Variant: NC_012920.1:m.9176T>G

CA340929

9650 (ClinVar)

Gene: MT-ATP6

Condition: mitochondrial disease

Inheritance Mode: Mitochondrial inheritance

UUID: a799cd48-3a29-4e23-96fe-4f6445ba99d4

Approved on: 2022-03-24

Published on: 2022-03-24

HGVS expressions

NC_012920.1:m.9176T>G
J01415.2:m.9176T>G
ENST00000361899.2:n.650T>G

Likely Pathogenic

• Met criteria codes: PP3 PP1_Moderate PM2_Supporting PM5 PS4_Supporting PS3_Moderate

Expert Panel

Mitochondrial Diseases VCEP

Criteria Specification Information

Evidence submitted by expert panel

Mitochondrial Diseases VCEP

The m.9176T>G (p.L217R) variant in MT-ATP6 has been reported in 9 individuals with features of primary mitochondrial disease from 3 families. Affected individuals had variable ages of onset (first months of life to 3 years old, one case with onset in late teens). Features included Leigh syndrome, seizures, ataxia, muscle weakness, dystonia, developmental regression with illness, axonal neuropathy, optic atrophy, and retinal dystrophy. Some individuals had gradual progression including one with onset in childhood but surviving to at least 40s. Others have progressed to death within months. Brain imaging in some individuals was consistent with Leigh syndrome and others with diffuse brain atrophy. Elevated blood and CSF lactate were noted. Heteroplasmy levels were >95% in multiple tissues for those with onset in childhood, 70% for gradually-progressive phenotype, and healthy family members had 28-50% heteroplasmy (PS4_supporting; PMIDs: 11245730, 11731285; Khailany et al., 2020 with no PMID). There are no reports of de novo occurrence of this variant. This variant segregated with disease in multiple affected members in multiple families and several healthy family members had lower to undetectable levels of the variant (PP1_moderate; PMIDs: 11245730, 11731285; Khailany et al., 2020 with no PMID). This variant is absent in population databases after removing sequences from individuals with mitochondrial disease (one occurrence in GenBank sequences is from individual with mitochondrial disease; absent in gnomAD v3.1.2 and Helix databset; PM2_supporting). This variant is located at the same amino acid position as another well-known pathogenic variant, m.9176T>C (p.L217P) (PM5). Several studies in E. coli (PMID: 11119722), yeast (PMID: 19454486), and cybrids (PMID: 19160410) support the functional impact of this variant and independent studies showed independent deleterious effects of the variant (PS3_moderate). The computational predictor APOGEE gives a consensus rating of pathogenic with a score of 0.9 (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 February 28, 2022. Mitochondrial DNA-specific ACMG/AMP criteria applied: PS3_moderate, PS4_supporting, PP1_moderate, PM2_supporting, PM5, PP3.

Met criteria codes

• PP3: In silico tools (APOGEE) predict this variant to be pathogenic with a score of 0.9 (PP3).
• PP1_Moderate: At least 9 segregations across 2 kindreds
• PM2_Supporting: This variant is absent in population databases after removing sequences from individuals with mitochondrial disease (one occurrence in GenBank sequences is from individual with mitochondrial disease; absent in gnomAD and Helix databset; PM2_supporting).
• PM5: Another variant at this amino acid position leading to a different amino acid change is classified as pathogenic by this expert panel – m.9176T>C (p.L217P; PM5).
• PS4_Supporting: 3 unrelated probands with features consistent with mitochondrial disease
• PS3_Moderate: Several studies in E. coli (PMID: 11119722), yeast (PMID: 19454486), and cybrids (PMID: 19160410) support the functional impact of this variant and independent studies showed independent deleterious effects of the variant (PS3_moderate).