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

  • See Evidence submitted by expert panel for details.

Variant: NC_012920.1:m.9026G>A

CA414801916

693058 (ClinVar)

Gene: MT-ATP6
Condition: mitochondrial disease
Inheritance Mode: Mitochondrial inheritance
UUID: 8c4887bb-1511-411f-8136-172461d18622

HGVS expressions

NC_012920.1:m.9026G>A
J01415.2:m.9026G>A
ENST00000361899.2:n.500G>A

Uncertain Significance

Met criteria codes 3
PP4 PP1 PP3
Not Met criteria codes 10
PS3 PS2 PS1 PS4 BP4 PM6 PM2 PVS1 PM4 PM5

Evidence Links 0

Expert Panel

Criteria Specification Information

Criteria Specifications for this VCEP
Evidence submitted by expert panel
Mitochondrial Diseases VCEP
The m.9026G>A (p.G167D) variant in MT-ATP6 has been reported in one family to date and features in this family included exercise intolerance, vomiting, and a maternal family history of similar spectrum concerns (PMID: 30763462). Oxidative phosphorylation testing in fibroblasts from the proband were consistent with CV deficiency and all other potential etiologies were reasonably excluded (PP4). Per our literature review and a recently published review, there are no reported de novo occurrences of this variant (PMID: 30763462). This variant segregated with disease in the single reported family as the proband’s healthy brother had undetectable levels of variant in blood and his less severely affected mother (fatigue, migraines, neuropathy) had lower heteroplasmy (4% blood, 8% urine) than the proband (PP1, PMID: 30763462). In silico tools predict this variant to be pathogenic (PP3). There are no cybrid or single fiber studies reported on this variant. In summary, this variant meets criteria to be classified as uncertain significance for primary mitochondrial disease inherited in a maternal manner. This classification was approved by the NICHD U24 Mitochondrial Disease Variant Curation Expert Panel on March 22, 2021. Mitochondrial DNA-specific ACMG/AMP criteria applied: PP4, PP1, PP3).
Met criteria codes
PP4
All other known etiologies excluded. Fibroblasts from the proband had very low integrated oxygen consumption capacity in response to substrates for complexes I, II, and III that was relieved by uncoupling, consistent with a CV deficiency.
PP1
Per Ganetzky et al., 2019 (PMID: 30763462), healthy brother with undetectable level of variant in BLOOD; less severely affected mother (fatigue, migraines, neuropathy) with lower heteroplasmy (4% blood, 8% urine)
PP3
APOGEE score 0.56 (>0.5 so P)
Not Met criteria codes
PS3
No cybrid or single fiber studies performed to date.
PS2
No reports of de novo occurrence.
PS1
No other changes resulting in same aa change reported.
PS4
Present in only one proband and mother as of 1/26/2021: One reported individual (Ganetzky et al., 2019 - PMID: 30763462) with exercise intolerance (red flag feature) + vomiting (nonspecific feature) + maternal family history (nonspecific feature)
BP4
APOGEE score 0.56 (>0.5 so P)
PM6
No reports of de novo occurrence.
PM2
GenBank sequences queried 1/27/21; present in 3 individuals for a frequency of 0.006% (1 individual in H1a, 2 individuals in U5a). gnomAD queried 2/25/21 - 1 homoplasmic occurrence (in individual of African/African American background - haplogroup L3), 4 heteroplasmic occurrences (1 individual of Latino/Admixed American background and 3 European (non-Finnish); 3 heteroplasmic occurrences in individuals with haplogroup H and 1 with haplogroup C; 2 individuals with 10-20% heteroplasmy, 1 individual with 30-40% heteroplasmy; 1 individual with 80-90% heteroplasmy)
PVS1
Single nt change
PM4
No code specific comments provided, please refer to the summary above or general recommendations provided in the guideline
PM5
m.9025G>A (p.Gly167Ser) reported in one individual (PMID: 24986921) at homoplasmy, also homoplasmic in healthy mother and sibling. GenBank AF is 0.064%. Not definitely pathogenic so cannot apply this criterion.
Approved on: 2021-05-07
Published on: 2021-10-22
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