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

    Gene ID: 51480, updated on 10-Dec-2024

    Summary

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    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

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    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

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    Go to nucleotide: Graphics FASTA GenBank

    Expression

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    • Project title: Tissue-specific circular RNA induction during human fetal development
    • Description: 35 human fetal samples from 6 tissues (3 - 7 replicates per tissue) collected between 10 and 20 weeks gestational time were sequenced using Illumina TruSeq Stranded Total RNA
    • BioProject: PRJNA270632
    • Publication: PMID 26076956
    • Analysis date: Mon Apr 2 22:54:59 2018

    Bibliography

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    Related articles in PubMed

    1. 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. Cuevas-Covarrubias SA, et al. Br J Dermatol, 2008 Mar. PMID 18076704
    2. A human sex-chromosomal gene family expressed in male germ cells and encoding variably charged proteins. Lahn BT, et al. Hum Mol Genet, 2000 Jan 22. PMID 10607842
    3. A member of a gene family on Xp22.3, VCX-A, is deleted in patients with X-linked nonspecific mental retardation. Fukami M, et al. Am J Hum Genet, 2000 Sep. PMID 10903929, Free PMC Article
    4. Identification and characterization of the potential promoter regions of 1031 kinds of human genes. Suzuki Y, et al. Genome Res, 2001 May. PMID 11337467, Free PMC Article
    5. A reference map of the human binary protein interactome. Luck K, et al. Nature, 2020 Apr. PMID 32296183, Free PMC Article

    See all (8) citations in PubMed

    GeneRIFs: Gene References Into Functions

    Phenotypes

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    Review eQTL and phenotype association data in this region using PheGenI

    Variation

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    See variants in ClinVar

    See studies and variants in dbVar

    See Variation Viewer (GRCh37.p13)

    See Variation Viewer (GRCh38)

    Interactions

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    Products Interactant Other Gene Complex Source Pubs Description

    General gene information

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    Markers

    Homology

    Clone Names

    • MGC118977, MGC125729, MGC125794, MGC125795

    Gene Ontology Provided by GOA

    Process Evidence Code Pubs
    involved_in brain development IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  

    General protein information

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    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_016378.3 → NP_057462.2  variable charge X-linked protein 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:1 → 138
      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)
    Nucleotide Protein
    Heading Accession and Version
    Protein Accession Links
    GenPept Link UniProtKB Link
    Q9H322.3 GenPept UniProtKB/Swiss-Prot:Q9H322

    Gene LinkOut

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

    Chemical Information
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