NM_001382273.1(TNK2):c.1667_1668delinsAT (p.Gly556Asp) AND not provided

Germline classification:: Uncertain significance (1 submission)
Last evaluated:: Jan 4, 2024
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:: RCV003683004.1

Allele description [Variation Report for NM_001382273.1(TNK2):c.1667_1668delinsAT (p.Gly556Asp)]

NM_001382273.1(TNK2):c.1667_1668delinsAT (p.Gly556Asp)

Gene:

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

Variant type:

Indel

Cytogenetic location:

3q29

Genomic location:

Preferred name:

NM_001382273.1(TNK2):c.1667_1668delinsAT (p.Gly556Asp)

HGVS:

NC_000003.12:g.195868630_195868631delinsAT
NG_029779.1:g.45379_45380delinsAT
NM_001010938.2:c.1739_1740delinsAT
NM_001308046.2:c.1718_1719delinsAT
NM_001382271.1:c.1718_1719delinsAT
NM_001382272.1:c.1739_1740delinsAT
NM_001382273.1:c.1667_1668delinsATMANE SELECT
NM_001382274.1:c.1667_1668delinsAT
NM_001382275.1:c.1763_1764delinsAT
NM_001386164.1:c.1622_1623delinsAT
NM_001387707.1:c.1763_1764delinsAT
NM_001387708.1:c.1694_1695delinsAT
NM_001387709.1:c.1622_1623delinsAT
NM_001387710.1:c.1622_1623delinsAT
NM_001387711.1:c.1622_1623delinsAT
NM_001387712.1:c.1622_1623delinsAT
NM_001387713.1:c.1622_1623delinsAT
NM_001387714.1:c.1622_1623delinsAT
NM_001387715.1:c.1694_1695delinsAT
NM_001387716.1:c.1667_1668delinsAT
NM_001387717.1:c.1667_1668delinsAT
NM_001387718.1:c.1667_1668delinsAT
NM_001387719.1:c.1622_1623delinsAT
NM_001387720.1:c.1622_1623delinsAT
NM_001387721.1:c.1622_1623delinsAT
NM_005781.5:c.1622_1623delinsAT
NP_001010938.2:p.Gly580Asp
NP_001294975.1:p.Gly573Asp
NP_001369200.1:p.Gly573Asp
NP_001369201.1:p.Gly580Asp
NP_001369202.1:p.Gly556Asp
NP_001369203.1:p.Gly556Asp
NP_001369204.1:p.Gly588Asp
NP_001373093.1:p.Gly541Asp
NP_001374636.1:p.Gly588Asp
NP_001374637.1:p.Gly565Asp
NP_001374638.1:p.Gly541Asp
NP_001374639.1:p.Gly541Asp
NP_001374640.1:p.Gly541Asp
NP_001374641.1:p.Gly541Asp
NP_001374642.1:p.Gly541Asp
NP_001374643.1:p.Gly541Asp
NP_001374644.1:p.Gly565Asp
NP_001374645.1:p.Gly556Asp
NP_001374646.1:p.Gly556Asp
NP_001374647.1:p.Gly556Asp
NP_001374648.1:p.Gly541Asp
NP_001374649.1:p.Gly541Asp
NP_001374650.1:p.Gly541Asp
NP_005772.3:p.Gly541Asp
NC_000003.11:g.195595501_195595502delinsAT
NR_170678.1:n.1914_1915delinsAT
NR_170679.1:n.2218_2219delinsAT
NR_170680.1:n.1925_1926delinsAT
NR_170681.1:n.1880_1881delinsAT
NR_170682.1:n.2192_2193delinsAT
NR_170683.1:n.2147_2148delinsAT
NR_170684.1:n.1560_1561delinsAT
NR_170685.1:n.2063_2064delinsAT
NR_170686.1:n.1931_1932delinsAT
NR_170687.1:n.1906_1907delinsAT
NR_170688.1:n.2147_2148delinsAT
NR_170689.1:n.1661_1662delinsAT
NR_170690.1:n.1472_1473delinsAT
NR_170691.1:n.1819_1820delinsAT
NR_170692.1:n.1429_1430delinsAT

Protein change:

G541D

Molecular consequence:

NM_001010938.2:c.1739_1740delinsAT - missense variant - [Sequence Ontology: SO:0001583]
NM_001308046.2:c.1718_1719delinsAT - missense variant - [Sequence Ontology: SO:0001583]
NM_001382271.1:c.1718_1719delinsAT - missense variant - [Sequence Ontology: SO:0001583]
NM_001382272.1:c.1739_1740delinsAT - missense variant - [Sequence Ontology: SO:0001583]
NM_001382273.1:c.1667_1668delinsAT - missense variant - [Sequence Ontology: SO:0001583]
NM_001382274.1:c.1667_1668delinsAT - missense variant - [Sequence Ontology: SO:0001583]
NM_001382275.1:c.1763_1764delinsAT - missense variant - [Sequence Ontology: SO:0001583]
NM_001386164.1:c.1622_1623delinsAT - missense variant - [Sequence Ontology: SO:0001583]
NM_001387707.1:c.1763_1764delinsAT - missense variant - [Sequence Ontology: SO:0001583]
NM_001387708.1:c.1694_1695delinsAT - missense variant - [Sequence Ontology: SO:0001583]
NM_001387709.1:c.1622_1623delinsAT - missense variant - [Sequence Ontology: SO:0001583]
NM_001387710.1:c.1622_1623delinsAT - missense variant - [Sequence Ontology: SO:0001583]
NM_001387711.1:c.1622_1623delinsAT - missense variant - [Sequence Ontology: SO:0001583]
NM_001387712.1:c.1622_1623delinsAT - missense variant - [Sequence Ontology: SO:0001583]
NM_001387713.1:c.1622_1623delinsAT - missense variant - [Sequence Ontology: SO:0001583]
NM_001387714.1:c.1622_1623delinsAT - missense variant - [Sequence Ontology: SO:0001583]
NM_001387715.1:c.1694_1695delinsAT - missense variant - [Sequence Ontology: SO:0001583]
NM_001387716.1:c.1667_1668delinsAT - missense variant - [Sequence Ontology: SO:0001583]
NM_001387717.1:c.1667_1668delinsAT - missense variant - [Sequence Ontology: SO:0001583]
NM_001387718.1:c.1667_1668delinsAT - missense variant - [Sequence Ontology: SO:0001583]
NM_001387719.1:c.1622_1623delinsAT - missense variant - [Sequence Ontology: SO:0001583]
NM_001387720.1:c.1622_1623delinsAT - missense variant - [Sequence Ontology: SO:0001583]
NM_001387721.1:c.1622_1623delinsAT - missense variant - [Sequence Ontology: SO:0001583]
NM_005781.5:c.1622_1623delinsAT - missense variant - [Sequence Ontology: SO:0001583]
NR_170678.1:n.1914_1915delinsAT - non-coding transcript variant - [Sequence Ontology: SO:0001619]
NR_170679.1:n.2218_2219delinsAT - non-coding transcript variant - [Sequence Ontology: SO:0001619]
NR_170680.1:n.1925_1926delinsAT - non-coding transcript variant - [Sequence Ontology: SO:0001619]
NR_170681.1:n.1880_1881delinsAT - non-coding transcript variant - [Sequence Ontology: SO:0001619]
NR_170682.1:n.2192_2193delinsAT - non-coding transcript variant - [Sequence Ontology: SO:0001619]
NR_170683.1:n.2147_2148delinsAT - non-coding transcript variant - [Sequence Ontology: SO:0001619]
NR_170684.1:n.1560_1561delinsAT - non-coding transcript variant - [Sequence Ontology: SO:0001619]
NR_170685.1:n.2063_2064delinsAT - non-coding transcript variant - [Sequence Ontology: SO:0001619]
NR_170686.1:n.1931_1932delinsAT - non-coding transcript variant - [Sequence Ontology: SO:0001619]
NR_170687.1:n.1906_1907delinsAT - non-coding transcript variant - [Sequence Ontology: SO:0001619]
NR_170688.1:n.2147_2148delinsAT - non-coding transcript variant - [Sequence Ontology: SO:0001619]
NR_170689.1:n.1661_1662delinsAT - non-coding transcript variant - [Sequence Ontology: SO:0001619]
NR_170690.1:n.1472_1473delinsAT - non-coding transcript variant - [Sequence Ontology: SO:0001619]
NR_170691.1:n.1819_1820delinsAT - non-coding transcript variant - [Sequence Ontology: SO:0001619]
NR_170692.1:n.1429_1430delinsAT - non-coding transcript variant - [Sequence Ontology: SO:0001619]

Condition(s)

Synonyms:: none provided
Identifiers:: MedGen: C3661900

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FGFR1OP2 FGFR1 oncogene partner 2 [Homo sapiens]
FGFR1OP2 FGFR1 oncogene partner 2 [Homo sapiens]
Gene ID:26127

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BAG5 BAG cochaperone 5 [Homo sapiens]
BAG5 BAG cochaperone 5 [Homo sapiens]
Gene ID:9529

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Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV004410934	Invitae	criteria provided, single submitter (Invitae Variant Classification Sherloc (09022015))	Uncertain significance (Jan 4, 2024)	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

SCV004410934

Invitae

criteria provided, single submitter

(Invitae Variant Classification Sherloc (09022015))

Uncertain significance
(Jan 4, 2024)

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, SCV004410934.1

#	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 glycine, which is neutral and non-polar, with aspartic acid, which is acidic and polar, at codon 619 of the TNK2 protein (p.Gly619Asp). This variant is present in population databases (no rsID available, gnomAD 0.01%). This variant has not been reported in the literature in individuals affected with TNK2-related conditions. 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 disruptive. 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: Feb 28, 2024

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