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
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  • See Evidence submitted by expert panel for details.

Variant: NC_012920.1:m.9185T>C

CA340928

9647 (ClinVar)

Gene: MT-ATP6
Condition: mitochondrial disease
Inheritance Mode: Mitochondrial inheritance
UUID: dba7e884-95cc-4e63-87f1-7f3604a9dea5

HGVS expressions

NC_012920.1:m.9185T>C
J01415.2:m.9185T>C
ENST00000361899.2:n.659T>C

Pathogenic

Met criteria codes 6
PS3_Supporting PM2_Supporting PS4 PP3 PM6 PP1_Moderate
Not Met criteria codes 1
PP4

Evidence Links 0

Expert Panel

Criteria Specification Information

Criteria Specifications for this VCEP
Evidence submitted by expert panel
Mitochondrial Diseases VCEP
The m.9185T>C (p.L220P) variant in MT-ATP6 has been reported in more than 16 individuals with features of primary mitochondrial disease with manifestations including Leigh syndrome, MELAS, NARP, neuropathy, ataxia, exercise intolerance, muscle weakness, developmental delay, and seizures (PS4; PMIDs: 28429146, 33717984, 27290639, 24153443, 27783406, 32042921, 31500933, 29116603, 31187502, 22577227, 25548692, 18461509, 17352390, 29228836, 16217706). There are at least two reports of de novo occurrences of this variant (PM6; PMIDs: 33717984, 29228836). This variant segregated with disease in multiple affected members in multiple families and several healthy family members had lower levels of the variant (PP1_moderate; PMIDs: 16217706, 17352390,20546952). This variant is absent in population databases after removing sequences from individuals with mitochondrial disease (three occurrences in GenBank sequences are from individuals with mitochondrial disease; absent in gnomAD v3.1.2 and Helix dataset; PM2_supporting). Studies in cybrids support the functional impact of this variant (PS3_supporting; PMID: 24153443). The computational predictor APOGEE gives a consensus rating of pathogenic with a score of 0.94 (Min=0, Max=1), which predicts a damaging effect on gene function (PP3). In summary, this variant meets criteria to be classified as pathogenic for primary mitochondrial disease inherited in a mitochondrial manner. This classification was approved by the NICHD U24 Mitochondrial Disease Variant Curation Expert Panel on May 20, 2021. Mitochondrial DNA-specific ACMG/AMP criteria applied: PS4, PM6, PS3_supporting, PP1_moderate, PM2_supporting, PP3.
Met criteria codes
PS3_Supporting
Studies in cybrids support the functional impact of this variant (PS3_supporting; PMID: 24153443).
PM2_Supporting
This variant is absent in population databases after removing sequences from individuals with mitochondrial disease (three occurrences in GenBank sequences are from individuals with mitochondrial disease; absent in gnomAD v3.1.2 and Helix dataset; PM2_supporting).
PS4
This variant variant has been reported in more than 16 individuals with features of primary mitochondrial disease with manifestations including Leigh syndrome, MELAS, NARP, neuropathy, ataxia, exercise intolerance, muscle weakness, developmental delay, and seizures (PS4; PMIDs: 28429146, 33717984, 27290639, 24153443, 27783406, 32042921, 31500933, 29116603, 31187502, 22577227, 25548692, 18461509, 17352390, 29228836, 16217706).
PP3
The computational predictor APOGEE gives a consensus rating of pathogenic with a score of 0.94 (Min=0, Max=1), which predicts a damaging effect on gene function (PP3).
PM6
There are at least two reports of de novo occurrences of this variant (PM6; PMIDs: 33717984, 29228836).
PP1_Moderate
This variant segregated with disease in multiple affected members in multiple families and several healthy family members had lower levels of the variant (PP1_moderate; PMIDs: 16217706, 17352390,20546952).
Not Met criteria codes
PP4
Other causes of oxphos deficiency not ruled out.
Approved on: 2022-06-30
Published on: 2022-06-30
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