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Link to this search: https://omia.org/results/?search_type=advanced&gb_species_id=9925&result_type=variant&defect=yes&singlelocus=yes&characterised=yes
9 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 | Year Published | PubMed ID(s) | Acknowledgements |
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| 224 | OMIA:000698-9925 | goat | Myotonia | CLCN1 | missense | Naturally occurring variant | yes | ARS1.2 | 4 | NC_030811.1:g.13857007C>G | XM_013963554.2:c.2656G>C | XP_013819008.1:p.(A886P) | Previously listed in OMIA based on ENSEMBL Variant Effect Predictor: transcript ENSCHIT00000031898.1:c.2590G>C; p.(P864A); c. and p. updated based on NCBI transcript IDs [26/08/2024] | 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 | 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 | 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 | 2007 | 17931404 | The genomic location on ARS1 was determined by Katie Eager, EMAI, NSW Department of Primary Industries | |||
| 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 | |||
| 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 | |||||
| 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 |
| Overall Statistics | |
|---|---|
| Total number of variants | 9 |
| Variants with genomic location | 7 (77.8% ) |
| Variants in a variant database, i.e. with rs ID | 6 (66.7%) |
| Variant Type | Count | Percent |
|---|---|---|
| complex rearrangement | 1 | 11.1% |
| deletion, small (<=20) | 2 | 22.2% |
| insertion, gross (>20) | 1 | 11.1% |
| missense | 1 | 11.1% |
| nonsense (stop-gain) | 3 | 33.3% |
| regulatory | 1 | 11.1% |
| Year First Reported | Count | Percent |
|---|---|---|
| 1993 | 1 | 11.1% |
| 1994 | 1 | 11.1% |
| 1995 | 1 | 11.1% |
| 1996 | 2 | 22.2% |
| 1997 | 0 | 0.0% |
| 1998 | 0 | 0.0% |
| 1999 | 1 | 11.1% |
| 2000 | 0 | 0.0% |
| 2001 | 1 | 11.1% |
| 2002 | 0 | 0.0% |
| 2003 | 0 | 0.0% |
| 2004 | 0 | 0.0% |
| 2005 | 0 | 0.0% |
| 2006 | 0 | 0.0% |
| 2007 | 1 | 11.1% |
| 2008 | 0 | 0.0% |
| 2009 | 0 | 0.0% |
| 2010 | 0 | 0.0% |
| 2011 | 0 | 0.0% |
| 2012 | 0 | 0.0% |
| 2013 | 0 | 0.0% |
| 2014 | 0 | 0.0% |
| 2015 | 0 | 0.0% |
| 2016 | 0 | 0.0% |
| 2017 | 0 | 0.0% |
| 2018 | 0 | 0.0% |
| 2019 | 0 | 0.0% |
| 2020 | 1 | 11.1% |