OMIA:002449-94885 : Skin colour, LYST-related in Pantherophis guttatus (corn snake) |
Categories: Pigmentation phene
Possibly relevant human trait(s) and/or gene(s)s (MIM numbers): 606897 (gene) , 214500 (trait)
Links to MONDO diseases: No links.
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."
Genetic engineering:
Unknown
Have human generated variants been created, e.g. through genetic engineering and gene editing
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 |
Variants
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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 |
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| 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]. 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 | 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