Document Type
Article
Publication Date
9-1-2024
Original Citation
El Kassaby B,
Castellanos F,
Gerring M,
Kunde-Ramamoorthy G,
Bult C.
MVAR: A Mouse Variation Registry. J Mol Biol. 2024;436(17):168518
Keywords
JGM, Animals, Mice, Databases, Genetic, Genetic Variation, Polymorphism, Single Nucleotide, Registries, Molecular Sequence Annotation, INDEL Mutation, Software, Genomics, Humans, Computational Biology
JAX Source
J Mol Biol. 2024;436(17):168518
ISSN
1089-8638
PMID
38458603
DOI
https://doi.org/10.1016/j.jmb.2024.168518
Grant
MVAR was supported, in part, by funding from The Jackson Laboratory Director’s Innovation Fund and NHGRI U24HG000330 (CJB).
Abstract
The Mouse Variation Registry (MVAR) resource is a scalable registry of mouse single nucleotide variants and small indels and variant annotation. The resource accepts data in standard Variant Call Format (VCF) and assesses the uniqueness of the submitted variants via a canonicalization process. Novel variants are assigned a unique, persistent MVAR identifier; variants that are equivalent to an existing variant in the resource are associated with the existing identifier. Annotations for variant type, molecular consequence, impact, and genomic region in the context of specific transcripts and protein sequences are generated using Ensembl's Variant Effect Predictor (VEP) and Jannovar. Access to the data and annotations in MVAR are supported via an Application Programming Interface (API) and web application. Researchers can search the resource by gene symbol, genomic region, variant (expressed in Human Genome Variation Society syntax), refSNP identifiers, or MVAR identifiers. Tabular search results can be filtered by variant annotations (variant type, molecular consequence, impact, variant region) and viewed according to variant distribution across mouse strains. The registry currently comprises more than 99 million canonical single nucleotide variants for 581 strains of mice. MVAR is accessible from https://mvar.jax.org.
Creative Commons License
This work is licensed under a Creative Commons Attribution 4.0 International License.