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
  • The variant label for this record ("NC_012920.1(MT-ATP6"):m.9038T>C) does not appear to be in HGVS format


Variant: NC_012920.1(MT-ATP6):m.9038T>C

CA414801969

693062 (ClinVar)

Gene: MT-ATP6
Condition: mitochondrial disease
Inheritance Mode: Mitochondrial inheritance
UUID: 13da6c3a-c0f6-425b-a572-3f59b9754815
Approved on: 2023-04-17
Published on: 2023-05-19

HGVS expressions

NC_012920.1:m.9038T>C
J01415.2:m.9038T>C
ENST00000361899.2:n.512T>C

Uncertain Significance

Met criteria codes 1
BP4
Not Met criteria codes 6
PS2 PS3 PS4 PP1 PM6 PM2

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.9038T>C variant in MT-ATP6 was reviewed by the Mitochondrial Disease Nuclear and Mitochondrial Variant Curation Expert Panel on April 17, 2023. There are no individuals or families with this variant reported in the medical literature to our knowledge. There are several occurrences in population databases. This variant is present in 0.025% of individuals in GenBank MITOMAP sequences, in 0.012% of individuals in gnomAD v3.1.2 (homoplasmic in 22 individuals and heteroplasmic in five), and in 0.011% of individuals in the Helix dataset. The computational predictor APOGEE gives a consensus rating of neutral with a score of 0.45 (Min=0, Max=1), which predicts no damaging effect on gene function (BP4). There are no cybrid, single fiber, or other studies reported for 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 April 17, 2023. Mitochondrial DNA-specific ACMG/AMP criteria applied (PMID: 32906214): BP4.
Met criteria codes
BP4
The computational predictor APOGEE gives a consensus rating of pathogenic with a score of 0.47 (Min=0, Max=1), which predicts a benign effect on gene function (BP4).
Not Met criteria codes
PS2
There are no reported de novo occurrences of this variant to our knowledge.
PS3
There are no cybrids, single fiber studies, or other functional assays reported on this variant.
PS4
There are no individuals with this variant reported in the medical literature to our knowledge.
PP1
There are no large families reported in the medical literature to consider for evidence of segregation.
PM6
There are no reported de novo occurrences of this variant to our knowledge.
PM2
This variant is present in population databases (Mitomap's 51,863 sequences: AF=0.025%; Helix's 196,554 sequences: AF=0.011%; and gnomAD v3.1.2: AF=0.012% as this is homoplasmic in 22 individuals and heteroplasmic in 5 individuals). Given the frequency of this variant, it does not meet PM2 criterion.
Curation History
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