Seroatlas · Human Serome Atlas

VCX3B

Variable charge X-linked protein 3B

Also known as: VCX-C, VCX3B_HUMAN

Cross-references: UniProt · Ensembl · Human Protein Atlas · GeneCards · NCBI Gene

Protein identityUniProt · HPA

UniProt accession: Q9H321
Gene: VCX3B
Ensembl: ENSG00000205642
Chromosome: X
Canonical length: 246 aa
Protein class: Predicted intracellular proteins

OverviewNCBI Gene

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 the Y-linked members are two identical copies of the gene within a palindromic region on chromosome Yq11. The family members share a high degree of sequence identity, with the exception that a 30-nt 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. This family member, as represented by the reference genome allele, contains 14 copies of the 30-nt repeat unit. VCX/Y genes encode small and highly charged proteins containing putative bipartite nuclear localization signals. Although the exact function of this family member has yet to be determined, a role in mRNA stability regulation can be inferred from the ability of the highly similar family member, VCX-A, to inhibit mRNA decapping. A possible role in the regulation of ribosome assembly during spermatogenesis has also been suggested. [provided by RefSeq, Aug 2010]

Canonical amino-acid sequenceUniProt

246 residues, UniProt reviewed canonical sequence.

>Q9H321|VCX3B
     1  MSPKPRASGP PAKAKEAGKR KSSSQPSPSD PKKKTTKVAK KGKAVRRGRR GKKGAATKMA
    61  AVTAPEAESG PAAPGPSDQP SQELPQHELP PEEPVSEGTQ HDPLSQESEL EEPLSQESEV
   121  EEPLSQESQV EEPLSQESEV EEPLSQESQV EEPLSQESEV EEPLSQESEV EEPLSQESQV
   181  EEPLSQESEV EEPLSQESQV EEPLSQESEM EEPLSQESQV EEPLSQESEM EEPLSQESEM
   241  EELPSV

LocalizationUniProt · AlphaFold · HPA

Whether an antibody against VCX3B can act on the native protein depends on physical access: surface and secreted proteins are reachable by circulating antibodies, intracellular proteins usually are not.

Antibody reachability: Intracellular
Secreted: No
Transmembrane segments: 0
Mean surface accessibility (rSASA): 0.73
Highest tissue expression: 14 nTPM

Expression across tissuesHPA

Tissue

testis: 14 nTPM
retina: 0.3 nTPM
amygdala: 0.2 nTPM
thyroid gland: 0.2 nTPM
adrenal gland: 0.1 nTPM
basal ganglia: 0.1 nTPM

Single-cell type

early primary spermatocytes: 326 nCPM
differentiating spermatogonia: 182 nCPM
undifferentiated spermatogonia: 65 nCPM
late primary spermatocytes: 36 nCPM
late spermatids: 11 nCPM
early spermatids: 11 nCPM

Immune cell

basophil: 0 nTPM
classical monocyte: 0 nTPM
eosinophil: 0 nTPM
gdT-cell: 0 nTPM
intermediate monocyte: 0 nTPM
MAIT T-cell: 0 nTPM

Brain region

basal ganglia: 0.3 nTPM
cerebral cortex: 0.3 nTPM
hippocampal formation: 0.3 nTPM
hypothalamus: 0.3 nTPM
pons: 0.3 nTPM
thalamus: 0.3 nTPM

Genetic constraint and essentialitygnomAD · DepMap

Does the body need this protein intact? Low LOEUF or a strong DepMap dependency means loss or blockade of the protein is likely to be felt.

gnomAD LOEUF (loss-of-function intolerance): 1.83
gnomAD pLI: 0.34
gnomAD missense Z: -1.64

Cancer expressionTCGA

Across TCGA tumor cohorts, this protein is over-expressed in roughly 3% of surveyed tumor types (aggregate summary; per-cohort expression, alteration, and survival load in the interactive view).

OntologyGO

Biological processes

brain development

Cellular components

Protein domainsUniProt · Pfam · InterPro

KeywordsUniProt

Repeat

Antibody and autoantibody relevanceSeroatlas analysis

Seroatlas reads VCX3B as an antibody target. Whether an autoantibody or antibody against VCX3B could matter depends on whether native VCX3B is physically reachable, whether the body needs it intact, and whether it acts in a disease-relevant tissue.

VCX3B is annotated as predominantly intracellular. Intracellular proteins are common autoantibody markers, becoming visible to the immune system after cell injury or altered processing, but are usually markers of disease rather than direct drivers.

Annotation status

The present source text does not explicitly label VCX3B as an autoantigen. Seroatlas presents hypothesis context only and does not manufacture a known-serology claim.

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