ZP4
gene geneOn this page
Also known as ZPBZPB2ZP1B
Summary
ZP4 (zona pellucida glycoprotein 4, HGNC:15770) is a protein-coding gene on chromosome 1q43, encoding Zona pellucida sperm-binding protein 4 (Q12836). Component of the zona pellucida, an extracellular matrix surrounding oocytes which mediates sperm binding, induction of the acrosome reaction and prevents post-fertilization polyspermy.
The zona pellucida is an extracellular matrix that surrounds the oocyte and early embryo. It is composed primarily of three or four glycoproteins with various functions during fertilization and preimplantation development. The nascent protein contains a N-terminal signal peptide sequence, a conserved ZP domain, a consensus furin cleavage site, and a C-terminal transmembrane domain. It is hypothesized that furin cleavage results in release of the mature protein from the plasma membrane for subsequent incorporation into the zona pellucida matrix. However, the requirement for furin cleavage in this process remains controversial based on mouse studies. Previously, this gene has been referred to as ZP1 or ZPB and thought to have similar functions as mouse Zp1. However, a human gene with higher similarity and chromosomal synteny to mouse Zp1 has been assigned the symbol ZP1 and this gene has been assigned the symbol ZP4.
Source: NCBI Gene 57829 — RefSeq curated summary.
At a glance
- Gene–disease (curated): schizophrenia (No Known Disease Relationship, GenCC)
- GWAS associations: 8
- Clinical variants (ClinVar): 102 total
- Constraint (gnomAD): pLI 0.00 (LoF-tolerant), LOEUF 1.17 (unconstrained)
- MANE Select transcript:
NM_021186 - Notable: 102 clinical variants but no curated precision-oncology (CIViC) evidence yet
Identifiers
Gene identifiers
| Field | Value |
|---|---|
| HGNC ID | HGNC:15770 |
| Approved symbol | ZP4 |
| Name | zona pellucida glycoprotein 4 |
| Location | 1q43 |
| Locus type | gene with protein product |
| Status | Approved |
| Aliases | ZPB, ZPB2, ZP1B |
| Ensembl gene | ENSG00000116996 |
| Ensembl biotype | protein_coding |
| OMIM | 613514 |
| Entrez | 57829 |
Gene structure
Transcript identifiers
Ensembl transcripts: 2 — 2 protein_coding
MANE Select: ENST00000366570
Transcript support level (Ensembl TSL; 1 = fully mRNA-supported): TSL 1: 1, TSL 5: 1
ENST00000366570, ENST00000611898
RefSeq mRNA: 1 — MANE Select: NM_021186
NM_021186
CCDS: CCDS1615
Canonical transcript exons
ENST00000366570 — 12 exons
| Exon | Start | End |
|---|---|---|
| ENSE00000793657 | 237890055 | 237890176 |
| ENSE00000793658 | 237889867 | 237889969 |
| ENSE00000793659 | 237888358 | 237888510 |
| ENSE00000793660 | 237887374 | 237887561 |
| ENSE00000793661 | 237886771 | 237886868 |
| ENSE00000793662 | 237885756 | 237885886 |
| ENSE00000793663 | 237885391 | 237885580 |
| ENSE00000793664 | 237885165 | 237885315 |
| ENSE00000805426 | 237882742 | 237882846 |
| ENSE00000805427 | 237884769 | 237884847 |
| ENSE00001442058 | 237882404 | 237882549 |
| ENSE00003733451 | 237890461 | 237890922 |
Expression profiles
Bgee: expression breadth broad, 18 present calls, max score 98.96.
Highest expression (Bgee): oocyte, secondary oocyte, pancreatic ductal cell, tibialis anterior, cartilage tissue.
Top tissues by expression
showing 100 of 242 tissues by Bgee expression score (0-100, higher = more expressed):
| Tissue | Anatomy ID | Expression score | Quality |
|---|---|---|---|
| oocyte | CL:0000023 | 98.96 | gold quality |
| secondary oocyte | CL:0000655 | 97.90 | gold quality |
| pancreatic ductal cell | CL:0002079 | 83.09 | silver quality |
| tibialis anterior | UBERON:0001385 | 80.23 | gold quality |
| cartilage tissue | UBERON:0002418 | 76.05 | gold quality |
| ileal mucosa | UBERON:0000331 | 74.01 | gold quality |
| deltoid | UBERON:0001476 | 62.23 | silver quality |
| cardiac muscle of right atrium | UBERON:0003379 | 54.88 | gold quality |
| left ventricle myocardium | UBERON:0006566 | 54.23 | gold quality |
| kidney epithelium | UBERON:0004819 | 53.93 | gold quality |
| upper arm skin | UBERON:0004263 | 53.52 | gold quality |
| upper leg skin | UBERON:0004262 | 53.24 | gold quality |
| skin of hip | UBERON:0001554 | 52.43 | silver quality |
| myocardium | UBERON:0002349 | 50.48 | gold quality |
| quadriceps femoris | UBERON:0001377 | 48.44 | gold quality |
| nasal cavity epithelium | UBERON:0005384 | 47.03 | gold quality |
| vastus lateralis | UBERON:0001379 | 45.40 | gold quality |
| layer of synovial tissue | UBERON:0007616 | 43.55 | gold quality |
| buccal mucosa cell | CL:0002336 | 43.53 | gold quality |
| skeletal muscle tissue of rectus abdominis | UBERON:0004511 | 43.37 | gold quality |
| placenta | UBERON:0001987 | 41.85 | gold quality |
| superficial temporal artery | UBERON:0001614 | 41.33 | gold quality |
| palpebral conjunctiva | UBERON:0001812 | 41.10 | gold quality |
| mucosa of paranasal sinus | UBERON:0005030 | 40.98 | gold quality |
| amniotic fluid | UBERON:0000173 | 40.69 | gold quality |
| jejunal mucosa | UBERON:0000399 | 40.59 | gold quality |
| biceps brachii | UBERON:0001507 | 40.57 | gold quality |
| epithelium of nasopharynx | UBERON:0001951 | 40.45 | gold quality |
| gingival epithelium | UBERON:0001949 | 40.43 | gold quality |
| germinal epithelium of ovary | UBERON:0001304 | 40.33 | gold quality |
| esophagus squamous epithelium | UBERON:0006920 | 40.29 | gold quality |
| skeletal muscle tissue of biceps brachii | UBERON:0004502 | 40.27 | gold quality |
| jejunum | UBERON:0002115 | 40.18 | gold quality |
| epithelium of mammary gland | UBERON:0003244 | 40.14 | gold quality |
| oviduct epithelium | UBERON:0004804 | 40.03 | gold quality |
| mammary duct | UBERON:0001765 | 39.98 | gold quality |
| mucosa of sigmoid colon | UBERON:0004993 | 39.95 | gold quality |
| saphenous vein | UBERON:0007318 | 39.83 | gold quality |
| parotid gland | UBERON:0001831 | 39.81 | gold quality |
| urethra | UBERON:0000057 | 39.80 | gold quality |
| heart right ventricle | UBERON:0002080 | 39.79 | gold quality |
| pericardium | UBERON:0002407 | 39.77 | gold quality |
| endothelial cell | CL:0000115 | 39.75 | gold quality |
| synovial joint | UBERON:0002217 | 39.70 | gold quality |
| dorsal root ganglion | UBERON:0000044 | 39.68 | gold quality |
| nipple | UBERON:0002030 | 39.68 | gold quality |
| bronchial epithelial cell | CL:0002328 | 39.65 | gold quality |
| decidua | UBERON:0002450 | 39.65 | gold quality |
| penis | UBERON:0000989 | 39.64 | gold quality |
| gingiva | UBERON:0001828 | 39.64 | gold quality |
| bronchus | UBERON:0002185 | 39.64 | gold quality |
| trigeminal ganglion | UBERON:0001675 | 39.63 | gold quality |
| tendon of biceps brachii | UBERON:0008188 | 39.60 | gold quality |
| colonic mucosa | UBERON:0000317 | 39.57 | gold quality |
| inferior vagus X ganglion | UBERON:0005363 | 39.57 | gold quality |
| superior surface of tongue | UBERON:0007371 | 39.56 | gold quality |
| pylorus | UBERON:0001166 | 39.55 | gold quality |
| renal medulla | UBERON:0000362 | 39.53 | gold quality |
| pons | UBERON:0000988 | 39.51 | gold quality |
| thymus | UBERON:0002370 | 39.50 | gold quality |
| medulla oblongata | UBERON:0001896 | 39.48 | gold quality |
| superior vestibular nucleus | UBERON:0007227 | 39.47 | gold quality |
| cardia of stomach | UBERON:0001162 | 39.46 | gold quality |
| parietal pleura | UBERON:0002400 | 39.45 | gold quality |
| Brodmann (1909) area 23 | UBERON:0013554 | 39.40 | gold quality |
| dorsal plus ventral thalamus | UBERON:0001897 | 39.38 | gold quality |
| granulocyte | CL:0000094 | 39.37 | gold quality |
| tongue | UBERON:0001723 | 39.37 | gold quality |
| cerebellar vermis | UBERON:0004720 | 39.37 | gold quality |
| oral cavity | UBERON:0000167 | 39.35 | gold quality |
| subthalamic nucleus | UBERON:0001906 | 39.35 | gold quality |
| ventral tegmental area | UBERON:0002691 | 39.35 | gold quality |
| trachea | UBERON:0003126 | 39.33 | gold quality |
| parietal lobe | UBERON:0001872 | 39.32 | gold quality |
| vena cava | UBERON:0004087 | 39.31 | gold quality |
| pharyngeal mucosa | UBERON:0000355 | 39.27 | gold quality |
| substantia nigra pars compacta | UBERON:0001965 | 39.23 | gold quality |
| visceral pleura | UBERON:0002401 | 39.23 | gold quality |
| postcentral gyrus | UBERON:0002581 | 39.23 | gold quality |
| body of tongue | UBERON:0011876 | 39.22 | gold quality |
| medial globus pallidus | UBERON:0002477 | 39.18 | gold quality |
| trabecular bone tissue | UBERON:0002483 | 39.18 | gold quality |
| globus pallidus | UBERON:0001875 | 39.15 | gold quality |
| substantia nigra pars reticulata | UBERON:0001966 | 39.11 | gold quality |
| entorhinal cortex | UBERON:0002728 | 39.05 | gold quality |
| lateral nuclear group of thalamus | UBERON:0002736 | 39.00 | gold quality |
| corpus epididymis | UBERON:0004359 | 38.98 | gold quality |
| tibia | UBERON:0000979 | 38.93 | gold quality |
| lateral globus pallidus | UBERON:0002476 | 38.81 | gold quality |
| seminal vesicle | UBERON:0000998 | 38.75 | gold quality |
| caput epididymis | UBERON:0004358 | 38.75 | gold quality |
| cauda epididymis | UBERON:0004360 | 38.74 | gold quality |
| middle temporal gyrus | UBERON:0002771 | 38.72 | gold quality |
| mammalian vulva | UBERON:0000997 | 38.66 | gold quality |
| pigmented layer of retina | UBERON:0001782 | 38.55 | gold quality |
| bone marrow cell | CL:0002092 | 38.52 | gold quality |
| sperm | CL:0000019 | 38.32 | gold quality |
| sural nerve | UBERON:0015488 | 38.12 | gold quality |
| Brodmann (1909) area 46 | UBERON:0006483 | 37.40 | gold quality |
| superior frontal gyrus | UBERON:0002661 | 37.39 | gold quality |
Single-cell (SCXA)
Detected in 2 experiment(s), a significant marker in 2.
| Experiment | Marker? | Max mean expression |
|---|---|---|
| E-GEOD-36552 | yes | 163.58 |
| E-ANND-3 | yes | 3.78 |
HPA expression
RNA tissue specificity: Tissue enriched
7 HPA tissues / cells by nTPM:
| Tissue / cell | Axis | nTPM | Protein (IHC) |
|---|---|---|---|
| Ovary | tissue | 3.6 | high |
| Midbrain | tissue | 0.2 | |
| Tonsil | tissue | 0.2 | not detected |
| Pons | tissue | 0.1 | |
| Placenta | tissue | 0.1 | not detected |
| Thymus | tissue | 0.1 | |
| Hippocampal formation | tissue | 0.1 |
Brain sub-regions (HPA Brain Atlas): detected in 3; highest nTPM — Dorsal motor vagal complex (0.1), Nucleus tractus solitarii (0.1), Subiculum (0.1).
Regulation
Is transcription factor: no
Functional genomics
gnomAD constraint: pLI 7.33e-21, LOEUF 1.17, missense Z -1.19 — population loss-of-function intolerance (pLI ≥ 0.9 = LoF-intolerant; lower LOEUF = more constrained). gnomAD
Regional missense constraint (gnomAD RMC): no regional variation along ENST00000366570 — one region, missense o/e 1.18.
Literature-anchored findings (GeneRIF, showing 10)
- ZPB induces acrosomal exocytosis through a Gi independent pathway. (PMID:15805145)
- Binding sites for recombinant zona pellucida B (ZPB) glycoprotein are located both at the N- and C-terminus of proacrosin (PMID:15950651)
- Exposure of sperm to ZP proteins promoted acrosomal exocytosis and changed motility patterns. (PMID:16407501)
- induces acrosome reactions which are protein kinase-C, protein tyrosine kinase, T-type Ca2+ channels, and extracellular Ca2+ dependent (PMID:18667750)
- a significant decrease in acrosomal exocytosis mediated by both recombinant human ZP3 (p<0.005) and ZP4 (p<0.005) was observed in presence of the immune sera (PMID:19004505)
- Human ZP4 is not sufficient to support human sperm binding to the zona pellucida in transgenic mice; other zona proteins may be needed for human gamete recognition. (PMID:21173071)
- ZO4 is highly expressed in ovarian tissue in PCOS patients with regular cycle and without hyperandrogenism; in some patients with PCOS and infertility, ZP4 mutation can be found. (PMID:25740067)
- ZP4 gene SNPs rs547984, rs540782, rs693421, rs2499601 are not associated with open-angle glaucoma among ethnic Hans from Sichuan. (PMID:30298508)
- Zona Pellucida Proteins, Fibrils, and Matrix. (PMID:32569527)
- Mutations in ZP4 are associated with abnormal zona pellucida and female infertility. (PMID:33461974)
Cross-species orthologs
2 orthologs
| Organism | Symbol | Gene ID |
|---|---|---|
| ENSDARG00000113246 | ||
| rattus_norvegicus | Zp4 | ENSRNOG00000027506 |
Paralogs (4): ZP2 (ENSG00000103310), QRICH2 (ENSG00000129646), ZP1 (ENSG00000149506), C16orf96 (ENSG00000205832)
Additional cross-species homologs
Sequence homologs in species beyond Ensembl Compara’s model organisms, by Diamond local protein alignment (% sequence identity; best hit per species). Lower-identity rows are more distant homologs. The matched accessions’ gene symbols aren’t in biobtree yet, so each row shows the UniProt accession.
| Organism | UniProt | Identity | Method |
|---|---|---|---|
| Mus musculus | O08524 | 94.2% | Diamond |
| Macaca radiata | O77726 | 94.2% | Diamond |
| Canis lupus familiaris | P47983 | 83.0% | Diamond |
| Felis catus | P47984 | 83.0% | Diamond |
| Sus scrofa | P42099 | 78.0% | Diamond |
| Bos taurus | Q9BH10 | 78.0% | Diamond |
| Oryctolagus cuniculus | Q00193 | 69.6% | Diamond |
Genomic neighbors (locus context)
Genes flanking this one on the chromosome (NCBI/Entrez gene neighborhood). Positional context only — some neighbors share regulatory elements (bidirectional promoters, antisense/overlapping transcripts), but chromosomal adjacency is not itself a functional relationship (see Interactions for that).
| Symbol | Type | Entrez |
|---|---|---|
| MIR4428 | ncRNA | 100616141 |
| RYR2 | protein-coding | 6262 |
| MT1HL1 | protein-coding | 645745 |
Protein
Protein identifiers
Zona pellucida sperm-binding protein 4 — Q12836 (reviewed: Q12836)
Alternative names: Zona pellucida glycoprotein 4, Zona pellucida protein B
All UniProt accessions (1): Q12836
UniProt curated annotations — full annotation on UniProt →
Function. Component of the zona pellucida, an extracellular matrix surrounding oocytes which mediates sperm binding, induction of the acrosome reaction and prevents post-fertilization polyspermy. The zona pellucida is composed of 3 to 4 glycoproteins, ZP1, ZP2, ZP3, and ZP4. ZP4 may act as a sperm receptor.
Subcellular location. Zona pellucida Cell membrane.
Tissue specificity. Expressed in oocytes.
Post-translational modifications. Proteolytically cleaved before the transmembrane segment to yield the secreted ectodomain incorporated in the zona pellucida.
Domain organisation. The ZP domain is involved in the polymerization of the ZP proteins to form the zona pellucida.
Similarity. Belongs to the ZP domain family. ZPB subfamily.
RefSeq proteins (1): NP_067009* (*=MANE)
Domains & families (InterPro)
| ID | Name | Type |
|---|---|---|
| IPR000519 | P_trefoil_dom | Domain |
| IPR001507 | ZP_dom | Domain |
| IPR017957 | P_trefoil_CS | Conserved_site |
| IPR017977 | ZP_dom_CS | Conserved_site |
| IPR042235 | ZP-C_dom | Homologous_superfamily |
| IPR044913 | P_trefoil_dom_sf | Homologous_superfamily |
| IPR048290 | ZP_chr | Domain |
| IPR051148 | Zona_Pellucida_Domain_gp | Family |
| IPR054554 | ZP1/4_Ig-like | Domain |
| IPR055355 | ZP-C | Domain |
| IPR055356 | ZP-N | Domain |
Pfam: PF00088, PF00100, PF22821, PF23344
UniProt features (19 total): glycosylation site 7, chain 2, sequence variant 2, topological domain 2, domain 2, signal peptide 1, disulfide bond 1, propeptide 1, transmembrane region 1
Structure
Predicted structure (AlphaFold)
| Model | pLDDT | Fraction very-high |
|---|---|---|
| AF-Q12836-F1 | 74.90 | 0.24 |
Human Protein Atlas
Protein class: Predicted membrane proteins, Predicted secreted proteins
Protein evidence: Evidence at protein level
Antibody reliability (HPA): IH enhanced
Functional residue map
Curated UniProt residues grouped by drug-discovery relevance — catalytic, ligand-binding, modification, and mutation-validated positions. Source: UniProtKB sequence features.
Disulfide bonds (1)
| Type | Positions |
|---|---|
| Disulfide bond | 367–442 |
Glycosylation sites (7)
| Type | Positions |
|---|---|
| N-linked (glcnac…) asparagine | 202, 219, 267, 470, 474, 69 |
| O-linked (galnac…) threonine | 302 |
Function
Pathways and Gene Ontology
Reactome pathways
1 curated (TAS) of 3; 0 disease pathways. Curated-first; evidence = TAS (manually curated) vs IEA (electronic inference).
3 pathways:
| ID | Pathway | Evidence |
|---|---|---|
| R-HSA-2534343 | Interaction With Cumulus Cells And The Zona Pellucida | curated |
| R-HSA-1187000 | Fertilization | — |
| R-HSA-1474165 | Reproduction | — |
MSigDB gene sets: 77 (showing top):
GOBP_REGULATION_OF_CELL_ACTIVATION, GOBP_SINGLE_FERTILIZATION, GOBP_NEGATIVE_REGULATION_OF_REPRODUCTIVE_PROCESS, GOBP_REGULATION_OF_LEUKOCYTE_PROLIFERATION, GOBP_POSITIVE_REGULATION_OF_REPRODUCTIVE_PROCESS, GOBP_VESICLE_MEDIATED_TRANSPORT, GOBP_POSITIVE_REGULATION_OF_CELL_ADHESION, GOBP_POSITIVE_REGULATION_OF_LEUKOCYTE_PROLIFERATION, GOBP_CELL_CELL_ADHESION, GOBP_EXOCYTOSIS, GOBP_REGULATION_OF_IMMUNE_RESPONSE, GOBP_LEUKOCYTE_PROLIFERATION, GOMF_EXTRACELLULAR_MATRIX_STRUCTURAL_CONSTITUENT, GOBP_SPERM_EGG_RECOGNITION, GOBP_POSITIVE_REGULATION_OF_CELL_ACTIVATION
GO Biological Process (8): positive regulation of humoral immune response (GO:0002922), binding of sperm to zona pellucida (GO:0007339), positive regulation of T cell proliferation (GO:0042102), prevention of polyspermy (GO:0060468), acrosomal vesicle exocytosis (GO:0060478), positive regulation of acrosome reaction (GO:2000344), negative regulation of binding of sperm to zona pellucida (GO:2000360), single fertilization (GO:0007338)
GO Molecular Function (4): acrosin binding (GO:0032190), structural constituent of egg coat (GO:0035804), identical protein binding (GO:0042802), protein binding (GO:0005515)
GO Cellular Component (3): extracellular region (GO:0005576), plasma membrane (GO:0005886), egg coat (GO:0035805)
Reactome top-level categories
2 top-level categories:
| Category | Pathways |
|---|---|
| Fertilization | 1 |
| Reproduction | 1 |
GO top-level categories
28 GO namespaces:
| Category | Terms |
|---|---|
| acrosome reaction | 2 |
| regulation of humoral immune response | 1 |
| humoral immune response | 1 |
| positive regulation of immune response | 1 |
| sperm-egg recognition | 1 |
| T cell proliferation | 1 |
| regulation of T cell proliferation | 1 |
| positive regulation of lymphocyte proliferation | 1 |
| positive regulation of T cell activation | 1 |
| egg activation | 1 |
| negative regulation of fertilization | 1 |
| calcium-ion regulated exocytosis | 1 |
| regulation of acrosome reaction | 1 |
| positive regulation of reproductive process | 1 |
| binding of sperm to zona pellucida | 1 |
| negative regulation of cellular process | 1 |
| negative regulation of reproductive process | 1 |
| regulation of binding of sperm to zona pellucida | 1 |
| fertilization | 1 |
| enzyme binding | 1 |
| extracellular matrix structural constituent | 1 |
| egg coat | 1 |
| protein binding | 1 |
| binding | 1 |
| cellular anatomical structure | 1 |
| membrane | 1 |
| cell periphery | 1 |
| specialized extracellular matrix | 1 |
Experimentally-supported GO annotations
GO terms backed by direct experimental evidence (ECO experimental codes) — 8 of 15 annotations. The rest are phylogenetic / computational / electronic (IEA).
8 experimentally-supported GO terms:
| GO term | NS | Evidence |
|---|---|---|
| acrosomal vesicle exocytosis | BP | mutant phenotype |
| negative regulation of binding of sperm to zona pellucida | BP | direct assay |
| positive regulation of T cell proliferation | BP | direct assay |
| positive regulation of acrosome reaction | BP | direct assay |
| positive regulation of humoral immune response | BP | direct assay |
| egg coat | CC | direct assay |
| acrosin binding | MF | physical interaction |
| identical protein binding | MF | physical interaction |
Protein interactions and networks
STRING
showing 15 of 740 interactions by confidence (×1000):
| Protein A | Protein B | Partner UniProt | Score |
|---|---|---|---|
| ZP4 | ZP3 | P21754 | 981 |
| ZP4 | GDF9 | O60383 | 775 |
| ZP4 | FIGLA | Q6QHK4 | 721 |
| ZP4 | ZP2 | Q05996 | 698 |
| ZP4 | CACNA1G | O43497 | 648 |
| ZP4 | BMP15 | O95972 | 641 |
| ZP4 | ASTL | Q6HA08 | 606 |
| ZP4 | P4HA2 | O15460 | 591 |
| ZP4 | IZUMO1 | Q8IYV9 | 577 |
| ZP4 | NOBOX | O60393 | 577 |
| ZP4 | MMUT | P22033 | 556 |
| ZP4 | DAZL | Q92904 | 499 |
| ZP4 | ZAR1 | Q86SH2 | 497 |
| ZP4 | NLRP5 | P59047 | 491 |
| ZP4 | CACNA1C | Q13936 | 490 |
IntAct
Human interaction partners of ZP4 in IntAct, one row per partner (best MIscore; records = supporting IntAct interaction records).
9 partners by confidence:
| Partner | Interaction type | MIscore | Records |
|---|---|---|---|
| GSTM3 | physical association | 0.520 | 2 |
| ACR | direct interaction | 0.440 | 3 |
| ALDOA | physical association | 0.400 | 1 |
| ENO1 | physical association | 0.400 | 1 |
| GAPDHS | physical association | 0.400 | 1 |
| GPX4 | physical association | 0.400 | 1 |
| ODF2 | physical association | 0.400 | 1 |
| PKM | physical association | 0.400 | 1 |
| TPI1 | physical association | 0.400 | 1 |
Disease & clinical
Genetic variants
Variant evidence for ZP4: 102 ClinVar records (0 pathogenic / likely pathogenic); 8 GWAS associations.
ClinVar
102 variants total. Per-class counts are floors (≥ shown; pagination cap):
| Classification | Count (floor) |
|---|---|
| Pathogenic | 0 |
| Likely pathogenic | 0 |
| Uncertain significance | 83 |
| Likely benign | 13 |
| Benign | 4 |
SpliceAI
Top 10 splice-impact sites by Δscore (adjacent positions with the same effect merged into one range; 28 predictions of 898):
| Position(s) | Effect | Δscore | Sites |
|---|---|---|---|
| 1:237882847–237882848 | acceptor_loss | 1.0000 | 5 |
| 1:237885581–237885582 | acceptor_loss | 1.0000 | 3 |
| 1:237885592 | acceptor_gain | 1.0000 | |
| 1:237886769–237886770 | donor_loss | 1.0000 | 5 |
| 1:237888511–237888512 | acceptor_loss | 1.0000 | 5 |
| 1:237888518 | acceptor_gain | 1.0000 | |
| 1:237890053–237890054 | donor_loss | 1.0000 | 5 |
| 1:237890185 | acceptor_gain | 1.0000 | |
| 1:237882847 | acceptor_loss | 0.9900 | |
| 1:237882850 | acceptor_gain | 0.9900 |
AlphaMissense
524 missense substitutions predicted likely pathogenic (of 3,512 scored), across 159 residues. Top 20 hotspot residues, ranked by the number of likely-pathogenic substitutions (of those reachable by a single-nucleotide change), then by mean score:
| Residue | Likely-pathogenic substitutions | Mean am_pathogenicity | Max am_pathogenicity |
|---|---|---|---|
| F422 | 8 | 0.940 | 0.994 |
| F417 | 8 | 0.910 | 0.989 |
| F424 | 8 | 0.902 | 0.980 |
| D393 | 8 | 0.898 | 0.958 |
| C367 | 7 | 0.959 | 0.983 |
| C442 | 7 | 0.957 | 0.981 |
| W381 | 7 | 0.917 | 0.987 |
| C285 | 7 | 0.915 | 0.946 |
| F235 | 7 | 0.913 | 0.961 |
| C388 | 7 | 0.909 | 0.969 |
| C189 | 7 | 0.897 | 0.942 |
| C242 | 7 | 0.867 | 0.906 |
| C128 | 7 | 0.853 | 0.948 |
| C164 | 7 | 0.852 | 0.907 |
| W368 | 7 | 0.850 | 0.978 |
| C169 | 7 | 0.849 | 0.931 |
| C179 | 7 | 0.845 | 0.889 |
| C154 | 7 | 0.837 | 0.905 |
| C34 | 7 | 0.822 | 0.912 |
| F279 | 7 | 0.822 | 0.912 |
HPA cancer prognostics
RNA cancer specificity: Not detected
Disease associations
OMIM: gene MIM:613514 | disease phenotypes:
GenCC curated gene-disease
1 curated gene-disease records:
| Disease | Classification | Inheritance | Records |
|---|---|---|---|
| schizophrenia | No Known Disease Relationship | Unknown |
Mondo (1): schizophrenia (MONDO:0005090)
GWAS associations
8 associations:
| Study | Trait | p-value |
|---|---|---|
| GCST010002_8 | Refractive error | 7e-10 |
| GCST005436_1 | C-peptide levels in type I diabetes | 4e-8 |
| GCST000041_1 | Hypertension | 8e-7 |
| GCST000767_4 | Non-alcoholic fatty liver disease histology (AST) | 2e-6 |
| GCST009391_855 | Metabolite levels | 3e-6 |
| GCST005435_1 | Stimulated C-peptide levels in type I diabetes | 4e-6 |
| GCST009391_1241 | Metabolite levels | 4e-6 |
| GCST009391_705 | Metabolite levels | 6e-6 |
EFO canonical traits (from GWAS)
4 canonical traits:
| EFO ID | Trait name |
|---|---|
| EFO:0005187 | C-peptide measurement |
| EFO:0010404 | triacylglycerol 48:1 measurement |
| EFO:0010356 | lysophosphatidylcholine 14:0 measurement |
| EFO:0010401 | triacylglycerol 46:1 measurement |
Drugs & pharmacology
Drug and pharmacology data
Is drug target: no
PharmGKB: 1 entry (CPIC guideline: no)
CTD chemical–gene interactions
8 total (human), top 8 by PubMed support.
| Chemical | Actions (top 5) | PubMed papers |
|---|---|---|
| sodium arsenite | increases expression | 1 |
| CGP 52608 | affects binding, increases reaction | 1 |
| abrine | increases expression | 1 |
| Resveratrol | affects cotreatment, decreases expression | 1 |
| Acetaminophen | decreases expression | 1 |
| Benzo(a)pyrene | affects methylation, increases methylation | 1 |
| Plant Extracts | affects cotreatment, decreases expression | 1 |
| Aflatoxin B1 | increases methylation | 1 |
Clinical trials (associated diseases)
Via MONDO — disease-level, not drug-specific.
showing 60 of 600 trials:
| NCT | Phase | Status | Title |
|---|---|---|---|
| NCT00000374 | Phase 4 | COMPLETED | Treatment for First-Episode Schizophrenia |
| NCT00001656 | Phase 4 | COMPLETED | Comparison of Clozapine vs Olanzapine in Childhood-Onset Psychotic Disorders |
| NCT00007774 | Phase 4 | COMPLETED | To Determine if Olanzapine is More Cost Effective Than Haloperidol for the Treatment of Schizophrenia |
| NCT00014001 | Phase 4 | COMPLETED | CATIE- Schizophrenia Trial |
| NCT00018668 | Phase 4 | COMPLETED | Antipsychotic Response in Schizophrenia |
| NCT00034801 | Phase 4 | COMPLETED | Olanzapine Versus Active Comparator in the Treatment of Depression in Patients With Schizophrenia |
| NCT00034905 | Phase 4 | COMPLETED | A Comparison of Seroquel vs. Risperidone in Schizophrenia |
| NCT00036088 | Phase 4 | COMPLETED | Olanzapine Versus An Active Comparator in the Treatment of Schizophrenia |
| NCT00044187 | Phase 4 | COMPLETED | The Assessment of a Weight-Gain Agent for the Treatment of Olanzapine-Associated Anti-Obesity Agent in Patients With Schizophrenia, Schizophreniform Disorder, Schizoaffective Disorder, and Bipolar I Disorder |
| NCT00044655 | Phase 4 | COMPLETED | Switching Medication to Treat Schizophrenia |
| NCT00048828 | Phase 4 | COMPLETED | Treating Drug-Resistant Childhood Schizophrenia |
| NCT00053703 | Phase 4 | COMPLETED | Treatment of Early Onset Schizophrenia Spectrum Disorders (TEOSS) |
| NCT00056498 | Phase 4 | COMPLETED | Risperidone Treatment in Schizophrenia Patients Who Are Currently Taking Clozapine |
| NCT00061802 | Phase 4 | COMPLETED | Efficacy and Safety of Two Atypical Antipsychotics vs. Placebo in Patients With an Acute Exacerbation of Either Schizophrenia or Schizoaffective Disorder |
| NCT00080327 | Phase 4 | COMPLETED | Study of Three Doses of Aripiprazole in Patients With Acute Schizophrenia |
| NCT00088049 | Phase 4 | COMPLETED | Study of Olanzapine vs. Aripiprazole in the Treatment of Schizophrenia |
| NCT00090012 | Phase 4 | COMPLETED | Comparison of Continuing Olanzapine to Switching to Quetiapine in Overweight or Obese Patients With Schizophrenia and Schizoaffective Disorder |
| NCT00100776 | Phase 4 | COMPLETED | Efficacy of High Dose Olanzapine for the Treatment of Schizophrenia and Schizoaffective Disorder |
| NCT00103571 | Phase 4 | COMPLETED | Olanzapine Versus Aripiprazole in the Treatment of Acutely Ill Patients With Schizophrenia |
| NCT00108368 | Phase 4 | COMPLETED | The Effects of Risperidone and Olanzapine on Thinking |
| NCT00114595 | Phase 4 | COMPLETED | Ethyl-Eicosapentaenoic Acid and Tardive Dyskinesia |
| NCT00130923 | Phase 4 | COMPLETED | Risperidone Long-acting Versus Oral Risperidone in Patients With Schizophrenia and Alcohol Use Disorder |
| NCT00137020 | Phase 4 | COMPLETED | Clinical Effect Of Cross Titration Of Antipsychotics With Ziprasidone In Schizophrenia Or Schizoaffective Disorder |
| NCT00140166 | Phase 4 | COMPLETED | Treatment of Acute Schizophrenia With Vitamin Therapy |
| NCT00145847 | Phase 4 | COMPLETED | Naltrexone Treatment of Alcohol Abuse in Schizophrenia |
| NCT00148564 | Phase 4 | COMPLETED | Energy Homeostasis Under Treatment With Atypical Antipsychotics |
| NCT00156715 | Phase 4 | COMPLETED | Efficacy of Quetiapine in the Treatment of Patients With Schizophrenia and a Comorbid Substance Use Disorder |
| NCT00158223 | Phase 4 | COMPLETED | Effectiveness of Pimozide in Augmenting the Effects of Clozapine in the Treatment of Schizophrenia |
| NCT00159081 | Phase 4 | COMPLETED | One Year Drug Treatment in First-Episode Schizophrenia |
| NCT00159120 | Phase 4 | COMPLETED | Maintenance Treatment vs. Stepwise Drug Discontinuation in First-Episode Schizophrenia |
| NCT00159133 | Phase 4 | COMPLETED | Prodrome-Based Early Intervention With Antipsychotics vs. Benzodiazepines in First-Episode Schizophrenia |
| NCT00159757 | Phase 4 | TERMINATED | 12 Week Open, Non-Comparative Switch Study Of Oral Ziprazidone In Previously Treated Schizophrenic Patients |
| NCT00167817 | Phase 4 | COMPLETED | Effect of Switch to Aripiprazole on Health and Smoking Parameters in Patients With Schizophrenia: A Pilot Study |
| NCT00169026 | Phase 4 | TERMINATED | Alcoholism and Schizophrenia: Effects of Clozapine |
| NCT00169039 | Phase 4 | TERMINATED | Clozapine Versus Chlorpromazine for Treatment-Unresponsive Schizophrenia |
| NCT00169065 | Phase 4 | COMPLETED | Effectiveness of Clozapine Versus Olanzapine for Treatment-resistant Schizophrenia |
| NCT00169091 | Phase 4 | TERMINATED | Clozapine Versus Haloperidol for Treating the First Episode of Schizophrenia |
| NCT00176423 | Phase 4 | COMPLETED | Efficacy Study of Galantamine for Cognitive Impairments in Schizophrenia |
| NCT00176436 | Phase 4 | COMPLETED | Atomoxetine for Treatment of Weight Gain in Olanzapine or Clozapine Patients |
| NCT00177008 | Phase 4 | COMPLETED | Aripiprazole for the Treatment of Schizophrenia With Co-Morbid Social Anxiety |
| NCT00177580 | Phase 4 | COMPLETED | Improving Symptoms of Schizophrenia and Schizoaffective Disorder by Supplementing Medications With Pravastatin |
| NCT00182442 | Phase 4 | COMPLETED | Cognition, Functioning and Quality of Life |
| NCT00182494 | Phase 4 | UNKNOWN | Diabetes Prevention Program in Schizophrenia [DPPS] |
| NCT00183625 | Phase 4 | COMPLETED | Supported Employment and Skills Training in Conjunction With Pharmacotherapy in Schizophrenia Patients |
| NCT00186771 | Phase 4 | UNKNOWN | Magnetic Stimulation as a Treatment for Auditory Hallucinations in Schizophrenia |
| NCT00190749 | Phase 4 | COMPLETED | Safety Study of Olanzapine and a Comparator in Patients With Schizophrenia and Schizoaffective Disorder |
| NCT00191555 | Phase 4 | COMPLETED | Efficacy Study of Switching Stabilized Schizophrenic Patients From Conventional to Atypical Antipsychotic Treatment |
| NCT00194025 | Phase 4 | COMPLETED | Valproate in Late Life Schizophrenia |
| NCT00199940 | Phase 4 | COMPLETED | Safety And Efficacy Study Of Ziprasidone In Pediatric Psychotic Illness |
| NCT00202306 | Phase 4 | COMPLETED | Indicated Prevention of Psychotic Disorders With Low-dose Lithium |
| NCT00203788 | Phase 4 | COMPLETED | Improving Work Outcome in People With Recent-onset Schizophrenia |
| NCT00204061 | Phase 4 | COMPLETED | Early Pharmacological and Psychological Intervention for Late Prodromal States of Psychosis |
| NCT00205660 | Phase 4 | COMPLETED | Changes in Adiposity, Metabolic Measures From Atypicals to Aripiprazole |
| NCT00206102 | Phase 4 | COMPLETED | A Study of the Cataractogenic Potential of Seroquel and Risperdal in the Treatment of Participants With Schizophrenia or Schizoaffective Disorder |
| NCT00208143 | Phase 4 | COMPLETED | Seroquel Therapy for Substance Use Disorders Comorbid With Schizophrenia |
| NCT00208169 | Phase 4 | COMPLETED | Abilify Therapy for Reducing Comorbid Substance Abuse |
| NCT00214578 | Phase 4 | COMPLETED | Seroquel on Glucose Metabolism |
| NCT00215579 | Phase 4 | COMPLETED | Determining the Effects of Risperdal Consta in Patients With Psychotic Disorders and Incomplete Adherence |
| NCT00216528 | Phase 4 | COMPLETED | A Study to Evaluate Symptomatic Remission in Schizophrenia With Long Acting Risperidone Microspheres |
| NCT00216632 | Phase 4 | COMPLETED | A Study of Treatment Success in Changing From Olanzapine to Long-acting Injectable Risperidone (RISPERDAL® CONSTA™) |
Related Atlas pages
- Associated diseases: schizophrenia
- Disease cohort memberships (association, not causation — diseases whose associated-gene cohort lists this gene; a subset are also under Associated diseases): cirrhosis of liver, hypertensive disorder, metabolic dysfunction-associated steatotic liver disease