mvTool V2 – Universal mtDNA Variant Converter and One Stop Annotation

mvTool V2 – Universal mtDNA Variant Converter and One Stop Annotation


Input mtDNA variants in any of the major formats, mixed formats input is supported.

The results are returned as multiple html tables, as well as a downloadable combined Excel file.

An API is implemented, which takes inputs in VCF, HGVS, or classical mtDNA variant nomenclatures, and returns annotated vcf or json outputs


Mitochondrial DNA variant nomenclature has multiple existing systems used in literature and in different institutes. The major ways are:
1. HGVS Committee: m.8993T>G. This is its recommended format and is widely used in literature.
2. HGVS NCBI/ClinVar: NC_012920.1:m.8993T>G, reference version is required.
3. HGVS Ensembl: MT:g.8993T>G
4. HGVS Mutalyzer: NC_012920.1:g.8993T>G
5. Classical I: used in literature, PhyloTree, Haplogrep, 8527, 8993G, 8993d, 5787_5789d, 1494.1T, 7472.XA
6. Classical II: T8993G
7. Potential non-standard: 8527A>G
8. VCF-style input: Tab-delimted, with at least the first 5 columns in vcf format

Adding to the complexity, the chromosome names can be used as any of the following:
chrM, chM, chrMT, chMT, M, MT, NC_012920.1.

The current mtDNA variant data is mostly based on the default revised Cambridge sequence (rCRS, accession number NC_012920.1), but some commercial SNP array platforms used YRI (accession number AF347015) reference.

The MSeqDR universal variant converter can convert the various combinations of these formats into a standard variant list in the rCRS-based HGVS (1-4) formats. It can convert YRI-based positions into rCRS-based positions.

*Note: Unlimited converter input size. The annotation is currently limited to first 100 entries, due to burden of calling external Ensembl web services. The limit will be lifted in future.

Annotate both mtDNA and nuclear DNA variants? Switch to One-Stop Variant Annotation.
Novel pathogenic variant? Please submit.

The major mvTool collaborators and data sources:
MSeqDR Logo Mitomap  MitoTIP tRNA Scoring     dbNSFP   HmtDB Ensembl PhyloTree GeneDX Inc. OMIM ClinVar human-phenotype-ontology

Dr. Lishuang SHEN

Lishuang Shen MSeqDR WebMaster, Sr. Bioinformatics Scientist, Center for Personalized Medicine, Children's Hospital of Los Angeles, Email:,, Suite 300, 2100 W 3rd St, Los Angeles, CA 90057

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