NM_000222.3(KIT):c.1369G>A (p.Val457Met) AND Gastrointestinal stromal tumor

Germline classification:: Uncertain significance (1 submission)
Last evaluated:: Dec 19, 2022
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:: RCV003638281.2

Allele description [Variation Report for NM_000222.3(KIT):c.1369G>A (p.Val457Met)]

NM_000222.3(KIT):c.1369G>A (p.Val457Met)

Gene:

KIT:KIT proto-oncogene, receptor tyrosine kinase [Gene - OMIM - HGNC]

Variant type:

single nucleotide variant

Cytogenetic location:

4q12

Genomic location:

Preferred name:

NM_000222.3(KIT):c.1369G>A (p.Val457Met)

HGVS:

NC_000004.12:g.54725879G>A
NG_007456.1:g.72885G>A
NM_000222.3:c.1369G>AMANE SELECT
NM_001093772.2:c.1369G>A
NM_001385284.1:c.1372G>A
NM_001385285.1:c.1369G>A
NM_001385286.1:c.1369G>A
NM_001385288.1:c.1372G>A
NM_001385290.1:c.1372G>A
NM_001385292.1:c.1372G>A
NP_000213.1:p.Val457Met
NP_000213.1:p.Val457Met
NP_001087241.1:p.Val457Met
NP_001372213.1:p.Val458Met
NP_001372214.1:p.Val457Met
NP_001372215.1:p.Val457Met
NP_001372217.1:p.Val458Met
NP_001372219.1:p.Val458Met
NP_001372221.1:p.Val458Met
LRG_307t1:c.1369G>A
LRG_307:g.72885G>A
LRG_307p1:p.Val457Met
NC_000004.11:g.55592045G>A
NM_000222.2:c.1369G>A

Protein change:

V457M

Molecular consequence:

NM_000222.3:c.1369G>A - missense variant - [Sequence Ontology: SO:0001583]
NM_001093772.2:c.1369G>A - missense variant - [Sequence Ontology: SO:0001583]
NM_001385284.1:c.1372G>A - missense variant - [Sequence Ontology: SO:0001583]
NM_001385285.1:c.1369G>A - missense variant - [Sequence Ontology: SO:0001583]
NM_001385286.1:c.1369G>A - missense variant - [Sequence Ontology: SO:0001583]
NM_001385288.1:c.1372G>A - missense variant - [Sequence Ontology: SO:0001583]
NM_001385290.1:c.1372G>A - missense variant - [Sequence Ontology: SO:0001583]
NM_001385292.1:c.1372G>A - missense variant - [Sequence Ontology: SO:0001583]

Condition(s)

Name:: Gastrointestinal stromal tumor
Synonyms:: Gastrointestinal Stromal Sarcoma; Gastrointestinal stromal tumor, somatic; Gastrointestinal stroma tumor
Identifiers:: MONDO: MONDO:0011719; MeSH: D046152; MedGen: C0238198; Orphanet: 44890; OMIM: 606764; Human Phenotype Ontology: HP:0100723

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LOC116019930 [Ipomoea triloba]
LOC116019930 [Ipomoea triloba]
Gene ID:116019930

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Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV004477977	Labcorp Genetics (formerly Invitae), Labcorp	criteria provided, single submitter (Invitae Variant Classification Sherloc (09022015))	Uncertain significance (Dec 19, 2022)	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

SCV004477977

Labcorp Genetics (formerly Invitae), Labcorp

criteria provided, single submitter

(Invitae Variant Classification Sherloc (09022015))

Uncertain significance
(Dec 19, 2022)

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, SCV004477977.1

#	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. Algorithms developed to predict the effect of missense changes on protein structure and function output the following: SIFT: "Tolerated"; PolyPhen-2: "Benign"; Align-GVGD: "Class C0". The methionine amino acid residue is found in multiple mammalian species, which suggests that this missense change does not adversely affect protein function. This variant has not been reported in the literature in individuals affected with KIT-related conditions. This variant is not present in population databases (gnomAD no frequency). This sequence change replaces valine, which is neutral and non-polar, with methionine, which is neutral and non-polar, at codon 457 of the KIT protein (p.Val457Met).

#	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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