ClinVar Miner

Submissions for variant NC_012920.1(MT-TL1):m.3302A>G

dbSNP: rs1603218878
Minimum review status: Collection method:
Minimum conflict level:
ClinVar version:
Total submissions: 5
Download table as spreadsheet
Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
ClinGen Mitochondrial Disease Nuclear and Mitochondrial Variant Curation Expert Panel, ClinGen RCV003153873 SCV003842287 likely pathogenic Mitochondrial disease 2022-11-14 reviewed by expert panel curation The m.3302A>G variant in MT-TL1 has been reported in four unrelated individuals with primary mitochondrial disease. Three individuals had features consistent with MELAS and the fourth had myopathy and respiratory failure. The heteroplasmy levels of the variant in affected individuals ranged from 45% to homoplasmic (PS4_moderate; PMIDs: 19370763, 8366098). This variant segregated with disease in one family as the proband and his mother harbored the variant at high heteroplasmy levels (values not provided) in fibroblasts and the variant was homoplasmic in muscle in the proband. An unaffected maternal aunt did not harbor the variant in her white blood cells (PP1; PMID: 8366098). There are no reports of de novo occurrences to our knowledge. Cybrid studies supported the functional impact of this variant as cybrids with the variant present at 98% heteroplasmy had a 6-fold reduction of respiration compared to those with 77% heteroplasmy showing no respiration defect (PS3_supporting; PMID: 17130166). The computational predictor MitoTIP suggests this variant is pathogenic (85.9 percentile) and HmtVAR predicts it to be pathogenic score of 0.85 (PP3). This variant is absent in the GenBank dataset, Helix dataset, and gnomAD v3.1.2 (PM2_supporting). 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 November 14, 2022. Mitochondrial DNA-specific ACMG/AMP criteria applied (PMID: 32906214): PS4_moderate, PP1, PS3_supporting, PM2_supporting, PP3.
Wong Mito Lab, Molecular and Human Genetics, Baylor College of Medicine RCV000850712 SCV000992945 pathogenic Juvenile myopathy, encephalopathy, lactic acidosis AND stroke 2019-07-12 criteria provided, single submitter clinical testing The NC_012920.1:m.3302A>G variant in MT-TL1 gene is interpreted to be a Pathogenic variant based on the modified ACMG guidelines (unpublished). This variant meets the following evidence codes reported in the guidelines: PS3, PS5, PM7
Mendelics RCV000850712 SCV002517713 pathogenic Juvenile myopathy, encephalopathy, lactic acidosis AND stroke 2022-05-04 criteria provided, single submitter clinical testing
OMIM RCV004555600 SCV005044061 pathogenic MITOCHONDRIAL SKELETAL MYOPATHY 2024-05-15 no assertion criteria provided literature only
OMIM RCV004555599 SCV005044062 pathogenic MITOCHONDRIAL CARDIOMYOPATHY WITH OR WITHOUT SKELETAL MYOPATHY 2024-05-15 no assertion criteria provided literature only

The information on this website is not intended for direct diagnostic use or medical decision-making without review by a genetics professional. Individuals should not change their health behavior solely on the basis of information contained on this website. Neither the University of Utah nor the National Institutes of Health independently verfies the submitted information. If you have questions about the information contained on this website, please see a health care professional.