The ClinGen Evidence Repository is an FDA-recognized human genetic variant database containing expert-curated assertions regarding variants' pathogenicity and supporting evidence summaries. [Disclaimer]
  • Despite there being a valid 'cspec' property in the messages there's a discrepancy in message contents and CSPEC data: * Message Gene: MT-TS1 CSPEC Genes: [] * Message MONDOs: MONDO:0044970 CSPEC MONDO: []
  • No CSPEC computed assertion could be determined for this classification!


Variant: NC_012920.1(MT-TS1):m.7512T>C

CA120546

9562 (ClinVar)

Gene: MT-TS1
Condition: mitochondrial disease
Inheritance Mode: Mitochondrial inheritance
UUID: 1cdf5a8b-79ba-4cde-ab35-80894be67e37
Approved on: 2024-07-08
Published on: 2025-04-28

HGVS expressions

NC_012920.1:m.7512T>C
J01415.2:m.7512T>C

Likely Pathogenic

Met criteria codes 5
PP3 PM2_Supporting PS3_Supporting PS4_Moderate PP1_Moderate

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.7512T>C variant in MT-TS1 has been reported in four unrelated individuals with primary mitochondrial disease (PS4_moderate; PMIDs: 7669057, 17894844, 9778262). Clinical features in affected individuals include mitochondrial encephalomyopathy, lactic acidosis, and stroke-like episodes (MELAS) as well as seizures, cognitive decline, dementia, muscle atrophy, muscle weakness, ataxia, developmental regression, and sensorineural hearing loss. Muscle biopsy in some cases showed ragged red fibers. Heteroplasmy levels in affected individuals ranged from 24% to homoplasmy. There are no reported de novo occurrences of this variant reported to our knowledge. The variant segregated with clinical features in all reported families (PP1_moderate; PMIDs: 7669057, 17894844, 9778262). This variant is absent in the GenBank dataset and gnomAD v3.1.2, and there is one heteroplasmic occurrence in the Helix dataset (PM2_supporting). The computational predictor MitoTIP suggests this variant is pathogenic (64.2 percentile) and HmtVAR predicts it to be pathogenic score of 0.75 (PP3). Single fiber analysis showed significantly higher levels of the variant in COX-negative fibers (n=10, median 97%, range: 94–99%) compared with COX-positive fibers (n=10, median 36%, range: 12–91%) (PS3_supporting, PMID: 17894844). 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 ClinGen Mitochondrial Disease Variant Curation Expert Panel on July 8, 2024. Mitochondrial DNA-specific ACMG/AMP criteria applied (PMID: 32906214): PS4_moderate, PP1_moderate, PM2_supporting, PP3, PS3_supporting.
Met criteria codes
PP3
The computational predictor MitoTIP suggests this variant is pathogenic (64.2 percentile) and HmtVAR predicts it to be pathogenic score of 0.75 (PP3).
PM2_Supporting
This variant is absent in the GenBank dataset and gnomAD v3.1.2, and there is one heteroplasmic occurrence in the Helix dataset (PM2_supporting).
PS3_Supporting
Single fiber analysis showed significantly higher levels of the variant in COX-negative fibers (n=10, median 97%, range: 94–99%) compared with COX-positive fibers (n=10, median 36%, range: 12–91%)(PS3_supporting, PMID: 17894844).
PS4_Moderate
No code specific comments provided, please refer to the summary above or general recommendations provided in the guideline
PP1_Moderate
No code specific comments provided, please refer to the summary above or general recommendations provided in the guideline
Curation History
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