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
  • The variant label for this record ("m.7497G>A") does not appear to be in HGVS format


Variant: m.7497G>A

9569 (ClinVar)

Gene: MT-TS1
Condition: mitochondrial disease
Inheritance Mode: Mitochondrial inheritance
UUID: 0a631f06-39e0-42e0-9268-4342fbc6f7e5
Approved on: 2023-04-17
Published on: 2023-05-19

HGVS expressions

NC_012920.1:m.7497G>A

Likely Pathogenic

The Expert Panel has overridden the computationally generated classification - "Uncertain Significance - Insufficient Evidence"
Met criteria codes 5
PM2 PS3_Supporting PS4_Supporting PP3 PP1_Moderate
Not Met criteria codes 2
PM6 PS2

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

Criteria Specification Approval History
Criteria Specifications for this VCEP
Evidence submitted by expert panel
Mitochondrial Diseases VCEP
The m.7497G>A variant in MT-TS1 has been reported in three unrelated individuals with primary mitochondrial disease with shared features of exercise intolerance, proximal myopathy, lactic acidosis, and myalgia. Age at presentation ranged from three years old to the 30s. Muscle biopsies showed ragged red fibers, COX-negative fibers, and reduced activities of complexes I and IV. All probands were homoplasmic for the variant in muscle and it was present in various other tissues at levels >90%. (PS4_supporting; PMIDs: 14605505, 9778262). This variant segregated with disease in each of the three families reported (PP1_moderate). The probands were homoplasmic for the variant muscle and/or blood. In one family, the unaffected mother harbored the variant at 10% in blood (PMID: 14605505). In the second family, the unaffected mother harbored the variant at 62% and the unaffected brother had the variant at 62% in blood (PMID: 9778262). In the third family, an affected daughter with myalgia had the variant at 90% in blood and an unaffected brother has the variant at 70% (PMID: 9778262). There are no reported de novo occurrences of this variant to our knowledge. The computational predictor MitoTIP suggests this variant is pathogenic (92.9 percentile) and HmtVAR predicts it to be pathogenic score of 0.5 (PP3). This variant is absent in the GenBank dataset, Helix dataset, and gnomAD v3.1.2 (PM2_supporting). Cybrid studies showed a correlation between higher heteroplasmy level and lower complex I and IV activities (PS3_supporting, PMID: 16199753). 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 April 17, 2023. Mitochondrial DNA-specific ACMG/AMP criteria applied (PMID: 32906214): PS4_supporting, PP1_moderate, PS3_supporting, PM2_supporting, PP3.
Met criteria codes
PM2
This variant is absent in the GenBank dataset, Helix dataset, and gnomAD v3.1.2 (PM2_supporting).
PS3_Supporting
Cybrid studies showed a correlation between higher heteroplasmy level and lower complex I and IV activity (PS3_supporting, PMID: 16199753).

PS4_Supporting
The m.7497 G>A variant in MT-TS1 has been reported in 3 unrelated individuals with primary mitochondrial disease with shared features of exercise intolerance, proximal myopathy, lactic acidosis, myalgia, ages at presentation ranged from 3 years of age to 30's; muscle biopsies noted ragged red fibers, COX negative fibers, and reduce complexes I and IV (PS4_supporting; PMIDs: 14605505, 9778262). All probands were homoplasmic in muscle and other tissues > 90%.
PP3
The computational predictor MitoTIP suggests this variant is pathogenic (92.9 percentile) and HmtVAR predicts it to be pathogenic score of 0.5 (PP3).
PP1_Moderate
This variant segregated with disease in 3 families reported. The probands all had homoplasmic levels in muscle or blood. One family (PMID: 14605505) the unaffected mother harbored the variant at 10% in blood. In the second family (PMID: 9778262) the unaffected mother harbored the variant at 62% and the unaffected brother had the variant at 62% in blood. The third family (PMID: 9778262) the affected daughter with myalgia had the variant at 90% in blood and an unaffected brother has the variant at 70% (PP1).
Not Met criteria codes
PM6
There are no reported de novo occurrences of this variant to our knowledge.
PS2
There are no reported de novo occurrences of this variant to our knowledge.
Curation History
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