OMIA:002651-499056 : Skin colour, SMARCE1-related in Ahaetulla prasina (Asian vine snakes)

Possibly relevant human trait(s) and/or gene(s) (MIM number): 603111 (gene)

Links to MONDO diseases: No links.

Mendelian trait/disorder: yes

Mode of inheritance: Probably autosomal recessive

Considered a defect: no

Key variant known: yes

Year key variant first reported: 2023

Species-specific description: Tang et al. (2023) "investigate color morph-enriched Asian vine snakes (Ahaetulla prasina), to explore the mechanism underpinning color variations. Transmission electron microscopy imaging and metabolomics analysis indicates that chromatophore morphology (mainly iridophores) is the main basis for differences in skin color."

Mapping: Tang et al. (2023) "applied a genome-wide association study (GWAS) ... [and] identified an interval on chromosome 4 that contained 903 genome-wide significant SNPs ... . Population genomic analysis was also performed to detect signatures of selection underlying the yellow phenotype. Genomic scans for population genetic differentiation ... revealed that the region strongly associated with GWAS-based color also carried a signature of high differentiation between the two morphs .... The region spanned 426.29 kb (Chr04: 42,912,390–43,338,676) ... and harbored 11 protein-coding genes ... ."

Molecular basis: Tang et al. (2023) "Based on the 903 genome-wide significant SNPs in the signal region, variant annotation and functional prediction identified three missense variants ... . However, only one variant (Chr04: 432,332,81, c.58C > T, p.P20S) was predicted to have a deleterious impact on proteins ... . The p.P20S missense mutation occurred specifically in the yellow Asian vine snakes and was positioned within the 3rd exon of the protein-coding gene SMARCE1. ... Most yellow snakes were homozygotes based on the SNP loci, suggesting a key effect of mutation on skin color differences ... . The existence of the SMARCE1 subunit likely functions to maintain proper subunit composition of the SWI/SNF complex ... and the N-terminal proline-rich region of SMARCE1, where the mutation is located, is important for complex assembly ... . Here, protein variation analysis and structural prediction likewise verified the significance of the p.P20S to SMARCE1 ... . Furthermore, the SMARCE1 knockout zebrafish suggested the involvement of SMARCE1 in NCC differentiation ... . ... abnormal iridophores appeared in the eyes and body of morphants during early embryonic development ... ."

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
SMARCE1 Ahaetulla prasina 4 NC_080542.1 (43211233..43255543) SMARCE1 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
1537 Skin colour, yellow SMARCE1 missense Naturally occurring variant 4 g.43233281C>T c.58C>T p.(P20S) 2023 36895044

Cite this entry

Nicholas, F. W., Tammen, I., & Sydney Informatics Hub. (2023). OMIA:002651-499056: Online Mendelian Inheritance in Animals (OMIA) [dataset]. https://omia.org/. https://doi.org/10.25910/2AMR-PV70

Reference

2023 Tang, C.Y., Zhang, X., Xu, X., Sun, S., Peng, C., Song, M.H., Yan, C., Sun, H., Liu, M., Xie, L., Luo, S.J., Li, J.T. :
Genetic mapping and molecular mechanism behind color variation in the Asian vine snake. Genome Biol 24:46, 2023. Pubmed reference: 36895044. DOI: 10.1186/s13059-023-02887-z.

Edit History


  • Created by Imke Tammen2 on 11 Mar 2023
  • Changed by Imke Tammen2 on 11 Mar 2023