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    VCX2 variable charge X-linked 2 [ Homo sapiens (human) ]

    Gene ID: 51480, updated on 2-Nov-2024

    Summary

    Official Symbol
    VCX2provided by HGNC
    Official Full Name
    variable charge X-linked 2provided by HGNC
    Primary source
    HGNC:HGNC:18158
    See related
    Ensembl:ENSG00000177504 MIM:300532; AllianceGenome:HGNC:18158
    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
    VCXB; VCX2R; VCX-2r
    Summary
    This gene belongs to the VCX/Y gene family, which has multiple members on both X and Y chromosomes that are expressed exclusively in male germ cells. The VCX gene cluster is polymorphic in terms of copy number; different individuals may have a different number of VCX genes. This gene contains two copies of a 30 nt tandem repeat. Deletion of a nearby member of this family was implicated in cognitive disability. [provided by RefSeq, Feb 2015]
    Expression
    Restricted expression toward testis (RPKM 16.4) See more
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    Genomic context

    See VCX2 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 (8169944..8171267, complement)
    RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) X NC_060947.1 (7734626..7735949, complement)
    RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) X NC_000023.10 (8137985..8139308, complement)

    Chromosome X - NC_000023.11Genomic Context describing neighboring genes 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 patatin like phospholipase domain containing 4 Neighboring gene Sharpr-MPRA regulatory region 2843 Neighboring gene OCT4-NANOG hESC enhancer GRCh37_chrX:8073020-8073627 Neighboring gene S232-VCX2 recombination region Neighboring gene uncharacterized LOC107985676 Neighboring gene microRNA 651 Neighboring gene P300/CBP strongly-dependent group 1 enhancer GRCh37_chrX:8313181-8314380 Neighboring gene variable charge X-linked 3B

    Genomic regions, transcripts, and products

    Expression

    • 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

    Interactions

    Products Interactant Other Gene Complex Source Pubs Description

    General gene information

    Markers

    Clone Names

    • MGC118977, MGC125729, MGC125794, MGC125795

    Gene Ontology Provided by GOA

    Function Evidence Code Pubs
    enables molecular_function ND
    No biological Data available
    more info
     
    Process Evidence Code Pubs
    involved_in biological_process ND
    No biological Data available
    more info
     
    involved_in brain development IBA
    Inferred from Biological aspect of Ancestor
    more info
     
    Component Evidence Code Pubs
    is_active_in cellular_component ND
    No biological Data available
    more info
     

    General protein information

    Preferred Names
    variable charge X-linked protein 2
    Names
    variable charge protein on X with two repeats
    variably charged protein X-B
    variably charged, X chromosome 2
    variably charged, X chromosome B
    variably charged, X chromosome, with 2 repeats

    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_016378.3NP_057462.2  variable charge X-linked protein 2

      See identical proteins and their annotated locations for NP_057462.2

      Status: REVIEWED

      Source sequence(s)
      AC097626, AF167079, AI015625, BC134350
      Consensus CDS
      CCDS35200.1
      UniProtKB/Swiss-Prot
      A3KPB6, Q4V9T2, Q9H322, Q9P0H5
      UniProtKB/TrEMBL
      Q3SXQ9
      Related
      ENSP00000321309.4, ENST00000317103.5
      Conserved Domains (1) summary
      pfam15231
      Location:1138
      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
      8169944..8171267 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    Alternate T2T-CHM13v2.0

    Genomic

    1. NC_060947.1 Alternate T2T-CHM13v2.0

      Range
      7734626..7735949 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)