BPY2 basic charge Y-linked 2 [Homo sapiens (human)] - Gene

Summary

Official Symbol: BPY2provided by HGNC
Official Full Name: basic charge Y-linked 2provided by HGNC
Primary source: HGNC:HGNC:13508
See related: Ensembl:ENSG00000183753 MIM:400013; AllianceGenome:HGNC:13508
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: VCY2; BPY2A; VCY2A
Summary: This gene is located in the nonrecombining portion of the Y chromosome, and expressed specifically in testis. The encoded protein interacts with ubiquitin protein ligase E3A and may be involved in male germ cell development and male infertility. Three nearly identical copies of this gene exist on chromosome Y; two copies are part of a palindromic region. This record represents the copy outside of the palidromic region. [provided by RefSeq, Jul 2008]
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Genomic context

Location:: Yq11.223

Exon count:: 9

Annotation release	Status	Assembly	Chr	Location
RS_2024_08	current	GRCh38.p14 (GCF_000001405.40)	Y	NC_000024.10 (22984263..23005465)
RS_2024_08	current	T2T-CHM13v2.0 (GCF_009914755.1)	Y	NC_060948.1 (23819939..23841142)
RS_2024_09	previous assembly	GRCh37.p13 (GCF_000001405.25)	Y	NC_000024.9 (25130410..25151612)

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?

genetic association study in Chinese population: Data suggest that combined patterns of copy number abnormality in BPY2 (basic charge Y-linked protein 2) and/or DAZ1 (deleted in azoospermia 1) are associated with spermatogenic impairment/azoospermia.
Title: Gene copy number alterations in the azoospermia-associated AZFc region and their effect on spermatogenic impairment.
Observational study of gene-disease association. (HuGE Navigator)
Title: Differential effect of specific gr/gr deletion subtypes on spermatogenesis in the Chinese Han population.
VCY2 was weakly expressed at the spermatogonia and immunonegative in spermatocytes and round spermatids in testicular biopsy specimens with maturation arrest or hypospermatogenesis.
Title: Specific expression of VCY2 in human male germ cells and its involvement in the pathogenesis of male infertility.
VCY2 protein interacts with the HECT domain of ubiquitin-protein ligase E3A
Title: VCY2 protein interacts with the HECT domain of ubiquitin-protein ligase E3A.

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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

Copy number response

Description
Copy number response Haploinsufficency No evidence available (Last evaluated 2012-08-22) ClinGen Genome Curation Page Triplosensitivity No evidence available (Last evaluated 2012-08-22) 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)

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:480540

G34986 (e-PCR)
- UniSTS:30325

G65869 (e-PCR)
- UniSTS:230535

Gene Ontology Provided by GOA

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

Process	Evidence Code	Pubs
involved_in single fertilization	TAS Traceable Author Statement more info	PubMed
involved_in spermatogenesis	IMP Inferred from Mutant Phenotype more info	PubMed

Component	Evidence Code	Pubs
located_in nucleus	IDA Inferred from Direct Assay more info	PubMed

General protein information

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Preferred Names: testis-specific basic protein Y 2

Names: basic protein on Y chromosome 2; testis-specific basic protein on Y, 2; variable charge, Y-linked, 2; variably charged protein Y 2

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.