chr4:55593613:T>A Detail (hg19) (KIT)

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Summary
Information
Links
Disease area statistics
MGeND
ClinVar
CIViC
DisGeNET
Annotation
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Information

Genome

Assembly	Position
hg19	chr4:55,593,613-55,593,613
hg38	chr4:54,727,447-54,727,447 View the variant detail on this assembly version.

HGVS

KIT

Type	Transcript	Protein
RefSeq	NM_000222.2:c.1679T>A	NP_000213.1:p.Val560Asp
	NM_001093772.1:c.1670T>A	NP_001087241.1:p.Val557Asp
Ensemble	ENST00000288135.6:c.1679T>A	ENST00000288135.6:p.Val560Asp
	ENST00000412167.7:c.1670T>A	ENST00000412167.7:p.Val557Asp
	ENST00000686011.1:c.1667T>A	ENST00000686011.1:p.Val556Asp
	ENST00000687109.1:c.1682T>A	ENST00000687109.1:p.Val561Asp
	ENST00000687246.1:c.1667T>A	ENST00000687246.1:p.Val556Asp
	ENST00000687295.1:c.1667T>A	ENST00000687295.1:p.Val556Asp
	ENST00000689832.1:c.1682T>A	ENST00000689832.1:p.Val561Asp
	ENST00000689994.1:c.1169T>A	ENST00000689994.1:p.Val390Asp
	ENST00000690543.1:c.1670T>A	ENST00000690543.1:p.Val557Asp
	ENST00000692783.1:c.1679T>A	ENST00000692783.1:p.Val560Asp

Summary

MGeND

Clinical significance	not provided
Variant entry	2
GWAS entry
Disease area statistics	Show details

Frequency

[No Data.]

Prediction

ClinVar

Clinical Significance	Likely pathogenic
Review star
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Links

KIT

Type	Database	ID	Link
Gene	MIM	164920	OMIM
	HGNC	6342	HGNC
	Ensembl	ENSG00000157404	Ensembl
	NCBI		NCBI
	Gene Cards		Gene Cards
	OncoKB		OncoKB

Type	Database	ID	Link
Variant	TogoVar
	COSMIC	COSM1257	COSMIC
	MONDO

Disease area statistics

MGeND

Clinical significance	Last evaluated	Condition	Origin	Submission ID	Submitter	Institute	Citation	Comment	Image
not provided		other	somatic	MGS000039 (TMGS000092)	Hitoshi Nakagama	National Cancer Center Japan	29659903
not provided		small intestine, unspecified	not provided	MGS000042 (TMGS000093)	Hitoshi Nakagama	National Cancer Center Japan

ClinVar

Clinical significance	Last evaluated	Review status	Condition	Origin	Links
Pathogenic	2015-07-14	no assertion criteria provided	melanoma	somatic	Detail
Likely pathogenic	2016-05-13	no assertion criteria provided	gastrointestinal stromal tumor	somatic	Detail
Likely pathogenic	2024-02-23	criteria provided, single submitter	Hereditary cancer-predisposing syndrome	germline	Detail

CIViC

Disease	Drug	EL	ET	ED	CS	VO	TR	Pubmed	Links
cancer	Sunitinib	D	Predictive	Does Not Support	Resistance	Somatic	2	18955458	Detail
gastrointestinal stromal tumor	Sunitinib	C	Predictive	Supports	Resistance	Somatic	3	18955458	Detail
gastrointestinal stromal tumor	Sunitinib,Regorafenib,Ponatinib,Imatinib	D	Predictive	Supports	Sensitivity/Response	Somatic	3	25239608	Detail
cancer	Imatinib Mesylate	D	Predictive	Supports	Sensitivity/Response	Somatic	2	18955458	Detail

DisGeNET

Score	Disease name	Description	Source	Pubmed	Links
0.760	Gastrointestinal Stromal Tumors	Previously, we found 2 types of gain-of-function mutation of the PDGFRA gene, Va...	BeFree	15221957	Detail
0.616	Gastrointestinal Stromal Tumors	Previously, we found 2 types of gain-of-function mutation of the PDGFRA gene, Va...	BeFree	15221957	Detail
0.019	urticaria pigmentosa	Distinct signalling pathways for mutated KIT(V560G) and KIT(D816V) in mastocytos...	BeFree	23777495	Detail
0.118	mastocytosis	Distinct signalling pathways for mutated KIT(V560G) and KIT(D816V) in mastocytos...	BeFree	23777495	Detail
0.126	Leukemia, Mast-Cell	Ponatinib was found to inhibit the kinase activity of KIT G560V and KIT D816V in...	BeFree	23539538	Detail
0.019	leukemia	Two subclones of the HMC1 mast leukaemia cell line were used; both express an id...	BeFree	19804454	Detail
0.760	Gastrointestinal Stromal Tumors	We expressed c-KIT cDNA constructs encoding the V654A substitution alone and in ...	BeFree	17363509	Detail

Annotation

Annotations

Descrption	Source	Links
In an in vitro study, Chinese hamster ovary cells expressing KIT V560D demonstrated comparable sensi...	CIViC Evidence	Detail
Patient 72 from a larger cohort of genotyped patients (n= 78) with imatinib resistant or intolerant ...	CIViC Evidence	Detail
In an in vitro study, an IL3 independent Ba/F3 cell line expressing KIT V560D primary activating mut...	CIViC Evidence	Detail
In an in vitro study, Chinese hamster ovary cells expressing KIT V560D mutation demonstrated sensiti...	CIViC Evidence	Detail
NM_000222.3(KIT):c.1679T>A (p.Val560Asp) AND Melanoma	ClinVar	Detail
NM_000222.3(KIT):c.1679T>A (p.Val560Asp) AND Gastrointestinal stromal tumor	ClinVar	Detail
NM_000222.3(KIT):c.1679T>A (p.Val560Asp) AND Hereditary cancer-predisposing syndrome	ClinVar	Detail
Previously, we found 2 types of gain-of-function mutation of the PDGFRA gene, Val561 to Asp and Asp8...	DisGeNET	Detail
Previously, we found 2 types of gain-of-function mutation of the PDGFRA gene, Val561 to Asp and Asp8...	DisGeNET	Detail
Distinct signalling pathways for mutated KIT(V560G) and KIT(D816V) in mastocytosis.	DisGeNET	Detail
Distinct signalling pathways for mutated KIT(V560G) and KIT(D816V) in mastocytosis.	DisGeNET	Detail
Ponatinib was found to inhibit the kinase activity of KIT G560V and KIT D816V in the human mast cell...	DisGeNET	Detail
Two subclones of the HMC1 mast leukaemia cell line were used; both express an identical KIT allele-s...	DisGeNET	Detail
We expressed c-KIT cDNA constructs encoding the V654A substitution alone and in combination with a t...	DisGeNET	Detail

Overlapped Transcript Coordinates

Gene	Transcript ID	Exon Number	Chromosome	Start	Stop	Type	Amino Mutation	Transcript Position	Links

Overlapped Transcript

Gene	Transcript ID	Chromosome	Start	Stop	Links

Gene: -
dbSNP: rs121913521 dbSNP
Genome: hg19
Position: chr4:55,593,613-55,593,613
Variant Type: snv
Reference Allele: T
Alternative Allele: A
Variant (CIViC) (CIViC Variant): V560D
Transcript 1 (CIViC Variant): ENST00000288135.5
Variant URL (CIViC Variant): https://civic.genome.wustl.edu/links/variants/971

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