ZP4

zona pellucida glycoprotein 4, the group of Zona pellucida glycoproteins

Basic information

Region (hg38): 1:237877864-237890922

Links

ENSG00000116996 ∙ NCBI:57829 ∙ OMIM:613514 ∙ HGNC:15770 ∙ Uniprot:Q12836 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

Phenotypes

GenCC

Source: genCC

• schizophrenia (No Known Disease Relationship), mode of inheritance: Unknown

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the ZP4 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the ZP4 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			34	6	4	44
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	34	7	4

Variants in ZP4

This is a list of pathogenic ClinVar variants found in the ZP4 region.

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

Position	Type	Phenotype	Significance	ClinVar
1-237882466-C-A		not specified	Uncertain significance (Feb 14, 2023)
1-237882534-G-A			Benign (Jun 29, 2018)
1-237882756-G-A			Benign (Jul 06, 2018)
1-237882807-G-A		not specified	Uncertain significance (May 02, 2024)
1-237882829-T-G		not specified	Uncertain significance (Jun 17, 2022)
1-237884789-A-G		not specified	Uncertain significance (Mar 07, 2023)
1-237885196-G-C		not specified	Uncertain significance (Jun 21, 2023)
1-237885221-T-C		not specified	Uncertain significance (Jan 10, 2023)
1-237885229-C-A		not specified	Uncertain significance (Sep 06, 2022)
1-237885229-C-T		not specified	Uncertain significance (Dec 26, 2023)
1-237885241-G-A		not specified	Uncertain significance (Jul 13, 2021)
1-237885429-G-T		not specified	Uncertain significance (Mar 01, 2023)
1-237885434-T-C		not specified	Uncertain significance (Feb 15, 2023)
1-237885479-G-T		not specified	Uncertain significance (Mar 07, 2023)
1-237885509-C-T		not specified	Uncertain significance (Nov 27, 2023)
1-237885523-C-T		not specified	Uncertain significance (Dec 11, 2023)
1-237885557-C-T		not specified	Uncertain significance (Sep 20, 2023)
1-237885565-G-A		not specified	Uncertain significance (Jan 26, 2022)
1-237885776-A-G		not specified	Uncertain significance (Sep 29, 2022)
1-237885797-G-C		not specified	Uncertain significance (May 24, 2023)
1-237885821-G-T		not specified	Uncertain significance (Jun 21, 2022)
1-237885840-T-C		not specified	Likely benign (Oct 26, 2022)
1-237885843-G-A			Benign (Jul 06, 2018)
1-237886786-C-T		not specified	Uncertain significance (Mar 31, 2023)
1-237886798-C-A		not specified	Uncertain significance (Apr 20, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
ZP4	protein_coding	protein_coding	ENST00000366570	12	8390

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
1.74e-18	0.00635	125438	0	310	125748	0.00123

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	-1.24	357	297	1.20	0.0000154	3496
Missense in Polyphen		83	79.429	1.045		989
Synonymous	-1.60	137	115	1.19	0.00000630	1098
Loss of Function	0.207	28	29.2	0.959	0.00000173	288

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.00693	0.00693
Ashkenazi Jewish	0.00	0.00
East Asian	0.00332	0.00201
Finnish	0.000139	0.000139
European (Non-Finnish)	0.000697	0.000695
Middle Eastern	0.00332	0.00201
South Asian	0.00133	0.00127
Other	0.000490	0.000489

dbNSFP

Source: dbNSFP

• Function: FUNCTION: The mammalian zona pellucida, which mediates species- specific sperm binding, induction of the acrosome reaction and prevents post-fertilization polyspermy, is composed of three to four glycoproteins, ZP1, ZP2, ZP3, and ZP4. ZP4 may act as a sperm receptor.
• Pathway: Interaction With The Zona Pellucida;Fertilization;Reproduction (Consensus)

Recessive Scores

• pRec: 0.178

Intolerance Scores

• loftool: 0.451
• rvis_EVS: -0.11
• rvis_percentile_EVS: 45.61

Haploinsufficiency Scores

• pHI: 0.130
• hipred: N
• hipred_score: 0.112
• ghis: 0.405

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.292

Gene Damage Prediction

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

Gene ontology

• Biological process: positive regulation of humoral immune response;binding of sperm to zona pellucida;positive regulation of T cell proliferation;acrosomal vesicle exocytosis;positive regulation of acrosome reaction;negative regulation of binding of sperm to zona pellucida
• Cellular component: extracellular region;plasma membrane;integral component of membrane
• Molecular function: protein binding;acrosin binding;identical protein binding