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VCX2 Gene

protein-coding GIFtS: 42
GCID: GC0XM008097

Variable Charge, X-Linked 2

See VCX2-related disease
at

MalaCards

(According to ¹HGNC, ²Entrez Gene,
³UniProtKB/Swiss-Prot, ⁴UniProtKB/TrEMBL, ⁵OMIM, ⁶GeneLoc, ⁷Ensembl, ⁸DME, ⁹miRBase, ¹⁰fRNAdb, ¹²H-InvDB, ¹³NCBI, ¹⁴NONCODE, and/or ¹⁵RNAdb)
About This Section

Aliases
Variable Charge, X-Linked 2¹ ²		VCX-2r² ³
VCX2R² ³ ⁵		VCX-B² ³
VCXB² ³ ⁵		Variable Charge X-Linked Protein 2²
Variable Charge Protein On X With Two Repeats² ³		Variably Charged X-B²
Variably Charged Protein X-B² ³

External Ids:	HGNC: 18158¹	Entrez Gene: 51480²	Ensembl: ENSG00000177504⁷	OMIM: 300532⁵	UniProtKB: Q9H322³

Export aliases for VCX2 gene to outside databases

Previous GC identifers: GC0XM007550 GC0XM007947 GC0XM005966

(According to Entrez Gene, GeneCards, Tocris Bioscience, Wikipedia's Gene Wiki, PharmGKB,
UniProtKB/Swiss-Prot, and/or UniProtKB/TrEMBL)
About This Section

Entrez Gene summary for VCX2 Gene:

This gene belongs to the VCX/Y gene family, which has multiple members on both X and Y chromosomes, and all are

expressed exclusively in male germ cells. The X-linked members are clustered on chromosome Xp22 and Y-linked

members are two identical copies of the gene within a palindromic region on Yq11. The family members share a high

degree of sequence identity, with the exception that a 30-bp unit is tandemly repeated in X-linked members but

occurs only once in Y-linked members. The VCX gene cluster is polymorphic in terms of copy number; different

individuals may have a different number of VCX genes. VCX/Y genes encode small and highly charged proteins of

unknown function. The presence of a putative bipartite nuclear localization signal suggests that VCX/Y members

are nuclear proteins. This gene contains 2 repeats of the 30-bp unit. (provided by RefSeq, Jul 2008)

GeneCards Summary for VCX2 Gene:

VCX2 (variable charge, X-linked 2) is a protein-coding gene. Diseases associated with VCX2 include x-linked ichthyosis. An important paralog of this gene is VCX3B.

UniProtKB/Swiss-Prot: VCX2_HUMAN, Q9H322

Function: May mediate a process in spermatogenesis or may play a role in sex ratio distortion

(According to GeneLoc and/or HGNC, and/or
Entrez Gene (NCBI build 37),
and/or miRBase,
Genomic Views according to UCSC (hg19) and Ensembl (release 75), Regulatory elements and Epigenetics data according to QIAGEN, and/or SwitchGear Genomics)
About This Section

RefSeq DNA sequence at NCBI GenBank:

NC_000023.10 NC_018934.2 NT_167197.2

Regulatory elements:

Regulatory transcription factor binding sites in the VCX2 gene promoter:
FOXF2 FOXO1a FOXO1
Other transcription factors

SwitchGear Promoter luciferase reporter plasmids (see all 2): VCX2 promoter sequence

Search Chromatin IP Primers for VCX2

Epigenetics:

DNA Methylation CpG Assay Predesigned for Pyrosequencing in human, mouse, rat VCX2

Genomic Location:
Genomic View: UCSC Golden Path with GeneCards custom track

Entrez Gene cytogenetic band: Xp22.32 Ensembl cytogenetic band: Xp22.31 HGNC cytogenetic band: Xp22.32

VCX2 Gene in genomic location: bands according to Ensembl, locations according to (and/or Entrez Gene and/or Ensembl if different)
VCX2 gene location

GeneLoc information about chromosome X GeneLoc Exon Structure

GeneLoc location for GC0XM008097: view genomic region (about GC identifiers)

Start:	8,137,985 bp from pter	End:	8,139,308 bp from pter
Size:	1,324 bases	Orientation:	minus strand

(According to ¹UniProtKB, HORDE, ²neXtProt, Ensembl, and/or Reactome, Modification sites according to PhosphoSitePlus, Specific Peptides from DME, RefSeq according to NCBI, PDB rendering according to OCA and/or Proteopedia, Recombinant Proteins from EMD Millipore, R&D Systems, GenScript, Enzo Life Sciences, OriGene, Novus Biologicals, Sino Biological, ProSpec, Cloud-Clone Corp., eBioscience, antibodies-online, and/or GeneTex,
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About This Section

UniProtKB/Swiss-Prot: VCX2_HUMAN, Q9H322 (See protein sequence)

Recommended Name: Variable charge X-linked protein 2

Size: 139 amino acids; 14661 Da

Secondary accessions: A3KPB6 Q4V9T2 Q9P0H5

Explore the universe of human proteins at neXtProt for VCX2: NX_Q9H322

Explore proteomics data for VCX2 at MOPED

Post-translational modifications:

Modification sites at neXtProt

Modification sites at PhosphoSitePlus

See VCX2 Protein Expression from SPIRE MOPED, PaxDB, and MaxQB

REFSEQ proteins: NP_057462.2

ENSEMBL proteins:

ENSP00000321309

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(According to HGNC, IUPHAR, InterPro, ProtoNet, UniProtKB, and/or BLOCKS, Sets of similar genes according to GenesLikeMe)
About This Section

1 InterPro protein domain:

IPR026653 VCX/VCY1

Graphical View of Domain Structure for InterPro Entry Q9H322

ProtoNet protein and cluster: Q9H322

UniProtKB/Swiss-Prot: VCX2_HUMAN, Q9H322

Similarity: Belongs to the VCX/VCY family

Find genes that share domains with VCX2 About GenesLikeMe

(According to ¹UniProtKB, Genatlas, LifeMap Discovery™, IUBMB, and/or ²DME, Human phenotypes from GenomeRNAi, Animal models from MGI Mar 06 2013, genOway,
transcription factor targeting from QIAGEN and/or HOMER, miRNA Gene Targets from miRTarBase, shRNA from OriGene, siRNAs from OriGene, QIAGEN, microRNA from QIAGEN, SwitchGear Genomics, Gene Editing from DNA2.0, Clones from OriGene, GenScript, Sino Biological, DNA2.0, Vector BioLabs and/or Addgene, Cell Lines from GenScript, ESI BIO, In Situ Hybridization Assays from Advanced Cell Diagnostics, Flow cytometry from eBioscience, Ontologies according to Gene Ontology Consortium 01 Apr 2014 via Entrez Gene, Sets of similar genes according to GenesLikeMe)
About This Section

Molecular Function:

UniProtKB/Swiss-Prot Summary: VCX2_HUMAN, Q9H322

Function: May mediate a process in spermatogenesis or may play a role in sex ratio distortion

Gene Ontology (GO): 1 molecular function term: About this table

GO ID	Qualified GO term	Evidence	PubMed IDs
GO:0003674	molecular_function	ND	--

Find genes that share ontologies with VCX2 About GenesLikeMe

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(According to UniProtKB, COMPARTMENTS Subcellular localization database, Ontologies according to Gene Ontology Consortium 01 Apr 2014 via Entrez Gene, Sets of similar genes according to GenesLikeMe)
About This Section

Subcellular locations from COMPARTMENTS:

Compartment	Confidence
nucleus	3
cytoskeleton	1
cytosol	1
extracellular	1
mitochondrion	1

About this image

Gene Ontology (GO): 1 cellular component term: About this table

GO ID	Qualified GO term	Evidence	PubMed IDs
GO:0005575	cellular_component	ND	--

Find genes that share ontologies with VCX2 About GenesLikeMe

(SuperPaths according to PathCards, Pathways according to R&D Systems, Cell Signaling Technology, KEGG, PharmGKB, BioSystems, Sino Biological, Reactome, Tocris Bioscience, GeneGo (Thomson Reuters), QIAGEN, and/or UniProtKB, Sets of similar genes according to GenesLikeMe, Interaction Networks according to QIAGEN, and/or STRING, Interactions according to ¹UniProtKB, ²MINT, ³I2D, and/or ⁴STRING, with links to IntAct and Ensembl, Ontologies according to Gene Ontology Consortium 01 Apr 2014 via Entrez Gene, Sets of similar genes according to GenesLikeMe)
About This Section

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Interactions:

Search GeneGlobe Interaction Network for VCX2

Gene Ontology (GO): 1 biological process term: About this table

GO ID	Qualified GO term	Evidence	PubMed IDs
GO:0008150	biological_process	ND	--

Find genes that share ontologies with VCX2 About GenesLikeMe

(Chemical Compounds according to UniProtKB, Enzo Life Sciences, EMD Millipore, Tocris Bioscience, ApexBio, HMDB, BitterDB, and/or Novoseek, Ligands according to IUPHAR, and Drugs according to DrugBank, Enzo Life Sciences, and/or PharmGKB, Sets of similar genes according to GenesLikeMe)
About This Section

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(Secondary structures according to fRNAdb,
GenBank/EMBL/DDBJ Accessions according to
Unigene (Build 236 Homo sapiens; Apr 25 2013) or GenBank,
RefSeq according to Entrez Gene,
DOTS (version 10), and/or AceView, transcript ids from Ensembl with links to UCSC,
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About This Section

REFSEQ mRNAs for VCX2 gene:

NM_016378.2

Unigene Cluster for VCX2:

Variable charge, X-linked 2

Hs.279737 [show with all ESTs]

Unigene Representative Sequence: AF167079

1 Ensembl transcript including schematic representation, and UCSC links where relevant:

ENST00000317103(uc004csb.3)

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Additional mRNA sequence:

AF159127.1 AF167079.1 BC096715.1 BC098101.1 BC098113.1 BC098163.1 BC104153.2 BC104167.1

BC104168.1 BC134350.1

2 DOTS entries:

DT.313845 DT.313846

11 AceView cDNA sequences:

AF167081 AA565702 AF159129 NM_013452 BE504628 AA206042 BF885187 AU099954

BV184446 AI824821 AA897187

GeneLoc Exon Structure

(RNA expression data according to H-InvDB, NONCODE, miRBase, and RNAdb, Expression images according to data from BioGPS, Illumina Human BodyMap, and CGAP SAGE, Sets of similar genes according to GenesLikeMe, in vivo and in vitro expression data from LifeMap Discovery™, Protein expression images according to data from SPIRE ¹MOPED, ²PaxDb, and ³MaxQB, plus additional links to SOURCE, and/or BioGPS, and/or UniProtKB,
PCR Arrays from QIAGEN, Primers from OriGene, and/or QIAGEN, In Situ Hybridization Assays from Advanced Cell Diagnostics)
About This Section

VCX2 expression in normal human tissues (normalized intensities)
See probesets specificity/sensitivity at GeneAnnot
About this imageBioGPS <intensity>^2/3
CGAP TAG: --

About this image

VCX2 Protein expression data from MOPED¹, PaxDb² and MaxQB³:

About this image

VCX2 Protein Expression

SOURCE GeneReport for Unigene cluster: Hs.279737

UniProtKB/Swiss-Prot: VCX2_HUMAN, Q9H322

Tissue specificity: Expressed exclusively in testis

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(Orthologs according to ^1,2HomoloGene (²older version, for species not in ¹newer version), ³euGenes, ⁴SGD , ⁵MGI Mar 06 2013, with possible further links to Flybase and/or WormBase, and/or ⁶Ensembl pan taxonomic compara , Gene Trees according to Ensembl and TreeFam)
About This Section

This gene was present in the common ancestor of human and chimp.

Orthologs for VCX2 gene from 1 species (see representative species ) About this table

Organism	Taxonomic classification	Gene	Description	Human Similarity	Orthology Type	Details
chimpanzee (Pan troglodytes)	Mammalia	LOC742075¹	variable charge X-linked protein 3B-like	95.66(n) 91.87(a)		742075 XM_003318999.2 XP_003319047.2

ENSEMBL Gene Tree for VCX2 (if available)
TreeFam Gene Tree for VCX2 (if available)

(Paralogs according to ¹HomoloGene,
²Ensembl, and ³SIMAP, Pseudogenes according to ⁴Pseudogene.org Build 68,Sets of similar genes according to GenesLikeMe)
About This Section

Paralogs for VCX2 gene

VCY¹ ² VCY1B¹ ² VCX3B² VCX² VCX3A² ENSG00000268080²

5 SIMAP similar genes for VCX2 using alignment to 4 protein entries: VCX2_HUMAN (see all proteins):

VCY VCY1B VCX3A VCX VCX3B

Find genes that share paralogs with VCX2 About GenesLikeMe

(SNPs/Variants according to the ¹NCBI SNP Database, ²Ensembl, ³PupaSUITE, ⁴UniProtKB, and DNA2.0, Linkage Disequilibrium by HapMap, Structural Variations(CNVs/InDels/Inversions) from the Database of Genomic Variants, Mutations from the Human Gene Mutation Database (HGMD), the Human Cytochrome P450 Allele Nomenclature Database, and the Locus Specific Mutation Databases (LSDB), Blood group antigen gene mutations by BGMUT, Resequencing Primers, Cancer Mutation PCR Arrays and Assays, and Copy Number PCR Arrays from QIAGEN)
About This Section

SNP ID	Valid	Clinical significance	Chr X pos	Sequence	#	AA Chg	Type	More	#	Allele freq	Pop	Total sample	More
Genomic Data					Transcription Related Data				Allele Frequencies
				--	--	--		--	--
rs186123665^1,2	C	--	8137917(+)	`CCCTCA/CCCACA`	1	--	ds500¹		0	--	--	--	--
rs77398535^1,2	C	--	8137936(+)	`CTTCCT/CCCCTC`	1	--	ds500¹		1		NA	2
rs190542322^1,2	C	--	8137972(+)	`AACACA/GGAGTC`	1	--	ds500¹		0	--	--	--	--
rs182724706^1,2	C	--	8138030(+)	`AAGCAC/TCCCGC`	1	--	ut3¹		0	--	--	--	--
rs201568637^1,2	C	--	8138039(+)	`GCTGGC/TGAGAT`	1	--	ut3¹		0	--	--	--	--
rs200935795^1,2	C	--	8138058(+)	`TCTGGA/CGGCTG`	1	--	ut3¹		0	--	--	--	--
rs145708656^1,2	C,F	--	8138078(+)	`TTAGTC/TGGTGC`	2	N D	mis¹		1		NA	4540
rs1058239^1,2,,4	C,F,H	--	8138080(-)	`GAGCAG/CCGACT`	2	/T /S	mis¹ ese³		11		MN NS EA NA WA CSA	5139
rs77780768^1,2	C,F	--	8138088(-)	`GTCTCC/G/TGAGAG`	3	S	syn¹		2		CSA NA	4543
rs148114540^1,2	C	--	8138093(+)	`GGAGAC/TAGGGG`	2	I V	mis¹		1		NA	4542

HapMap Linkage Disequilibrium report for VCX2 (8137985 - 8139308 bp)

Structural Variations
Database of Genomic Variants (DGV) 8 variations for VCX2: About this table

Variant ID	Type	Subtype	PubMed ID
nsv6788	CNV	Insertion	18451855
nsv508752	CNV	Insertion	20534489
esv2752335	CNV	Gain	17911159
nsv528203	CNV	Gain	19592680
nsv524164	CNV	Gain	19592680
nsv470340	CNV	Gain	18288195
dgv499n21	CNV	Gain	19592680
nsv511081	CNV	Complex	20534489

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(in which this Gene is Involved, According to MalaCards, OMIM, UniProtKB, the University of Copenhagen DISEASES database, Genatlas, GeneTests, GAD, HuGE Navigator, and/or TGDB, Sets of similar genes according to GenesLikeMe)
About This Section

OMIM gene information: 300532 OMIM disorders: --

1 disease for VCX2:
About MalaCards

x-linked ichthyosis

2 inferred disease relationships from the University of Copenhagen DISEASES database for VCX2:

X-linked ichthyosis Kallmann syndrome

Find genes that share disorders with VCX2 About GenesLikeMe

Genetic Association Database (GAD): VCX2

Export disorders for VCX2 gene to outside databases

(in PubMed. Associations of this gene to articles via ¹Entrez Gene, ²UniProtKB/Swiss-Prot, ³HGNC, ⁴GAD, ⁵PharmGKB, ⁶HMDB, ⁷DrugBank, ⁸UniProtKB/TrEMBL, ⁹ Novoseek, and/or ¹⁰fRNAdb)
About This Section

PubMed articles for VCX2 gene, integrated from 10 sources (see all 11):
(articles sorted by number of sources associating them with VCX2)

A human sex-chromosomal gene family expressed in male germ cells and encoding variably charged proteins. (PubMed id 10607842)^{1, 2, 3} Lahn B.T. and Page D.C. (Hum. Mol. Genet. 2000)
The status, quality, and expansion of the NIH full-length cDNA project: the Mammalian Gene Collection (MGC). (PubMed id 15489334)^{1, 2} Gerhard D.S.... Malek J. (Genome Res. 2004)
A member of a gene family on Xp22.3, VCX-A, is deleted in patients with X-linked nonspecific mental retardation. (PubMed id 10903929)^{1, 2} Fukami M.... Rappold G.A. (Am. J. Hum. Genet. 2000)
A genome-wide study of common SNPs and CNVs in cognitive performance in the CANTAB. (PubMed id 19734545)⁴ Need A.C....Goldstein D.B. (Hum. Mol. Genet. 2009)
The DNA sequence of the human X chromosome. (PubMed id 15772651)² Ross M.T.... Bentley D.R. (Nature 2005)
Generation and initial analysis of more than 15,000 full-length human and mouse cDNA sequences. (PubMed id 12477932)¹ Strausberg R.L....Marra M.A. (Proc. Natl. Acad. Sci. U.S.A. 2002)
Identification and characterization of the potential promoter regions of 1031 kinds of human genes. (PubMed id 11337467)¹ Suzuki Y....Sugano S. (Genome Res. 2001)
Analysis of the VCX3A, VCX2 and VCX3B genes shows that VCX3A gene deletion is not sufficient to result in mental retardation in X-linked ichthyosis. (PubMed id 18076704)⁹ Cuevas-Covarrubias S.A. and GonzA!lez-Huerta L.M. (Br. J. Dermatol. 2008)
Sushi repeat protein X-linked 2, a novel mediator of angiogenesis. (PubMed id 19667118)⁹ Miljkovic-Licina M....Imhof B.A. (FASEB J. 2009)
Deletion of VCX-A due to NAHR plays a major role in the occurrence of mental retardation in patients with X-linked ichthyosis. (PubMed id 15888481)⁹ Van Esch H....Froyen G. (Hum. Mol. Genet. 2005)

(in PubMed, OMIM, and NCBI Bookshelf)
About This Section

		AND	OR
Aliases
Free Text

Query String		PubMed OMIM NCBI Bookshelf
	(Note: In FireFox, select the above section and copy using Ctrl-C)

(According to Entrez Gene, HGNC, AceView, euGenes, Ensembl, miRBase, ECgene, Kegg, and/or H-InvDB)
About This Section

Entrez Gene: 51480	HGNC: 18158	AceView: VCX	Ensembl:ENSG00000177504	euGenes: HUgn51480
ECgene: VCX2	H-InvDB: VCX2

(According to HUGE)
About This Section

(According to PharmGKB, ATLAS, HORDE, IMGT, LEIDEN, UniProtKB/Swiss-Prot, UniProtKB/TrEMBL, and/or others, e.g. Wikipedia and GeneReviews, via UniProtKB/Swiss-Prot)
About This Section

Name	Description
PharmGKB entry for VCX2	Pharmacogenomics, SNPs, Pathways

Intellectual Property for VCX2 gene
(Patent information from GeneIP, Licensable technologies from WIS Yeda, Salk, Tufts, IP news from LifeMap Sciences, Inc.)

About This Section

Patent Information for VCX2 gene:
Search GeneIP for patents involving VCX2

GeneCards and IP:
Japan Patent Office Licenses GeneCards European Patent Office Licenses GeneCards Improving the IP Search

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VCX2 Gene

Variable Charge, X-Linked 2

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VCX2 Human Recombinant Protein Products:

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Export list of displayed genes

VCX2 Gene

Variable Charge, X-Linked 2

Aliasesfor VCX2 gene

Summariesfor VCX2 gene

Genomic Viewsfor VCX2 gene

Proteinsfor VCX2 gene

VCX2 Human Recombinant Protein Products:

VCX2 Antibody Products:

VCX2 Assay Products:

Domains /Familiesfor VCX2 gene

Functionfor VCX2 gene

Localizationfor VCX2 gene

Pathways & Interactionsfor VCX2 gene

Drugs & Compoundsfor VCX2 gene

Transcriptsfor VCX2 gene

Expression for VCX2 gene

Orthologsfor VCX2 gene

Paralogsfor VCX2 gene

Genomic Variantsfor VCX2 gene

Disorders / Diseasesfor VCX2 gene

Publicationsfor VCX2 gene

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Genome Databases showing VCX2 gene

Other Databases showing VCX2 gene

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Aliases
for VCX2 gene

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for VCX2 gene

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for VCX2 gene

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for VCX2 gene

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Families
for VCX2 gene

Function
for VCX2 gene

Localization
for VCX2 gene

Pathways & Interactions
for VCX2 gene

Drugs & Compounds
for VCX2 gene

Transcripts
for VCX2 gene

Expression
for VCX2 gene

Orthologs
for VCX2 gene

Paralogs
for VCX2 gene

Genomic Variants
for VCX2 gene

Disorders / Diseases
for VCX2 gene

Publications
for VCX2 gene

Intellectual Property
for VCX2 gene

Products
for VCX2 gene