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NM_000222.3(KIT):c.1951A>T (p.Met651Leu) AND Hereditary cancer-predisposing syndrome

Germline classification:
Benign (1 submission)
Last evaluated:
Feb 14, 2023
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:
RCV002418399.4

Allele description [Variation Report for NM_000222.3(KIT):c.1951A>T (p.Met651Leu)]

NM_000222.3(KIT):c.1951A>T (p.Met651Leu)

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.1951A>T (p.Met651Leu)
HGVS:
  • NC_000004.12:g.54728082A>T
  • NG_007456.1:g.75088A>T
  • NM_000222.3:c.1951A>TMANE SELECT
  • NM_001093772.2:c.1939A>T
  • NM_001385284.1:c.1954A>T
  • NM_001385285.1:c.1951A>T
  • NM_001385286.1:c.1939A>T
  • NM_001385288.1:c.1942A>T
  • NM_001385290.1:c.1954A>T
  • NM_001385292.1:c.1942A>T
  • NP_000213.1:p.Met651Leu
  • NP_000213.1:p.Met651Leu
  • NP_001087241.1:p.Met647Leu
  • NP_001372213.1:p.Met652Leu
  • NP_001372214.1:p.Met651Leu
  • NP_001372215.1:p.Met647Leu
  • NP_001372217.1:p.Met648Leu
  • NP_001372219.1:p.Met652Leu
  • NP_001372221.1:p.Met648Leu
  • LRG_307t1:c.1951A>T
  • LRG_307:g.75088A>T
  • LRG_307p1:p.Met651Leu
  • NC_000004.11:g.55594248A>T
  • NM_000222.2:c.1951A>T
Protein change:
M647L
Links:
dbSNP: rs534209826
NCBI 1000 Genomes Browser:
rs534209826
Molecular consequence:
  • NM_000222.3:c.1951A>T - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001093772.2:c.1939A>T - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001385284.1:c.1954A>T - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001385285.1:c.1951A>T - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001385286.1:c.1939A>T - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001385288.1:c.1942A>T - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001385290.1:c.1954A>T - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001385292.1:c.1942A>T - missense variant - [Sequence Ontology: SO:0001583]

Condition(s)

Name:
Hereditary cancer-predisposing syndrome
Synonyms:
Neoplastic Syndromes, Hereditary; Tumor predisposition; Cancer predisposition; See all synonyms [MedGen]
Identifiers:
MONDO: MONDO:0015356; MeSH: D009386; MedGen: C0027672

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Assertion and evidence details

Help
Submission AccessionSubmitterReview Status
(Assertion method)		Clinical Significance
(Last evaluated)		OriginMethodCitations
SCV002718798Ambry Genetics
criteria provided, single submitter

(Ambry Variant Classification Scheme 2023)		Benign
(Feb 14, 2023) 		germlineclinical testing

PubMed (2)
[See all records that cite these PMIDs]

Citation Link

Help

Summary from all submissions

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

Citations

PubMed

Rare germline variant contributions to myeloid malignancy susceptibility.

Li ST, Wang J, Wei R, Shi R, Adema V, Nagata Y, Kerr CM, Kuzmanovic T, Przychodzen B, Sole F, Maciejewski JP, LaFramboise T.

Leukemia. 2020 Jun;34(6):1675-1678. doi: 10.1038/s41375-019-0701-8. Epub 2020 Jan 7. No abstract available.

PubMed [citation]
PMID:
31911633
PMCID:
PMC8908771

Comparison of BRCA versus non-BRCA germline mutations and associated somatic mutation profiles in patients with unselected breast cancer.

Chen B, Zhang G, Li X, Ren C, Wang Y, Li K, Mok H, Cao L, Wen L, Jia M, Li C, Guo L, Wei G, Lin J, Li Y, Zhang Y, Han-Zhang H, Liu J, Lizaso A, Liao N.

Aging (Albany NY). 2020 Feb 24;12(4):3140-3155. doi: 10.18632/aging.102783. Epub 2020 Feb 24.

PubMed [citation]
PMID:
32091409
PMCID:
PMC7066887

Details of each submission

From Ambry Genetics, SCV002718798.3

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1not providednot providednot providednot providedclinical testing PubMed (2)

Description

This alteration is classified as benign based on a combination of the following: seen in unaffected individuals, population frequency, intact protein function, lack of segregation with disease, co-occurrence, RNA analysis, in silico models, amino acid conservation, lack of disease association in case-control studies, and/or the mechanism of disease or impacted region is inconsistent with a known cause of pathogenicity.

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

Last Updated: Sep 1, 2024