Search Results
Advanced search
Link to this search: https://omia.org/results/?gb_species_id=9925&search_type=advanced&result_type=variant
30 variant records found |
[show instead phene records] |
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 |
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| 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 | |||||||
| 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 | |||||||
| 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 | ||||||
| 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 | ||||||
| 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 | ||||||
| 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 | rs5334475115 | 1996 | 8855341 | ||||
| 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 | |||
| 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 | |||
| 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 | |||||||||
| 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 | ||||||||
| 265 | OMIA:000665-9925 | goat | Mucopolysaccharidosis IIID | GNS | nonsense (stop-gain) | Naturally occurring variant | yes | ARS1 | 5 | g.48406875C>T | c.304C>T | p.(R102*) | rs5334475114 | 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 | OMIA:000806-9925 | goat | Polyceraty | HOXD1 | delins, gross (>20) | Naturally occurring variant | no | ARS1 | 2 | g.115652290_116155699delins137kb | 2021 | 33528505 | ||||||||
| 1201 | OMIA:001737-9925 | goat | Bezoar (Goat) | 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 | OMIA:001737-9925 | goat | Barbari (Goat) | 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 | OMIA:000209-9925 | goat | Pak Angora, Pakistan (Goat) | 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 | OMIA:000626-9925 | 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 | OMIA:001199-9925 | goat | Murcia-Granada (Goat) | 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 | rs669694251 | 2009 | 19706191 | |||
| 1310 | OMIA:000944-9925 | goat | Resistance to scrapie | PRNP | missense | Naturally occurring variant | yes | ARS1 | 13 | p.(H143R) | 2002 | 11842266 | ||||||||
| 1146 | OMIA:000944-9925 | goat | Norsk melkegeit, Norway (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 | OMIA:000944-9925 | 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 | rs268292978 | 2011 | 22040234 | The genomic location on ARS1 was determined by Katie Eager, EMAI, NSW Department of Primary Industries | ||
| 828 | OMIA:000944-9925 | 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 | rs268292980 | 1996 | 8922485 | The genomic location on ARS1 was determined by Katie Eager, EMAI, NSW Department of Primary Industries | ||
| 830 | OMIA:000944-9925 | 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 | OMIA:000944-9925 | 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 | OMIA:000944-9925 | 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 | rs268292981 | 2009 | 19218225 | The genomic location on ARS1 was determined by Katie Eager, EMAI, NSW Department of Primary Industries | ||
| 832 | OMIA:000944-9925 | 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 | rs268292982 | 2009 | 19218225 | The genomic location on ARS1 was determined by Katie Eager, EMAI, NSW Department of Primary Industries | ||
| 833 | OMIA:000944-9925 | 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 | rs268292983 | 2006 | 16603543 | The genomic location on ARS1 was determined by Katie Eager, EMAI, NSW Department of Primary Industries | ||
| 264 | OMIA:000424-9925 | goat | Nederlandse Landgeit, Netherlands (Goat) | 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*) | rs5334475116 | 1993 | 8380383 | The genomic location on ARS1 was determined by Katie Eager, EMAI, NSW Department of Primary Industries | ||
| 1059 | OMIA:001249-9925 | goat | Toggenburg (Goat) Valais Copperneck | Brown | TYRP1 | missense | Naturally occurring variant | no | ARS1 | 8 | g.31503165C>T | c.1487G>A | p.(G496D) | rs5334475101 | 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% |