VCX3A variable charge X-linked 3A [Homo sapiens (human)] - Gene

Summary

Official Symbol: VCX3Aprovided by HGNC
Official Full Name: variable charge X-linked 3Aprovided by HGNC
Primary source: HGNC:HGNC:18159
See related: Ensembl:ENSG00000169059 MIM:300533; AllianceGenome:HGNC:18159
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: VCX3; VCXA; VCX-A; VCX8R; VCX-8r
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 8 repeats of the 30-bp unit. [provided by RefSeq, Jul 2008]
Expression: Restricted expression toward testis (RPKM 27.7) See more
Orthologs: all
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Genomic context

Location:: Xp22.31

Exon count:: 3

Annotation release	Status	Assembly	Chr	Location
RS_2023_10	current	GRCh38.p14 (GCF_000001405.40)	X	NC_000023.11 (6533618..6535118, complement)
RS_2023_10	current	T2T-CHM13v2.0 (GCF_009914755.1)	X	NC_060947.1 (6086887..6088477, complement)
105.20220307	previous assembly	GRCh37.p13 (GCF_000001405.25)	X	NC_000023.10 (6451659..6453159, complement)

Chromosome X - NC_000023.11 Genomic Context describing neighboring genes

Genomic regions, transcripts, and products

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Genomic Sequence:

Go to nucleotide: Graphics FASTA GenBank

Expression

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See details

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

Bibliography

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GeneRIFs: Gene References Into Functions

What's a GeneRIF?

We demonstrate that VCX-A can specifically bind a subset of mRNAs involved in neuritogenesis and is also capable of promoting translational silencing.
Title: Modulation of neuritogenesis by a protein implicated in X-linked mental retardation.
two different deletion patterns were observed: the first group included 62 patients with deletion of VCX3A & VCX genes. The second group included 18 patients with breakpoints at several regions on either side of the STS gene not including the VCX3A gene.
Title: 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.
Our data demonstrate that VCX-A can regulate mRNA stability and that it is an example of a tissue-specific decapping regulator.
Title: Identification of an mRNA-decapping regulator implicated in X-linked mental retardation.

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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

Copy number response

Description
Copy number response Haploinsufficency No evidence available (Last evaluated 2012-10-12) ClinGen Genome Curation Page Triplosensitivity Dosage sensitivity unlikely (Last evaluated 2012-10-12) ClinGen Genome Curation Page

Variation

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See variants in ClinVar

See studies and variants in dbVar

See Variation Viewer (GRCh37.p13)

See Variation Viewer (GRCh38)

General gene information

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Markers

DXS7973 (e-PCR)
- UniSTS:154372

DXS7974 (e-PCR)
- UniSTS:154373

DXS7976 (e-PCR)
- UniSTS:154374

NoName (e-PCR)
- UniSTS:485487

DXS1255 (e-PCR)
- UniSTS:99724

DXS7728 (e-PCR)
- UniSTS:6035

NoName (e-PCR)
- UniSTS:483989

NoName (e-PCR)
- UniSTS:481203

NoName (e-PCR)
- UniSTS:489685

NoName (e-PCR)
- UniSTS:482528

DXS8175 (e-PCR)
- UniSTS:154594

Gene Ontology Provided by GOA

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

Component	Evidence Code	Pubs
located_in nucleolus	ISS Inferred from Sequence or Structural Similarity more info
located_in nucleus	ISS Inferred from Sequence or Structural Similarity more info

General protein information

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Preferred Names: variable charge X-linked protein 3

Names: variable charge protein on X with eight repeats; variably charged X-A; variably charged protein X-A

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.