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.586G>A") 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-TF CSPEC Genes: [] * Message MONDOs: MONDO:0044970 CSPEC MONDO: []
  • No CSPEC computed assertion could be determined for this classification!


Variant: m.586G>A

CA128831

30005 (ClinVar)

Gene: MT-TF
Condition: mitochondrial disease
Inheritance Mode: Mitochondrial inheritance
UUID: f333f6f6-be97-4d97-899b-db6db92f26e8
Approved on: 2024-06-10
Published on: 2024-12-06

HGVS expressions

NC_012920.1:m.586G>A
J01415.2:m.586G>A

Uncertain Significance

Met criteria codes 5
PS4_Supporting PP3 PM2_Supporting PS3_Supporting PM6_Supporting

Evidence Links 1

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.586G>A variant in MT-TF has been reported in two unrelated individuals with primary mitochondrial disease (PS4_supporting; PMIDs: 21060018, 31463198). One individual was a 57-year-old woman with hearing loss onset in her mid 40s that progressed to profound hearing loss in her 50s, myopathy and progressive exercise intolerance with reduced mobility and falls onset in her late 40s, and spasticity, facial grimacing, dementia, and psychiatric manifestations in her mid 50s (PMID: 21060018). Brain imaging showed generalized cerebral, cerebellar, and brainstem atrophy. Cerebrospinal fluid lactate was elevated. Muscle biopsy showed ragged red fibers and COX-deficient fibers. The variant was present in muscle at 85% heteroplasmy, urinary epithelia at 29%, and blood at 3%. Her mother had died however DNA from paraffin-embedded breast tissue was obtained and revealed the variant at 13% heteroplasmy. The other individual was a 14-year-old boy with exercise intolerance and muscle weakness that followed a stable course (PMID: 31463198). Brain imaging was normal. Lactate was elevated in blood. Muscle biopsy showed ragged red fibers, COX-negative fibers, and mitochondrial respiratory chain complexes I, III, and IV deficiency. The variant was present at >90% in muscle, 40% in urinary epithelia, and was present at trace levels in blood. The variant was undetectable in his mother’s blood and urinary epithelia (PM6_supporting; PMID: 31463198). This variant is absent in the GenBank dataset, Helix dataset, and gnomAD v3.1.2 (PM2_supporting). The computational predictor MitoTIP suggests this variant is pathogenic (89.7 percentile) and HmtVAR predicts it to be pathogenic score of 0.6 (PP3). Single fiber testing showed higher levels of the variant in COX-deficient fibers (99.4±0.2%, n=11) than in COX-positive fibers (72.1±8.5%, n=9; p<0.001; PS3_supporting, PMID: 21060018). 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 June 10, 2024. Mitochondrial DNA-specific ACMG/AMP criteria applied (PMID: 32906214): PS4_supporting, PM6_supporting, PP3, PS3_supporting, PM2_supporting.
Met criteria codes
PS4_Supporting
The m.586G>A variant in MT-TF has been reported in two unrelated individuals with primary mitochondrial disease. One individual was a 57-year-old woman with hearing loss onset in her mid 40s that progressed to profound hearing loss in her 50s, myopathy and progressive exercise intolerance with reduced mobility and falls onset in her late 40s, and spasticity, facial grimacing, dementia, and psychiatric manifestations in her mid 50s (PMID: 21060018). Brain imaging showed generalized cerebral, cerebellar, and brainstem atrophy. Cerebrospinal fluid lactate was elevated. Muscle biopsy showed ragged red fibers and COX-deficient fibers. The variant was present in muscle at 85% heteroplasmy, urinary epithelia at 29%, and blood at 3%. Her mother had died however DNA from paraffin-embedded breast tissue was obtained and revealed the variant at 13% heteroplasmy. The other individual was a 14-year-old boy with exercise intolerance and muscle weakness that was following a stable course. Brain imaging was normal (PMID: 31463198). Lactate was elevated in blood. Muscle biopsy showed ragged red fibers, COX-negative fibers, and mitochondrial respiratory chain complex I, III, and IV deficiency.
PP3
The computational predictor MitoTIP suggests this variant is pathogenic (89.7 percentile) and HmtVAR predicts it to be pathogenic score of 0.6 (PP3).
PM2_Supporting
This variant is absent in the GenBank dataset, Helix dataset, and gnomAD v3.1.2 (PM2_supporting).
PS3_Supporting
Single fiber testing showed higher levels of the variant in COX-deficient fibers (99.4%) than in COX-positive fibers (72.1%; PS3_supporting, PMID: 21060018).

PM6_Supporting
The variant was present at >90% in muscle, 40% in urinary epithelia, and was present at trace levels in blood from the proband. The variant was undetectable in his mother’s blood and urinary epithelia (PM6_supporting; PMID: 31463198).
Curation History
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