ZPBP2

zona pellucida binding protein 2, the group of Immunoglobulin like domain containing

Basic information

Region (hg38): 17:39868202-39877896

Links

ENSG00000186075 ∙ NCBI:124626 ∙ OMIM:608499 ∙ HGNC:20678 ∙ Uniprot:Q6X784 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

Phenotypes

GenCC

Source: genCC

No genCC data.

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the ZPBP2 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the ZPBP2 gene is commonly pathogenic or not.

In the table, we include only reliable ClinVar variants with their consequences to MANE Select, Mane Plus Clinical transcripts, or transcripts with TSL equals 1. Click the count to view the source variants.

Warning: slight differences between displayed counts and the number of variants in ClinVar may occur, primarily due to (1) the application of a different transcript and/or consequence by our variant effect predictor or (2) differences in clinical significance: we classify Benign/Likely benign variants as Likely benign and Pathogenic/Likely pathogenic variants as Likely pathogenic.

Variant type	Pathogenic	Likely pathogenic	VUS	Likely benign	Benign	Sum
synonymous					1	1
missense			15	1	1	17
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	15	1	2

Variants in ZPBP2

This is a list of pathogenic ClinVar variants found in the ZPBP2 region.

You can filter this list by clicking the number of variants in the Variants pathogenicity by type table.

Position	Type	Phenotype	Significance	ClinVar
17-39868576-A-G		not specified	Uncertain significance (Jul 25, 2023)
17-39871532-G-A		not specified	Uncertain significance (Sep 07, 2022)
17-39871561-G-C		not specified	Uncertain significance (Jul 09, 2021)
17-39871571-G-A			Benign (Apr 04, 2018)
17-39871618-G-C		not specified	Uncertain significance (Apr 17, 2024)
17-39872276-G-A		not specified	Uncertain significance (Jun 11, 2024)
17-39872327-G-A		not specified	Uncertain significance (Jan 30, 2024)
17-39872360-T-G		not specified	Uncertain significance (Jun 14, 2023)
17-39872382-T-C			Benign (Apr 04, 2018)
17-39872416-C-T		not specified	Uncertain significance (Jan 26, 2023)
17-39872478-A-G		not specified	Uncertain significance (Aug 13, 2021)
17-39873083-G-A		not specified	Uncertain significance (Feb 28, 2024)
17-39875278-T-G		not specified	Uncertain significance (Mar 29, 2022)
17-39875306-A-G		not specified	Uncertain significance (Mar 25, 2024)
17-39875357-A-G		not specified	Uncertain significance (Nov 07, 2022)
17-39875366-G-A		not specified	Uncertain significance (May 04, 2023)
17-39875395-A-G			Likely benign (Jun 15, 2018)
17-39876685-T-C		not specified	Uncertain significance (Dec 17, 2021)
17-39876727-G-T		not specified	Uncertain significance (May 31, 2023)
17-39876803-A-C		not specified	Uncertain significance (Nov 17, 2022)
17-39876804-G-A		not specified	Uncertain significance (Jun 03, 2022)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
ZPBP2	protein_coding	protein_coding	ENST00000348931	8	9733

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
1.22e-8	0.349	125717	0	31	125748	0.000123

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.421	171	187	0.913	0.0000101	2228
Missense in Polyphen		48	66.27	0.72431		827
Synonymous	1.49	49	64.2	0.763	0.00000348	602
Loss of Function	0.751	14	17.4	0.806	9.45e-7	211

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000612	0.000609
Ashkenazi Jewish	0.000399	0.000298
East Asian	0.000222	0.000217
Finnish	0.00	0.00
European (Non-Finnish)	0.0000913	0.0000879
Middle Eastern	0.000222	0.000217
South Asian	0.0000664	0.0000653
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Is implicated in sperm-oocyte interaction during fertilization. {ECO:0000250|UniProtKB:Q6X786}.

Intolerance Scores

• loftool: 0.953
• rvis_EVS: 0.37
• rvis_percentile_EVS: 75.43

Haploinsufficiency Scores

• pHI: 0.0429
• hipred: N
• hipred_score: 0.212

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.187

Gene Damage Prediction

	All	Recessive	Dominant
Mendelian	Medium	Medium	Medium
Primary Immunodeficiency	Medium	Medium	High
Cancer	Medium	Medium	Medium

Mouse Genome Informatics

• Gene name: Zpbp2
• Phenotype: reproductive system phenotype; cellular phenotype; endocrine/exocrine gland phenotype

Gene ontology

• Biological process: acrosome assembly;binding of sperm to zona pellucida
• Cellular component: acrosomal vesicle;zona pellucida receptor complex;extracellular region;nucleus;cell body