NM_000222.3(KIT):c.1480T>A (p.Tyr494Asn) AND Gastrointestinal stromal tumor

Germline classification:: Uncertain significance (1 submission)
Last evaluated:: Nov 23, 2021
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:: RCV001991399.5

Allele description [Variation Report for NM_000222.3(KIT):c.1480T>A (p.Tyr494Asn)]

NM_000222.3(KIT):c.1480T>A (p.Tyr494Asn)

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.1480T>A (p.Tyr494Asn)

HGVS:

NC_000004.12:g.54725990T>A
NG_007456.1:g.72996T>A
NM_000222.3:c.1480T>AMANE SELECT
NM_001093772.2:c.1480T>A
NM_001385284.1:c.1483T>A
NM_001385285.1:c.1480T>A
NM_001385286.1:c.1480T>A
NM_001385288.1:c.1483T>A
NM_001385290.1:c.1483T>A
NM_001385292.1:c.1483T>A
NP_000213.1:p.Tyr494Asn
NP_001087241.1:p.Tyr494Asn
NP_001372213.1:p.Tyr495Asn
NP_001372214.1:p.Tyr494Asn
NP_001372215.1:p.Tyr494Asn
NP_001372217.1:p.Tyr495Asn
NP_001372219.1:p.Tyr495Asn
NP_001372221.1:p.Tyr495Asn
LRG_307:g.72996T>A
NC_000004.11:g.55592156T>A

Protein change:

Y494N

Links:

dbSNP: rs2109769353

NCBI 1000 Genomes Browser:

rs2109769353

Molecular consequence:

NM_000222.3:c.1480T>A - missense variant - [Sequence Ontology: SO:0001583]
NM_001093772.2:c.1480T>A - missense variant - [Sequence Ontology: SO:0001583]
NM_001385284.1:c.1483T>A - missense variant - [Sequence Ontology: SO:0001583]
NM_001385285.1:c.1480T>A - missense variant - [Sequence Ontology: SO:0001583]
NM_001385286.1:c.1480T>A - missense variant - [Sequence Ontology: SO:0001583]
NM_001385288.1:c.1483T>A - missense variant - [Sequence Ontology: SO:0001583]
NM_001385290.1:c.1483T>A - missense variant - [Sequence Ontology: SO:0001583]
NM_001385292.1:c.1483T>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

Recent activity

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Rattus norvegicus leucine rich repeat neuronal 3 (Lrrn3), mRNA
Rattus norvegicus leucine rich repeat neuronal 3 (Lrrn3), mRNA
gi|1937369847|ref|NM_030856.2|

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Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV002283480	Labcorp Genetics (formerly Invitae), Labcorp	criteria provided, single submitter (Invitae Variant Classification Sherloc (09022015))	Uncertain significance (Nov 23, 2021)	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

SCV002283480

Labcorp Genetics (formerly Invitae), Labcorp

criteria provided, single submitter

(Invitae Variant Classification Sherloc (09022015))

Uncertain significance
(Nov 23, 2021)

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, SCV002283480.3

#	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 (SIFT, PolyPhen-2, Align-GVGD) all suggest that this variant is likely to be tolerated. 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 tyrosine, which is neutral and polar, with asparagine, which is neutral and polar, at codon 494 of the KIT protein (p.Tyr494Asn).

#	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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