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29 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.
| 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 | Peacock Valais Grüenochte | Peacock | ASIP | A^pc | repeat variation | no | "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 | |||||||
| OMIA 000201-9925 | goat | Bezoar Valais Blackneck Valais Copperneck | 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 | Appenzell Girgentana Saanen | White or tan | ASIP | A^Wt | repeat variation | 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 | |||||
| OMIA 000201-9925 | goat | Grisons Striped Toggenburg | Swiss markings | ASIP | A^sm | repeat variation | 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 | |||||
| OMIA 000201-9925 | goat | Chamois Colored St. Gallen Booted | Badgerface | ASIP | A^b | repeat variation | 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 | |||||
| OMIA 000698-9925 | goat | Myotonia | CLCN1 | missense | yes | ARS1 | 4 | g.13857007C>G | c.2590G>C | 1996 | 8855341 | ||||||
| OMIA 000852-9925 | goat | Casein, alpha-S1, reduced concentration | CSN1S1 | insertion, gross (>20) | 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 | ||||||||
| OMIA 001623-9925 | goat | Casein, alpha-S2, absence | CSN1S2 | nonsense (stop-gain) | no | ARS1 | 6 | g.86085134G>A | c.763G>A | p.(T110*) | rs268293093 | 2001 | 11419340 | The genomic location on ARS1 was determined by Katie Eager, EMAI, NSW Department of Primary Industries | |||
| OMIA 001424-9925 | goat | absence of β‐casein | CSN2 | CSN2^0 | deletion, small (<=20) | no | ARS1 | 6 | g.86008401delA | 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." | 1999 | 10612234 | The genomic location on ARS1 was determined by Katie Eager, EMAI, NSW Department of Primary Industries | ||||
| OMIA 001424-9925 | goat | absence of β‐casein | CSN2 | CSN2^01 | regulatory | no | ARS1 | 6 | g.86015651A>G | Cosenza et al. (2016): "nucleotide C .... negatively affects the promoter activity of the CSN2 gene" | 2007 | 17931404 | The genomic location on ARS1 was determined by Katie Eager, EMAI, NSW Department of Primary Industries | ||||
| 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 | ARS1 | 5 | g.48406875C>T | c.322C>T | p.(R102*) | 1995 | 7623459 | The genomic location on ARS1 was determined by Katie Eager, EMAI, NSW Department of Primary Industries | ||||
| OMIA 000806-9925 | goat | Polyceraty | HOXD1 | delins, gross (>20) | no | ARS1 | 2 | g.115652290_116155699delins137kb | 2021 | 33528505 | |||||||
| 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.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 | ||||
| OMIA 000209-9925 | goat | Pak angora | White | KIT | KIT^ANG | repeat variation | 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 | ||||
| OMIA 000626-9925 | goat | Mannosidosis, beta | MANBA | deletion, small (<=20) | yes | ARS1 | 6 | g.22409150delG | c.1398delG | 1996 | 8921369 | The genomic location on ARS1 was determined by Katie Eager, EMAI, NSW Department of Primary Industries | |||||
| OMIA 000944-9925 | goat | Resistance to scrapie | PRNP | missense | yes | ARS1 | 13 | p.(H143R) | 2002 | 11842266 | |||||||
| OMIA 000944-9925 | goat | Norwegian Dairy Goat | Complete resistance to scrapie | PRNP | Ter | nonsense (stop-gain) | no | ARS1 | 13 | g.46469788G>T | c.???G>T | p.(Gly32*) | 2012 | 23249298 | The genomic location on ARS1 was determined by Katie Eager, EMAI, NSW Department of Primary Industries | ||
| OMIA 000944-9925 | goat | Resistance to scrapie | PRNP | missense | yes | ARS1 | 13 | g.46470073G>A | p.(G127S) | rs268292978 | 2011 | 22040234 | The genomic location on ARS1 was determined by Katie Eager, EMAI, NSW Department of Primary Industries | ||||
| OMIA 000944-9925 | goat | Resistance to scrapie | PRNP | missense | yes | ARS1 | 13 | g.46470120A>G | p.(I142M) | rs268292980 | 1996 | 8922485 | The genomic location on ARS1 was determined by Katie Eager, EMAI, NSW Department of Primary Industries | ||||
| OMIA 000944-9925 | goat | Resistance to scrapie | PRNP | missense | no | ARS1 | 13 | g.46470130A>G | p.(N146D) | 2007 | 16314132 | The genomic location on ARS1 was determined by Katie Eager, EMAI, NSW Department of Primary Industries | |||||
| OMIA 000944-9925 | goat | Resistance to scrapie | PRNP | missense | no | ARS1 | 13 | g.46470131A>G | p.(N146S) | 2007 | 16314132 | The genomic location on ARS1 was determined by Katie Eager, EMAI, NSW Department of Primary Industries | |||||
| OMIA 000944-9925 | goat | Resistance to scrapie | PRNP | missense | yes | ARS1 | 13 | g.46470155G>A | p.(H154R) | rs268292981 | 2009 | 19218225 | The genomic location on ARS1 was determined by Katie Eager, EMAI, NSW Department of Primary Industries | ||||
| OMIA 000944-9925 | goat | Resistance to scrapie | PRNP | missense | yes | ARS1 | 13 | g.46470326G>A | p.(Q211R) | rs268292982 | 2009 | 19218225 | The genomic location on ARS1 was determined by Katie Eager, EMAI, NSW Department of Primary Industries | ||||
| OMIA 000944-9925 | goat | Resistance to scrapie | PRNP | missense | yes | ARS1 | 13 | g.46470358C>A | p.(Q222K) | rs268292983 | 2006 | 16603543 | The genomic location on ARS1 was determined by Katie Eager, EMAI, NSW Department of Primary Industries | ||||
| OMIA 000424-9925 | goat | Dutch Landrace | Goitre, familial | TG | nonsense (stop-gain) | yes | ARS1 | 14 | g.73537317C>G | c.945C>G | p.(Y296*) | 1993 | 8380383 | The genomic location on ARS1 was determined by Katie Eager, EMAI, NSW Department of Primary Industries | |||
| OMIA 001249-9925 | goat | Toggenburg Valais Copperneck | Brown | TYRP1 | missense | 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 | 29 |
| Variants with genomic location | 24 (82.8% ) |
| Variants in a variant database, i.e. with rs ID | 6 (20.7%) |
| Variant Type | Count | Percent |
|---|---|---|
| complex rearrangement | 1 | 3.4% |
| deletion, small (<=20) | 2 | 6.9% |
| delins, gross (>20) | 1 | 3.4% |
| insertion, gross (>20) | 1 | 3.4% |
| missense | 10 | 34.5% |
| nonsense (stop-gain) | 4 | 13.8% |
| regulatory | 1 | 3.4% |
| repeat variation | 7 | 24.1% |
| wild type (i.e. normal) | 2 | 6.9% |
| Year First Reported | Count | Percent |
|---|---|---|
| 1993 | 1 | 3.4% |
| 1994 | 1 | 3.4% |
| 1995 | 1 | 3.4% |
| 1996 | 3 | 10.3% |
| 1997 | 0 | 0.0% |
| 1998 | 0 | 0.0% |
| 1999 | 1 | 3.4% |
| 2000 | 0 | 0.0% |
| 2001 | 1 | 3.4% |
| 2002 | 1 | 3.4% |
| 2003 | 0 | 0.0% |
| 2004 | 0 | 0.0% |
| 2005 | 0 | 0.0% |
| 2006 | 1 | 3.4% |
| 2007 | 3 | 10.3% |
| 2008 | 0 | 0.0% |
| 2009 | 3 | 10.3% |
| 2010 | 0 | 0.0% |
| 2011 | 1 | 3.4% |
| 2012 | 1 | 3.4% |
| 2013 | 0 | 0.0% |
| 2014 | 0 | 0.0% |
| 2015 | 1 | 3.4% |
| 2016 | 1 | 3.4% |
| 2017 | 0 | 0.0% |
| 2018 | 0 | 0.0% |
| 2019 | 7 | 24.1% |
| 2020 | 1 | 3.4% |
| 2021 | 1 | 3.4% |