OMIA:001249-9643 : Coat colour, brown, TYRP1-related in Ursus americanus (American black bear)

In other species: Rhesus monkey , dog , domestic cat , horse , pig , taurine cattle , goat , sheep , rabbit , golden hamster , North American deer mouse , Mongolian gerbil , American mink

Categories: Pigmentation phene

Links to possible relevant human trait(s) and/or gene(s) in OMIM: 612271 (trait) , 203290 (trait) , 115501 (gene)

Mendelian trait/disorder: yes

Considered a defect: no

Key variant known: yes

Year key variant first reported: 2023

Species-specific description: Puckett et al. (2023): "The American black bear, Ursus americanus (U. americanus), exhibits a range of colors including the cinnamon morph, which has a similar color to the brown bear, U. arctos, and is found at high frequency in the American southwest. ... Our analyses indicate that the cinnamon TYRP1 variant arose within the western lineage of U. americanus and likely provided a selective advantage in the southwest."

Mapping: Puckett et al. (2023): "A genome-wide association study ... for quantitative hair reflectance values from 151 bears identified 120 single-nucleotide variants (SNVs) above a significance threshold of 10−8 ... . A single peak had the lowest p values and spanned the pigmentation gene TYRP1 ... ."

Molecular basis: Puckett et al. (2023) "identified a significant (p = 1.99 × 10−13) G to A SNV, HiC_scaffold_24:6724152g>a that predicts a missense alteration, p.Arg153Cys ... . This alteration within the luminal domain of TYRP1, a type I transmembrane protein, is within a critical region near the zinc cofactor binding site and thus is likely deleterious ... ."

Associated gene:

Symbol Description Species Chr Location OMIA gene details page Other Links
TYRP1 Ursus americanus NW_025578481.1 (30501445..30484072) TYRP1 Homologene, Ensembl , NCBI gene

Variants

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 Breed(s) Variant Phenotype Gene Allele Type of Variant Source of Genetic Variant Reference Sequence Chr. g. or m. c. or n. p. Verbal Description EVA ID Year Published PubMed ID(s) Acknowledgements
1518 Cinnamon coat colour TYRP1 missense Naturally occurring variant HiC_scaffold_24 g.6724152G>A p.(R153C) 2023 36528024

Cite this entry

Nicholas, F. W., Tammen, I., & Sydney Informatics Hub. (2023). OMIA:001249-9643: Online Mendelian Inheritance in Animals (OMIA) [dataset]. https://omia.org/. https://doi.org/10.25910/2AMR-PV70

References

Note: the references are listed in reverse chronological order (from the most recent year to the earliest year), and alphabetically by first author within a year.

2023 Caro, T. :
Bear essentials. Trends Genet , 2023. Pubmed reference: 36828727. DOI: 10.1016/j.tig.2023.02.011.
Puckett, E.E., Davis, I.S., Harper, D.C., Wakamatsu, K., Battu, G., Belant, J.L., Beyer, D.E., Carpenter, C., Crupi, A.P., Davidson, M., DePerno, C.S., Forman, N., Fowler, N.L., Garshelis, D.L., Gould, N., Gunther, K., Haroldson, M., Ito, S., Kocka, D., Lackey, C., Leahy, R., Lee-Roney, C., Lewis, T., Lutto, A., McGowan, K., Olfenbuttel, C., Orlando, M., Platt, A., Pollard, M.D., Ramaker, M., Reich, H., Sajecki, J.L., Sell, S.K., Strules, J., Thompson, S., van Manen, F., Whitman, C., Williamson, R., Winslow, F., Kaelin, C.B., Marks, M.S., Barsh, G.S. :
Genetic architecture and evolution of color variation in American black bears. Curr Biol 33:86-97.e10, 2023. Pubmed reference: 36528024. DOI: 10.1016/j.cub.2022.11.042.

Edit History


  • Created by Imke Tammen2 on 09 Jan 2023
  • Changed by Imke Tammen2 on 09 Jan 2023
  • Changed by Imke Tammen2 on 23 Jan 2023