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NM_000222.3(KIT):c.2564A>G (p.Tyr855Cys) AND multiple conditions

Germline classification:
Uncertain significance (1 submission)
Last evaluated:
Aug 4, 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:
RCV003224519.2

Allele description [Variation Report for NM_000222.3(KIT):c.2564A>G (p.Tyr855Cys)]

NM_000222.3(KIT):c.2564A>G (p.Tyr855Cys)

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.2564A>G (p.Tyr855Cys)
HGVS:
  • NC_000004.12:g.54736577A>G
  • NG_007456.1:g.83583A>G
  • NM_000222.3:c.2564A>GMANE SELECT
  • NM_001093772.2:c.2552A>G
  • NM_001385284.1:c.2567A>G
  • NM_001385285.1:c.2561A>G
  • NM_001385286.1:c.2549A>G
  • NM_001385288.1:c.2555A>G
  • NM_001385290.1:c.2564A>G
  • NM_001385292.1:c.2552A>G
  • NP_000213.1:p.Tyr855Cys
  • NP_001087241.1:p.Tyr851Cys
  • NP_001372213.1:p.Tyr856Cys
  • NP_001372214.1:p.Tyr854Cys
  • NP_001372215.1:p.Tyr850Cys
  • NP_001372217.1:p.Tyr852Cys
  • NP_001372219.1:p.Tyr855Cys
  • NP_001372221.1:p.Tyr851Cys
  • LRG_307t1:c.2564A>G
  • LRG_307:g.83583A>G
  • NC_000004.11:g.55602743A>G
  • NM_000222.2:c.2564A>G
Protein change:
Y850C
Links:
dbSNP: rs1722933723
NCBI 1000 Genomes Browser:
rs1722933723
Molecular consequence:
  • NM_000222.3:c.2564A>G - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001093772.2:c.2552A>G - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001385284.1:c.2567A>G - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001385285.1:c.2561A>G - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001385286.1:c.2549A>G - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001385288.1:c.2555A>G - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001385290.1:c.2564A>G - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001385292.1:c.2552A>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
Name:
Piebaldism
Synonyms:
Piebald skin depigmentation
Identifiers:
MONDO: MONDO:0008244; MedGen: C0080024; Orphanet: 2884; OMIM: 172800; Human Phenotype Ontology: HP:0007544
Name:
Acute myeloid leukemia (AML)
Synonyms:
Acute myeloid leukemia, adult; AML adult; Acute myelogenous leukemia; See all synonyms [MedGen]
Identifiers:
MONDO: MONDO:0018874; MeSH: D015470; MedGen: C0023467; Orphanet: 519; OMIM: 601626; Human Phenotype Ontology: HP:0004808
Name:
Cutaneous mastocytosis
Synonyms:
MASTOCYTOSIS, MACULOPAPULAR CUTANEOUS; MASTOCYTOSIS, DIFFUSE CUTANEOUS
Identifiers:
MONDO: MONDO:0019023; MedGen: C1136033; OMIM: 154800; Human Phenotype Ontology: HP:0200151
Name:
Germ cell tumor of testis (TGCT)
Synonyms:
GERM CELL TUMOR, SOMATIC; Testicular germ cell tumor
Identifiers:
MONDO: MONDO:0010108; MedGen: C1336708; OMIM: 273300

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Assertion and evidence details

Help
Submission AccessionSubmitterReview Status
(Assertion method)		Clinical Significance
(Last evaluated)		OriginMethodCitations
SCV003920114Center for Genomics, Ann and Robert H. Lurie Children's Hospital of Chicago
criteria provided, single submitter

(ACMG Guidelines, 2015)		Uncertain significance
(Aug 4, 2022) 		germlineclinical testing

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

Help

Summary from all submissions

EthnicityOriginAffectedIndividualsFamiliesChromosomes testedNumber TestedFamily historyMethod
not providedgermlineunknownnot providednot providednot providednot providednot providedclinical testing

Citations

PubMed

Standards and guidelines for the interpretation of sequence variants: a joint consensus recommendation of the American College of Medical Genetics and Genomics and the Association for Molecular Pathology.

Richards S, Aziz N, Bale S, Bick D, Das S, Gastier-Foster J, Grody WW, Hegde M, Lyon E, Spector E, Voelkerding K, Rehm HL; ACMG Laboratory Quality Assurance Committee..

Genet Med. 2015 May;17(5):405-24. doi: 10.1038/gim.2015.30. Epub 2015 Mar 5.

PubMed [citation]
PMID:
25741868
PMCID:
PMC4544753

Details of each submission

From Center for Genomics, Ann and Robert H. Lurie Children's Hospital of Chicago, SCV003920114.1

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

Description

This variant has not been reported in the literature and is not present in large control databases. This variant is present in ClinVar (Variation ID:857642). Evolutionary conservation and computational predictive tools suggest that this variant may impact the protein. In summary, data on this variant is insufficient for disease classification. Therefore, the clinical significance of this variant is uncertain.

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

Last Updated: May 12, 2024