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8 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
1 OMIA000240-8932 rock pigeon Crest EPHB2 cr missense Naturally occurring variant no c.???C>T p.(R758C) 2013 23371554
1209 OMIA001654-8932 rock pigeon Almond MLANA st repeat variation Naturally occurring variant yes "The CNV captures a 77-kb segment of the reference genome (ScoHet5_227: 5,181,467–5,259,256), with an additional increase in coverage in a nested 25-kb segment (ScoHet5_227: 5,201,091–5,226,635). Read-depth analysis confirmed 7 copies of the outer 77-kb segment and 14 copies of the inner 25-kb segment in the genomes of female (ZStW) Almond pigeons, which have an St locus on only one chromosome. We used PCR to amplify across the outer and inner CNV breakpoints of Almond pigeons and determined that the CNV consists of tandem repeats of the 77-kb and nested 25-kb segments (Fig 3)." (Bruders et al., 2020) 2020 32433666
1064 OMIA002189-8932 rock pigeon Barless NDP c start-lost Naturally occurring variant no Cliv_1.0 Vickrey et al. (2018): "a nonsynonymous protein-coding change at the start codon of NDP". 2018 30014848
1212 OMIA002270-8932 rock pigeon Feathered shank PITX1 deletion, gross (>20) Naturally occurring variant no "a 44-kb deletion (from 6.719–6.763 Mb)" (Domyan et al., 2016) 2016 26977633
1349 OMIA001308-8932 rock pigeon Short beak ROR2 Ku2 missense Naturally occurring variant no Cliv_2.1 c.1087C>T Genomic position on scaffold ScoHet5_445.1:6568443; non-reference allele causes an arginine-to-cysteine substitution in the seventh exon of ROR2 (Boer et al., 2021) 2021 34551284
1298 OMIA002416-8932 rock pigeon Pearl-eye SLC2A11B tr nonsense (stop-gain) Naturally occurring variant no AKCR02000030.1 g.1895934G>A p.(W49X) Andrade et al. (2021): "This mutation creates a premature STOP codon in exon 3 of the likely canonical SLC2A11B transcript." 2021 33621224
1065 OMIA002190-8932 rock pigeon Recessive red SOX10 e^1 deletion, gross (>20) Naturally occurring variant no Domyan et al. (2014) reported a 7.5kb deletion that spans "a conserved enhancer element that drives Sox10 expression in melanocytes" 2014 24508169
1066 OMIA002190-8932 rock pigeon Recessive red SOX10 e^2 deletion, gross (>20) Naturally occurring variant no Domyan et al. (2014) reported a 2.5kb deletion that spans "a conserved enhancer element that drives Sox10 expression in melanocytes" 2014 24508169
Overall Statistics
Total number of variants 8
Variants with genomic location 3 (37.5% )
Variants in a variant database, i.e. with rs ID 0 (0.0%)
Variant Type Count Percent
deletion, gross (>20) 3 37.5%
missense 2 25.0%
nonsense (stop-gain) 1 12.5%
repeat variation 1 12.5%
start-lost 1 12.5%
Year First Reported Count Percent
2013 1 12.5%
2014 2 25.0%
2015 0 0.0%
2016 1 12.5%
2017 0 0.0%
2018 1 12.5%
2019 0 0.0%
2020 1 12.5%
2021 2 25.0%