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
  • The variant label for this record ("m.11777C>A") does not appear to be in HGVS format


Variant: m.11777C>A

CA120636

9711 (ClinVar)

Gene: MT-ND4
Condition: mitochondrial disease
Inheritance Mode: Mitochondrial inheritance
UUID: 5c213439-72fe-44b9-972e-30aec7a96987
Approved on: 2022-06-30
Published on: 2022-06-30

HGVS expressions

NC_012920.1:m.11777C>A
J01415.2:m.11777C>A
ENST00000361381.2:n.1018C>A

Likely Pathogenic

Met criteria codes 6
PM2_Supporting PM5 PP1 PP3 PS3_Supporting PS4_Moderate
Not Met criteria codes 2
PM6 PS2

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

PDF
Criteria Specification Approval History
Criteria Specifications for this VCEP
Evidence submitted by expert panel
Mitochondrial Diseases VCEP
The m.11777C>A (p.R340S) variant in MT-ND4 has been reported in at least eight unrelated individuals with primary mitochondrial disease and features including Leigh syndrome, stroke-like episodes, and cardiomyopathy (PS4_moderate; PMIDs: 12707444, 16120329, 15576045, 20502985, 24642831, 29428506). Ages of onset varied from the first few days of life to the 60s and heteroplasmy levels in affected individuals ranged from 50-93%. There is one report of the variant being absent in mother’s blood (PMID: 16120329) however no additional tissues were tested and technology performed at the time of publication would not detect low heteroplasmy levels of the variant. This variant segregated with disease in one family, as two healthy family members had lower to undetectable levels of the variant (PP1; PMID: 20502985). This variant is absent in the GenBank dataset, Helix dataset, and gnomAD v3.1.2 (PM2_supporting). Another variant at this amino acid position leading to a different amino acid change is a known pathogenic variant – m.11778G>A (p.R340H, PM5). Cybrid studies supported the functional impact of this variant (PS3_supporting; PMID: 16120329). The computational predictor APOGEE gives a consensus rating of pathogenic with a score of 0.83 (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 May 24, 2022. Mitochondrial DNA-specific ACMG/AMP criteria applied (PMID: 32906214): PS4_moderate, PP1, PS3_supporting, PM2_supporting, PM5, PP3.
Met criteria codes
PM2_Supporting
This variant is absent in the GenBank dataset, Helix dataset, and gnomAD v3.1.2 (PM2_supporting).
PM5
Another variant at this amino acid position leading to a different amino acid change is a known pathogenic variant – m.11778G>A (p.R340H, PM5).
PP1
This variant segregated with disease in one family, as two healthy family members had lower to undetectable levels of the variant (PP1_supporting; PMID: 20502985).
PP3
The computational predictor APOGEE gives a consensus rating of pathogenic with a score of 0.83 (Min=0, Max=1), which predicts a damaging effect on gene function (PP3).
PS3_Supporting
Cybrid studies supported the functional impact of this variant (PS3_supporting; PMID: 16120329). Cybrid studies performed: "Primary cultures" from patients 1 and 2 (likely myoblasts in which decreased ATP synthesis was reported); ATP synthesis decreases with increasing heteroplasmy level.
PS4_Moderate
The m.11777C>A (p.R340S) variant in MT-ND4 has been reported in at least eight unrelated individuals with primary mitochondrial disease and features including Leigh syndrome, stroke-like episodes, and cardiomyopathy (PS4_moderate; PMIDs: 12707444, 16120329, 15576045, 20502985, 24642831, 29428506). Ages of onset varied from the first few days of life to the 60s and heteroplasmy levels in affected individuals ranged from 50-93%.
Not Met criteria codes
PM6
There is one report of the variant being absent in mother’s blood (PMID: 16120329) however no additional tissues were tested and technology performed at the time of publication would not detect low heteroplasmy levels of the variant.
PS2
There is one report of the variant being absent in mother’s blood (PMID: 16120329) however no additional tissues were tested and technology performed at the time of publication would not detect low heteroplasmy levels of the variant.
Curation History
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