ClinVar Miner

Submissions for variant NM_020442.6(VARS2):c.2467-2A>G

gnomAD frequency: 0.00011  dbSNP: rs200075594
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Total submissions: 4
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Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
CeGaT Center for Human Genetics Tuebingen RCV001312050 SCV001502478 pathogenic not provided 2020-10-01 criteria provided, single submitter clinical testing
Labcorp Genetics (formerly Invitae), Labcorp RCV001312050 SCV002211693 pathogenic not provided 2024-11-15 criteria provided, single submitter clinical testing This sequence change affects an acceptor splice site in intron 25 of the VARS2 gene. It is expected to disrupt RNA splicing. Variants that disrupt the donor or acceptor splice site typically lead to a loss of protein function (PMID: 16199547), and loss-of-function variants in VARS2 are known to be pathogenic (PMID: 29313548). This variant is present in population databases (rs200075594, gnomAD 0.03%). Disruption of this splice site has been observed in individual(s) with VARS2-related mitochondrial disease (PMID: 29314548). In at least one individual the data is consistent with being in trans (on the opposite chromosome) from a pathogenic variant. ClinVar contains an entry for this variant (Variation ID: 933237). Algorithms developed to predict the effect of sequence changes on RNA splicing suggest that this variant may disrupt the consensus splice site. For these reasons, this variant has been classified as Pathogenic.
Fulgent Genetics, Fulgent Genetics RCV001201411 SCV002810746 likely pathogenic Combined oxidative phosphorylation defect type 20 2021-07-16 criteria provided, single submitter clinical testing
OMIM RCV001201411 SCV001372478 pathogenic Combined oxidative phosphorylation defect type 20 2020-07-10 no assertion criteria provided literature only

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