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-ATP6 CSPEC Genes: [] * Message MONDOs: MONDO:0044970 CSPEC MONDO: []
  • No CSPEC computed assertion could be determined for this classification!


Variant: NC_012920.1(MT-TK):m.8296A>G

CA120557

9584 (ClinVar)

Gene: MT-ATP6
Condition: mitochondrial disease
Inheritance Mode: Mitochondrial inheritance
UUID: 2723e9dc-d079-4e5c-98b7-07425e227416
Approved on: 2025-02-04
Published on: 2025-05-28

HGVS expressions

NC_012920.1:m.8296A>G
J01415.2:m.8296A>G

Uncertain Significance

Met criteria codes 1
PP3
Not Met criteria codes 6
PS3 PS2 PS4 PP1 PM2 PM6

Evidence Links 2

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.8296A>G variant in MT-TK has been reported in 18 unrelated individuals with primary mitochondrial disease with varying phenotypes (diabetes, hypertrophic cardiomyopathy, optic atrophy, sensorineural hearing loss, and generalized epilepsy; 10 subjects reported in PMIDs: 9802769, 9571188, 10525672; additional subjects reported in PMIDs: 10737988, 12504210, 18651333, 20143911, 37573175), however analyses for other genetic etiologies were limited in these affected individuals precluding their inclusion in this curation. The variant was present in some affected individuals at homoplasmy and in others at heteroplasmy. In at least one family, the variant was present at homoplasmy in the proband and in his healthy mother and sister (PMID: 18651333). There are no reported de novo occurrences to our knowledge. This variant is present in population databases and is seen in individuals from several different haplogroups (MITOMAP: 0.061%, 38/61,883; gnomAD v3.1.2: 0.044%, 25/56,432 homoplasmic occurrences, one heteroplasmic occurrence; Helix: 0.048%, 94/195,893 homoplasmic occurrences). The computational predictor MitoTIP suggests this variant is pathogenic (72.3 percentile) and HmtVAR predicts it to be pathogenic score of 0.85 (PP3). Single fiber testing showed similar levels of the variant in COX-negative ragged red fibers and normal fibers (PMID: 9932960), and cybrid studies showed no significant differences from wild type (PMID: 11857739). 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 February 4, 2025. Mitochondrial DNA-specific ACMG/AMP criteria applied (PMID: 32906214): PP3.
Met criteria codes
PP3
The computational predictor MitoTIP suggests this variant is pathogenic (72.3 percentile) and HmtVAR predicts it to be pathogenic score of 0.85 (PP3).
Not Met criteria codes
PS3
Single fiber testing showed similar levels of the variant in COX-negative ragged red fibers and normal fibers (PMID: 9932960), and cybrid studies showed no significant differences from wild type (PMID: 11857739).

PS2
There are no reported de novo occurrences to our knowledge.
PS4
The m.8296A>G variant in MT-TK has been reported in 18 unrelated individuals with primary mitochondrial disease with varying phenotypes (diabetes, hypertrophic cardiomyopathy, optic atrophy, sensorineural hearing loss, and generalized epilepsy; 10 subjects reported in PMIDs: 9802769, 9571188, 10525672; additional subjects reported in PMIDs: 10737988, 12504210, 18651333, 20143911, 37573175), however analyses for other genetic etiologies were limited in these affected individuals precluding their inclusion in this curation. The variant was present in some affected individuals at homoplasmy and in others at heteroplasmy.
PP1
In at least one family, the variant was present at homoplasmy in the proband and in his healthy mother and sister (PMID: 18651333).
PM2
This variant is present in population databases and is seen in individuals from several different haplogroups (MITOMAP: 0.061%, 38/61,883; gnomAD v3.1.2: 0.044%, 25/56,432 homoplasmic occurrences, 1 heteroplasmic occurrence; Helix: 0.048%, 94/195,893 homoplasmic occurrences).
PM6
There are no reported de novo occurrences to our knowledge.
Curation History
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