OMIA:001737-9925 : Coat colour, white spotting, KIT-related in Capra hircus
Categories: Pigmentation phene
Links to MONDO diseases: No links.
Mendelian trait/disorder: yes
Considered a defect: no
Key variant known: yes
Year key variant first reported: 2019
Cross-species summary: Variable degree of white spotting ranging from tiny white spots up to completely white animals. The absence of pigment is caused by the absence of skin melanocytes ("leucism, leucistic"), not by failure in the biochemical reactions required for pigment synthesis.
Molecular basis: Henkel et al. (2019) reported two "CNVs were located in the 3’-flanking region of KIT and associated with a completely white coat color phenotype in Pak Angora goats [see OMIA 000209-9925] and a white-spotted coat color phenotype in Barbari goats [this OMIA entry], respectively".
|Symbol||Description||Species||Chr||Location||OMIA gene details page||Other Links|
|KIT||v-kit Hardy-Zuckerman 4 feline sarcoma viral oncogene homolog||Capra hircus||6||NC_030813.1 (70711232..70793908)||KIT||Homologene, Ensembl , NCBI gene|
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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||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||Inferred EVA rsID||Year Published||PubMed ID(s)||Acknowledgements|
|1201||Bezoar (Goat)||Wild type or Bezoar||KIT||reference sequence allele||Naturally occurring variant||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|
|1187||Barbari (Goat)||White-spotted||KIT||KIT^BAR||repeat variation||Naturally occurring variant||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|
Cite this entry
|2019||Henkel, J., Saif, R., Jagannathan, V., Schmocker, C., Zeindler, F., Bangerter, E., Herren, U., Posantzis, D., Bulut, Z., Ammann, P., Drögemüller, C., Flury, C., Leeb, T. :|
|Selection signatures in goats reveal copy number variants underlying breed-defining coat color phenotypes. PLoS Genet 15:e1008536, 2019. Pubmed reference: 31841508 . DOI: 10.1371/journal.pgen.1008536.|
- Changed by Frank Nicholas on 09 Apr 2020
- Created by Frank Nicholas on 09 Apr 2020
- Changed by Frank Nicholas on 17 May 2020