NM_000222.3(KIT):c.1407T>G (p.Phe469Leu) AND Hereditary cancer-predisposing syndrome

Germline classification:: Uncertain significance (1 submission)
Last evaluated:: Jun 28, 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:: RCV002388019.3

Allele description [Variation Report for NM_000222.3(KIT):c.1407T>G (p.Phe469Leu)]

NM_000222.3(KIT):c.1407T>G (p.Phe469Leu)

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.1407T>G (p.Phe469Leu)

HGVS:

NC_000004.12:g.54725917T>G
NG_007456.1:g.72923T>G
NM_000222.3:c.1407T>GMANE SELECT
NM_001093772.2:c.1407T>G
NM_001385284.1:c.1410T>G
NM_001385285.1:c.1407T>G
NM_001385286.1:c.1407T>G
NM_001385288.1:c.1410T>G
NM_001385290.1:c.1410T>G
NM_001385292.1:c.1410T>G
NP_000213.1:p.Phe469Leu
NP_000213.1:p.Phe469Leu
NP_001087241.1:p.Phe469Leu
NP_001372213.1:p.Phe470Leu
NP_001372214.1:p.Phe469Leu
NP_001372215.1:p.Phe469Leu
NP_001372217.1:p.Phe470Leu
NP_001372219.1:p.Phe470Leu
NP_001372221.1:p.Phe470Leu
LRG_307t1:c.1407T>G
LRG_307:g.72923T>G
LRG_307p1:p.Phe469Leu
NC_000004.11:g.55592083T>G
NM_000222.2:c.1407T>G

Protein change:

F469L

Links:

dbSNP: rs1553891415

NCBI 1000 Genomes Browser:

rs1553891415

Molecular consequence:

NM_000222.3:c.1407T>G - missense variant - [Sequence Ontology: SO:0001583]
NM_001093772.2:c.1407T>G - missense variant - [Sequence Ontology: SO:0001583]
NM_001385284.1:c.1410T>G - missense variant - [Sequence Ontology: SO:0001583]
NM_001385285.1:c.1407T>G - missense variant - [Sequence Ontology: SO:0001583]
NM_001385286.1:c.1407T>G - missense variant - [Sequence Ontology: SO:0001583]
NM_001385288.1:c.1410T>G - missense variant - [Sequence Ontology: SO:0001583]
NM_001385290.1:c.1410T>G - missense variant - [Sequence Ontology: SO:0001583]
NM_001385292.1:c.1410T>G - 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

Recent activity

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LOC122636064 [Vespula pensylvanica]
LOC122636064 [Vespula pensylvanica]
Gene ID:122636064

Gene
LOC127246502 [Andrographis paniculata]
LOC127246502 [Andrographis paniculata]
Gene ID:127246502

Gene

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Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV002699208	Ambry Genetics	criteria provided, single submitter (Ambry Variant Classification Scheme 2023)	Uncertain significance (Jun 28, 2022)	germline	clinical testing	Citation Link

Submission Accession

Submitter

Review Status
(Assertion method)

Clinical Significance
(Last evaluated)

Origin

Method

Citations

SCV002699208

Ambry Genetics

criteria provided, single submitter

(Ambry Variant Classification Scheme 2023)

Uncertain significance
(Jun 28, 2022)

germline

clinical testing

Citation Link

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

Details of each submission

From Ambry Genetics, SCV002699208.2

#	Ethnicity	Individuals	Chromosomes Tested	Family History	Method	Citations
1	not provided	not provided	not provided	not provided	clinical testing	not provided

Description

The p.F469L variant (also known as c.1407T>G), located in coding exon 9 of the KIT gene, results from a T to G substitution at nucleotide position 1407. The phenylalanine at codon 469 is replaced by leucine, an amino acid with highly similar properties. This amino acid position is well conserved in available vertebrate species. In addition, this alteration is predicted to be tolerated by in silico analysis. Since supporting evidence is limited at this time, the clinical significance of this alteration remains unclear.

#	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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