NM_000222.3(KIT):c.2489G>C (p.Arg830Pro) AND Gastrointestinal stromal tumor

Germline classification:: Uncertain significance (1 submission)
Last evaluated:: Dec 11, 2020
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:: RCV002009472.7

Allele description [Variation Report for NM_000222.3(KIT):c.2489G>C (p.Arg830Pro)]

NM_000222.3(KIT):c.2489G>C (p.Arg830Pro)

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.2489G>C (p.Arg830Pro)

HGVS:

NC_000004.12:g.54736502G>C
NG_007456.1:g.83508G>C
NM_000222.2:c.2489G>C
NM_000222.3:c.2489G>CMANE SELECT
NM_001093772.2:c.2477G>C
NM_001385284.1:c.2492G>C
NM_001385285.1:c.2486G>C
NM_001385286.1:c.2474G>C
NM_001385288.1:c.2480G>C
NM_001385290.1:c.2489G>C
NM_001385292.1:c.2477G>C
NP_000213.1:p.Arg830Pro
NP_001087241.1:p.Arg826Pro
NP_001372213.1:p.Arg831Pro
NP_001372214.1:p.Arg829Pro
NP_001372215.1:p.Arg825Pro
NP_001372217.1:p.Arg827Pro
NP_001372219.1:p.Arg830Pro
NP_001372221.1:p.Arg826Pro
LRG_307t1:c.2489G>C
LRG_307:g.83508G>C
NC_000004.11:g.55602668G>C

Protein change:

R825P

Links:

dbSNP: rs772311731

NCBI 1000 Genomes Browser:

rs772311731

Molecular consequence:

NM_000222.3:c.2489G>C - missense variant - [Sequence Ontology: SO:0001583]
NM_001093772.2:c.2477G>C - missense variant - [Sequence Ontology: SO:0001583]
NM_001385284.1:c.2492G>C - missense variant - [Sequence Ontology: SO:0001583]
NM_001385285.1:c.2486G>C - missense variant - [Sequence Ontology: SO:0001583]
NM_001385286.1:c.2474G>C - missense variant - [Sequence Ontology: SO:0001583]
NM_001385288.1:c.2480G>C - missense variant - [Sequence Ontology: SO:0001583]
NM_001385290.1:c.2489G>C - missense variant - [Sequence Ontology: SO:0001583]
NM_001385292.1:c.2477G>C - 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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PREDICTED: nodulin homeobox isoform X2 [Cucumis melo]
PREDICTED: nodulin homeobox isoform X2 [Cucumis melo]
gi|659115328|ref|XP_008457501.1|

Protein

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Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV002290145	Labcorp Genetics (formerly Invitae), Labcorp	criteria provided, single submitter (Invitae Variant Classification Sherloc (09022015))	Uncertain significance (Dec 11, 2020)	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

SCV002290145

Labcorp Genetics (formerly Invitae), Labcorp

criteria provided, single submitter

(Invitae Variant Classification Sherloc (09022015))

Uncertain significance
(Dec 11, 2020)

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, SCV002290145.3

#	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 disruptive, but these predictions have not been confirmed by published functional studies and their clinical significance is uncertain. This variant has not been reported in the literature in individuals with KIT-related conditions. This variant is not present in population databases (ExAC no frequency). This sequence change replaces arginine with proline at codon 830 of the KIT protein (p.Arg830Pro). The arginine residue is highly conserved and there is a moderate physicochemical difference between arginine and proline.

#	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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