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25 variant records found

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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.

OMIA ID(s) Species Name Breed(s) Variant Phenotype Gene Allele Type of Variant Deleterious? Reference Sequence Chr. g. or m. c. or n. p. Verbal Description EVA ID Year Published PubMed ID(s) Acknowledgements
OMIA 000201-9925 goat Bezoar Wild type or Bezaur ASIP A^bz wild type (i.e. normal) no "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
OMIA 000201-9925 goat Peacock Peacock ASIP A^pc repeat variation no g.63,130,175-63,245,658 (3 copies) "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) 2019 31841508
OMIA 000201-9925 goat Grisons Striped Toggenburg Swiss markings ASIP A^sm repeat variation no ARS1 13 g.63,129,198-63,142,631 (8 copies) "8 tandem copies of a 13,433 bp sequence from the 5’-flanking region of ASIP" (Henkel et al., 2019) 2019 31841508
OMIA 000201-9925 goat Chamois Colored St. Gallen Booted Badgerface ASIP A^b repeat variation no ARS1 13 g.63,158,171-63,203,851 (5 copies) "a five-fold amplification of45,680 bp located ~61 kb downstream ofthe Asm amplification" (Henkel et al., 2019) 2019 31841508
OMIA 000201-9925 goat Appenzell Girgentana Saanen White or tan ASIP A^Wt repeat variation no ARS1 13 g.63,226,824-63,381,501 (3 copies) "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) 2009 20016133
OMIA 000698-9925 goat Myotonia CLCN1 missense yes G>C 1996 8855341
OMIA 000852-9925 goat Casein, alpha-S1, reduced concentration CSN1S1 insertion, gross (>20) yes "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
OMIA 001623-9925 goat Casein, alpha-S2, absence CSN1S2 nonsense (stop-gain) yes c.763G>A p.T110* 2001 11419340
OMIA 002164-9925 goat Coat colour, white spotting, EDNRA-related EDNRA repeat variation no "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
OMIA 000483-9925 goat Polled intersex syndrome ERG PIS complex rearrangement 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
OMIA 000665-9925 goat Mucopolysaccharidosis IIID GNS nonsense (stop-gain) yes c.322C>T p.R102* 1995 7623459
OMIA 001737-9925 goat Bezoar Wild type or Bezoar KIT wild type (i.e. normal) 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
OMIA 001737-9925 goat Barbari White-spotted KIT KIT^BAR repeat variation no ARS1 6 g.70,859,258-70,959,918 (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
OMIA 000209-9925 goat Pak angora White KIT KIT^ANG repeat variation no ARS1 6 g.70,859,258-70,959,918 (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
OMIA 000626-9925 goat Mannosidosis, beta MANBA deletion, small (<=20) yes c.1398delG 1996 8921369
OMIA 000944-9925 goat Resistance to scrapie PRNP missense yes p.G127S 2011 22040234
OMIA 000944-9925 goat Resistance to scrapie PRNP missense yes p.H154R 2009 19218225
OMIA 000944-9925 goat Resistance to scrapie PRNP missense yes p.I142M 1996 8922485
OMIA 000944-9925 goat Resistance to scrapie PRNP missense no p.N146D 2007 16314132
OMIA 000944-9925 goat Resistance to scrapie PRNP missense no p.N146S 2007 16314132
OMIA 000944-9925 goat Resistance to scrapie PRNP missense yes p.Q211R 2009 19218225
OMIA 000944-9925 goat Resistance to scrapie PRNP missense yes p.Q222K 2006 16603543
OMIA 000944-9925 goat Norwegian Dairy Goat Complete resistance to scrapie PRNP Ter nonsense (stop-gain) no c.???G>T p.(Gly32*) 2012 23249298
OMIA 000424-9925 goat Dutch Landrace Goitre, familial TG nonsense (stop-gain) yes c.945C>G p.Y296* 1993 8380383
OMIA 001249-9925 goat Brown TYRP1 missense no c.1487G>A p.Gly496Asp 2015 25392961
Overall Statistics
Total number of variants 25
Variants with genomic location 6 (24.0% )
Variants in a variant database, i.e. with rs ID 0 (0.0%)
Variant Type Count Percent
complex rearrangement 1 4.0%
deletion, small (<=20) 1 4.0%
insertion, gross (>20) 1 4.0%
missense 9 36.0%
nonsense (stop-gain) 4 16.0%
repeat variation 7 28.0%
wild type (i.e. normal) 2 8.0%
Year First Reported Count Percent
1993 1 4.0%
1994 1 4.0%
1995 1 4.0%
1996 3 12.0%
1997 0 0.0%
1998 0 0.0%
1999 0 0.0%
2000 0 0.0%
2001 1 4.0%
2002 0 0.0%
2003 0 0.0%
2004 0 0.0%
2005 0 0.0%
2006 1 4.0%
2007 2 8.0%
2008 0 0.0%
2009 3 12.0%
2010 0 0.0%
2011 1 4.0%
2012 1 4.0%
2013 0 0.0%
2014 0 0.0%
2015 1 4.0%
2016 1 4.0%
2017 0 0.0%
2018 0 0.0%
2019 7 28.0%
2020 1 4.0%