intact endogenous retrovirus that was not found in chickens representing 31 different breeds not showing henny feathering or in samples of the ancestral red junglefowl. The sequence shows over 99% sequence identity to the avian leukosis virus ev-1 and ev-21 strains, suggesting a recent integration. The ERV 3’LTR, containing a powerful transcriptional enhancer and core promoter with TATA box together with binding sites for EFIII and Ig/EBP inside the CYP19A1 5′ untranslated region" (Li et al., 2019)			1991	1939054	Genomic location and size of the insertion provided by Li et al. (2019)
274	OMIA:001405-9615	dog	Beagle	Metabolizer of a cognitive enhancer	CYP1A2		nonsense (stop-gain)	Naturally occurring variant	yes	CanFam3.1	30	g.37821686C>T	c.1117C>T	p.(R373*)		rs852922442	rs852922442	2004	15564884	Variant coordinates obtained from or confirmed by EBI's Variant Effect Predictor (VEP) tool
1251	OMIA:002288-9913	cattle	Hereford (Cattle)	Mandibulofacial dysostosis	CYP26C1		missense	Naturally occurring variant	yes	ARS-UCD1.2	26	g.14404993T>C	c.563T>G	p.(L188P)	ENSBTAT00000056396.3:c.563T>G; ENSBTAP00000050244.2:p.Leu188Arg	rs431913023	rs431913023	2020	33105751
656	OMIA:000837-9823	pig		Vitamin D-deficiency rickets, type I	CYP27B1		deletion, gross (>20)	Naturally occurring variant	yes		5				the first of two deletions (173 bp or 329 bp) in the gene for cytochromome P450C1 (otherwise known as CYP27B1)			2003	12915218
657	OMIA:000837-9823	pig		Vitamin D-deficiency rickets, type I	CYP27B1		deletion, gross (>20)	Naturally occurring variant	yes		5				the second of two deletions (173 bp or 329 bp) in the gene for cytochromome P450C1 (otherwise known as CYP27B1)			2003	12915218
502	OMIA:000837-9685	domestic cat		Vitamin D-deficiency rickets, type I	CYP27B1		deletion, small (<=20)	Naturally occurring variant	yes	Felis_catus_9.0	B4	g.86180281del	c.731del	p.(R244Pfs*32)	XM_003988966.3; XP_003989015.1; published as c.731delG			2009	19138382	Genomic position in Felis_catus_9.0 provided by Leslie Lyons and Reuben Buckley.
315	OMIA:000837-9685	domestic cat		Vitamin D-deficiency rickets, type I	CYP27B1		nonsense (stop-gain)	Naturally occurring variant	yes	Felis_catus_9.0	B4	g.86180375C>A	c.637G>T	p.(E213*)	XM_003988966.3; XP_003989015.1;			2012	22553308	Variant coordinates obtained from or confirmed by EBI's Some Effect Predictor (VEP) tool
1411	OMIA:002508-9913	cattle	Simmental (Cattle)	Haplotype with homozygous deficiency SH8	CYP2B6	SH8	missense	Naturally occurring variant	yes	ARS-UCD1.2	18	g.50296371A>T	c.938T>A	p.(I313N)	NM_001075173.1			2021	34944310
52	OMIA:002684-9615	dog	Australian Cattle Dog Shetland Sheepdog	Leucodystrophy	CYTB		missense	Naturally occurring variant	yes	CanFam3.1	M	m.14474G>A	c.14474G>A	p.(V98M)				2006	16026996	Variant coordinates obtained from or confirmed by EBI's Some Effect Predictor (VEP) tool
784	OMIA:001986-9823	pig		Severe combined immunodeficiency disease, autosomal, T cell-negative, B cell-negative, NK cell-positive, with sensitivity to ionizing radiation	DCLRE1C		splicing	Naturally occurring variant	yes	Sscrofa11.1	10	g.46845535G>A						2015	26320255
785	OMIA:001986-9823	pig		Severe combined immunodeficiency disease, autosomal, T cell-negative, B cell-negative, NK cell-positive, with sensitivity to ionizing radiation	DCLRE1C		nonsense (stop-gain)	Naturally occurring variant	yes	Sscrofa11.1	10	g.46851262G>A		p.(Trp267*)				2015	26320255
167	OMIA:000735-9796	horse	Belgian Draft (Horse) Connemara Pony (Horse) Haflinger (Horse) Rocky Mountain, United States of America (Bighorn sheep)	Ocular squamous cell carcinoma	DDB2		missense	Naturally occurring variant	yes	EquCab3.0	12	g.11726667C>T	c.1013C>T	p.(T338M)	The EquCab2 coordinates, obtained from or confirmed by EBI's Some Effect Predictor (VEP) tool, are g.11608667, c.1013C>T and p.T338M	rs1139682898	rs1139682898	2017	28425625	The EquCab3 g. coordinates were provided by by Meredith O’Connell, working under the guidance of Professor Ernie Bailey, 5 March 2019
1335	OMIA:002377-8845	swan goose	Lion Head (Goose (domestic)) Sichuan White, China (Goose (domestic))	Knob, basal	DIO2		missense	Naturally occurring variant	no	AnsCyg_PRJNA183603_v1.0	NW_013185827.1	g.642923G>A		p.(P265L)				2021	34193033
565	OMIA:002095-9615	dog	Rhodesian Ridgeback	Epilepsy, generalized myoclonic, with photosensitivity	DIRAS1		deletion, small (<=20)	Naturally occurring variant	yes	CanFam3.1	20	g.56474668_56474671del	c.564_567del	p.(D189Afs*11)	XM_005633100.3; XP_005633157.1; published as DIRAS1:c.564_567delAGAC			2017	28223533	Genomic and protein coordinates in CanFam3.1 provided by Robert Kuhn
1412	OMIA:002505-9913	cattle	Simmental (Cattle)	Haplotype with homozygous deficiency SH5	DIS3	SH5	insertion, small (<=20)	Naturally occurring variant	unknown	ARS-UCD1.2	12	g.47511687_47511687insT	c.2032dup	p.(I678N*2)	NP_025000110.1, XM_025000110.1			2021	34944310
1308	OMIA:001484-9685	domestic cat	Abyssinian (Cat) Burmese (Cat) Maine Coon (Cat) Oriental Shorthair (Cat)	Ticked	DKK4	Ti^CK	missense	Naturally occurring variant	no	Felis_catus_9.0	B1	g.42620835C>T	c.53C>T	p.(A18V)				2021	33780570	ENSFCAT00000034752:c.53C>T; XM_023252567.1:c53C>T
1307	OMIA:001484-9685	domestic cat	Abyssinian (Cat)	Ticked	DKK4	Ti^A	missense	Naturally occurring variant	no	Felis_catus_9.0	B1	g.42621481G>A	c.188G>A	p.(C63Y)	published as g.41621481G>A		rs785541575	2021	33780570	(XM_023252567.1; ENSFCAT00000034752: c.188G>A)
914	OMIA:001354-9940	sheep		Muscular hypertrophy (double muscling), Callipyge	DLK1		regulatory	Naturally occurring variant	unknown	Oar_rambouillet_v1.0	18	g.66187430A>G			"a single A/G polymorphism located at position 103,894 of GenBank AF354168 and position 267 of the GenBank STS AF401294" (Freking et al., 2002) "the CLPG mutation, an A to G transition in a highly conserved dodecamer motif located in the 90-Kb intergenic region separating the Delta-like 1 homologue (DLK1) and Gene trap locus 2 (GTL2) genes in the eponymous imprinted domain" (Xu et al., 2015; PubMed 26474044) In relation to the Oar_v4.0/oviAri4 genome assembly, the location of the causative SNP is OAR18:g.64294536A>G (Ross Tellam, pers. comm. to FN 5 Nov 2020)	rs10721113		2002	12368241	The genomic location on Oar_rambouillet_v1.0 was determined by Katie Eager & Shernae Woolley, EMAI, NSW Department of Primary Industries.
615	OMIA:002109-9913	cattle	Brown Swiss (Cattle)	Tricho-dento-osseous-like syndrome	DLX3		insertion, small (<=20)	Naturally occurring variant	yes	ARS-UCD1.2	19	g.36665831_36665832insGGAGCACA	c.584_585insGGAGCACAGG	p.(S198Rfs*99)	NM_001081622 position is g.37298375_37298376insGGAGCACA			2017	28670783	The genomic location on ARS-UCD1.2 was determined by Katie Eager and Shernae Woolley, EMAI, NSW. Department of Primary Industries.
728	OMIA:001919-9615	dog	Nova Scotia Duck Tolling retriever	Cleft palate 1	DLX6		insertion, gross (>20)	Naturally occurring variant	yes	CanFam3.1	14	g.22068082_22068083insN[2056]			"2056 bp insertion [including LINE1] . . within a highly conserved region of DLX6 intron 2 at cfa14.25016716"[CanFam2.0]			2014	24699068
957	OMIA:001081-9615	dog	Rottweiler	Muscular dystrophy, Duchenne type	DMD		nonsense (stop-gain)	Naturally occurring variant	yes		X				"nonsense mutation in exon 58"			1994	Reference not in PubMed; see OMIA 001081-9615 for reference details
536	OMIA:001081-9615	dog	Cocker Spaniel	Muscular dystrophy, Duchenne type	DMD		deletion, small (<=20)	Naturally occurring variant	yes		X				deletion of four nucleotides in exon 65, with a reading frame shift predicting a premature stop codon at the site of the deletion			2012	22218699
680	OMIA:001081-9615	dog	German Shorthaired Pointer	Muscular dystrophy, Duchenne type	DMD		deletion, gross (>20)	Naturally occurring variant	yes		X				a "deletion encompassing the entire dystrophin [DMD] gene"			1999	10407848
681	OMIA:001081-9615	dog	Tibetan Terrier	Muscular dystrophy, Duchenne type	DMD		deletion, gross (>20)	Naturally occurring variant	yes		X				"a large deletion of exons 8-29"			2012	22218699
922	OMIA:001081-9685	domestic cat	Domestic Shorthair	Muscular dystrophy, Duchenne type	DMD		deletion, gross (>20)	Naturally occurring variant	yes		X				A deletion of the muscle promoter and first exon and the Purkinje neuronal first exon of the DMD gene			1994	7881288
923	OMIA:001081-9685	domestic cat	Domestic Shorthair	Muscular dystrophy, Duchenne type	DMD		deletion, gross (>20)	Naturally occurring variant	yes		X				A large deletion that "involved regions of the dystrophin gene that are poorly characterized, including the cortical neuronal promoter and its first exon and the skeletal neuronal promoter and its first exon"			2014	24446404
989	OMIA:001081-9615	dog	Miniature Poodle	Muscular dystrophy, Duchenne type	DMD		deletion, gross (>20)	Naturally occurring variant	yes		X				"a >5 Mb deletion on the X chromosome, encompassing the entire DMD gene"			2018	29474464
729	OMIA:001081-9615	dog	Labrador Retriever	Muscular dystrophy, Duchenne type	DMD		insertion, gross (>20)	Naturally occurring variant	yes		X				"184 nucleotide [pseudoexon] insertion between exon 19 and exon 20, which results in a premature stop codon at the next codon downstream of the insertion"			2012	22218699 Reference not in PubMed; see OMIA 001081-9615 for reference details
1395	OMIA:001081-9823	pig		Duchenne muscular dystrophy	DMD	DMD^ex52del	delins, gross (>20)	Transgenesis via somatic cell nuclear transfer (SCNT)	yes		X				gene targeting and somatic cell nuclear transfer was used to replace DMD exon 52 with a neomycin resistance cassette			2013	23784375
367	OMIA:001081-9615	dog	Cavalier King Charles Spaniel	Muscular dystrophy, Duchenne type	DMD		splicing	Naturally occurring variant	yes	CanFam3.1	X	g.26956239G>A	c.7294+5G>T		NM_001003343.1; NP_001003343.1; experimentally confirmed splice defect; a single nucleotide variant in the 5'-splice site of intron 51 that results in skipping of exon 50 in mRNA transcripts and a predicted premature truncation of the translated protein			2010	20072625
562	OMIA:001081-9615	dog	Cavalier King Charles Spaniel	Muscular dystrophy, Duchenne type	DMD		deletion, small (<=20)	Naturally occurring variant	yes	CanFam3.1	X	g.27442996_27443002del	c.6057_6063del	p.(N2021Pfs)	NM_001003343.1; NP_001003343.1; published as c.6051_6057delTCTCAAT based on different transcript			2016	28028563
542	OMIA:001081-9615	dog	Norfolk Terrier	Muscular dystrophy, Duchenne type	DMD		deletion, small (<=20)	Naturally occurring variant	yes	CanFam3.1	X	g.27606021del	c.3084delG	p.(G1029Nfs*30)				2015	26401335
1249	OMIA:001081-9615	dog	Jack Russell Terrier	Duchenne-type muscular dystrophy	DMD		deletion, gross (>20)	Naturally occurring variant	yes	CanFam3.1	X	g.27615280_27982912del	c.94-10346_2807-6207del		XM_005641029.1			2020	33049940
1236	OMIA:001081-9615	dog	Australian Labradoodle	Australian Labradoodle dystrophinopathy	DMD		nonsense (stop-gain)	Naturally occurring variant	yes	CanFam3.1	X	g.27621845G>A	c.2668C>T	p.(R890*)	NM_001003343.1; NP_001003343.1; "a C to T transition at base pair 43 in exon 21 of the dystrophin gene" (Shrader et al., 2018)			2018	30286978
1234	OMIA:001081-9615	dog	Labrador Retriever	Labrador Retriever muscular dystrophy (LRMD)	DMD		inversion	Naturally occurring variant	yes	CanFam3.1	X	g.27622834_29823788inv	c.-1490357_2626-947inv		XM_005641029.1			2020	32767978
1235	OMIA:001081-9615	dog	Border Collie	Muscular dystrophy, Duchenne	DMD		deletion, small (<=20)	Naturally occurring variant	yes	CanFam3.1	X	g.27626466del	c.2841delT					2018	29843823
750	OMIA:001081-9615	dog	Japanese Spitz	Muscular dystrophy, Duchenne type	DMD		inversion	Naturally occurring variant	yes	CanFam3.1	X	g.27631972_33069482inv	c.-4736051_2384-5339inv		XM_005641029.1; "an inversion of a 5.4-Mb fragment of the X chromosome, with one break point (BP1) in the DMD gene . . . and a second break point (BP2) in a gene farther toward the centromere, the RPGR gene".			2015	25644216
708	OMIA:001081-9615	dog	Pembroke Welsh Corgi	Muscular dystrophy, Duchenne type	DMD		insertion, gross (>20)	Naturally occurring variant	yes	CanFam3.1	X	g.27721607_27721608insN[(4800)]			"a long interspersed repetitive element-1 (LINE-1) insertion in intron 13, which introduced a new exon containing an in-frame stop codon"			2011	20714321
1492	OMIA:001081-9615	dog	Labrador Retriever	Muscular dystrophy, Duchenne type	DMD		duplication	Naturally occurring variant	yes	CanFam3.1	X	g.27851768_28247504dup			Shelton et al. (2022): "chrX:27,851,768-27,852,122 bp position (Intron 7 . . .) and chrX:28,247,150-28,247,504 bp position (Intron 1 . . .)"			2022	36041985
366	OMIA:001081-9615	dog	Golden Retriever	Muscular dystrophy, Duchenne type	DMD		splicing	Naturally occurring variant	yes	CanFam3.1	X	g.27926946T>C	c.531-2A>G		NM_001003343.1; a point mutation in the consensus splice acceptor site in exon 6 , such that exon 7 is skipped	rs1152388423	rs1152388423	1992	1577476
1531	OMIA:001888-9685	domestic cat		Becker muscular dystrophy	DMD		missense	Naturally occurring variant	yes	F.catus_Fca126_mat1.0	X	g.27988938G>A	c.4186C>T	p.(H1396Y)	XM_045050787.1; XP_044906722.1			2023	36834603
1510	OMIA:001081-9685	domestic cat	Maine Coon (Cat)	Muscular dystrophy, Duchenne type	DMD		nonsense (stop-gain)	Naturally occurring variant	yes	F.catus_Fca126_mat1.0	X	g.28208148G>A	c.1180C>T	p.(R394*)	XM_045050794.1; XP_044906729.1			2022	36359052
1457	OMIA:001888-9823	pig		Becker muscular dystrophy	DMD		insertion, gross (>20)	Naturally occurring variant	yes	Sscrofa11.1	X				Aihara et al. (2022): "Analysis of dystrophin mRNA showed a 62 base pair insertion between exons 26 and 27. The insertion was derived from intron 26."			2022	35220848
179	OMIA:001685-9823	pig		Stress syndrome	DMD		missense	Naturally occurring variant	yes	Sscrofa11.1	X	g.28309227G>A	c.5872C>T	p.(R1958W)	Ensembl VEP was used to identify cDNA position in transcript ENSSSCT00000089893.1, SIFT score 0.01	rs196952080	rs196952080	2012	22691118
908	OMIA:001542-9940	sheep	Corriedale (Sheep)	Hypophosphatemic rickets, autosomal recessive, 1	DMP1		nonsense (stop-gain)	Naturally occurring variant	yes	Oar_rambouillet_v1.0	6	g.112910614C>T	c.433C>T	p.(R145*)	Published as g.112213795C>T / c.250C>T. Protein and cDNA positions in this table are based on XP_012035717.1 and XM_012180327.3.			2011	21747952	The genomic location on Oar_rambouillet_v1.0 was determined by Katie Eager, EMAI, NSW Department of Primary Industries.
1352	OMIA:002442-9823	pig	Large White (Pig)	Sperm flagella defect	DNAH17		deletion, small (<=20)	Naturally occurring variant	yes	Sscrofa11.1	12	g.3556402_3556414del			Nosková et al. (2021): "intronic 13-bp deletion ... causes exon skipping which results in the in-frame loss of 89 amino acids from DNAH17"			2021	33724408
39	OMIA:001466-9615	dog	Chesapeake Bay Retriever Curly-coated retriever Labrador Retriever	Exercise-induced collapse	DNM1		missense	Naturally occurring variant	yes	CanFam3.1	9	g.55282762C>A	c.767G>T	p.(R256L)	ROS_Cfam_1.0:g.56204742C>A ENSCAFT00845051951.1:c.767G>T ENSCAFP00845040760.1:p.Arg256Leu	rs852832685	rs852832685	2008	18806795	Variant coordinates obtained from or confirmed by EBI's Some Effect Predictor (VEP) tool
1434	OMIA:002534-9615	dog	Border Collie	Centronuclear myopathy 1	DNM2		missense	Naturally occurring variant	yes	CanFam3.1	20	g.50423497G>A	c.1393C>T	p.(R465W)	XM_005632882.3; XP_005632939.1.			2022	35244154
125	OMIA:001776-9685	domestic cat		Dihydropyrimidinase deficiency	DPYS		missense	Naturally occurring variant	yes	Felis_catus_9.0	F2	g.52064442C>T	c.1303G>A	p.(G435R)	XM_023248231.1; XP_023103999.1			2012	23430934	Genomic position in Felis_catus_9.0 provided by Leslie Lyons and Reuben Buckley.
1194	OMIA:002266-9615	dog	Rottweiler	Hyperkeratosis, palmoplantar, DSG1-related	DSG1		deletion, small (<=20)	Naturally occurring variant	yes	CanFam3.1	7	g.58163636_58163640del	c.2541_2545del	p.(G848Wfs*2)	NM_001002939.1; NP_001002939.1; published as c.2541_2545delGGGCT			2020	32344723
1392	OMIA:002452-9685	domestic cat	Domestic Shorthair	Hair shaft dysplasia	DSG4		deletion, small (<=20)	Naturally occurring variant	yes	Felis_catus_9.0	D3	g.55315010del	c.76del	p.(I26Lfs*4)	XM_019815116.1; XP_019670675.1			2022	34878611
1393	OMIA:002452-9685	domestic cat	Domestic Shorthair	Hair shaft dysplasia	DSG4		deletion, small (<=20)	Naturally occurring variant	yes	Felis_catus_9.0	D3	g.55336127del	c.1777del	p.(H593Tfs*23)	XM_019815116.1; XP_019670675.1			2022	34878611
1408	OMIA:002243-9913	cattle	Highland (Cattle)	Ichthyosis, DSP-related	DSP		missense	Naturally occurring variant	yes	ARS-UCD1.2	23	g.47826600G>T	c.6893C>A	p.(A2298D)	NM_001192368.2; NP_001179297.1			2022	34996433
1115	OMIA:002210-9823	pig	Bama Xiang Zhu, China (Pig)	Congenital hypothyroidosis	DUOX2		missense	Naturally occurring variant	yes	Sscrofa11.1	1	g.126625620A>G	c.1226A>G	p.(D409G)	ENU mutagenesis was used to create these pigs, the mutation is located within an exonic splicing enhancer motif and causes aberrant splicing of DUOX2 transcripts (Cao et al., 2019)			2019	30651277
1056	OMIA:002186-9615	dog	Boston Terrier Bulldog French Bulldog	Screw tail	DVL2		deletion, small (<=20)	Naturally occurring variant	yes	CanFam3.1	5	g.32195051del	c.2051del	p.(P684Lfs*26)	XM_005619960.3; XP_005620017.1; published as g.32195043_32195044del; c.2044delC and changed to HGVS nomenclature in this table			2018	30521570
711	OMIA:000543-9913	cattle	Danish Holstein (Cattle)	Anhidrotic ectodermal dysplasia	EDA	HED6	insertion, gross (>20)	Naturally occurring variant	yes		X				"a LINE1-derived pseudoexon between EDA exons 1 and 2. The 161-bp-long pseudoexon introduces a shift in reading frame and a premature stop codon early in EDA exon 2"			2011	22034998	Allele id was copied from Table 1 of Capuzzello et al. (2022)
645	OMIA:000543-9913	cattle	Deutsche Holstein Schwarzbunt, Germany (Cattle)	Anhidrotic ectodermal dysplasia	EDA	HED1	deletion, gross (>20)	Naturally occurring variant	yes		X		c.397_502del	p.(M133Vfs*111)	a large deletion including exon 3 in the gene for ectodysplasin (ED1; now called EDA) 200922: g. info moved to here (g.85821470) until it can be standardised			2001	11591646	Variant information kindly provided or confirmed by Hubert Pausch, including information from Additional Table 6 of Jansen et al. (2013) BMC Genomics201314:446 https://doi.org/10.1186/1471-2164-14-446 Allele id and p. information were copied from Table 1 of Capuzzello et al. (2022)
1120	OMIA:000543-9913	cattle	Prim'Holstein, France (Cattle)	Generalized hypohidrotic ectodermal dysplasia	EDA	HED8	inversion	Naturally occurring variant	yes	ARS-UCD1.2	X	g.77174882_80737442inv			Escouflaire et al. (2019): The "first breakpoint . . . [is] between positions 82,271,052 and 82,271,053 bp on chromosome X . . . The second breakpoint is situated at position 86,034,441 bp within the EDA intron 1"			2019	31533624	Allele id was copied from Table 1 of Capuzzello et al. (2022).
1293	OMIA:000543-9913	cattle	Red Angus-Simmental cross	Hypohidrotic ectodermal dysplasia	EDA	HED9	deletion, gross (>20)	Naturally occurring variant	yes	ARS-UCD1.2	X	g.80382423_80435202del			GCF_002263795.1 (O'Toole et al., 2021)			2021	33801223	Allele id was copied from Table 1 of Capuzzello et al. (2022).
373	OMIA:000543-9913	cattle	Deutsche Holstein Schwarzbunt, Germany (Cattle)	Anhidrotic ectodermal dysplasia	EDA	HED2	splicing	Naturally occurring variant	yes	ARS-UCD1.2	X	g.80411671A>C	c.924+2T>G		c.DNA position is based on NM_001081743.2			2002	12021844	The genomic location on ARS-UCD1.2 was determined by Katie Eager and Shernae Woolley, EMAI, NSW. Department of Primary Industries. Allele id was copied from Table 1 of Capuzzello et al. (2022)
1295	OMIA:000543-9913	cattle	Holstein Friesian (Cattle)	Anhidrotic ectodermal dysplasia	EDA	HED5	splicing	Naturally occurring variant	yes	ARS-UCD1.2	X	g.80411795C>A	c.802C>A		"a single nucleotide polymorphism (SNP) G/A at the 9th base of exon 8 [GenBank: AJ278907.1 position 30.549] ... Sequencing of the RT-PCR products revealed that the amplified fragment of the affected animals lacked ... exon 8. At the protein level, the exon skipping leads to a frameshift and consequently to a premature stop codon." (Gargani et al., 2011)			2011	21740563	Allele id and c. information were copied from Table 1 of Capuzzello et al. (2022)
1294	OMIA:000543-9913	cattle	Red Angus-Charolais-Simmental cross	Anhidrotic ectodermal dysplasia	EDA	HED3	nonsense (stop-gain)	Naturally occurring variant	yes	ARS-UCD1.2	X	g.80415626G>A	c.730C>T	p.(R244*)				2007	17616058 Reference not in PubMed; see OMIA 000543-9913 for reference details	The g. coordinate for the named reference genome assembly, together with the c. coordinate, were kindly provided by Tosso Leeb (22 March 2021). Allele id was copied from Table 1 of Capuzzello et al. (2022).
1484	OMIA:000543-9913	cattle	British Blue x Holstein-Friesian cross	Anhidrotic ectodermal dysplasia, EDA-related	EDA	HED10	deletion, gross (>20)	Naturally occurring variant	yes	ARS-UCD1.2	X	g.80516615_80538514del	c.397_502del	p.(M133Vfs*111)	NM_001081743.2; NP_001075212.1			2022	36068608	Allele id was copied from Table 1 of Capuzzello et al. (2022).
586	OMIA:000543-9913	cattle	Japanese Black, Japan (Cattle)	Anhidrotic ectodermal dysplasia	EDA	HED7	insertion, small (<=20)	Naturally occurring variant	yes	ARS-UCD1.2	X	g.80802800_80802801insCCCT	c.280_281insAGGG	p.(G94Qfs*49)				2012	22497423	The genomic location on ARS-UCD1.2 was determined by Katie Eager and Shernae Woolley, EMAI, NSW. Department of Primary Industries. Allele id was copied from Table 1 of Capuzzello et al. (2022).
482	OMIA:000543-9913	cattle	Holstein (black and white) (Cattle)	Anhidrotic ectodermal dysplasia	EDA	HED4	deletion, small (<=20)	Naturally occurring variant	yes	ARS-UCD1.2	X	g.80803015_80803033del	c.48_66del	p.(A16S22fs*55)	"a 19-bp deletion at nucleotides c.48_66 in exon 1 ... . This mutation is predicted to generate a truncated 49 aa protein."			2011	21410470	Allele id and p. information were copied from Table 1 of Capuzzello et al. (2022)
1458	OMIA:000543-9615	dog	Mixed breed (dog)	X-linked hypohidrotic ectodermal dysplasia	EDA		splicing	Naturally occurring variant	yes	CanFam3.1	X		r.385_487del	p.M129fs*112	NM_001014770.2; NP_001014770.1; EDA transcript lacks 103 nucleotides encoded by exon 2, exon skipping is likely to be caused by an intronic splice variant			2016	27449516
1017	OMIA:000543-9615	dog	Dachshund	X-linked hypohidrotic ectodermal dysplasia	EDA		deletion, small (<=20)	Naturally occurring variant	yes	CanFam3.1	X	g.54509504del	c.842delT	p.(L281Hfs*22)				2018	30276836
361	OMIA:000543-9615	dog	German Shepherd Dog	Anhidrotic ectodermal dysplasia	EDA		splicing	Naturally occurring variant	yes	CanFam3.1	X	g.54511433G>A	c.910-1G>A		NM_001014770.2	rs1152388425	rs1152388425	2005	16151697	Genomic coordinates in CanFam3.1 und EVA Id provided by Zoe Shmidt and Robert Kuhn.
724	OMIA:001695-8090	Japanese medaka		Reduced scale-3	edar		insertion, gross (>20)	Naturally occurring variant	yes						"several kb of extra sequence in the 5' UTR that . . . contains out-of-frame start codons and stop codons, [and consequently] the mutant transcript is likely to result in premature initiation and termination of translation and, as a result, the EDAR protein is not synthesized"			2001	11516953
843	OMIA:002128-9913	cattle	Charolais (Cattle)	Anhidrotic ectodermal dysplasia, EDAR-related	EDAR		insertion, small (<=20)	Naturally occurring variant	yes	ARS-UCD1.2	11	g.44599876_44599877insC		p.(P161Rfs*97)	UMD3.1 position is g.44462236_44462237insC			2017	28904385	The genomic location on ARS-UCD1.2 was determined by Katie Eager and Shernae Woolley, EMAI, NSW. Department of Primary Industries.
1550	OMIA:002687-9940	sheep		Fleece variation, wool density	EDAR		regulatory	Naturally occurring variant	no	Oar_v4.0	3	g.61927840T>C			the T allele is associated denser wool production in fine wool sheep	rs408766096		2023	37137429
1474	OMIA:002560-9913	cattle	Lidia, Spain (Cattle)	Growth and respiratory lethal syndrome	EDN2		missense	Naturally occurring variant	yes	ARS-UCD1.2	3	g.104701617G>A	c.149G>A	p.(C50Y)	ENSBTAG00000021434; ENSBTAT00000028571.3			2022	35912509
722	OMIA:001671-9031	chicken	Bohuslän - Dals svarthöna, Sweden (Chicken) H'mong, Viet Nam (Chicken) Kedu, Indonesia (Chicken) Silkie (Chicken)	Silky/Silkie pigmentation (Fibromelanosis)	EDN3	FM	complex rearrangement	Naturally occurring variant	no		20				the FM mutation actually involves "the duplication of two genomic regions, each larger than 100 kb and separated by 417 kb on wild-type [GGA20] chromosomes"			2011	22216010
760	OMIA:002164-9925	goat		Coat colour, white spotting, EDNRA-related	EDNRA		repeat variation	Naturally occurring variant	no		17				"a 1Mb copy number variant (CNV) harboring 5 genes including EDNRA. The analysis of 358 Boer goats revealed 3 alleles with one, two, and three copies of this CNV. The copy number is correlated with the degree of white spotting in goats"			2016	27329507
160	OMIA:000629-9796	horse	American Paint (Horse) Miniature Horse (Horse) Quarter Horse (Horse) Thoroughbred (Horse)	Megacolon	EDNRB	frame overo	delins, small (<=20)	Naturally occurring variant	yes	EquCab3.0	17	g.50503041_50503042delinsCT	c.353_354delinsAG	p.(I118K)	NM_001081837.2; NP_001075306.2			1998	9530628
930	OMIA:001765-9940	sheep	West African Dwarf (Sheep)	Waardenburg syndrome, type 4A	EDNRB		deletion, gross (>20)	Naturally occurring variant	yes	Oar_rambouillet_v1.0	10				"a deletion of about 110 kb on sheep chromosome [OAR]10, comprising the entire EDNRB gene"			2012	23300849
1562	OMIA:002701-51751	ball python		Skin colour, EDNRB1-related	EDNRB1	yellowbelly	deletion, small (<=20)	Naturally occurring variant	unknown				c.1646del		OP589186.1; 1-bp deletion introduces a frameshift, which removes or alters three of the seven transmembrane helices			2023	37191439
1563	OMIA:002701-51751	ball python		Skin colour, EDNRB1-related	EDNRB1	yellowbelly	deletion, small (<=20)	Naturally occurring variant	unknown				c.1747_1763del		OP589186.1; "17-bp deletion introduces a frameshift into the transcript, which removes or alters two of the seven transmembrane helices"			2023	37191439
1564	OMIA:002701-51751	ball python		Skin colour, EDNRB1-related	EDNRB1	specter	missense	Naturally occurring variant	unknown				c.2601G>C	p.(R315P)	OP589186.1			2023	37191439
1567	OMIA:002701-51751	ball python		Skin colour, EDNRB1-related	EDNRB1	asphalt	splicing	Naturally occurring variant	unknown				c.3118G>A		OP589186.1; G-to-A substitution in the sixth splice donor for the sixth intron			2023	37191439
1565	OMIA:002701-51751	ball python		Skin colour, EDNRB1-related	EDNRB1	spark	missense	Naturally occurring variant	unknown				c.481G>C	p.(L152F)	OP589186.1			2023	37191439
1566	OMIA:002701-51751	ball python		Skin colour, EDNRB1-related	EDNRB1	gravel	splicing	Naturally occurring variant	unknown				c.499G>A		OP589186.1; G-to-A substitution at the splice donor for the first intron			2023	37191439
257	OMIA:000375-93934	Japanese quail		Feather colour, panda/dotted white	EDNRB2		missense	Naturally occurring variant	no				c.995G>A	p.(R332H)				2007	17313575
1164	OMIA:001252-8843	domestic goose	Gang, China (Goose (domestic))	Feather colour, recessive white	EDNRB2		insertion, small (<=20)	Naturally occurring variant	no	AnsCyg_PRJNA183603_v1.0		g.750748_750735insCACAGGTGAGCTCT			"NW_013185915.1: g. 750,748-750,735 insertion. CACAGGTGAGCTCT" (Xi et al., 2020)			2020	32066369
16	OMIA:001904-9031	chicken		Feather colour, recessive white	EDNRB2	mo^w	missense	Naturally occurring variant	no	GRCg6a	4	g.11164302G>T	c.731G>T	p.(C244F)	NM_204120.1; NP_989451.1; published as c.1008G>T and p.(C244F); coordinates in the table have been updated to a recent reference genome and / or transcript			2014	24466053	Genomic position in GRCg6a provided by Joshua Khamis.
17	OMIA:001904-9031	chicken		Feather colour, mottled	EDNRB2	mo	missense	Naturally occurring variant	no	GRCg6a	4	g.11166001G>A	c.999G>A	p.(R332H)	NM_204120.1; NP_989451.1; published as c.1272G>A and p.(R332H); coordinates in the table have been updated to a recent reference genome and / or transcript			2014	24466053	Genomic position in GRCg6a provided by Joshua Khamis.
1483	OMIA:002564-9615	dog	Labrador Retriever	Congenital dyserythropoietic anemia and polymyopathy	EHBP1L1		nonsense (stop-gain)	Naturally occurring variant	yes	CanFam4	18	g.52128140G>A	c.388C>T	p.(R130*)	XM_038563927.1;			2022	36011338
1481	OMIA:002564-9615	dog	English Springer Spaniel	Dyserythropoietic anemia and myopathy syndrome (DAMS)	EHBP1L1		deletion, small (<=20)	Naturally occurring variant	yes	UU_Cfam_GSD_1.0	18	g.52123541delG	c.3120delC	p.(F1041Sfs*30)	XM_038563927.1; XP_038419855.1			2022	36140701
1044	OMIA:001805-9615	dog	Parson Russell Terrier	Amelogenesis imperfecta	ENAM		missense	Naturally occurring variant	yes	CanFam3.1	13	g.59945218C>T	c.716C>T	p.(P239L)	XM_539305.4; XP_539305.3			2019	30877375	Genomic coordinates in CanFam3.1 provided by Robert Kuhn and Zoe Shmidt.
452	OMIA:001805-9615	dog	Italian Greyhound	Amelogenesis imperfecta	ENAM		deletion, small (<=20)	Naturally occurring variant	yes	CanFam3.1	13	g.59946493_59946497del	c.1991_1995delTTTCC	p.(F665Rfs*3)	XM_539305.4; XP_539305.3; published as c.1991_1995delTTTCC			2013	23638899	Genomic coordinates in CanFam3.1 provided by Robert Kuhn
759	OMIA:000296-9031	chicken		Duplex comb	EOMES		duplication	Naturally occurring variant	no		2				"a 20 Kb tandem duplication containing several conserved putative regulatory elements located 200 Kb upstream of the eomesodermin gene (EOMES)"			2015	25789773
1	OMIA:000240-8932	rock pigeon		Crest	EPHB2	cr	missense	Naturally occurring variant	no				c.???C>T	p.(R758C)				2013	23371554
1454	OMIA:002550-9615	dog	Rhodesian Ridgeback	Early onset adult deafness	EPS8L2		deletion, small (<=20)	Naturally occurring variant	yes	UMICH_Zoey_3.1/canFam5	18	g.25868739_25868750del	c.1033_1044del	p.(V345_L348del)	XM_038500406.1; XP_038356334.1; published as 12-bp inframe deletion in EPS8L2 (CFA18:25,868,739-25,868,751 in the UMICH_Zoey_3.1) corresponding to deletion of amino acids VHFL			2022	35385474
191	OMIA:001716-9913	cattle	Holstein (black and white) (Cattle)	Ehlers-Danlos syndrome, Holstein variant	EPYC		missense	Naturally occurring variant	yes	ARS-UCD1.2	5	g.20856381C>A	c.258G>T	p.(S87N)				1999	10357109	Variant information kindly provided or confirmed by Hubert Pausch, including information from Additional Table 6 of Jansen et al. (2013) BMC Genomics201314:446 https://doi.org/10.1186/1471-2164-14-446
1161	OMIA:000483-9925	goat		Polled intersex syndrome	ERG	PIS	complex rearrangement	Naturally occurring variant	yes		1				"a deletion with a total length of 10 159 bp and an inversely inserted approximately 480 kb-sized duplicated segment of a region located approximately 21 Mb further downstream on chromosome 1 containing two genes, KCNJ15 and ERG" (Simon et al., 2020)			2020	32060960
1169	OMIA:002543-9031	chicken		Cleft primary palate	ESRP2		deletion, small (<=20)	Naturally occurring variant	yes	GRCg6a	11	g.3284041del				ss5200091912	❌ rs3386590816	2020	32162363
1439	OMIA:001457-9685	domestic cat		Multiple acyl-CoA dehydrogenase deficiency	ETFDH		missense	Naturally occurring variant	yes	Felis_catus_9.0	B1	g.71374631A>C	c.692T>G	p.(F231C)	NM_001290236.1; NP_001277165.1			2014	24142280	Thanks to Heidi Anderson for alerting OMIA to this paper; 31 March 2022
375	OMIA:002540-9913	cattle	Japanese Brown, Japan (Cattle)	Chondrodysplasia	EVC2		splicing	Naturally occurring variant	yes	ARS-UCD1.2	6	g.103594013C>T	c.1356C>T		Variant creates a cryptic splice donor site in exon 11 which is leading to improper splicing at position c.1355 and resulting in the 56-base RNA deletion between 1355 and 1410. The deletion causes a frameshift and premature termination.			2002	12136126	The genomic location on ARS-UCD1.2 was determined by Katie Eager and Shernae Woolley, EMAI, NSW. Department of Primary Industries.
617	OMIA:002540-9913	cattle	Japanese Brown, Japan (Cattle)	Chondrodysplasia	EVC2		delins, small (<=20)	Naturally occurring variant	yes	ARS-UCD1.2	6	g.103609778_103609779delinsG	c.2327_2328delinsG	p.(A776Gfs*22)	Published as c.2054_2055delCAinsG, cDNA and protein position in this table based on ENSBTAT00000005613.6			2002	12136126	The genomic location on ARS-UCD1.2 was determined by Katie Eager and Shernae Woolley, EMAI, NSW. Department of Primary Industries.
534	OMIA:002540-9913	cattle	Tirolean gray cattle (Cattle)	Chondrodysplasia	EVC2		deletion, small (<=20)	Naturally occurring variant	yes	ARS-UCD1.2	6	g.103651709_103651710del	c.2993_2994del	p.(D998Efs*13)				2014	24733244	The genomic location on ARS-UCD1.2 was determined by Katie Eager and Shernae Woolley, EMAI, NSW. Department of Primary Industries. 210909 FN: given that the variant is a 2bp del (AC), g.103651710_103651710del needs to be changed. BLASTing with AGAGGAGCAAGAAGAC from Fig.4 indicates that it is 719 and 710 that are deleted. THus the entry is changed to g.103651709_103651710del; and AC is removed from the c. entry.
346	OMIA:002042-9913	cattle	Belgian Blue (Cattle)	Abortion (embryonic lethality), EXOSC4	EXOSC4		nonsense (stop-gain)	Naturally occurring variant	yes	ARS-UCD1.2	14	g.755826G>A	c.190G>A	p.(R64*)			rs3423357300	2016	27646536	Variant coordinates obtained from or confirmed by EBI's Some Effect Predictor (VEP) tool
1467	OMIA:002554-9685	domestic cat	Mixed breed (dog)	Osteochondromatosis (feline leukemia virus-negative)	EXT1		duplication	Naturally occurring variant	yes	F.catus_Fca126_mat1.0?	F2	g.61870704dup	c.1468dup	p.(L490Pfs*31)	XM_023248762.2;			2022	35719100
980	OMIA:001214-9615	dog	American Staffordshire Terrier	Osteochondromatosis	EXT2		nonsense (stop-gain)	Naturally occurring variant	yes	CanFam3.1	18	g.45101754G>T	c.924C>A	p.(Y308*)	XM_014121199.2; XP_013976674.1; published as c.969C>A and p.(Y323*); coordinates in the table have been updated to a recent reference genome and / or transcript			2018	29485212
713	OMIA:000363-9913	cattle	Holstein (black and white) (Cattle) Sahiwal (Cattle)	Factor XI deficiency	F11		insertion, gross (>20)	Naturally occurring variant	yes		27				a 76-bp insertion in exon 12 of the Factor XI gene 200922: g. and c. info moved here (g.15367048; c.1406ins76) until can be standardised			2004	15566468	Variant information kindly provided or confirmed by Hubert Pausch, including information from Additional Table 6 of Jansen et al. (2013) BMC Genomics201314:446 https://doi.org/10.1186/1471-2164-14-446
591	OMIA:000363-9913	cattle	Japanese Black, Japan (Cattle) Sahiwal (Cattle)	Factor XI deficiency	F11		delins, small (<=20)	Naturally occurring variant	yes	ARS-UCD1.2	27	g.16305660delinsATATGTGCAGAATATA	c.870delinsATATGTGCAGAATATA	P.(F290delinsLYVQNI)				2005	16104386	Breed and variant information kindly provided or confirmed by Matt McClure and Jennifer McClure from "Understanding Genetics and Complete Genetic Disease and Trait Definition (Expanded 2016 Edition)" (https://www.icbf.com/wp/?page_id=2170). The genomic location on ARS-UCD1.2 was determined by Katie Eager and Shernae Woolley, EMAI, NSW. Department of Primary Industries.
702	OMIA:000363-9615	dog	Kerry Blue Terrier	Factor XI deficiency	F11		insertion, gross (>20)	Naturally occurring variant	yes	CanFam3.1	16	g.44477343_44477344ins90	c.819_820ins90		NM_001135123.1 "an insertion of 90 bp (SINE) inside of coding exon 7" resulting in a "30 amino acids insertion in the A3 domain of FXI serine protease" (Tcherneva et al., 2007).			2007	Reference not in PubMed; see OMIA 000363-9615 for reference details	g. and c. coordinates kindly provided by Professor Urs Giger (27 August 2022)
1472	OMIA:000363-9685	domestic cat	Maine Coon (Cat)	Factor XI deficiency	F11		missense	Naturally occurring variant	yes	Felis catus 9.0	B1	g.17176154G>A	c.1546G>A	p.(V516M)	XM_003984601.5; XP_003984650.2			2022	35627175
533	OMIA:000364-9685	domestic cat		Factor XII deficiency	F12		deletion, small (<=20)	Naturally occurring variant	yes	Felis_catus_9.0	A1	g.175381114del	c.1321del	p.(L441Cfs*119)	NM_001168212.2; NP_001161684.2; published as c.1321delC			2015	24793828	Genomic position in Felis_catus_9.0 provided by Leslie Lyons and Reuben Buckley.
147	OMIA:000364-9685	domestic cat	Domestic Shorthair	Factor XII deficiency	F12		missense	Naturally occurring variant	yes	Felis_catus_9.0	A1	g.175382065G>C	c.1631G>C	p.(G544A)	NM_001168212.2; NP_001161684.2			2017	28392508	Genomic position in Felis_catus_9.0 provided by Leslie Lyons and Reuben Buckley.
1532	OMIA:001818-9913	cattle	Japanese Black, Japan (Cattle)	Factor XIII deficiency	F13A1		missense	Naturally occurring variant	yes	UMD_3.1.1	23	g.48649432T>C	c.248T>C	p.(F83S)	NM_001167894.1; NP_001161366.1			1996	Reference not in PubMed; see OMIA 001818-9913 for reference details	Variant was first reported by Ogawa and Iga (1996). Variant information in this table is based on supplementary table 1 by Shibutani et al. (2023).
148	OMIA:000361-9783	Asiatic elephant		Factor VII deficiency	F7		missense	Naturally occurring variant	yes				c.202A>G	p.(R68G)				2017	28118558
40	OMIA:000361-9615	dog	Beagle	Factor VII deficiency	F7		missense	Naturally occurring variant	yes	CanFam3.1	22	g.60578895G>A	c.407G>A	p.(G136E)				2006	16961583	Variant coordinates obtained from or confirmed by EBI's Some Effect Predictor (VEP) tool
363	OMIA:000437-9615	dog	Irish Setter Miniature Schnauzer	Haemophilia A	F8		splicing	Naturally occurring variant	yes		X				intronic inversion that results in "aberrant splicing and premature termination"			2002	12008949
1038	OMIA:000437-9913	cattle	Fleckvieh-Simmental, Germany (Cattle)	Haemophilia A	F8		missense	Naturally occurring variant	yes	ARS-UCD1.2	X	g.36017426A>T	c.134A>T	p.(H45L)	ENSBTAT00000036726.5:c.134A>T; ENSBTAP00000036581.4:p.His45Leu	rs1117392179	rs1117392179	2018	29774585
194	OMIA:000437-9913	cattle	Japanese Brown, Japan (Cattle)	Haemophilia A	F8		missense	Naturally occurring variant	yes	ARS-UCD1.2	X	g.36145188T>A	c.6458T>A	p.(L2153H)				2009	19456318	Variant coordinates obtained from or confirmed by EBI's Some Effect Predictor (VEP) tool
350	OMIA:000437-9615	dog	Old English Sheepdog	Haemophilia A	F8		nonsense (stop-gain)	Naturally occurring variant	yes	CanFam3.1	X	g.122973422G>A	c.1786C>T	p.(R596*)				2016	27780008	Variant coordinates obtained from or confirmed by EBI's Some Effect Predictor (VEP) tool
100	OMIA:000437-9615	dog	German Shepherd Dog	Haemophilia A	F8		missense	Naturally occurring variant	yes	CanFam3.1	X	g.122975611C>T	c.1700G>A	p.(C567Y)	NM_001003212.1; NP_001003212.1; published as c.1643G>A & p.(C548Y); coordinates in the table have been updated to a recent reference genome and / or transcript.			2014	25040606
99	OMIA:000437-9615	dog	Boxer	Haemophilia A	F8		missense	Naturally occurring variant	yes	CanFam3.1	X	g.122981181G>C	c.1469C>G	p.(P490R)	NM_001003212.1; NP_001003212.1; published as c.1412C>G & p.(P471R); coordinates in the table have been updated to a recent reference genome and/ or transcript			2014	25040606
272	OMIA:000437-9615	dog	German Shepherd Dog	Haemophilia A	F8		nonsense (stop-gain)	Naturally occurring variant	yes	CanFam3.1	X	g.123043081C>T	c.98G>A	p.(W33*)				2011	21949058	Variant coordinates obtained from or confirmed by EBI's Some Effect Predictor (VEP) tool
1284	OMIA:000437-9615	dog	Rhodesian Ridgeback	Haemophilia A	F8		insertion, gross (>20)	Naturally occurring variant	yes	CanFam3.1	X	g.1240738676_1240738677insN[221]	c.4824_4825insN[221]		NM_001003212.1; published as c.4824_25ins221			2021	33494213
621	OMIA:000437-9940	sheep	Weißes Alpenschaf, Switzerland (Sheep)	Haemophilia A	F8		delins, small (<=20)	Naturally occurring variant	yes	Oar_rambouillet_v1.0	X	g.86301507_86301516delinsTAATTAATACC	c.3108_3117delinsGGTATTAATTA		The 11 bp region in exon 14 that differed between the wild-type and the hemophiliac introduced a premature stop codon			2010	19943872	The genomic location on Oar_rambouillet_v1.0 was determined by Katie Eager, EMAI, NSW Department of Primary Industries. 210906 After checking the cDNA sequence in Fig. 3 of the paper, FN concluded that the 10bp deletion starts at c.3108 and ends at c.3117 and that the 11bp inserted sequence is GGTATTAATTA. Thus the HGVS-consistent notation is c.3108_3117delinsGGTATTAATTA, instead of c.3107del10ins11.
636	OMIA:000438-9615	dog	Labrador Retriever	Haemophilia B	F9		deletion, gross (>20)	Naturally occurring variant	yes		X				a deletion of the entire gene			1997	9394892
637	OMIA:000438-9615	dog	Pit Bull Terrier	Haemophilia B	F9		deletion, gross (>20)	Naturally occurring variant	yes		X				Gu et al. (1999): "A large deletion mutation was found in 1 breed variant, spanning the entire 5' region of the factor IX gene extending to exon 6".			1999	10544912	Following Table 3 from Kuder et al. (2021), the breed for this variant has been changed to Pit Bull Terrier. (18th October 2021)
1039	OMIA:000438-9615	dog	Hovawart	Haemophilia B	F9		regulatory	Naturally occurring variant	yes	CanFam3.1	X	g.109501492del	c.-73del		NM_001003323.2; Brenig et al. (2019): NC_006621.3:g.109501492delC; "The deletion is located 73 bp upstream of the F9 start codon in the conserved overlapping DNA binding sites of hepatocyte nuclear factor 4alpha and androgen receptor."			2019	30846504
705	OMIA:000438-9615	dog	German Wirehaired Pointer	Haemophilia B	F9		insertion, gross (>20)	Naturally occurring variant	yes	CanFam3.1	X	g.109521130_109521131insN[(1500)]			NM_001003323.2; published as "insert consists of a 5' truncated canine Line-1 followed by an approximately 200-bp 3' poly (A) tract, flanked by a 15-bp direct repeat"; g. coordinate of insertion obtained from Brenig et al. (2019)			2003	14722728	CanFam3.1 coordinates copied from Table 3 of Kuder et al. (2021) (18 Oct 2021)
467	OMIA:000438-9615	dog	Lhasa Apso	Haemophilia B	F9		deletion, small (<=20)	Naturally occurring variant	yes	CanFam3.1	X	g.109521356_109521361delinsT	c.548_553delinsT	p.(R183Lfs*3)	NM_001003323.2; NP_001003323.1; published as "a deletion including nucleotides 772-776 and a C-->T transition at nucleotide 777", coordinates in the table have been updated to a recent reference genome and / or transcript and to HGVS nomenclature			1996	8896410	CanFam3.1 coordinates copied from Table 3 of Kuder et al. (2021) (18 Oct 2021)
47	OMIA:000438-9615	dog	Rhodesian Ridgeback	Haemophilia B	F9		missense	Naturally occurring variant	yes	CanFam3.1	X	g.109530868G>A	c.731G>A	p.(G244E)	NM_001003323.2; NP_001003323.1; published as p.(G244E) by Mischke et al. (2011), g. and p. coordinates were copied on the 18th October 2021 from Table 3 of Kuder et al. (2021) (relating to NP_001003323.1 ) as g.109530847G>A and p.(G237E). These g. and p. positions were incorrect. After review of Figure 1 published by Mischke et al. (2011) it was confirmed that the published p. coordinates are consistent with NM_001003323.2:c.731G>A and NP_001003323.1:p.(G244E). The g. coordinates have been updated to a recent reference genome (5th April 2022)			2011	20303304	Thank you to Agustín Arasanz for identifying that the coordinates published by Kuder et al. (2021) were inconsistent with the originally published information by Mischke et al. (2011) (5th April 2022).
1363	OMIA:000438-9615	dog	Newfoundland	Haemophilia B	F9		insertion, small (<=20)	Naturally occurring variant	yes	CanFam3.1	X	g.109531586_109531587insA	c.821_822insA	p.(N274Kfs*23)	NM_001003323.2; NP_001003323.1			2021	34680886
704	OMIA:000438-9615	dog	Airedale Terrier	Haemophilia B	F9		insertion, gross (>20)	Naturally occurring variant	yes	CanFam3.1	X	g.109532012_109532013insN[(5000)]	c.1247_1248insN[(5000)]		NM_001003323.2; Gu et al. (1999): "An approximately 5 kb insertion disrupted exon 8 ... associated with alternative splicing between a donor site 5' and acceptor site 3' to the normal exon 8 splice junction, with introduction of a new stop codon. The resultant transcript lacked most of the factor IX catalytic domain and 3' untranslated region."			1999	10544912	CanFam3.1 coordinates copied from Table 3 of Kuder et al. (2021) (18 Oct 2021)
46	OMIA:000438-9615	dog	Cairn Terrier	Haemophilia B	F9		missense	Naturally occurring variant	yes	CanFam3.1	X	g.109532018G>A	c.1253G>A	p.(G418E)	NM_001003323.2; NP_001003323.1, published as p.(G379E) by Evans et al. (1989), coordinates in the table have been updated to a recent reference genome and / or transcript			1989	2481310	c. and p. coordinates updated from Kuder et al. (2021)
127	OMIA:000438-9685	domestic cat	Domestic Longhair	Haemophilia B	F9		missense	Naturally occurring variant	yes	Felis_catus_9.0	X	g.117091961G>A	c.383G>A	p.(C128Y)	NM_001009377.3; NP_001009377.1; published as p.(C82Y); coordinates in the table have been updated to a recent reference genome and / or transcript			2005	15822564	Genomic position in Felis_catus_9.0 provided by Leslie Lyons and Reuben Buckley.
310	OMIA:000438-9685	domestic cat		Haemophilia B	F9		nonsense (stop-gain)	Naturally occurring variant	yes	Felis_catus_9.0	X	g.117111577C>T	c.1150C>T	p.(R384*)	NM_001009377.3; NP_001009377.1; published as p.(R338*); coordinates in the table have been updated to a recent reference genome and / or transcript			2005	15822564	Genomic position in Felis_catus_9.0 provided by Leslie Lyons and Reuben Buckley.
1360	OMIA:002450-9913	cattle	Chianina (Cattle)	Ichthyosis congenita	FA2H		insertion, small (<=20)	Naturally occurring variant	yes	ARS-UCD1.2	18	g.2205625_2205626insG	c.9dupC	p.(A4Rfs*142)	NM_001192455.1; NP_001179384.1			2021	34599683
752	OMIA:002032-9615	dog	Border Collie Mixed breed (duplicate)	Neuropathy, sensory	FAM134B		inversion	Naturally occurring variant	yes	CanFam3.1	4	g.80439639_86910352inv			"6.47 Mb inversion was identified with breakpoints in intron 3 of FAM134B (chr4:86,910,352) and in an upstream intergenic region (chr4:80,439,639) ... … Analysis of RNAseq data revealed FAM134B was majorly disrupted by the inversion, with novel exons occurring 3′ of the final normally transcribed exon before the inversion, due to cryptic splicing."			2016	27527794
1342	OMIA:002032-9615	dog	Mixed breed (duplicate)	Neuropathy, sensory	FAM134B		missense	Naturally occurring variant	yes	CanFam3.1	4	g.86916562C>T	c.656C>T	p.(P219L)	NM_001314111.1; NP_001301040.1			2021	34387380
925	OMIA:001918-9615	dog	Tibetan Spaniel Tibetan Terrier	Progressive retinal atrophy, type 3, FAM161A-related	FAM161A		insertion, gross (>20)	Naturally occurring variant	yes	CanFam3.1	10	g.61822372_61822373insN[(230)]			A ~230bp insertion containing a 132bp short interspersed nuclear element (SINE), near the splice acceptor site of exon 5 CanFam2.0 coordinate published as g.64974130			2014	24705771
1183	OMIA:002259-9913	cattle	Montbéliarde (Cattle)	de novo mutation in an AI sire	FAM189A1		missense	Naturally occurring variant	yes	ARS-UCD1.2	21	g.28112913T>C		p.(N192S)	Bourneuf et al. (2017) detected FAM189A1 g.28644665T>C; p.N192S as a de novo recessive potentially lethal mutation from an analysis of whole-genome-sequence of a Montbéliarde AI bull. No information was provided on the descendants of this bull.			2017	28904385
102	OMIA:002015-9615	dog	Border Collie	Dental hypomineralization	FAM20C		missense	Naturally occurring variant	yes	CanFam3.1	6	g.16452327G>A	c.899C>T	p.(A300V)				2016	27187611	Variant coordinates obtained from or confirmed by EBI's Some Effect Predictor (VEP) tool
89	OMIA:001327-9615	dog	Irish Terrier Kromfohrländer	Hyperkeratosis, palmoplantar	FAM83G		missense	Naturally occurring variant	yes	CanFam3.1	5	g.41055619G>C	c.155G>C	p.(R52P)				2014	24832243	Variant coordinates obtained from or confirmed by EBI's Some Effect Predictor (VEP) tool
1511	OMIA:002600-9986	rabbit	New Zealand White (Rabbit)	Amelogenesis imperfecta	FAM83H		deletion, gross (>20)	Genome-editing (CRISPR-Cas9)	yes						large deletion of more then 900bp in exon 5			2022	36300761
460	OMIA:001683-9615	dog	Cavalier King Charles Spaniel	Congenital keratoconjunctivitis sicca and ichthyosiform dermatosis	FAM83H		deletion, small (<=20)	Naturally occurring variant	yes	CanFam3.1	13	g.37328057del	c.977del	p.(P326Hfs*258)	NM_001289427.1; NP_001276356.1; genomic position in accordance with HGVS 3'-rule			2012	22253609	Genomic coordinates in CanFam3.1 provided by Zoe Shmidt and Robert Kuhn.
683	OMIA:002683-9615	dog	Basenji	Fanconi syndrome	FAN1		deletion, gross (>20)	Naturally occurring variant	yes		3				"317 bp of exon 14 were deleted starting at the second exon14 nucleotide and extending into the 3' untranslated region of FAN1"			2011	Reference not in PubMed; see OMIA 002683-9615 for reference details
646	OMIA:000151-9913	cattle	Holstein (black and white) (Cattle)	Brachyspina	FANCI		deletion, gross (>20)	Naturally occurring variant	yes	ARS-UCD1.2	21	g.20773899_20777226del		p.(V877Lfs*27)				2012	22952632	Breed and variant information kindly provided or confirmed by Matt McClure and Jennifer McClure from "Understanding Genetics and Complete Genetic Disease and Trait Definition (Expanded 2016 Edition)" (https://www.icbf.com/wp/?page_id=2170)
613	OMIA:002064-9685	domestic cat	British Shorthair (Cat)	Autoimmune lymphoproliferative syndrome	FASLG		duplication	Naturally occurring variant	yes	Felis_catus_9.0	F1	g.16871916dup	c.418dup	p.(R140Kfs*37)	NM_001009352.1; NP_001009352.1; published as c.413_414insA "insertion of an adenine at position 14,607,400 [Felis_Catus_6.2]" (Aberdein et al., 2017); changed in this table to a recent reference genome and HGVS nomenclature			2017	27770190
201	OMIA:000628-9913	cattle	Limousin (Cattle)	Marfan syndrome	FBN1		missense	Naturally occurring variant	yes	ARS-UCD1.2	10	g.61831200G>A	c.3598G>A	p.(E1200K)				2005	15776436	Variant coordinates obtained from or confirmed by EBI's Some Effect Predictor (VEP) tool
377	OMIA:000628-9913	cattle	Japanese Black, Japan (Cattle)	Marfan syndrome	FBN1		splicing	Naturally occurring variant	yes	ARS-UCD1.2	10	g.61917867G>A	c.8227-1G>A					2012	22221020	Variant information kindly provided or confirmed by Hubert Pausch, including information from Additional Table 6 of Jansen et al. (2013) BMC Genomics201314:446 https://doi.org/10.1186/1471-2164-14-446
1402	OMIA:000628-9823	pig		Marfan syndrome	FBN1		deletion, small (<=20)	Genome-editing (ZFN)	yes	Sscrofa11.1	1	g.123246159del		p.(E433Nfs98*)				2016	27074716
910	OMIA:000836-9913	cattle	Blonde d'Aquitaine (Cattle) Limousin (Cattle)	Protoporphyria	FECH		extension (stop-lost)	Naturally occurring variant	yes	ARS-UCD1.2	24	g.56787697C>A	c.1250G>T	p.(417Lext27)				1998	9784594	Variant coordinates obtained from or confirmed by EBI's Some Effect Predictor (VEP) tool; Breed information kindly provided or confirmed by Matt McClure and Jennifer McClure from "Understanding Genetics and Complete Genetic Disease and Trait Definition (Expanded 2016 Edition)" (https://www.icbf.com/wp/?page_id=2170)
576	OMIA:001525-9615	dog	German Shepherd Dog	Leukocyte adhesion deficiency, type III	FERMT3		insertion, small (<=20)	Naturally occurring variant	yes	CanFam3.1	18	g.52835932_52835933insGGCAGCCGTCTT	c.1349_1350insAAGACGGCTGCC	p.(L450_A451insRRLP)	XM_038425194.1; XP_038281122.1; 12-base pair insertion			2010	20126836
1336	OMIA:002382-9615	dog	Miniature Wirehaired Dachshund	Afibrinogenaemia	FGA		deletion, small (<=20)	Naturally occurring variant	yes	CanFam3.1	15	g.52240694del	c.1665delT	p.(I555Mfs*33)	Transcript XM_532697.6 / ENSCAFT00000043702.3	rs1152388481	rs1152388481	2021	34356081
1529	OMIA:002625-9913	cattle	Japanese Black, Japan (Cattle)	Skeletal dysplasia, FGD3 related	FGD3		delins, small (<=20)	Naturally occurring variant	yes	UMD_3.1.1	8	g.85826989_85826990delinsTG		p.(H171C)				2015	26306008
1326	OMIA:002374-9913	cattle	Holstein Friesian (Cattle) Jersey (Cattle)	Charcot Marie Tooth disease	FGD4		splicing	Naturally occurring variant	yes	ARS-UCD1.2	5	g.77262490C>T	c.1671+1G>A		Splice donor mutation based on XM_005206883.3			2021	34045765
941	OMIA:001723-9940	sheep	Romney Marsh (Sheep)	Familial episodic ataxia	FGF14		nonsense (stop-gain)	Naturally occurring variant	yes	Oar_rambouillet_v1.0	10	g.88095843G>A	c.46C>T	p.(Q16*)	Oar_v3.1 position is g.77593415			2017	29253853	The genomic location on Oar_rambouillet_v1.0 was determined by Katie Eager, EMAI, NSW Department of Primary Industries.
327	OMIA:000889-9031	chicken	Israeli experimental line, Israel (Chicken) Storrs Connecticut scaleless low line, United States of America (Chicken) UC Davis line, United States of America (Chicken)	Scaleless	FGF20		nonsense (stop-gain)	Naturally occurring variant	yes	GRCg6a	4	g.63270401A>T	c.535A>T	p.(R179*)				2012	22712610	Variant coordinates obtained from or confirmed by EBI's Some Effect Predictor (VEP) tool
929	OMIA:000272-9615	dog	Rhodesian Ridgeback Thai Ridgeback	Ridge & dermoid sinus	FGF3	Ridge allele	duplication	Naturally occurring variant	yes	CanFam3.1	18	g.48372578_48505893dup133316			A large ~133,000 bp duplication on chromosome 18, encompassing three FGF genes (FGF3, FGF4, FGF19) and another gene ORAOV1. There is an additional single T inserted between the two copies of the duplication. This is not indicated in the genomic variant designation.			2007	17906623
694	OMIA:002542-9615	dog	Basset Hound Cairn Terrier Cardigan Welsh Corgi Dachshund Dandie Dinmont Terrier Lancashire heeler Norwich Terrier Pekingese Pembroke Welsh Corgi Petit Basset Griffon Vendéen Shih-Tzu Skye Terrier Swedish Vallhund Tibetan Spaniel West Highland Terrier	Chondrodysplasia	FGF4 retrogene CFA18	FGF4L1	insertion, gross (>20)	Naturally occurring variant	yes		18				a 5kb insertion containing a FGF4 retrogene, i.e. a processed pseudogene of FGF4: The insertion containing the FGF4 retrogene starts at 23,431,136 on CFA18, which is 25Mb away from the complete (original) FGF4 gene, which is located at CFA18 48413479-48415205			2009	19608863
855	OMIA:000157-9615	dog	American Cocker Spaniel Basset Hound Beagle Cardigan Welsh Corgi Chesapeake Bay Retriever Chihuahua Coton de Tulear Dachshund English Springer Spaniel French Bulldog Nova Scotia Duck Tolling retriever	Intervertebral disc disease, type I	FGF4 retrogene in CFA12	FGF4L2	insertion, gross (>20)	Naturally occurring variant	yes	CanFam3.1	12				" the insertion on CFA12 is 3,209 bp long (GenBank accession no. MF040221) and includes parental FGF4 cDNA (i.e., FGF4 exons spliced without introns) . . . ." 200922: g. info moved here (g.33710178_33710179insMF040221) until it can be standardised			2017	29073074
853	OMIA:002133-9615	dog	Nova Scotia Duck Tolling retriever	Skeletal dysplasia, FGF4-retrogene-related	FGF4 retrogene on CFA12	FGF4L2	insertion, gross (>20)	Naturally occurring variant	yes	CanFam3.1	12				" the insertion on CFA12 is 3,209 bp long (GenBank accession no. MF040221) and includes parental FGF4 cDNA (i.e., FGF4 exons spliced without introns) . . . ." 200922: g. info moved here (g.33710178_33710179insMF040221) until can be standardised			2017

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1524 variant records found