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.14495A>G") does not appear to be in HGVS format


Variant: m.14495A>G

CA340933

9691 (ClinVar)

Gene: MT-ND6
Condition: mitochondrial disease
Inheritance Mode: Mitochondrial inheritance
UUID: 1fc90c88-4e8f-4daa-a2b8-25cdd87f5188

HGVS expressions

NC_012920.1:m.14495A>G
J01415.2:m.14495A>G
ENST00000361681.2:n.179T>C

Likely Pathogenic

The Expert Panel has overridden the computationally generated classification - "Uncertain Significance - Insufficient Evidence"
Met criteria codes 4
PM2_Supporting PP1_Moderate PS4_Supporting PP3
Not Met criteria codes 3
PS3 PS2 PM6

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

PDF
Criteria Specification Approval History
Criteria Specifications for this VCEP
Evidence submitted by expert panel
Mitochondrial Diseases VCEP
The m.14495A>G (p.L60S) variant in MT-ND6 has been reported in five individuals from three families, all of whom had LHON (PS4_supporting; PMIDs: 2287992, 11133798). There are no reports of de novo occurrences to our knowledge. This variant segregated with disease in one family with LHON (all testing was performed in blood; affected individuals: proband/mother with variant present at 51% heteroplasmy, sons with variant at 93% and 92%; unaffected individuals: sister with variant at 23%, maternal niece with variant at 53%, and maternal nephew with variant at 37%; PP1_moderate; PMID: 11133798). This variant is absent in the GenBank dataset, Helix dataset, and gnomAD v3.1.2 (PM2_supporting). The computational predictor APOGEE gives a consensus rating of pathogenic with a score of 0.87 (Min=0, Max=1), which predicts a damaging effect on gene function (PP3). There are no cybrid studies, single fiber studies, or other functional assays reported for this variant. This variant meets criteria to be classified as uncertain significance however, after extensive discussion, this Expert Panel elected to modify the classification to likely pathogenic given the strong segregation evidence and consistent phenotype in affected individuals. This classification was approved by the NICHD/NINDS U24 Mitochondrial Disease Variant Curation Expert Panel on April 11, 2022. Mitochondrial DNA-specific ACMG/AMP criteria applied (PMID: 32906214): PS4_supporting, PP1_moderate, PM2_supporting, PP3.
Met criteria codes
PM2_Supporting
This variant is absent in the GenBank dataset, Helix dataset, and gnomAD v3.1.2 (PM2_supporting).
PP1_Moderate
This variant segregated with disease in one family with LHON (all testing was performed in blood; affected individuals: proband/mother with variant present at 51% heteroplasmy, sons with variant at 93% and 92%; unaffected individuals: sister with variant at 23%, maternal niece with variant at 53%, and maternal nephew with variant at 37%; PP1_moderate; PMID: 11133798).
PS4_Supporting
The m.14495A>G (p.L60S) variant in MT-ND6 has been reported in five individuals from three families, all of whom had LHON (PS4_supporting; PMIDs: 2287992, 11133798).
PP3
The computational predictor APOGEE gives a consensus rating of pathogenic with a score of 0.87 (Min=0, Max=1), which predicts a damaging effect on gene function (PP3).
Not Met criteria codes
PS3
There are no cybrid studies, single fiber studies, or other functional assays reported for this variant.
PS2
There are no reports of de novo occurrences to our knowledge.
PM6
There are no reports of de novo occurrences to our knowledge.
Approved on: 2022-06-30
Published on: 2022-06-30
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