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    VCX variable charge X-linked [ Homo sapiens (human) ]

    Gene ID: 26609, updated on 2-Nov-2024

    Summary

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    Official Symbol
    VCXprovided by HGNC
    Official Full Name
    variable charge X-linkedprovided by HGNC
    Primary source
    HGNC:HGNC:12667
    See related
    Ensembl:ENSG00000182583 MIM:300229; AllianceGenome:HGNC:12667
    Gene type
    protein coding
    RefSeq status
    REVIEWED
    Organism
    Homo sapiens
    Lineage
    Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Primates; Haplorrhini; Catarrhini; Hominidae; Homo
    Also known as
    VCX1; VCXB1; VCX-B1; VCX10R; VCX-10r
    Summary
    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 10 repeats of the 30-bp unit. [provided by RefSeq, Jul 2008]
    Expression
    Restricted expression toward testis (RPKM 23.7) See more
    Orthologs
    all
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    Genomic context

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    See VCX in Genome Data Viewer
    Location:
    Xp22.31
    Exon count:
    3
    Annotation release Status Assembly Chr Location
    RS_2024_08 current GRCh38.p14 (GCF_000001405.40) X NC_000023.11 (7842262..7844143)
    RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) X NC_060947.1 (7395939..7397760)
    RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) X NC_000023.10 (7810303..7812184)

    Chromosome X - NC_000023.11Genomic Context describing neighboring genes Neighboring gene pseudouridine 5'-phosphatase Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 20649 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 29389 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 29390 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 29391 Neighboring gene OCT4-NANOG hESC enhancer GRCh37_chrX:7154725-7155349 Neighboring gene Sharpr-MPRA regulatory region 5189 Neighboring gene microRNA 4767 Neighboring gene NANOG hESC enhancer GRCh37_chrX:7208639-7209140 Neighboring gene steroid sulfatase Neighboring gene MED14-independent group 3 enhancer GRCh37_chrX:7290864-7292063 Neighboring gene NANOG hESC enhancer GRCh37_chrX:7366971-7367514 Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chrX:7510918-7511520 Neighboring gene uncharacterized LOC124905241 Neighboring gene OCT4-NANOG-H3K27ac hESC enhancer GRCh37_chrX:7682068-7682794 Neighboring gene OCT4-NANOG-H3K27ac hESC enhancer GRCh37_chrX:7682795-7683521 Neighboring gene BRD4-independent group 4 enhancer GRCh37_chrX:7889540-7890739 Neighboring gene Sharpr-MPRA regulatory region 9499 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 29393 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 29394 Neighboring gene uncharacterized LOC107985675 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 29395 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 29396 Neighboring gene Sharpr-MPRA regulatory region 2843 Neighboring gene patatin like phospholipase domain containing 4 Neighboring gene OCT4-NANOG hESC enhancer GRCh37_chrX:8073020-8073627 Neighboring gene microRNA 651

    Genomic regions, transcripts, and products

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    Go to nucleotide: Graphics FASTA GenBank

    Expression

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    • Project title: HPA RNA-seq normal tissues HPA RNA-seq normal tissues
    • Description: RNA-seq was performed of tissue samples from 95 human individuals representing 27 different tissues in order to determine tissue-specificity of all protein-coding genes
    • BioProject: PRJEB4337
    • Publication: PMID 24309898
    • Analysis date: Wed Apr 4 07:08:55 2018

    Bibliography

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    Related articles in PubMed

    1. DNA Methylation and SNPs in VCX are Correlated with Sex Differences in the Response to Chronic Hepatitis B. Hu XQ, et al. Virol Sin, 2019 Oct. PMID 31161555, Free PMC Article
    2. Copy number gain of VCX, X-linked multi-copy gene, leads to cell proliferation and apoptosis during spermatogenesis. Ji J, et al. Oncotarget, 2016 Nov 29. PMID 27705943, Free PMC Article
    3. Genetic alterations of lung adenocarcinoma in relation to smoking and ethnicity. Sy SM, et al. Lung Cancer, 2003 Jul. PMID 12826317
    4. A search for novel cancer/testis antigens in lung cancer identifies VCX/Y genes, expanding the repertoire of potential immunotherapeutic targets. Taguchi A, et al. Cancer Res, 2014 Sep 1. PMID 24970476, Free PMC Article
    5. Expression and localization of VCX/Y proteins and their possible involvement in regulation of ribosome assembly during spermatogenesis. Zou SW, et al. Cell Res, 2003 Jun. PMID 12862317

    See all (11) citations in PubMed

    GeneRIFs: Gene References Into Functions

    What's a GeneRIF?
    1. SNPs and DNA methylation at the CHR X: 7810800 locus cooperatively regulate VCX expression in chronic hepatitis B (CHB). The upregulated VCX expression in female CHB patients might represent a mechanism of protection from more severe liver dysfunction and extensive fibrosis, as observed in male CHB patients.
      Title: DNA Methylation and SNPs in VCX are Correlated with Sex Differences in the Response to Chronic Hepatitis B.
    2. Increasing copy number of VCX could upregulate the gene expression and regulate cell proliferation and apoptosis during spermatogenesis in non-obstructive azoospermia.
      Title: Copy number gain of VCX, X-linked multi-copy gene, leads to cell proliferation and apoptosis during spermatogenesis.
    3. Identified members of the VCX/Y gene family as novel CT antigens.
      Title: A search for novel cancer/testis antigens in lung cancer identifies VCX/Y genes, expanding the repertoire of potential immunotherapeutic targets.
    4. Human VCX/Y, SPANX, and CSAG2 gene families together with the murine SPANX gene and the CYPT family may share a common ancestor.
      Title: A shared promoter region suggests a common ancestor for the human VCX/Y, SPANX, and CSAG gene families and the murine CYPT family.
    Submit: New GeneRIF Correction

    Phenotypes

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    Find tests for this gene in the NIH Genetic Testing Registry (GTR)

    Review eQTL and phenotype association data in this region using PheGenI

    Variation

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    See Variation Viewer (GRCh37.p13)

    Pathways from PubChem

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    Interactions

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    Products Interactant Other Gene Complex Source Pubs Description

    General gene information

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    Markers

    Homology

    Clone Names

    • MGC118975, MGC118976

    Gene Ontology Provided by GOA

    Function Evidence Code Pubs
    enables chromatin binding TAS
    Traceable Author Statement
    more info
    		 PubMed 
    Process Evidence Code Pubs
    involved_in brain development IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    involved_in chromatin organization TAS
    Traceable Author Statement
    more info
    		 PubMed 
    involved_in ribosome assembly NAS
    Non-traceable Author Statement
    more info
    		 PubMed 
    involved_in spermatogenesis TAS
    Traceable Author Statement
    more info
    		 PubMed 
    Component Evidence Code Pubs
    located_in nucleolus IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    located_in nucleus IDA
    Inferred from Direct Assay
    more info
    		 PubMed 

    General protein information

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    Preferred Names
    variable charge X-linked protein 1
    Names
    variable charge protein on X with ten repeats
    variable charge, X chromosome
    variably charged protein X-B1

    NCBI Reference Sequences (RefSeq)

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    RefSeqs maintained independently of Annotated Genomes

    These reference sequences exist independently of genome builds. Explain

    These reference sequences are curated independently of the genome annotation cycle, so their versions may not match the RefSeq versions in the current genome build. Identify version mismatches by comparing the version of the RefSeq in this section to the one reported in Genomic regions, transcripts, and products above.

    mRNA and Protein(s)

    1. NM_001393662.1 → NP_001380591.1  variable charge X-linked protein 1

      Status: REVIEWED

      Source sequence(s)
      AC005296
      Consensus CDS
      CCDS14128.1
      UniProtKB/Swiss-Prot
      A0JNS5, Q4V774, Q9H320, Q9P0H3
      Related
      ENSP00000509688.1, ENST00000688183.1
      Conserved Domains (2) summary
      PTZ00341
      Location:78 → 192
      PTZ00341; Ring-infected erythrocyte surface antigen; Provisional
      pfam15231
      Location:1 → 129
      VCX_VCY; Variable charge X/Y family

    2. NM_013452.3 → NP_038480.2  variable charge X-linked protein 1

      See identical proteins and their annotated locations for NP_038480.2

      Status: REVIEWED

      Source sequence(s)
      AC005296
      Consensus CDS
      CCDS14128.1
      UniProtKB/Swiss-Prot
      A0JNS5, Q4V774, Q9H320, Q9P0H3
      Related
      ENSP00000370447.3, ENST00000381059.7
      Conserved Domains (2) summary
      PTZ00341
      Location:78 → 192
      PTZ00341; Ring-infected erythrocyte surface antigen; Provisional
      pfam15231
      Location:1 → 129
      VCX_VCY; Variable charge X/Y family

    RefSeqs of Annotated Genomes: GCF_000001405.40-RS_2024_08

    The following sections contain reference sequences that belong to a specific genome build. Explain

    Reference GRCh38.p14 Primary Assembly

    Genomic

    1. NC_000023.11 Reference GRCh38.p14 Primary Assembly

      Range
      7842262..7844143
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_011545490.4 → XP_011543792.1  variable charge X-linked protein 1 isoform X1

      Related
      ENSP00000508920.1, ENST00000692567.1
      Conserved Domains (1) summary
      pfam15231
      Location:1 → 141
      VCX_VCY; Variable charge X/Y family

    Alternate T2T-CHM13v2.0

    Genomic

    1. NC_060947.1 Alternate T2T-CHM13v2.0

      Range
      7395939..7397760
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)
    Nucleotide Protein
    Heading Accession and Version
    Protein Accession Links
    GenPept Link UniProtKB Link
    Q9H320.1 GenPept UniProtKB/Swiss-Prot:Q9H320

    Gene LinkOut

    The following LinkOut resources are supplied by external providers. These providers are responsible for maintaining the links.

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