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.6742T>C") 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-CO1 CSPEC Genes: [] * Message MONDOs: MONDO:0044970 CSPEC MONDO: []
  • No CSPEC computed assertion could be determined for this classification!


Variant: m.6742T>C

CA120608

9664 (ClinVar)

Gene: MT-CO1
Condition: mitochondrial disease
Inheritance Mode: Mitochondrial inheritance
UUID: ee155be2-54f3-415b-8979-f01899860d7c
Approved on: 2023-12-21
Published on: 2024-03-15

HGVS expressions

NC_012920.1:m.6742T>C
J01415.2:m.6742T>C
ENST00000361624.2:c.839T>C

Uncertain Significance

Met criteria codes 2
PM2_Supporting PP3
Not Met criteria codes 5
PM6 PS3 PS2 PS4 PP1

Evidence Links 0

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.6742T>C (p.I280T) variant in MT-CO1 has been reported in one individual to date, in a man with sideroblastic anemia (PMID: 9389715). The variant was present at 52% in bone marrow, 59% in peripheral blood, 71% in platelets, and was undetectable in buccal and fibroblasts. As this is the only case reported to date, PS4 could not be applied. There was no mention of family member testing precluding consideration for de novo status or segregation. The computational predictor APOGEE gives a consensus rating of pathogenic with a score of 0.63 (Min=0, Max=1), which predicts a damaging effect on gene function (PP3). This variant is absent in the GenBank dataset and gnomAD v3.1.2, and there is one heteroplasmic occurrence in the Helix dataset (0.001%, haplogroup I; PM2_supporting). There are no cybrids, single fiber studies, or other functional assays reported on this variant. 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 December 21, 2023. Mitochondrial DNA-specific ACMG/AMP criteria applied (PMID: 32906214): PM2_supporting, PP3.
Met criteria codes
PM2_Supporting
This variant is absent in the GenBank dataset and gnomAD v3.1.2, and there is one heteroplasmic occurrence in the Helix dataset (0.001%, haplogroup I; PM2_supporting).
PP3
The computational predictor APOGEE gives a consensus rating of pathogenic with a score of 0.63 (Min=0, Max=1), which predicts a damaging effect on gene function (PP3).
Not Met criteria codes
PM6
There was no mention of family member testing precluding consideration for de novo status or segregation.
PS3
There are no cybrids, single fiber studies, or other functional assays reported on this variant.
PS2
There was no mention of family member testing precluding consideration for de novo status or segregation.
PS4
The m.6742T>C (p.I280T) variant in MT-CO1 has been reported in one individual to date, in a man with sideroblastic anemia (PMID: 9389715). The variant was present at 52% in bone marrow, 59% in peripheral blood, 71% in platelets, and was undetectable in buccal and fibroblasts. As this is the only case reported to date, PS4 could not be applied.
PP1
There was no mention of family member testing precluding consideration for de novo status or segregation.
Curation History
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