The ClinGen Evidence Repository is an FDA-recognized human genetic variant database containing expert-curated assertions regarding variants' pathogenicity and supporting evidence summaries. [Disclaimer]
  • There was no gene found in the curated document received from the VCI/VCEP
  • Gene listed was thus derived from ClinVar and/or CAR


Variant: NC_012920.1:m.3291T>C

CA337096487

223247 (ClinVar)

Gene: MT-TL1
Condition: mitochondrial disease
Inheritance Mode: Mitochondrial inheritance
UUID: a73e8ba0-8b36-46d2-bbf4-f57935653d8c
Approved on: 2022-10-03
Published on: 2022-10-13

HGVS expressions

NC_012920.1:m.3291T>C
J01415.2:m.3291T>C

Likely Pathogenic

Met criteria codes 6
PM2_Supporting PP1_Moderate PS4_Moderate PP3 PM6 PS3_Supporting

Evidence Links 1

Expert Panel

Criteria Specification Information

Criteria Specification: ClinGen Mitochondrial Disease Nuclear and Mitochondrial Expert Panel Specifications to the ACMG/AMP Variant Interpretation Guidelines Version 1_mtDNA

PDF
Criteria Specification Approval History
Criteria Specifications for this VCEP
Evidence submitted by expert panel
Mitochondrial Diseases VCEP
The m.3291T>C variant in MT-TL1 has been reported in at least eight unrelated individuals with primary mitochondrial disease. Ages of onset varied from 6- to 40-years old. Affected individuals had variable features including those consistent with MELAS (Mitochondrial Encephalopathy, Lactic Acidosis, and Stroke-like episodes) as well as myopathy, sensorineural hearing loss, and cognitive decline. Muscle biopsies in affected individuals showed ragged red fibers (RRF), whereas respiratory chain enzyme deficiencies were variable. Heteroplasmy levels ranged from 20-95% (PS4_moderate; PMIDs: 7520241, 10899447, 18977334, 20943236, 21996807, 21863273, 23273904). There are at least two de novo occurrences of this variant reported (PM6_moderate; PMIDs: 20943236, 7520241). Heteroplasmy levels tracked with disease manifestations in at least three families (PP1_moderate; PMIDs: 23273904, 21863273, 10899447). 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 and HmtVAR predicts it to be pathogenic score of 1 (PP3). Single fiber testing showed greater abundance of mutant genomes in COX-deficient (89.1± 9.9%, n=18) than in COX-positive fibers (51.1±27.1%, n=17; P < 0.001; PS3_supporting, PMID: 23273904). 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 October 3, 2022. Mitochondrial DNA-specific ACMG/AMP criteria applied: PS4_moderate, PM6_moderate, PP1_moderate, PM2_supporting, PP3, PS3_supporting.
Met criteria codes
PM2_Supporting
This variant is absent in the GenBank dataset, Helix dataset, and gnomAD v3.1.2 (PM2_supporting).
PP1_Moderate
Heteroplasmy levels tracked with disease manifestations in at least three families (PP1_moderate; PMIDs: 23273904, 21863273, 10899447).
PS4_Moderate
The m.3291T>C variant in MT-TL1 has been reported in at least eight unrelated individuals with primary mitochondrial disease. Ages of onset varied from 6- to 40-years old. Affected individuals had variable features including those consistent with MELAS (Mitochondrial Encephalopathy, Lactic Acidosis, and Stroke-like episodes) as well as myopathy, sensorineural hearing loss, and cognitive decline. Muscle biopsies in affected individuals showed ragged red fibers (RRF), whereas respiratory chain enzyme deficiencies were variable. Heteroplasmy levels ranged from 20-95% (PS4_moderate; PMIDs: 7520241, 10899447, 18977334, 20943236, 21996807, 21863273, 23273904).
PP3
The computational predictor MitoTIP suggests this variant is pathogenic and HmtVAR predicts it to be pathogenic score of 1 (PP3).
PM6
There are at least two de novo occurrences of this variant reported (PM6_moderate; PMIDs: 20943236, 7520241).
PS3_Supporting
Single fiber testing showed greater abundance of mutant genomes in COX-deficient (89.1± 9.9%, n=18), than in COX-positive fibers (51.1±27.1%, n=17; P < 0.001; PS3_supporting, PMID: 23273904).

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