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Link to this search: https://omia.org/results/?gb_species_id=8932&result_type=variant&search_type=advanced
12 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 | Inferred EVA rsID | Year Published | PubMed ID(s) | Acknowledgements |
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| 1632 | OMIA:000375-8932 | rock pigeon | Piebald | EDNRB2 | Group 4 | duplication | Naturally occurring variant | yes | tandem duplication of a 37-kb region spanning from intron 1 of VAMP7 to just 5’ of EDNRB2 | 2023 | 37546953 | |||||||||
| 1631 | OMIA:000375-8932 | rock pigeon | Piebald | EDNRB2 | Group2 | missense | Naturally occurring variant | yes | p.(A42E) | 2023 | 37546953 | |||||||||
| 1630 | OMIA:000375-8932 | rock pigeon | Piebald | EDNRB2 | Group1 | missense | Naturally occurring variant | yes | p.(R290C) | 2023 | 37546953 | |||||||||
| 1633 | OMIA:000375-8932 | rock pigeon | Recessive white and bull eye | EDNRB2 | missense | Naturally occurring variant | no | scaffold 507 | g.11167700C>T | p.(E256K) | 2023 | 37546953 | ||||||||
| 1 | OMIA:000240-8932 | rock pigeon | Crest | EPHB2 | cr | missense | Naturally occurring variant | no | c.???C>T | p.(R758C) | 2013 | 23371554 | ||||||||
| 1209 | OMIA:001654-8932 | 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 | OMIA:002189-8932 | 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 | OMIA:002270-8932 | 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 | OMIA:001308-8932 | 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 | OMIA:002416-8932 | 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 | OMIA:002190-8932 | 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 | OMIA:002190-8932 | 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 | 12 |
| Variants with genomic location | 3 (25.0% ) |
| Variants in a variant database, i.e. with rs ID | 0 (0.0%) |
| Variant Type | Count | Percent |
|---|---|---|
| deletion, gross (>20) | 3 | 25.0% |
| duplication | 1 | 8.3% |
| missense | 5 | 41.7% |
| nonsense (stop-gain) | 1 | 8.3% |
| repeat variation | 1 | 8.3% |
| start-lost | 1 | 8.3% |
| Year First Reported | Count | Percent |
|---|---|---|
| 2013 | 1 | 8.3% |
| 2014 | 2 | 16.7% |
| 2015 | 0 | 0.0% |
| 2016 | 1 | 8.3% |
| 2017 | 0 | 0.0% |
| 2018 | 1 | 8.3% |
| 2019 | 0 | 0.0% |
| 2020 | 1 | 8.3% |
| 2021 | 2 | 16.7% |
| 2022 | 0 | 0.0% |
| 2023 | 4 | 33.3% |