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NM_000222.3(KIT):c.1702T>G (p.Tyr568Asp) AND Gastrointestinal stromal tumor

Germline classification:
Uncertain significance (1 submission)
Last evaluated:
Mar 9, 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:
RCV001925826.6

Allele description [Variation Report for NM_000222.3(KIT):c.1702T>G (p.Tyr568Asp)]

NM_000222.3(KIT):c.1702T>G (p.Tyr568Asp)

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.1702T>G (p.Tyr568Asp)
HGVS:
  • NC_000004.12:g.54727470T>G
  • NG_007456.1:g.74476T>G
  • NM_000222.3:c.1702T>GMANE SELECT
  • NM_001093772.2:c.1690T>G
  • NM_001385284.1:c.1705T>G
  • NM_001385285.1:c.1702T>G
  • NM_001385286.1:c.1690T>G
  • NM_001385288.1:c.1693T>G
  • NM_001385290.1:c.1705T>G
  • NM_001385292.1:c.1693T>G
  • NP_000213.1:p.Tyr568Asp
  • NP_001087241.1:p.Tyr564Asp
  • NP_001372213.1:p.Tyr569Asp
  • NP_001372214.1:p.Tyr568Asp
  • NP_001372215.1:p.Tyr564Asp
  • NP_001372217.1:p.Tyr565Asp
  • NP_001372219.1:p.Tyr569Asp
  • NP_001372221.1:p.Tyr565Asp
  • LRG_307:g.74476T>G
  • NC_000004.11:g.55593636T>G
Protein change:
Y564D
Links:
dbSNP: rs1722310323
NCBI 1000 Genomes Browser:
rs1722310323
Molecular consequence:
  • NM_000222.3:c.1702T>G - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001093772.2:c.1690T>G - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001385284.1:c.1705T>G - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001385285.1:c.1702T>G - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001385286.1:c.1690T>G - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001385288.1:c.1693T>G - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001385290.1:c.1705T>G - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001385292.1:c.1693T>G - 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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Assertion and evidence details

Submission AccessionSubmitterReview Status
(Assertion method)
Clinical Significance
(Last evaluated)
OriginMethodCitations
SCV002178340Invitae
criteria provided, single submitter

(Invitae Variant Classification Sherloc (09022015))
Uncertain significance
(Mar 9, 2021)
germlineclinical testing

PubMed (1)
[See all records that cite this PMID]

Summary from all submissions

EthnicityOriginAffectedIndividualsFamiliesChromosomes testedNumber TestedFamily historyMethod
not providedgermlineunknownnot providednot providednot providednot providednot providedclinical 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):240-242.

PubMed [citation]
PMID:
28492532
PMCID:
PMC5632818

Details of each submission

From Invitae, SCV002178340.3

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1not providednot providednot providednot providedclinical testing PubMed (1)

Description

This variant has not been reported in the literature in individuals with KIT-related conditions. 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 is not present in population databases (ExAC no frequency). This sequence change replaces tyrosine with aspartic acid at codon 568 of the KIT protein (p.Tyr568Asp). The tyrosine residue is highly conserved and there is a large physicochemical difference between tyrosine and aspartic acid.

#SampleMethodObservation
OriginAffectedNumber testedTissuePurposeMethodIndividualsAllele frequencyFamiliesCo-occurrences
1germlineunknownnot providednot providednot providednot providednot providednot providednot provided

Last Updated: Apr 15, 2024