OMIA:002449-94885 : Skin colour, LYST-related in Pantherophis guttatus (corn snake)

Categories: Pigmentation phene

Links to possible relevant human trait(s) and/or gene(s) in OMIM: 606897 (gene) , 214500 (trait)

Mendelian trait/disorder: yes

Considered a defect: no

Key variant known: yes

Year key variant first reported: 2020

Species-specific name: lavender color morph

Species-specific description: "The lavender color morph in corn snakes is characterized by gray, rather than red, blotches on a pink, instead of orange, background." (Ullate-Agote et al., 2020)

Molecular basis: Ullate-Agote et al. (2020) "perform mapping-by-sequencing analyses and identify a 3.9-Mb genomic interval where the lavender variant resides. ... sequencing analyses reveal a single nucleotide polymorphism introducing a premature stop codon in the lysosomal trafficking regulator gene (LYST) that shortens the corresponding protein by 603 amino acids and removes evolutionary-conserved domains."

Associated gene:

Symbol Description Species Chr Location OMIA gene details page Other Links
LYST Pantherophis guttatus NW_026844038.1 (27364828..27266328) LYST Homologene, Ensembl , NCBI gene


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
1359 Skin colour, lavender LYST nonsense (stop-gain) Naturally occurring variant c.9508C>T p.(Q3169*) 2020 33020272

Cite this entry

Nicholas, F. W., Tammen, I., & Sydney Informatics Hub. (2021). OMIA:002449-94885: Online Mendelian Inheritance in Animals (OMIA) [dataset].


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 Guo, L., Kruglyak, L. :
Genetics and biology of coloration in reptiles: The curious case of the Lemon Frost geckos. Physiol Genomics , 2023. Pubmed reference: 37642275. DOI: 10.1152/physiolgenomics.00015.2023.
2021 Andrade, P., Carneiro, M. :
Pterin-based pigmentation in animals. Biol Lett 17:20210221, 2021. Pubmed reference: 34403644. DOI: 10.1098/rsbl.2021.0221.
2020 Ullate-Agote, A., Burgelin, I., Debry, A., Langrez, C., Montange, F., Peraldi, R., Daraspe, J., Kaessmann, H., Milinkovitch, M.C., Tzika, A.C. :
Genome mapping of a LYST mutation in corn snakes indicates that vertebrate chromatophore vesicles are lysosome-related organelles. Proc Natl Acad Sci U S A 117:26307-26317, 2020. Pubmed reference: 33020272. DOI: 10.1073/pnas.2003724117.

Edit History

  • Created by Imke Tammen2 on 03 Oct 2021
  • Changed by Imke Tammen2 on 03 Oct 2021