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
  • The variant label for this record ("m.8356T>C") does not appear to be in HGVS format


Variant: m.8356T>C

CA120554

9580 (ClinVar)

Gene: MT-TK
Condition: mitochondrial disease
Inheritance Mode: Mitochondrial inheritance
UUID: c803d965-c7ab-4569-bee1-92a570eb1fc9

HGVS expressions

NC_012920.1:m.8356T>C
J01415.2:m.8356T>C

Likely Pathogenic

The Expert Panel has overridden the computationally generated classification - "Uncertain Significance - Insufficient Evidence"
Met criteria codes 5
PS4_Supporting PP3 PP1_Moderate PS3_Supporting PM2_Supporting
Not Met criteria codes 2
PS2 PM6

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.8356T>C variant in MT-TK has been reported in at least 11 individuals from two kindreds with primary mitochondrial disease. Age of onset ranged from the first decade of life to adulthood. Features seen in affected individuals include myoclonic epilepsy with ragged red fibers (MERRF), ataxia, generalized seizures, hearing loss, and lactic acidosis. Heteroplasmy levels were consistently lower in blood and higher in muscle, ranging from 43.4% to homoplasmy (PMIDs: 8069654, 1361099; PS4_supporting). Of note, there is an additional family reported in the literature that was not considered for this variant curation given the presence of another pathogenic variant, m.3243A>G. These individuals had features similar to those seen in individuals with m.8356T>C, as well as features classic for mitochondrial encephalomyopathy, lactic acidosis, and stroke-like episodes (MELAS; PMID: 20610441). This variant segregated with disease manifestations in multiple members of one family reported (PMID: 8069654; PP1_moderate). There are no reported cases of de novo occurrences to our knowledge. The computational predictor MitoTIP suggests this variant impacts the function of this tRNA (88.8 percentile) as does HmtVar with a score of 0.75 (PP3). This variant is absent in the GenBank dataset, Helix dataset, and gnomAD v3.1.2 (PM2_supporting). In cybrid cell lines homoplasmic for this variant, reduced oxygen consumption was reported, supporting the functional impact of this variant (PMID: 7739567; PS3_supporting). In summary, this variant meets criteria to be classified as likely pathogenic for primary mitochondrial disease inherited in a maternal manner. This classification was approved by the NICHD/NINDS U24 ClinGen Mitochondrial Disease Variant Curation Expert Panel on March 13, 2023. Mitochondrial DNA-specific ACMG/AMP criteria applied (PMID: 32906214): PS3_supporting, PS4_supporting, PP1_moderate, PP3, PM2_supporting.
Met criteria codes
PS4_Supporting
The m.8356T>C variant in MT-TK has been reported in at least 11 individuals from two kindreds with primary mitochondrial disease. Age of onset ranged from the first decade of life to adulthood. Features seen in affected individuals include myoclonic epilepsy with ragged red fibers (MERRF), ataxia, generalized seizures, hearing loss, and lactic acidosis. Heteroplasmy levels were consistently lower in blood and higher in muscle, ranging from 43.4% to homoplasmy (PMIDs: 8069654, 1361099; PS4_supporting). Of note, there is an additional family reported in the literature that was not considered for this variant curation given the presence of another pathogenic variant, m.3243A>G. These individuals had features similar to those seen in individuals with m.8356T>C, as well as features classic for mitochondrial encephalomyopathy, lactic acidosis, and stroke-like episodes (MELAS; PMID: 20610441).
PP3
The computational predictor MitoTIP suggests this variant impacts the function of this tRNA (88.8 percentile) as does HmtVar with a score of 0.75 (PP3).
PP1_Moderate
This variant segregated with disease manifestations in multiple members of one family reported (PMID: 8069654; PP1_moderate).
PS3_Supporting
In cybrid cell lines homoplasmic for this variant, reduced oxygen consumption was reported, supporting the functional impact of this variant (PMID: 7739567; PS3_supporting).
PM2_Supporting
This variant is absent in the GenBank dataset, Helix dataset, and gnomAD v3.1.2 (PM2_supporting).
Not Met criteria codes
PS2
There are no reported cases of de novo occurrences to our knowledge.
PM6
There are no reported cases of de novo occurrences to our knowledge.
Approved on: 2023-03-13
Published on: 2023-03-14
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