The ClinGen Evidence Repository is an FDA-recognized human genetic variant database containing expert-curated assertions regarding variants' pathogenicity and supporting evidence summaries. [Disclaimer]
  • The variant label for this record ("m.5816A>G") does not appear to be in HGVS format
  • Despite there being a valid 'cspec' property in the messages there's a discrepancy in message contents and CSPEC data: * Message Gene: MT-TC CSPEC Genes: [] * Message MONDOs: MONDO:0044970 CSPEC MONDO: []
  • No CSPEC computed assertion could be determined for this classification!


Variant: m.5816A>G

CA128829

30002 (ClinVar)

Gene: MT-TC
Condition: mitochondrial disease
Inheritance Mode: Mitochondrial inheritance
UUID: ce3adc03-b5b1-40f4-b4b6-23d431156d65
Approved on: 2024-04-23
Published on: 2024-08-08

HGVS expressions

NC_012920.1:m.5816A>G
J01415.2:m.5816A>G

Uncertain Significance

Met criteria codes 3
PP3 PS4_Supporting PM2_Supporting
Not Met criteria codes 1
PS3

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

Criteria Specification Approval History
Criteria Specifications for this VCEP
Evidence submitted by expert panel
Mitochondrial Diseases VCEP
The m.5816A>G variant in MT-TC has been reported in two unrelated families with primary mitochondrial disease (PS4_supporting; PMIDs: 17724295, 37771542). The first reported family had four affected individuals with variable clinical features including dystonia, seizures, tremor, fatigue, ptosis, pigmentary retinopathy, and optic atrophy. Muscle biopsies in these family members showed mosaic COX deficiency, normal respiratory chain enzyme activities, and decreased steady state levels of mt-tRNA Cys. The variant was homoplasmic in muscle and blood in these individuals (PMID: 17724295). The second family reported had one affected individual, a girl, with dystonia, episodic vomiting, motor regression, tremor, and seizures. Skin fibroblast testing showed reduced basal resting oxygen consumption rate (OCR), ATP production, proton leak, maximal respiration, and reserve capacity OCR. The variant was present in blood and urine but heteroplasmy levels were not reported (PMID: 37771542). The variant was present in additional family members of this second family however phenotypes and heteroplasmy levels were not reported. This variant is absent in the GenBank dataset, Helix dataset, and gnomAD v3.1.2 (PM2_supporting). There are no cybrids, single fiber studies, or other functional assays reported on this variant. The computational predictor MitoTIP suggests this variant is pathogenic (59.9 percentile) and HmtVAR predicts it to be pathogenic score of 0.65 (PP3). In summary, this variant meets criteria to be classified as uncertain significance for primary mitochondrial disease inherited in a mitochondrial manner. This classification was approved by the NICHD/NINDS U24 ClinGen Mitochondrial Disease Variant Curation Expert Panel on April 23, 2024. Mitochondrial DNA-specific ACMG/AMP criteria applied (PMID: 32906214): PS4_supporting, PM2_supporting, PP3.
Met criteria codes
PP3
The computational predictor MitoTIP suggests this variant is pathogenic (59.9 percentile) and HmtVAR predicts it to be pathogenic score of 0.65 (PP3).
PS4_Supporting
The m.5816A>G variant in MT-TC has been reported in two unrelated families with primary mitochondrial disease (PS4_supporting; PMIDs: 17724295, 37771542). The first reported family had four affected individuals with variable clinical features including dystonia, seizures, tremor, fatigue, ptosis, pigmentary retinopathy, and optic atrophy. Muscle biopsies in these family members showed mosaic COX deficiency, normal respiratory chain enzyme activities, and decreased steady state levels of mt-tRNA Cys. The variant was homoplasmic in muscle and blood in these individuals (PMID: 17724295). The second family reported had one affected individual, a girl, with dystonia, episodic vomiting, motor regression, tremor, and seizures. Skin fibroblast testing showed reduced basal resting oxygen consumption rate (OCR), ATP production, proton leak, maximal respiration, and reserve capacity OCR. The variant was present in blood and urine but heteroplasmy levels were not reported (PMID: 37771542).
PM2_Supporting
This variant is absent in the GenBank dataset, Helix dataset, and gnomAD v3.1.2 (PM2_supporting).
Not Met criteria codes
PS3
There are no cybrids, single fiber studies, or other functional assays reported on this variant.
Curation History
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