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

Gene ID: 51480, updated on 23-Nov-2023


Official Symbol
VCX2provided by HGNC
Official Full Name
variable charge X-linked 2provided by HGNC
Primary source
See related
Ensembl:ENSG00000177504 MIM:300532; AllianceGenome:HGNC:18158
Gene type
protein coding
RefSeq status
Homo sapiens
Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Primates; Haplorrhini; Catarrhini; Hominidae; Homo
Also known as
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]
Restricted expression toward testis (RPKM 16.4) See more
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Genomic context

Exon count:
Annotation release Status Assembly Chr Location
RS_2023_10 current GRCh38.p14 (GCF_000001405.40) X NC_000023.11 (8169944..8171267, complement)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) X NC_060947.1 (7734626..7735949, complement)
105.20220307 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


  • Project title: 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


Products Interactant Other Gene Complex Source Pubs Description

General gene information


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
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
    A3KPB6, Q4V9T2, Q9H322, Q9P0H5
    ENSP00000321309.4, ENST00000317103.5
    Conserved Domains (1) summary
    VCX_VCY; Variable charge X/Y family

RefSeqs of Annotated Genomes: GCF_000001405.40-RS_2023_10

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

Reference GRCh38.p14 Primary Assembly


  1. NC_000023.11 Reference GRCh38.p14 Primary Assembly

    8169944..8171267 complement
    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0


  1. NC_060947.1 Alternate T2T-CHM13v2.0

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