NM_001382273.1(TNK2):c.1519C>T (p.Pro507Ser) AND not provided

Germline classification:: Uncertain significance (1 submission)
Last evaluated:: Apr 26, 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:: RCV003698635.3

Allele description [Variation Report for NM_001382273.1(TNK2):c.1519C>T (p.Pro507Ser)]

NM_001382273.1(TNK2):c.1519C>T (p.Pro507Ser)

Gene:

TNK2:tyrosine kinase non receptor 2 [Gene - OMIM - HGNC]

Variant type:

single nucleotide variant

Cytogenetic location:

3q29

Genomic location:

Preferred name:

NM_001382273.1(TNK2):c.1519C>T (p.Pro507Ser)

HGVS:

NC_000003.12:g.195870138G>A
NG_029779.1:g.43872C>T
NM_001010938.2:c.1591C>T
NM_001308046.2:c.1615C>T
NM_001382271.1:c.1615C>T
NM_001382272.1:c.1591C>T
NM_001382273.1:c.1519C>TMANE SELECT
NM_001382274.1:c.1519C>T
NM_001382275.1:c.1615C>T
NM_001386164.1:c.1519C>T
NM_001387707.1:c.1615C>T
NM_001387708.1:c.1591C>T
NM_001387709.1:c.1519C>T
NM_001387710.1:c.1519C>T
NM_001387711.1:c.1519C>T
NM_001387712.1:c.1519C>T
NM_001387713.1:c.1519C>T
NM_001387714.1:c.1519C>T
NM_001387715.1:c.1591C>T
NM_001387716.1:c.1519C>T
NM_001387717.1:c.1519C>T
NM_001387718.1:c.1519C>T
NM_001387719.1:c.1519C>T
NM_001387720.1:c.1519C>T
NM_001387721.1:c.1519C>T
NM_005781.5:c.1519C>T
NP_001010938.2:p.Pro531Ser
NP_001294975.1:p.Pro539Ser
NP_001369200.1:p.Pro539Ser
NP_001369201.1:p.Pro531Ser
NP_001369202.1:p.Pro507Ser
NP_001369203.1:p.Pro507Ser
NP_001369204.1:p.Pro539Ser
NP_001373093.1:p.Pro507Ser
NP_001374636.1:p.Pro539Ser
NP_001374637.1:p.Pro531Ser
NP_001374638.1:p.Pro507Ser
NP_001374639.1:p.Pro507Ser
NP_001374640.1:p.Pro507Ser
NP_001374641.1:p.Pro507Ser
NP_001374642.1:p.Pro507Ser
NP_001374643.1:p.Pro507Ser
NP_001374644.1:p.Pro531Ser
NP_001374645.1:p.Pro507Ser
NP_001374646.1:p.Pro507Ser
NP_001374647.1:p.Pro507Ser
NP_001374648.1:p.Pro507Ser
NP_001374649.1:p.Pro507Ser
NP_001374650.1:p.Pro507Ser
NP_005772.3:p.Pro507Ser
NC_000003.11:g.195597009G>A
NR_170678.1:n.1766C>T
NR_170679.1:n.2070C>T
NR_170680.1:n.1777C>T
NR_170681.1:n.1777C>T
NR_170682.1:n.2044C>T
NR_170683.1:n.2044C>T
NR_170684.1:n.1457C>T
NR_170685.1:n.1915C>T
NR_170686.1:n.1828C>T
NR_170687.1:n.1758C>T
NR_170688.1:n.2044C>T
NR_170689.1:n.1558C>T
NR_170690.1:n.1369C>T
NR_170691.1:n.1716C>T
NR_170692.1:n.1326C>T

Protein change:

P507S

Molecular consequence:

NM_001010938.2:c.1591C>T - missense variant - [Sequence Ontology: SO:0001583]
NM_001308046.2:c.1615C>T - missense variant - [Sequence Ontology: SO:0001583]
NM_001382271.1:c.1615C>T - missense variant - [Sequence Ontology: SO:0001583]
NM_001382272.1:c.1591C>T - missense variant - [Sequence Ontology: SO:0001583]
NM_001382273.1:c.1519C>T - missense variant - [Sequence Ontology: SO:0001583]
NM_001382274.1:c.1519C>T - missense variant - [Sequence Ontology: SO:0001583]
NM_001382275.1:c.1615C>T - missense variant - [Sequence Ontology: SO:0001583]
NM_001386164.1:c.1519C>T - missense variant - [Sequence Ontology: SO:0001583]
NM_001387707.1:c.1615C>T - missense variant - [Sequence Ontology: SO:0001583]
NM_001387708.1:c.1591C>T - missense variant - [Sequence Ontology: SO:0001583]
NM_001387709.1:c.1519C>T - missense variant - [Sequence Ontology: SO:0001583]
NM_001387710.1:c.1519C>T - missense variant - [Sequence Ontology: SO:0001583]
NM_001387711.1:c.1519C>T - missense variant - [Sequence Ontology: SO:0001583]
NM_001387712.1:c.1519C>T - missense variant - [Sequence Ontology: SO:0001583]
NM_001387713.1:c.1519C>T - missense variant - [Sequence Ontology: SO:0001583]
NM_001387714.1:c.1519C>T - missense variant - [Sequence Ontology: SO:0001583]
NM_001387715.1:c.1591C>T - missense variant - [Sequence Ontology: SO:0001583]
NM_001387716.1:c.1519C>T - missense variant - [Sequence Ontology: SO:0001583]
NM_001387717.1:c.1519C>T - missense variant - [Sequence Ontology: SO:0001583]
NM_001387718.1:c.1519C>T - missense variant - [Sequence Ontology: SO:0001583]
NM_001387719.1:c.1519C>T - missense variant - [Sequence Ontology: SO:0001583]
NM_001387720.1:c.1519C>T - missense variant - [Sequence Ontology: SO:0001583]
NM_001387721.1:c.1519C>T - missense variant - [Sequence Ontology: SO:0001583]
NM_005781.5:c.1519C>T - missense variant - [Sequence Ontology: SO:0001583]
NR_170678.1:n.1766C>T - non-coding transcript variant - [Sequence Ontology: SO:0001619]
NR_170679.1:n.2070C>T - non-coding transcript variant - [Sequence Ontology: SO:0001619]
NR_170680.1:n.1777C>T - non-coding transcript variant - [Sequence Ontology: SO:0001619]
NR_170681.1:n.1777C>T - non-coding transcript variant - [Sequence Ontology: SO:0001619]
NR_170682.1:n.2044C>T - non-coding transcript variant - [Sequence Ontology: SO:0001619]
NR_170683.1:n.2044C>T - non-coding transcript variant - [Sequence Ontology: SO:0001619]
NR_170684.1:n.1457C>T - non-coding transcript variant - [Sequence Ontology: SO:0001619]
NR_170685.1:n.1915C>T - non-coding transcript variant - [Sequence Ontology: SO:0001619]
NR_170686.1:n.1828C>T - non-coding transcript variant - [Sequence Ontology: SO:0001619]
NR_170687.1:n.1758C>T - non-coding transcript variant - [Sequence Ontology: SO:0001619]
NR_170688.1:n.2044C>T - non-coding transcript variant - [Sequence Ontology: SO:0001619]
NR_170689.1:n.1558C>T - non-coding transcript variant - [Sequence Ontology: SO:0001619]
NR_170690.1:n.1369C>T - non-coding transcript variant - [Sequence Ontology: SO:0001619]
NR_170691.1:n.1716C>T - non-coding transcript variant - [Sequence Ontology: SO:0001619]
NR_170692.1:n.1326C>T - non-coding transcript variant - [Sequence Ontology: SO:0001619]

Condition(s)

Synonyms:: none provided
Identifiers:: MedGen: C3661900

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Tmem30c transmembrane protein 30C [Rattus norvegicus]
Tmem30c transmembrane protein 30C [Rattus norvegicus]
Gene ID:288175

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Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV004473372	Labcorp Genetics (formerly Invitae), Labcorp	criteria provided, single submitter (Invitae Variant Classification Sherloc (09022015))	Uncertain significance (Apr 26, 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

SCV004473372

Labcorp Genetics (formerly Invitae), Labcorp

criteria provided, single submitter

(Invitae Variant Classification Sherloc (09022015))

Uncertain significance
(Apr 26, 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 Labcorp Genetics (formerly Invitae), Labcorp, SCV004473372.1

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

Description

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. An algorithm developed to predict the effect of missense changes on protein structure and function (PolyPhen-2) suggests that this variant¬† is likely to be tolerated. This variant has not been reported in the literature in individuals affected with TNK2-related conditions. This variant is present in population databases (rs35759128, gnomAD 0.1%), and has an allele count higher than expected for a pathogenic variant. This sequence change replaces proline, which is neutral and non-polar, with serine, which is neutral and polar, at codon 570 of the TNK2 protein (p.Pro570Ser).

#	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: Sep 29, 2024

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