ClinVar Miner

Submissions for variant NC_012920.1(MT-TK):m.8340G>A

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Total submissions: 1
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Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
ClinGen Mitochondrial Disease Nuclear and Mitochondrial Variant Curation Expert Panel, ClinGen RCV004595588 SCV005088555 likely pathogenic Mitochondrial disease 2023-05-22 reviewed by expert panel curation The m.8340G>A variant in MT-TK has been reported in five unrelated individuals with features of primary mitochondrial disease (PS4_moderate; PMIDs: 24161205, 29501485, 28729369, 36999085, 34969639). Affected individuals were variably affected and had myopathy, exercise intolerance, muscle weakness, and chronic progressive external ophthalmoplegia (CPEO). Additional features seen include sensorineural hearing loss, retinal dystrophy, cataracts, migraines, epilepsy, microcephaly, and poor growth, and one individual was reported to have congenital heart disease and urinary tract anomalies. There are at least three de novo occurrences reported in the literature (PM6; PMIDs: 29501485, 28729369, 24161205). This variant is absent in the GenBank dataset, Helix dataset, and gnomAD v3.1.2 (PM2_supporting). The computational predictor MitoTIP suggests this variant is pathogenic (65th percentile) and HmtVAR predicts it to be pathogenic score of 0.4 (PP3). Single fiber testing showed higher levels of the variant in COX-deficient fibers (93.1% ± 0.26%, N=17) than in COX-positive fibers (29.5% ± 8.97, N=16), p<0.0001 (PS3_supporting, PMID: 28729369). In summary, this variant meets criteria to be classified as likely pathogenic for primary mitochondrial disease inherited in a mitochondrial manner. This classification was approved by the NICHD/NINDS U24 ClinGen Mitochondrial Disease Variant Curation Expert Panel on May 22, 2023. Mitochondrial DNA-specific ACMG/AMP criteria applied (PMID: 32906214): PS4_moderate, PM6, PM2_supporting, PP3, PS3_supporting.

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