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.14482C>A") does not appear to be in HGVS format


Variant: m.14482C>A

CA340934

9693 (ClinVar)

Gene: MT-ND6
Condition: mitochondrial disease
Inheritance Mode: Mitochondrial inheritance
UUID: ee5d40f3-a71d-44c5-8d5a-b92a0bd6bead
Approved on: 2022-06-30
Published on: 2022-06-30

HGVS expressions

NC_012920.1:m.14482C>A
J01415.2:m.14482C>A
ENST00000361681.2:n.192G>T

Likely Pathogenic

Met criteria codes 4
PM2_Supporting PS4_Moderate PM5 PP3
Not Met criteria codes 4
PM6 PS3 PS2 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

PDF
Criteria Specification Approval History
Criteria Specifications for this VCEP
Evidence submitted by expert panel
Mitochondrial Diseases VCEP
The m.14482C>A (p.M64I) variant in MT-ND6 has been reported in at least five unrelated individuals with LHON (PS4_moderate; PMIDs: 19319978, 12112086, 11931086, 12150954). Ages of onset varied from 10-29-years-old. All affected individuals had the variant present at homoplasmy. There are no reports of de novo occurrences to our knowledge. Several extended families have been reported in the medical literature (PMIDs: 11931086, 12112086) however family member testing was not performed or the variant was homoplasmic and thus prevented consideration for PP1. There are two occurrences of this variant in GenBank dataset, however both are from individuals with known mitochondrial disease. This variant is absent in gnomAD v3.1.2 and in Helix dataset therefore this variant is absent in healthy individuals (PM2_supporting). Another variant at this amino acid position leading to a different amino acid change is one of the most common causes of LHON and is a known pathogenic variant – m.14484T>C (p.M64V, PM5). There are no cybrid studies, single fiber studies, or other functional assays reported for this variant. The computational predictor APOGEE gives a consensus rating of pathogenic with a score of 0.96 (Min=0, Max=1), which predicts a damaging effect on gene function (PP3). 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 Mitochondrial Disease Variant Curation Expert Panel on May 3, 2022. Mitochondrial DNA-specific ACMG/AMP criteria applied (PMID: 32906214): PS4_moderate, PM2_supporting, PM5, PP3.
Met criteria codes
PM2_Supporting
There are two occurrences of this variant in GenBank dataset, however both are from individuals with known mitochondrial disease. This variant is absent in gnomAD v3.1.2 and in Helix dataset therefore this variant is absent in healthy individuals (PM2_supporting).
PS4_Moderate
The m.14482C>A (p.M64I) variant in MT-ND6 has been reported in at least five unrelated individuals with LHON (PS4_moderate; PMIDs: 19319978, 12112086, 11931086, 12150954). Ages of onset varied from 10-29-years-old. All affected individuals had the variant present at homoplasmy.
PM5
Another variant at this amino acid position leading to a different amino acid change is one of the most common causes of LHON and is a known pathogenic variant – m.14484T>C (p.M64V, PM5).
PP3
The computational predictor APOGEE gives a consensus rating of pathogenic with a score of 0.96 (Min=0, Max=1), which predicts a damaging effect on gene function (PP3).
Not Met criteria codes
PM6
There are no reports of de novo occurrences to our knowledge.
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.
PP1
Several extended families have been reported in the medical literature (PMIDs: 11931086, 12112086) however family member testing was not performed or the variant was homoplasmic and thus prevented consideration for PP1.
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