The ClinGen Evidence Repository is an FDA-recognized human genetic variant database containing expert-curated assertions regarding variants' pathogenicity and supporting evidence summaries. [Disclaimer]
  • The variant label for this record ("m.7671T>A") does not appear to be in HGVS format
  • Despite there being a valid 'cspec' property in the messages there's a discrepancy in message contents and CSPEC data: * Message Gene: MT-TW CSPEC Genes: [] * Message MONDOs: MONDO:0044970 CSPEC MONDO: []
  • No CSPEC computed assertion could be determined for this classification!


Variant: m.7671T>A

CA120605

9660 (ClinVar)

Gene: MT-TW
Condition: mitochondrial disease
Inheritance Mode: Mitochondrial inheritance
UUID: 0cbce67d-7c2d-401a-aaad-1c480c9c0252
Approved on: 2023-11-28
Published on: 2024-11-26

HGVS expressions

NC_012920.1:m.7671T>A
J01415.2:m.7671T>A
ENST00000361739.1:c.86T>A

Uncertain Significance

Met criteria codes 4
PP3 PM2 PM6_Supporting PS3_Supporting
Not Met criteria codes 3
PS4 BA1 BS1

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.7671T>A (p.M29K) variant in MT-CO2 has been reported in two unrelated individuals with primary mitochondrial disease to date. The first individual was a 14 year old male with proximal myopathy, lactic acidosis, and a five year history of muscle weakness and fatigue. Skeletal muscle biopsies revealed severe COX deficiency, increased SDH staining, and absence of ragged red fibers. Variant heteroplasmy was 90% in muscle and 4.5% - 6% in blood. The second individual was a 48 year old male of European ancestry with mitochondrial myopathy characterized by progressive weakness. Serum creatine kinase levels were elevated and muscle biopsy revealed scattered COX-negative fibers with increased SDH staining. This variant was observed at 52% heteroplasmy, presumably in the muscle sample (PMID: 32800583). Haplogroup information was not reported for both cases precluding consideration for PS4. This variant occurred de novo in one individual (absent in blood from mother; PM6_supporting, PMID: 10486321). Single fiber testing showed higher levels of the variant in COX negative fibers (81%, n=13) than in COX positive fibers (45%, n=4), p<0.01 (PS3_supporting, PMID: 10486321). The computational predictors APOGEE1 and APOGEE2 give a consensus rating of pathogenic with raw scores of 0.90 and 0.942, respectively (Min=0, Max=1), which predict a damaging effect on gene function (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 uncertain significance 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 28, 2023. Mitochondrial DNA-specific ACMG/AMP criteria applied (PMID: 32906214): PM6_supporting, PS3_supporting, PM2_supporting, PP3.
Met criteria codes
PP3
The computational predictors APOGEE1 and APOGEE2 give a consensus rating of pathogenic with raw scores of 0.90 and 0.942, respectively (Min=0, Max=1), which predict a damaging effect on gene function (PP3).
PM2
This variant is absent in the GenBank dataset, Helix dataset, and gnomAD v3.1.2 (PM2_supporting).
PM6_Supporting
This variant occurred de novo in one individual (absent in blood from mother); PM6_supporting, PMID: 10486321).
PS3_Supporting
Single fiber testing showed higher levels of the variant in COX negative fibers (81%, n=13) than in COX positive fibers (45%, n=4), p<0.01 (PS3_supporting, PMID: 10486321).

Not Met criteria codes
PS4
The m.7671T>A (p.M29K) variant in MT-CO2 has been reported in two unrelated individuals with primary mitochondrial disease to date. The first individual was a 14 year old male with proximal myopathy, lactic acidosis, and a five year history of muscle weakness and fatigue. Skeletal muscle biopsies revealed severe COX deficiency, increased SDH staining, and absence of ragged red fibers. Variant heteroplasmy was 90% in muscle and 4.5% - 6% in blood. The second individual was a 48 year old male of European ancestry with mitochondrial myopathy characterized by progressive weakness. Serum creatine kinase levels were elevated and muscle biopsy revealed scattered COX-negative fibers with increased SDH staining. This variant was observed at 52% heteroplasmy, presumably in the muscle sample (PMID: 32800583). Haplogroup information was not reported for both cases precluding consideration for PS4.
BA1
No code specific comments provided, please refer to the summary above or general recommendations provided in the guideline
BS1
No code specific comments provided, please refer to the summary above or general recommendations provided in the guideline
Curation History
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