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NM_004614.5(TK2):c.323C>T (p.Thr108Met) AND TK2-related disorder

Germline classification:
Pathogenic (1 submission)
Last evaluated:
Jun 14, 2024
Review status:
(0/4) 0 stars out of maximum of 4 stars
no assertion criteria provided
Somatic classification
of clinical impact:
None
Review status:
(0/4) 0 stars out of maximum of 4 stars
no assertion criteria provided
Somatic classification
of oncogenicity:
None
Review status:
(0/4) 0 stars out of maximum of 4 stars
no assertion criteria provided
Record status:
current
Accession:
RCV004757106.1

Allele description [Variation Report for NM_004614.5(TK2):c.323C>T (p.Thr108Met)]

NM_004614.5(TK2):c.323C>T (p.Thr108Met)

Gene:
TK2:thymidine kinase 2 [Gene - OMIM - HGNC]
Variant type:
single nucleotide variant
Cytogenetic location:
16q21
Genomic location:
Preferred name:
NM_004614.5(TK2):c.323C>T (p.Thr108Met)
Other names:
p.T108M:ACG>ATG
HGVS:
  • NC_000016.10:g.66531432G>A
  • NG_016862.1:g.23981C>T
  • NM_001172643.1:c.230C>T
  • NM_001172644.2:c.248C>T
  • NM_001172645.2:c.269C>T
  • NM_001271934.2:c.176C>T
  • NM_001271935.1:c.230C>T
  • NM_001272050.2:c.32C>T
  • NM_004614.5:c.323C>TMANE SELECT
  • NP_001166114.1:p.Thr77Met
  • NP_001166115.1:p.Thr83Met
  • NP_001166116.1:p.Thr90Met
  • NP_001258863.1:p.Thr59Met
  • NP_001258864.1:p.Thr77Met
  • NP_001258979.1:p.Thr11Met
  • NP_004605.4:p.Thr108Met
  • NC_000016.9:g.66565335G>A
  • NM_001271934.2:c.176C>T
  • NM_004614.4:c.323C>T
  • NR_073520.2:n.1312C>T
  • O00142:p.Thr108Met
Protein change:
T108M; THR108MET
Links:
UniProtKB: O00142#VAR_019420; OMIM: 188250.0003; dbSNP: rs137854431
NCBI 1000 Genomes Browser:
rs137854431
Molecular consequence:
  • NM_001172643.1:c.230C>T - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001172644.2:c.248C>T - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001172645.2:c.269C>T - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001271934.2:c.176C>T - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001271935.1:c.230C>T - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001272050.2:c.32C>T - missense variant - [Sequence Ontology: SO:0001583]
  • NM_004614.5:c.323C>T - missense variant - [Sequence Ontology: SO:0001583]
  • NR_073520.2:n.1312C>T - non-coding transcript variant - [Sequence Ontology: SO:0001619]

Condition(s)

Name:
TK2-related disorder
Synonyms:
TK2-related condition
Identifiers:

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Assertion and evidence details

Help
Submission AccessionSubmitterReview Status
(Assertion method)		Clinical Significance
(Last evaluated)		OriginMethodCitations
SCV005344697PreventionGenetics, part of Exact Sciences
no assertion criteria provided
Pathogenic
(Jun 14, 2024) 		germlineclinical testing

Help

Summary from all submissions

EthnicityOriginAffectedIndividualsFamiliesChromosomes testedNumber TestedFamily historyMethod
not providedgermlineunknownnot providednot providednot providednot providednot providedclinical testing

Details of each submission

From PreventionGenetics, part of Exact Sciences, SCV005344697.1

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1not providednot providednot providednot providedclinical testingnot provided

Description

The TK2 c.323C>T variant is predicted to result in the amino acid substitution p.Thr108Met. This particular substitution has been shown to lead to an approximately 100-fold decrease in the enzyme efficiency of thymidine kinase 2 (TK2) (defined as “T77M” in Wang et al. 2005. PubMed ID: 15639197). The p.Thr108Met substitution has also been repeatedly reported as “T77M” or “T108M” in patients with mitochondrial DNA depletion syndrome (Mancuso et al. 2003. PubMed ID: 12873860; Mancuso et al. 2002. PubMed ID: 12391347; Oskoui et al. 2006. PubMed ID: 16908738). This variant is reported in 0.023% of alleles in individuals of Latino descent in gnomAD. This variant is interpreted as pathogenic.

#SampleMethodObservation
OriginAffectedNumber testedTissuePurposeMethodIndividualsAllele frequencyFamiliesCo-occurrences
1germlineunknownnot providednot providednot providednot providednot providednot providednot provided

Last Updated: Oct 20, 2024