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


Variant: NC_012920.1:m.13514A>G

CA345918

155889 (ClinVar)

Gene: MT-ND5
Condition: mitochondrial disease
Inheritance Mode: Mitochondrial inheritance
UUID: 965e5a6a-1c4b-4802-96d2-dd44fe81b825

HGVS expressions

NC_012920.1:m.13514A>G
J01415.2:m.13514A>G
ENST00000361567.2:n.1178A>G

Likely Pathogenic

Met criteria codes 6
PP3 PM5 PM2_Supporting PS4_Moderate PS3_Supporting PM6_Supporting
Not Met criteria codes 4
PP1 PM4 PVS1 PS1

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.13514A>G (p.D393G) variant in MT-ND5 has been reported in at least 12 unrelated individuals with primary mitochondrial disease with onset ranging from childhood to adulthood and features variably consistent with Leigh syndrome and MELAS, as well as hypertrophic cardiomyopathy, optic atrophy, and neuropathy (PS4_moderate; PMIDs: 26341968, 25974876, 32504279, 20972245, 23847141, 21712854, 15576045, 14684687, 11198278). Heteroplasmy levels in affected individuals ranged from 55-70% in muscle, 12-55% in fibroblasts, 4-50% in blood, and 90% heart. This variant has been identified as a de novo occurrence in at least two probands with primary mitochondrial disease (PM6_supporting; PMIDs: 14684687, 11198278). There are no large families reported in the medical literature to consider for evidence of segregation. 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 classified as pathogenic by this Expert Panel – m.13513G>A (p. D393N, PM5). Cybrid studies showed a tight correlation between higher heteroplasmy level and lower complex I activity (PS3_supporting, PMID: 11198278). The computational predictor APOGEE gives a consensus rating of pathogenic with a score of 0.95 (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 3, 2022. Mitochondrial DNA-specific ACMG/AMP criteria applied (PMID: 32906214): PS4_moderate, PM6_supporting, PM2_supporting, PM5, PS3_supporting, PP3.
Met criteria codes
PP3
The computational predictor APOGEE gives a consensus rating of pathogenic with a score of 0.95 (Min=0, Max=1), which predicts a damaging effect on gene function (PP3).
PM5
Another variant at this amino acid position leading to a different amino acid change is classified as pathogenic by this Expert Panel – m.13513G>A (p. D393N, PM5).
PM2_Supporting
This variant is absent in the GenBank dataset, Helix dataset, and gnomAD v3.1.2 (PM2_supporting).
PS4_Moderate
The m.13514A>G (p.D393G) variant in MT-ND5 has been reported in at least 12 unrelated individuals with primary mitochondrial disease with onset ranging from childhood to adulthood and features variably consistent with Leigh syndrome and MELAS, as well as hypertrophic cardiomyopathy, optic atrophy, and neuropathy (PS4_moderate; PMIDs: 26341968, 25974876, 32504279, 20972245, 23847141, 21712854, 15576045, 14684687, 11198278). Heteroplasmy levels in affected individuals ranged from 55-70% in muscle, 12-55% in fibroblasts, 4-50% in blood, and 90% heart.
PS3_Supporting
Cybrid studies showed a tight correlation between higher heteroplasmy level and lower complex I activity (PS3_supporting, PMID: 11198278).
PM6_Supporting
This variant has been identified as a de novo occurrence in at least two probands with primary mitochondrial disease (PM6_supporting; PMIDs: 14684687, 11198278).
Not Met criteria codes
PP1
There are no large families reported in the medical literature to consider for evidence of segregation.
PM4
This is a missense variant.
PVS1
This is a missense variant.
PS1
No other variants resulting in the same amino acid change have been reported.
Approved on: 2022-06-30
Published on: 2022-06-30
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