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.8993T>C

CA120596

9642 (ClinVar)

Gene: MT-ATP6
Condition: mitochondrial disease
Inheritance Mode: Mitochondrial inheritance
UUID: 78912cb6-b192-4466-9395-e4e013a9ef90

HGVS expressions

NC_012920.1:m.8993T>C
J01415.2:m.8993T>C
ENST00000361899.2:n.467T>C

Pathogenic

Met criteria codes 5
PS4 PP3 PP1_Moderate PS3_Supporting PM5
Not Met criteria codes 4
PVS1 PS2 PS1 PM6

Evidence Links 1

Expert Panel

Criteria Specification Information

Criteria Specifications for this VCEP
Evidence submitted by expert panel
Mitochondrial Diseases VCEP
The m.8993T>C (p.L156P) variant in MT-ATP6 has been reported in >16 individuals with primary mitochondrial disease with onset ranging from the first year of life to adulthood; and who had features variably consistent with Leigh syndrome and neurogenic muscle weakness, ataxia, and retinitis pigmentosa (NARP) (PS4; PMIDs: 8395787, 16532470, 30128709, 29101127, 28003964, 26265210, 22819295, 19046652, 18055910, 16049925, 10604142). Per our literature review and a recently published review, there are no published de novo occurrences of this variant (PMID: 30763462). This variant is located at the same amino acid position as another well-known pathogenic variant, m.8993T>G (p.L156R) (PM5). 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; PMID: 10604142). In silico tools predict this variant to be pathogenic (PP3). Cybrid studies (homoplasmic for this variant) showed reduced ATP production compared to Rho+ control cell lines (PS3_supporting; PMID: 19160410). In summary, this variant meets criteria to be classified as pathogenic for primary mitochondrial disease inherited in a maternal manner. This classification was approved by the NICHD U24 Mitochondrial Disease Variant Curation Expert Panel on February 17, 2021. Mitochondrial DNA-specific ACMG/AMP criteria applied: PS3_supporting, PS4, PM5, PP1_moderate, PP3).
Met criteria codes
PS4
Variant present in ≥16 unrelated probands all meeting criteria outlined in mito VCEP specifications
PP3
APOGEE: 0.95 (P) [also HmtVAR: 0.9 (P)]
PP1_Moderate
More than 5 segregations - White et al., 1999: Family 11 (I-2 is healthy with 53% het in blood; II-2 is healthy with 74% het in blood; III-1 is healthy with 88% het in blood; III-3 is healthy with 17% het in blood; III-4 is healthy with 44% het in blood; and III-5 is healthy with 0% het in blood; PROBAND (III-2) is affected with 90% het in blood and 96% het in FCL); Family 12 (I-2 is healthy with 0% het in blood; II-2 is healthy with 77% het in blood; II-3 is healthy with 0% het in blood; II-4 is healthy with 0% het in blood; III-2 is healthy with 33% het in blood; PROBAND (III-1) is affected with 85% het in blood and 92% het in FCL); Family 13 (I-2 is healthy with 0% het in blood and 14% het in lymphoblasts; II-2 is healthy with 62% het in blood and 74% het in lymphoblasts; III-2 is affected with 89% het in blood, 93% het in FCL, 92% het in lymphoblasts, and 935 het in skeletal muscle; III-3 is affected with 83% het in blood and 76% het in lymphoblasts; PROBAND (III-1) is most severely affected family member with 93% het in blood, 92% het in FCL, 94% het in lymphoblasts, and 95% het in skeletal muscle).
PS3_Supporting
PM5
m.8993T>G (p.L156R) is a well-characterized pathogenic variant
Not Met criteria codes
PVS1
This is a single nucleotide change.
PS2
Per our review and Ganetzky et al., 2019, no de novo occurrences of m.8993T>C.
PS1
No other pathogenic variants resulting in this amino acid change have been reported to date.
PM6
Per our review and Ganetzky et al., 2019, no de novo occurrences of m.8993T>C.
Approved on: 2021-05-05
Published on: 2021-06-10
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