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30 variant records found

[show instead phene records]

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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
1199 OMIA000201-9925 goat Peacock 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
1200 OMIA000201-9925 goat Bezoar Valais Blackneck 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
1196 OMIA000201-9925 goat Appenzell Girgentana Saanen 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 OMIA000201-9925 goat Grisons Striped Toggenburg 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 OMIA000201-9925 goat Chamois Colored St. Gallen Booted 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
224 OMIA000698-9925 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
692 OMIA000852-9925 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 OMIA001623-9925 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
1312 OMIA001424-9925 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 OMIA001424-9925 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
760 OMIA002164-9925 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
1161 OMIA000483-9925 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
265 OMIA000665-9925 goat Mucopolysaccharidosis IIID GNS nonsense (stop-gain) Naturally occurring variant yes ARS1 5 g.48406875C>T c.304C>T p.(R102*) 1995 7623459 The genomic location on ARS1 was determined by Katie Eager, EMAI, NSW Department of Primary Industries. Published as c.322C>T. Updated position based on ENSEMBL Variant Effect Predictor: transcript ENSCHIT00000018630.1
1286 OMIA000806-9925 goat Polyceraty HOXD1 delins, gross (>20) Naturally occurring variant no ARS1 2 g.115652290_116155699delins137kb 2021 33528505
1201 OMIA001737-9925 goat Bezoar Wild type or Bezoar KIT reference sequence allele Naturally occurring variant no ARS1 6 "The coverage plot of bezoars (BEZ) does not show any copy number variation and represents the wildtype allele." (Henkel et al., 2019) 2019 31841508
1187 OMIA001737-9925 goat Barbari White-spotted KIT KIT^BAR repeat variation Naturally occurring variant no ARS1 6 g.70859258_70959918 (2 copies) The CNV "started ~63 kb downstream of KIT and covered ~100 kb of the genome reference sequence without known coding DNA. The short read-aligments of read-pairs spanning the amplification breakpoints confirmed that the individual copies of the CNV were arranged in tandem in a head to tail orientation" (Henkel et al., 2019) "70'911'301-70'927'581: deleted; 89'210'545-89'233'246: 3 copies of which 2 are inserted at 70'911'302" (Table S5; Henkel et al., 2019) 2019 31841508
1188 OMIA000209-9925 goat Pak angora White KIT KIT^ANG repeat variation Naturally occurring variant no ARS1 6 g.70859258_70959918 (3 copies) This CNV "started ~63 kb downstream of KIT and covered ~100 kb of the genome reference sequence without known coding DNA. The short read-aligments of read-pairs spanning the amplification breakpoints confirmed that the individual copies of the CNV were arranged in tandem in a head to tail orientation" (Henkel et al.,2019) 2019 31841508
451 OMIA000626-9925 goat Mannosidosis, beta MANBA deletion, small (<=20) Naturally occurring variant yes ARS1 6 g.22409150del c.1398del 1996 8921369 The genomic location on ARS1 was determined by Katie Eager, EMAI, NSW Department of Primary Industries
1332 OMIA001199-9925 goat Murciana Granadina Black coat colour MC1R missense Naturally occurring variant no ARS1 18 g.16105786C>G c.801C>G p.(C267W) cDNA position based on transcript ENSCHIT00000014455.1 2009 19706191
1310 OMIA000944-9925 goat Resistance to scrapie PRNP missense Naturally occurring variant yes ARS1 13 p.(H143R) 2002 11842266
1146 OMIA000944-9925 goat Norwegian Dairy Goat Complete resistance to scrapie PRNP Ter nonsense (stop-gain) Naturally occurring variant no ARS1 13 g.46469788G>T c.94G>T p.(G32*) ENSEMBL Variant Effect Predictor: transcript ENSCHIT00000020215.1 2012 23249298 The genomic location on ARS1 was determined by Katie Eager, EMAI, NSW Department of Primary Industries
827 OMIA000944-9925 goat Resistance to scrapie PRNP missense Naturally occurring variant yes ARS1 13 g.46470073G>A c.379G>A p.(G127S) ENSEMBL Variant Effect Predictor: transcript ENSCHIT00000020215.1 rs268292978 2011 22040234 The genomic location on ARS1 was determined by Katie Eager, EMAI, NSW Department of Primary Industries
828 OMIA000944-9925 goat Resistance to scrapie PRNP missense Naturally occurring variant yes ARS1 13 g.46470120A>G c.426A>G p.(I142M) ENSEMBL Variant Effect Predictor: transcript ENSCHIT00000020215.1 rs268292980 1996 8922485 The genomic location on ARS1 was determined by Katie Eager, EMAI, NSW Department of Primary Industries
830 OMIA000944-9925 goat Resistance to scrapie PRNP missense Naturally occurring variant no ARS1 13 g.46470130A>G c.436A>G p.(N146D) ENSEMBL Variant Effect Predictor: transcript ENSCHIT00000020215.1 2007 16314132 The genomic location on ARS1 was determined by Katie Eager, EMAI, NSW Department of Primary Industries
829 OMIA000944-9925 goat Resistance to scrapie PRNP missense Naturally occurring variant no ARS1 13 g.46470131A>G c.437A>G p.(N146S) ENSEMBL Variant Effect Predictor: transcript ENSCHIT00000020215.1 2007 16314132 The genomic location on ARS1 was determined by Katie Eager, EMAI, NSW Department of Primary Industries
831 OMIA000944-9925 goat Resistance to scrapie PRNP missense Naturally occurring variant yes ARS1 13 g.46470155G>A c.461G>A p.(R154H) ENSEMBL Variant Effect Predictor: transcript ENSCHIT00000020215.1 rs268292981 2009 19218225 The genomic location on ARS1 was determined by Katie Eager, EMAI, NSW Department of Primary Industries
832 OMIA000944-9925 goat Resistance to scrapie PRNP missense Naturally occurring variant yes ARS1 13 g.46470326G>A c.632G>A p.(R211Q) ENSEMBL Variant Effect Predictor: transcript ENSCHIT00000020215.1 rs268292982 2009 19218225 The genomic location on ARS1 was determined by Katie Eager, EMAI, NSW Department of Primary Industries
833 OMIA000944-9925 goat Resistance to scrapie PRNP missense Naturally occurring variant yes ARS1 13 g.46470358C>A c.664C>A p.(Q222K) ENSEMBL Variant Effect Predictor: transcript ENSCHIT00000020215.1 rs268292983 2006 16603543 The genomic location on ARS1 was determined by Katie Eager, EMAI, NSW Department of Primary Industries
264 OMIA000424-9925 goat Dutch Landrace Goitre, familial TG nonsense (stop-gain) Naturally occurring variant yes ARS1 14 g.73537317C>G c.945C>G p.(Y296*) ENSEMBL Variant Effect Predictor: transcript ENSCHIT00000040333.1: p.(Y315*) 1993 8380383 The genomic location on ARS1 was determined by Katie Eager, EMAI, NSW Department of Primary Industries
1059 OMIA001249-9925 goat Toggenburg Valais Copperneck Brown TYRP1 missense Naturally occurring variant no ARS1 8 g.31503165C>T c.1487G>A p.(G496D) 2015 25392961 The genomic location on ARS1 was determined by Katie Eager, EMAI, NSW Department of Primary Industries
Overall Statistics
Total number of variants 30
Variants with genomic location 25 (83.3% )
Variants in a variant database, i.e. with rs ID 8 (26.7%)
Variant Type Count Percent
complex rearrangement 1 3.3%
deletion, small (<=20) 2 6.7%
delins, gross (>20) 1 3.3%
insertion, gross (>20) 1 3.3%
missense 11 36.7%
nonsense (stop-gain) 4 13.3%
reference sequence allele 2 6.7%
regulatory 1 3.3%
repeat variation 7 23.3%
Year First Reported Count Percent
1993 1 3.3%
1994 1 3.3%
1995 1 3.3%
1996 3 10.0%
1997 0 0.0%
1998 0 0.0%
1999 1 3.3%
2000 0 0.0%
2001 1 3.3%
2002 1 3.3%
2003 0 0.0%
2004 0 0.0%
2005 0 0.0%
2006 1 3.3%
2007 3 10.0%
2008 0 0.0%
2009 4 13.3%
2010 0 0.0%
2011 1 3.3%
2012 1 3.3%
2013 0 0.0%
2014 0 0.0%
2015 1 3.3%
2016 1 3.3%
2017 0 0.0%
2018 0 0.0%
2019 7 23.3%
2020 1 3.3%
2021 1 3.3%