ZPBP

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

Basic information

Region (hg38): 7:49850421-50121329

Links

ENSG00000042813 ∙ NCBI:11055 ∙ OMIM:608498 ∙ HGNC:15662 ∙ Uniprot:Q9BS86 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

Phenotypes

GenCC

Source: genCC

• spermatogenic failure 66 (Limited), mode of inheritance: Unknown

Clinical Genomic Database

Source: CGD

Condition	Inheritance	Intervention Categories	Intervention/Rationale	Manifestation Categories	References
Spermatogenic failure 66	AR	General	Genetic knowledge may be beneficial related to issues such as selection of optimal supportive care, informed medical decision-making, prognostic considerations, and avoidance of unnecessary testing	Genitourinary	31985809

ClinVar

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

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the ZPBP 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				2	1	3
missense			12	2	2	16
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region				2	2	4
non coding				2		2
Total	0	0	12	6	3

Variants in ZPBP

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

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

Position	Type	Phenotype	Significance	ClinVar
7-49912057-G-A		not specified	Uncertain significance (Jul 12, 2023)
7-49912145-G-A		not specified	Uncertain significance (May 16, 2022)
7-49937527-C-T		ZPBP-related disorder	Likely benign (Oct 28, 2019)
7-49937570-T-A		not specified	Uncertain significance (Apr 15, 2024)
7-49937589-T-A		not specified	Uncertain significance (Feb 22, 2023)
7-49937592-C-T		not specified	Uncertain significance (Aug 17, 2022)
7-49983372-G-A		Spermatogenic failure 66	Pathogenic (Mar 17, 2022)
7-49983389-C-A		not specified	Uncertain significance (Dec 07, 2021)
7-49983401-C-T		not specified	Uncertain significance (Sep 01, 2021)
7-49983410-C-G		not specified	Uncertain significance (Apr 15, 2024)
7-49983526-C-T		ZPBP-related disorder	Benign (Oct 17, 2019)
7-50018323-A-G		ZPBP-related disorder	Benign (Mar 12, 2019)
7-50031241-T-C		Spermatogenic failure 66	Uncertain significance (-)
7-50031277-G-C		ZPBP-related disorder	Benign (Oct 28, 2019)
7-50031300-C-T		ZPBP-related disorder	Likely benign (Mar 12, 2019)
7-50031319-A-C		ZPBP-related disorder	Likely benign (Oct 28, 2019)
7-50058049-C-T		not specified	Uncertain significance (Jan 23, 2023)
7-50058101-A-G		ZPBP-related disorder	Benign (Feb 18, 2020)
7-50058132-C-T		not specified	Uncertain significance (Jul 09, 2021)
7-50081796-C-T		ZPBP-related disorder	Likely benign (Mar 25, 2019)
7-50081818-T-G		not specified	Uncertain significance (May 18, 2022)
7-50081820-T-C		not specified	Uncertain significance (Jun 06, 2023)
7-50081848-G-A		not specified	Uncertain significance (Jun 29, 2022)
7-50081893-G-A		not specified	Likely benign (May 02, 2024)
7-50089625-A-C		ZPBP-related disorder	Likely benign (Jan 03, 2020)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
ZPBP	protein_coding	protein_coding	ENST00000046087	8	270909

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.000312	0.988	125710	0	10	125720	0.0000398

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.895	161	196	0.820	0.0000112	2244
Missense in Polyphen		51	80.353	0.6347		979
Synonymous	-1.27	82	68.6	1.19	0.00000366	669
Loss of Function	2.23	9	19.7	0.457	0.00000113	228

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.00	0.00
Ashkenazi Jewish	0.00	0.00
East Asian	0.0000545	0.0000544
Finnish	0.00	0.00
European (Non-Finnish)	0.0000796	0.0000791
Middle Eastern	0.0000545	0.0000544
South Asian	0.00	0.00
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Plays a role in acrosome compaction and sperm morphogenesis (PubMed:21911476). Is implicated in sperm-oocyte interaction during fertilization (By similarity). {ECO:0000250|UniProtKB:Q62522, ECO:0000269|PubMed:21911476}.

Recessive Scores

• pRec: 0.113

Intolerance Scores

• loftool: 0.574
• rvis_EVS: -0.49
• rvis_percentile_EVS: 22.36

Haploinsufficiency Scores

• pHI: 0.500
• hipred: N
• hipred_score: 0.328
• ghis: 0.398

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: S
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.233

Gene Damage Prediction

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

Mouse Genome Informatics

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

Gene ontology

• Biological process: binding of sperm to zona pellucida
• Cellular component: acrosomal membrane;extracellular region;nucleus