ZPBP2 zona pellucida binding protein 2 [Homo sapiens (human)] - Gene

Summary

Official Symbol: ZPBP2provided by HGNC
Official Full Name: zona pellucida binding protein 2provided by HGNC
Primary source: HGNC:HGNC:20678
See related: Ensembl:ENSG00000186075 MIM:608499; AllianceGenome:HGNC:20678
Gene type: protein coding
RefSeq status: VALIDATED
Organism: Homo sapiens
Lineage: Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Primates; Haplorrhini; Catarrhini; Hominidae; Homo
Also known as: ZPBPL
Summary: Predicted to be involved in acrosome assembly and binding activity of sperm to zona pellucida. Predicted to act upstream of or within membrane lipid metabolic process and regulation of gene expression. Located in nucleus. [provided by Alliance of Genome Resources, Oct 2024]
Expression: Restricted expression toward testis (RPKM 54.6) See more
Orthologs: mouse all
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Genomic context

Location:: 17q21.1

Exon count:: 8

Annotation release	Status	Assembly	Chr	Location
RS_2024_08	current	GRCh38.p14 (GCF_000001405.40)	17	NC_000017.11 (39868202..39877896)
RS_2024_08	current	T2T-CHM13v2.0 (GCF_009914755.1)	17	NC_060941.1 (40731925..40741619)
RS_2024_09	previous assembly	GRCh37.p13 (GCF_000001405.25)	17	NC_000017.10 (38024455..38034149)

Chromosome 17 - NC_000017.11 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 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?

The Germ Cell-Specific Markers ZPBP2 and PGK2 in Testicular Biopsies Can Predict the Presence as well as the Quality of Sperm in Non-obstructive Azoospermia Patients.
Title: The Germ Cell-Specific Markers ZPBP2 and PGK2 in Testicular Biopsies Can Predict the Presence as well as the Quality of Sperm in Non-obstructive Azoospermia Patients.
Study of diurnal expression profiles of ZPBP2/Zpbp2, gasdermin B, and ORMDL3/Ormdl3 in human and mouse tissues revealed that Ormdl3 and Zpbp2 were controlled by the circadian clock in a tissue-specific fashion provided the first evidence that disease-associated genes Zpbp2 and Ormdl3 are regulated by circadian rhythms and the Zpbp2 region influences expression of the core clock gene Nr1d1.
Title: Regulatory interaction between the ZPBP2-ORMDL3/Zpbp2-Ormdl3 region and the circadian clock.
modest changes (8-13%) in promoter methylation levels of ZPBP2 and GSDMA may cause substantial changes in RNA levels and allelic expression of ZPBP2 and ORMDL3 is mediated by DNA methylation
Title: Role of DNA methylation in expression control of the IKZF3-GSDMA region in human epithelial cells.
The local genotype influences methylation levels at SLC22A5 and ZPBP2 promoters independently of the asthma status. Further studies are necessary to confirm the relationship between GSDMA-ZPBP2 and SLC22A5 methylation and asthma in females and males separately.
Title: Local genotype influences DNA methylation at two asthma-associated regions, 5q31 and 17q21, in a founder effect population.
The allele T of rs10852936 surrounding the IKZF3-ZPBP2 locus confers risk for early-onset psoriasis.
Title: The allele T of rs10852936 confers risk for early-onset psoriasis.
allele-specific transcriptional regulation of genes in the asthma-associated chromosomal region 17q12-q21; rs4795397 influences activity of ZPBP2 promoter in an allele-dependent fashion and leads to nucleosome repositioning on the asthma-associated allele; methylation of exon 1 of ZPBP2 masks the genetic effect on ZPBP2 promoter; ORMDL3 promoter is unmethylated
Title: Interaction between genetic and epigenetic variation defines gene expression patterns at the asthma-associated locus 17q12-q21 in lymphoblastoid cell lines.
Four additional susceptibility loci (IRF8, TMEM39A, IKZF3, and ZPBP2) for systemic lupus erythematosus were robustly established a multiethnic population (European, African American, Asian, Hispanic, Gullah, and Amerindian).
Title: Identification of IRF8, TMEM39A, and IKZF3-ZPBP2 as susceptibility loci for systemic lupus erythematosus in a large-scale multiracial replication study.
The disease-linked haplotype and putative causal DNA variants of ZPBP2/GSDMB/ORMDL3 locus via a combination of genetic and functional analyses, were identified.
Title: Allele-specific chromatin remodeling in the ZPBP2/GSDMB/ORMDL3 locus associated with the risk of asthma and autoimmune disease.
Observational study of gene-disease association. (HuGE Navigator)
Title: Allele-specific chromatin remodeling in the ZPBP2/GSDMB/ORMDL3 locus associated with the risk of asthma and autoimmune disease.
Data show that loss of zona pellucida binding proteins 1 and 2 in the acrosomal matrix disrupts acrosome biogenesis and sperm morphogenesis.
Title: Loss of zona pellucida binding proteins in the acrosomal matrix disrupts acrosome biogenesis and sperm morphogenesis.

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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

EBI GWAS Catalog

Description
Fraction of exhaled nitric oxide values in childhood are associated with 17q11.2-q12 and 17q12-q21 variants. EBI GWAS Catalog EBI GWAS CatalogPubMed
Genome-wide association study identifies TNFSF15 and POU2AF1 as susceptibility loci for primary biliary cirrhosis in the Japanese population. EBI GWAS Catalog EBI GWAS CatalogPubMed
Genome-wide meta-analyses identify three loci associated with primary biliary cirrhosis. EBI GWAS Catalog EBI GWAS CatalogPubMed
Genome-wide meta-analysis increases to 71 the number of confirmed Crohn's disease susceptibility loci. EBI GWAS Catalog EBI GWAS CatalogPubMed
Host-microbe interactions have shaped the genetic architecture of inflammatory bowel disease. EBI GWAS Catalog EBI GWAS CatalogPubMed
Meta-analysis identifies 29 additional ulcerative colitis risk loci, increasing the number of confirmed associations to 47. EBI GWAS Catalog EBI GWAS CatalogPubMed

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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Gene Ontology Provided by GOA

Process	Evidence Code	Pubs
involved_in acrosome assembly	IBA Inferred from Biological aspect of Ancestor more info
involved_in binding of sperm to zona pellucida	IBA Inferred from Biological aspect of Ancestor more info
involved_in circadian regulation of gene expression	IEA Inferred from Electronic Annotation more info
involved_in membrane lipid catabolic process	IEA Inferred from Electronic Annotation more info
involved_in negative regulation of immunoglobulin production	IEA Inferred from Electronic Annotation more info
involved_in sphingolipid metabolic process	IEA Inferred from Electronic Annotation more info

Component	Evidence Code	Pubs
is_active_in acrosomal vesicle	IBA Inferred from Biological aspect of Ancestor more info
located_in cell body	IEA Inferred from Electronic Annotation more info
located_in extracellular region	IEA Inferred from Electronic Annotation more info
located_in nucleus	HDA more info	PubMed
part_of zona pellucida receptor complex	IBA Inferred from Biological aspect of Ancestor more info

General protein information

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Preferred Names: zona pellucida-binding protein 2

Names: ZPBP-like protein

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)

NM_198844.3 → NP_942141.2 zona pellucida-binding protein 2 isoform 1 precursor

See identical proteins and their annotated locations for NP_942141.2

Status: VALIDATED

Description

Transcript Variant: This variant (1) represents the shorter transcript and encodes the shorter protein (isoform 1).

Source sequence(s)

BC043152, DB056422

Consensus CDS

CCDS11353.2

UniProtKB/Swiss-Prot

Q6X784

Related

ENSP00000367174.3, ENST00000377940.3

Conserved Domains (1) summary

pfam07354
Location:34 → 305

Sp38; Zona-pellucida-binding protein (Sp38)
NM_199321.3 → NP_955353.1 zona pellucida-binding protein 2 isoform 2 precursor

See identical proteins and their annotated locations for NP_955353.1

Status: VALIDATED

Description

Transcript Variant: This variant (2) has an additional in-frame exon in the 5' coding region, compared to variant 1, which results in a longer protein (isoform 2), compared to isoform 1.

Source sequence(s)

AY251603, BC043152, DB056422

Consensus CDS

CCDS11352.1

UniProtKB/Swiss-Prot

A8K8L8, Q6X783, Q6X784, Q86XL5

Related

ENSP00000335384.5, ENST00000348931.9

Conserved Domains (1) summary

pfam07354
Location:56 → 327

Sp38; Zona-pellucida-binding protein (Sp38)