chr2:136872498:G>A Detail (hg19) (CXCR4)

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

Genome

Assembly	Position
hg19	chr2:136,872,498-136,872,498
hg38	chr2:136,114,928-136,114,928 View the variant detail on this assembly version.

HGVS

CXCR4

Type	Transcript	Protein
RefSeq	NM_003467.2:c.1000C>T	NP_003458.1:p.Arg334Ter
	NM_001008540.1:c.1012C>T	NP_001008540.1:p.Arg338Ter
Ensemble	ENST00000241393.4:c.1000C>T	ENST00000241393.4:p.Arg334Ter
	ENST00000409817.1:c.1012C>T	ENST00000409817.1:p.Arg338Ter
	ENST00000466288.1:c.955C>T	ENST00000466288.1:p.Arg319Ter
	ENST00000696136.1:c.988C>T	ENST00000696136.1:p.Arg330Ter
	ENST00000696137.1:c.955C>T	ENST00000696137.1:p.Arg319Ter
	ENST00000696152.1:c.955C>T	ENST00000696152.1:p.Arg319Ter
	ENST00000696228.1:c.988C>T	ENST00000696228.1:p.Arg330Ter

Summary

MGeND

Clinical significance	Pathogenic
Variant entry	1
GWAS entry
Disease area statistics	Show details

Frequency

[No Data.]

Prediction

ClinVar

Clinical Significance	Pathogenic
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Links

CXCR4

Type	Database	ID	Link
Gene	MIM	162643	OMIM
	HGNC	2561	HGNC
	Ensembl	ENSG00000121966	Ensembl
	NCBI		NCBI
	Gene Cards		Gene Cards
	OncoKB		OncoKB

Type	Database	ID	Link
Variant	TogoVar
	COSMIC	COSM4848797	COSMIC
	MONDO

Disease area statistics

MGeND

Clinical significance	Last evaluated	Condition	Origin	Submission ID	Submitter	Institute	Citation	Comment	Image
Pathogenic		other	germline	MGS000001 (TMGS000179)	Kenjiro Kosaki	Keio University

ClinVar

Clinical significance	Last evaluated	Review status	Condition	Origin	Links
Pathogenic	2023-11-07	criteria provided, multiple submitters, no conflicts	Warts, hypogammaglobulinemia, infections, and myelokathexis	germline	Detail
Pathogenic	2022-04-05	criteria provided, multiple submitters, no conflicts	not provided	germline	Detail
Pathogenic	2022-03-22	criteria provided, multiple submitters, no conflicts	WHIM syndrome 1	germline unknown	Detail

CIViC

[No Data.]

DisGeNET

Score	Disease name	Description	Source	Pubmed	Links
0.002	WHIM syndrome	CXCL12 stimulation triggered CXCR4(R334X) internalization in FLNA-deficient M2 c...	BeFree	25355818	Detail
0.450	WHIM syndrome	Accordingly, like CXCR4(R334X), the most common truncation mutation in WHIM synd...	BeFree	22596258	Detail
0.450	WHIM syndrome	A nonsense mutation (C-->T) truncating the CXC chemokine receptor 4 (CXCR4) C...	BeFree	19476565	Detail
0.450	WHIM syndrome	NA	CLINVAR		Detail
0.450	WHIM syndrome	AMD3100 is a potent antagonist at CXCR4(R334X) , a hyperfunctional mutant chemok...	BeFree	21070597	Detail

Annotation

Annotations

Descrption	Source	Links
NM_003467.3(CXCR4):c.1000C>T (p.Arg334Ter) AND Warts, hypogammaglobulinemia, infections, and myeloka...	ClinVar	Detail
NM_003467.3(CXCR4):c.1000C>T (p.Arg334Ter) AND not provided	ClinVar	Detail
NM_003467.3(CXCR4):c.1000C>T (p.Arg334Ter) AND WHIM syndrome 1	ClinVar	Detail
CXCL12 stimulation triggered CXCR4(R334X) internalization in FLNA-deficient M2 cells but not in the ...	DisGeNET	Detail
Accordingly, like CXCR4(R334X), the most common truncation mutation in WHIM syndrome, CXCR4(E343K) m...	DisGeNET	Detail
A nonsense mutation (C-->T) truncating the CXC chemokine receptor 4 (CXCR4) C-terminal cytoplasmi...	DisGeNET	Detail
NA	DisGeNET	Detail
AMD3100 is a potent antagonist at CXCR4(R334X) , a hyperfunctional mutant chemokine receptor and cau...	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: rs104893624 dbSNP
Genome: hg19
Position: chr2:136,872,498-136,872,498
Variant Type: snv
Reference Allele: G
Alternative Allele: A

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