VCY variable charge Y-linked [Homo sapiens (human)] - Gene

Summary

Official Symbol: VCYprovided by HGNC
Official Full Name: variable charge Y-linkedprovided by HGNC
Primary source: HGNC:HGNC:12668
See related: Ensembl:ENSG00000129864 MIM:400012; AllianceGenome:HGNC:12668
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: BPY1; VCY1; VCY1A
Summary: The protein encoded by this gene is a member of a family of human VCX/Y genes. This gene family has multiple members on both X and Y chromosomes, and all are expressed exclusively in male germ cells. Members of the VCX/Y family 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. VCX/Y genes encode small and highly charged proteins of unknown function. This gene encodes a small, positively charged protein. The presence of a putative bipartite nuclear localization signal suggests that this gene encodes a nuclear protein. The genome has two identical copies of this gene within a palindromic region; this record represents the more centromeric copy. [provided by RefSeq, Jul 2008]
Expression: Restricted expression toward testis (RPKM 20.6) See more
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Genomic context

Location:: Yq11.221

Exon count:: 2

Annotation release	Status	Assembly	Chr	Location
RS_2024_08	current	GRCh38.p14 (GCF_000001405.40)	Y	NC_000024.10 (13985772..13986473, complement)
RS_2024_08	current	T2T-CHM13v2.0 (GCF_009914755.1)	Y	NC_060948.1 (14892390..14893091, complement)
RS_2024_09	previous assembly	GRCh37.p13 (GCF_000001405.25)	Y	NC_000024.9 (16097652..16098353, complement)

Chromosome Y - NC_000024.10 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 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?

Identified members of the VCX/Y gene family as novel CT antigens.
Title: A search for novel cancer/testis antigens in lung cancer identifies VCX/Y genes, expanding the repertoire of potential immunotherapeutic targets.
Human VCX/Y, SPANX, and CSAG2 gene families together with the murine SPANX gene and the CYPT family may share a common ancestor.
Title: A shared promoter region suggests a common ancestor for the human VCX/Y, SPANX, and CSAG gene families and the murine CYPT family.

Submit: New GeneRIF Correction

Phenotypes

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Review eQTL and phenotype association data in this region using PheGenI

Associated conditions

Description	Tests
Spermatogenic failure, Y-linked, 2 MedGen: C1839071 OMIM: 415000 GeneReviews: Y Chromosome Infertility	Compare labs

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

NoName (e-PCR)
- UniSTS:485487

sY1220 (e-PCR)
- UniSTS:478837

NoName (e-PCR)
- UniSTS:483989

RH93694 (e-PCR)
- UniSTS:87733

G34985 (e-PCR)
- UniSTS:37073

DYS413 (e-PCR)
- UniSTS:154595

Gene Ontology Provided by GOA

Function	Evidence Code	Pubs
enables protein binding	IPI Inferred from Physical Interaction more info	PubMed

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: testis-specific basic protein Y 1

Names: basic charge, Y-linked 1; basic protein on Y chromosome, 1; testis-specific basic protein on Y, 1; variable charge, Y chromosome; variably charged protein Y

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.