NM_004614.5(TK2):c.473A>G (p.Tyr158Cys) AND not provided

Germline classification:: Uncertain significance (1 submission)
Last evaluated:: Nov 14, 2023
Review status:: 1 star out of maximum of 4 stars
criteria provided, single submitter

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:: RCV001973254.5

Allele description [Variation Report for NM_004614.5(TK2):c.473A>G (p.Tyr158Cys)]

NM_004614.5(TK2):c.473A>G (p.Tyr158Cys)

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.473A>G (p.Tyr158Cys)

HGVS:

NC_000016.10:g.66517854T>C
NG_016862.1:g.37559A>G
NM_001172643.1:c.380A>G
NM_001172644.2:c.398A>G
NM_001172645.2:c.419A>G
NM_001271934.2:c.326A>G
NM_001271935.1:c.357-4043A>G
NM_001272050.2:c.182A>G
NM_004614.5:c.473A>GMANE SELECT
NP_001166114.1:p.Tyr127Cys
NP_001166115.1:p.Tyr133Cys
NP_001166116.1:p.Tyr140Cys
NP_001258863.1:p.Tyr109Cys
NP_001258979.1:p.Tyr61Cys
NP_004605.4:p.Tyr158Cys
NC_000016.9:g.66551757T>C
NR_073520.2:n.1462A>G

Protein change:

Y109C

Links:

dbSNP: rs553354595

NCBI 1000 Genomes Browser:

rs553354595

Molecular consequence:

NM_001271935.1:c.357-4043A>G - intron variant - [Sequence Ontology: SO:0001627]
NM_001172643.1:c.380A>G - missense variant - [Sequence Ontology: SO:0001583]
NM_001172644.2:c.398A>G - missense variant - [Sequence Ontology: SO:0001583]
NM_001172645.2:c.419A>G - missense variant - [Sequence Ontology: SO:0001583]
NM_001271934.2:c.326A>G - missense variant - [Sequence Ontology: SO:0001583]
NM_001272050.2:c.182A>G - missense variant - [Sequence Ontology: SO:0001583]
NM_004614.5:c.473A>G - missense variant - [Sequence Ontology: SO:0001583]
NR_073520.2:n.1462A>G - non-coding transcript variant - [Sequence Ontology: SO:0001619]

Condition(s)

Synonyms:: none provided
Identifiers:: MedGen: C3661900

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Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV002249732	Invitae	criteria provided, single submitter (Invitae Variant Classification Sherloc (09022015))	Uncertain significance (Nov 14, 2023)	germline	clinical testing	PubMed (1) [See all records that cite this PMID]

Submission Accession

Submitter

Review Status
(Assertion method)

Clinical Significance
(Last evaluated)

Origin

Method

Citations

SCV002249732

Invitae

criteria provided, single submitter

(Invitae Variant Classification Sherloc (09022015))

Uncertain significance
(Nov 14, 2023)

germline

clinical testing

PubMed (1)
[See all records that cite this PMID]

Help

Summary from all submissions

Ethnicity	Origin	Affected	Individuals	Families	Chromosomes tested	Number Tested	Family history	Method
not provided	germline	unknown	not provided	not provided	not provided	not provided	not provided	clinical testing

Citations

PubMed

Sherloc: a comprehensive refinement of the ACMG-AMP variant classification criteria.

Nykamp K, Anderson M, Powers M, Garcia J, Herrera B, Ho YY, Kobayashi Y, Patil N, Thusberg J, Westbrook M; Invitae Clinical Genomics Group., Topper S.

Genet Med. 2017 Oct;19(10):1105-1117. doi: 10.1038/gim.2017.37. Epub 2017 May 11. Erratum in: Genet Med. 2020 Jan;22(1):240. doi: 10.1038/s41436-019-0624-9.

PubMed [citation]

PMID:: 28492532
PMCID:: PMC5632818

Details of each submission

From Invitae, SCV002249732.3

#	Ethnicity	Individuals	Chromosomes Tested	Family History	Method	Citations
1	not provided	not provided	not provided	not provided	clinical testing	PubMed (1)

Description

This sequence change replaces tyrosine, which is neutral and polar, with cysteine, which is neutral and slightly polar, at codon 158 of the TK2 protein (p.Tyr158Cys). This variant is present in population databases (rs553354595, gnomAD 0.008%). This variant has not been reported in the literature in individuals affected with TK2-related conditions. ClinVar contains an entry for this variant (Variation ID: 1470389). Advanced modeling of protein sequence and biophysical properties (such as structural, functional, and spatial information, amino acid conservation, physicochemical variation, residue mobility, and thermodynamic stability) has been performed at Invitae for this missense variant, however the output from this modeling did not meet the statistical confidence thresholds required to predict the impact of this variant on TK2 protein function. In summary, the available evidence is currently insufficient to determine the role of this variant in disease. Therefore, it has been classified as a Variant of Uncertain Significance.

#	Sample				Method		Observation
#	Origin	Affected	Number tested	Tissue	Purpose	Method	Individuals	Allele frequency	Families	Co-occurrences
1	germline	unknown	not provided	not provided	not provided		not provided	not provided	not provided	not provided

Last Updated: May 19, 2024

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