SH3BP4
geneOn this page
Summary
SH3BP4 (SH3 domain binding protein 4, HGNC:10826) is a protein-coding gene on chromosome 2q37.2, encoding SH3 domain-binding protein 4 (Q9P0V3). May function in transferrin receptor internalization at the plasma membrane through a cargo-specific control of clathrin-mediated endocytosis.
This gene encodes a protein with 3 Asn-Pro-Phe (NPF) motifs, an SH3 domain, a PXXP motif, a bipartite nuclear targeting signal, and a tyrosine phosphorylation site. This protein is involved in cargo-specific control of clathrin-mediated endocytosis, specifically controlling the internalization of a specific protein receptor.
Source: NCBI Gene 23677 — RefSeq curated summary.
At a glance
- GWAS associations: 12
- Clinical variants (ClinVar): 169 total
- MANE Select transcript:
NM_014521
Identifiers
Gene identifiers
| Field | Value |
|---|---|
| HGNC ID | HGNC:10826 |
| Approved symbol | SH3BP4 |
| Name | SH3 domain binding protein 4 |
| Location | 2q37.2 |
| Locus type | gene with protein product |
| Status | Approved |
| Ensembl gene | ENSG00000130147 |
| Ensembl biotype | protein_coding |
| OMIM | 605611 |
| Entrez | 23677 |
Gene structure
Transcript identifiers
Ensembl transcripts: 15 — 11 protein_coding, 4 protein_coding_CDS_not_defined
ENST00000344528, ENST00000392011, ENST00000409212, ENST00000416021, ENST00000444916, ENST00000446904, ENST00000454947, ENST00000462602, ENST00000484097, ENST00000489601, ENST00000493436, ENST00000875805, ENST00000875806, ENST00000924838, ENST00000961226
RefSeq mRNA: 6 — MANE Select: NM_014521
NM_001371302, NM_001371303, NM_001371304, NM_001371305, NM_001371306, NM_014521
CCDS: CCDS2513
Canonical transcript exons
ENST00000392011 — 6 exons
| Exon | Start | End |
|---|---|---|
| ENSE00001030217 | 235034871 | 235035120 |
| ENSE00001030218 | 234995303 | 234995376 |
| ENSE00001132676 | 235052562 | 235052750 |
| ENSE00001132679 | 235040888 | 235043247 |
| ENSE00001510416 | 235053592 | 235055714 |
| ENSE00001828184 | 234952017 | 234952170 |
Expression profiles
Bgee: expression breadth ubiquitous, 274 present calls, max score 99.60.
FANTOM5 (CAGE): breadth ubiquitous, TPM avg 25.1629 / max 172.4797, expressed in 1541 samples.
FANTOM5 promoters (17 alternative TSS)
| Promoter ID | TPM avg | Samples expressed |
|---|---|---|
| 26167 | 13.5688 | 1491 |
| 26168 | 6.3857 | 1350 |
| 26166 | 2.9862 | 1339 |
| 26182 | 0.4743 | 279 |
| 26180 | 0.3840 | 151 |
| 26183 | 0.3631 | 168 |
| 26173 | 0.2354 | 141 |
| 26169 | 0.2137 | 90 |
| 26179 | 0.1149 | 51 |
| 26171 | 0.0814 | 27 |
Top tissues by expression
285 total, by Bgee expression score (0-100, higher = more expressed):
| Tissue | Anatomy ID | Expression score | Quality |
|---|---|---|---|
| parotid gland | UBERON:0001831 | 99.60 | gold quality |
| trachea | UBERON:0003126 | 96.45 | gold quality |
| mucosa of paranasal sinus | UBERON:0005030 | 96.13 | gold quality |
| renal medulla | UBERON:0000362 | 96.12 | gold quality |
| germinal epithelium of ovary | UBERON:0001304 | 96.07 | gold quality |
| nasal cavity epithelium | UBERON:0005384 | 95.99 | gold quality |
| caput epididymis | UBERON:0004358 | 95.52 | gold quality |
| saliva-secreting gland | UBERON:0001044 | 94.90 | gold quality |
| nasal cavity mucosa | UBERON:0001826 | 94.81 | gold quality |
| choroid plexus epithelium | UBERON:0003911 | 94.69 | gold quality |
| tibia | UBERON:0000979 | 94.47 | gold quality |
| epithelium of mammary gland | UBERON:0003244 | 94.22 | gold quality |
| mammary duct | UBERON:0001765 | 94.17 | gold quality |
| minor salivary gland | UBERON:0001830 | 93.89 | gold quality |
| bronchial epithelial cell | CL:0002328 | 93.87 | gold quality |
| bronchus | UBERON:0002185 | 93.76 | gold quality |
| epithelium of bronchus | UBERON:0002031 | 93.73 | gold quality |
| stromal cell of endometrium | CL:0002255 | 93.64 | gold quality |
| corpus epididymis | UBERON:0004359 | 93.55 | gold quality |
| pylorus | UBERON:0001166 | 93.51 | gold quality |
| inferior vagus X ganglion | UBERON:0005363 | 93.43 | gold quality |
| parietal pleura | UBERON:0002400 | 93.32 | gold quality |
| mouth mucosa | UBERON:0003729 | 93.19 | gold quality |
| endothelial cell | CL:0000115 | 93.16 | silver quality |
| inferior olivary complex | UBERON:0002127 | 93.10 | gold quality |
| cardia of stomach | UBERON:0001162 | 93.08 | gold quality |
| gingival epithelium | UBERON:0001949 | 92.91 | gold quality |
| olfactory segment of nasal mucosa | UBERON:0005386 | 92.89 | gold quality |
| body of pancreas | UBERON:0001150 | 92.59 | gold quality |
| metanephric glomerulus | UBERON:0004736 | 92.57 | gold quality |
Single-cell (SCXA)
Detected in 3 experiment(s), a significant marker in 2.
| Experiment | Marker? | Max mean expression |
|---|---|---|
| E-GEOD-93593 | yes | 8.41 |
| E-ANND-3 | yes | 7.79 |
| E-GEOD-81383 | no | 303.84 |
Regulation
Is transcription factor: no
Literature-anchored findings (GeneRIF, showing 6)
- Results show that TTP (SH3BP4), a SH3-containing protein, specifically regulates the internalization of the transferrin receptor (TfR). (PMID:16325581)
- SH3BP4 is a negative regulator of the Rag GTPase complex and amino acid-dependent mTORC1 signaling. (PMID:22575674)
- SH3BP4 has been identified as a novel pigmentation gene. The SH3BP4 is a direct target of miR-125b. The SH3BP4 is transcriptionally regulated by MITF as its direct target. (PMID:28819321)
- A SNP in the 3’UTR of SH3BP4 (rs56161233) that overlaps predicted miR-100-binding sites and is predicted to disrupt several miRNA-mRNA interactions was associated with overall survival of laryngeal cancer. (PMID:29880533)
- The data uncover the tumor-suppressive role of SH3BP4 that functions as a negative feedback regulator of Wnt signaling through modulating beta-catenin’s subcellular localization. (PMID:30811977)
- SH3BP4 promotes neuropilin-1 and alpha5-integrin endocytosis and is inhibited by Akt. (PMID:33761321)
Cross-species orthologs
4 orthologs
| Organism | Symbol | Gene ID |
|---|---|---|
| danio_rerio | sh3bp4a | ENSDARG00000020000 |
| danio_rerio | sh3bp4 | ENSDARG00000030104 |
| mus_musculus | Sh3bp4 | ENSMUSG00000036206 |
| rattus_norvegicus | Sh3bp4 | ENSRNOG00000019316 |
Paralogs (1): MACC1 (ENSG00000183742)
Protein
Protein identifiers
SH3 domain-binding protein 4 — Q9P0V3 (reviewed: Q9P0V3)
Alternative names: EH-binding protein 10, Transferrin receptor-trafficking protein
All UniProt accessions (5): Q9P0V3, C9JED2, C9JF25, C9JRG1, C9JWW6
UniProt curated annotations — full annotation on UniProt →
Function. May function in transferrin receptor internalization at the plasma membrane through a cargo-specific control of clathrin-mediated endocytosis. Alternatively, may act as a negative regulator of the amino acid-induced TOR signaling by inhibiting the formation of active Rag GTPase complexes. Preferentially binds inactive Rag GTPase complexes and prevents their interaction with the mTORC1 complex inhibiting its relocalization to lysosomes and its activation. Thereby, may indirectly regulate cell growth, proliferation and autophagy.
Subunit / interactions. Homodimer or homooligomer. Interacts with DNM2, EPS15, clathrin, the adapter protein complex 2/AP-2 and TFRC. Interacts with the Rag GTPases RRAGA, RRAGB, RRAGC and RRAGD; the interaction is most probably direct, preferentially occurs with their inactive GDP-bound form and is negatively regulated by amino acids. (Microbial infection) Interacts with molluscum contagiosum virus protein MC159L; this interaction is important for the suppression of autophagy.
Subcellular location. Membrane. Clathrin-coated pit. Cytoplasmic vesicle. Clathrin-coated vesicle. Nucleus.
Tissue specificity. Expressed in all tissues tested with higher expression in pancreas. Expressed by retinal pigment epithelial cells (at protein level).
Post-translational modifications. Phosphorylated upon EGF stimulation. Phosphorylation prevents interaction with DNM2.
Domain organisation. The SH3 domain mediates localization to the clathrin-coated pits and vesicles. The SH3 domain mediates interaction with DNM2 and the cytoplasmic part of TFRC with a lower affinity. The SH3 domain also mediates interaction with RRAGB, RRAGC and is required for the negative regulation of mTORC1.
Miscellaneous. Overexpression or depletion of SH3BP4 result in a specific decrease of the transferrin receptor endocytosis that can be rescued by DNM2 overexpression. Dubious isoform produced through aberrant splice sites.
Isoforms (2)
| UniProt ID | Names | Canonical? |
|---|---|---|
| Q9P0V3-1 | 1 | yes |
| Q9P0V3-2 | 2 |
RefSeq proteins (6): NP_001358231, NP_001358232, NP_001358233, NP_001358234, NP_001358235, NP_055336* (*=MANE)
Domains & families (InterPro)
| ID | Name | Type |
|---|---|---|
| IPR000906 | ZU5_dom | Domain |
| IPR001452 | SH3_domain | Domain |
| IPR035456 | SH3BP4_SH3 | Domain |
| IPR036028 | SH3-like_dom_sf | Homologous_superfamily |
| IPR056181 | SH3BP4_C | Domain |
| IPR056182 | UPA_SH3BP4 | Domain |
| IPR056183 | DEATH_SH3BP4 | Domain |
Pfam: PF00018, PF00791, PF07653, PF23637, PF23640, PF24094
UniProt features (15 total): modified residue 6, domain 3, sequence variant 2, chain 1, splice variant 1, mutagenesis site 1, sequence conflict 1
Structure
Experimental structures (PDB)
0 structures.
Predicted structure (AlphaFold)
| Model | pLDDT | Fraction very-high |
|---|---|---|
| AF-Q9P0V3-F1 | 70.15 | 0.29 |
Functional residue map
Curated UniProt residues grouped by drug-discovery relevance — catalytic, ligand-binding, modification, and mutation-validated positions. Source: UniProtKB sequence features.
Post-translational modifications (6): 131, 246, 251, 279, 296, 637
Mutagenesis-validated functional residues (1):
| Position | Phenotype |
|---|---|
| 92 | loss of function. loss of targeting to the clathrin-coated pits and vesicles. loss of interaction with dnm2, rragb and r |
Function
Pathways and Gene Ontology
Reactome pathways
4 pathways
| ID | Pathway |
|---|---|
| R-HSA-9639288 | Amino acids regulate mTORC1 |
| R-HSA-2262752 | Cellular responses to stress |
| R-HSA-8953897 | Cellular responses to stimuli |
| R-HSA-9711097 | Cellular response to starvation |
MSigDB gene sets: 224 (showing top):
GCACCTT_MIR18A_MIR18B, VERHAAK_AML_WITH_NPM1_MUTATED_DN, GOBP_REGULATION_OF_AUTOPHAGY, GOBP_RESPONSE_TO_ACID_CHEMICAL, GOBP_NEGATIVE_REGULATION_OF_CELL_GROWTH, GOBP_NEGATIVE_REGULATION_OF_HYDROLASE_ACTIVITY, GEORGES_CELL_CYCLE_MIR192_TARGETS, GOBP_GROWTH, GOBP_REGULATION_OF_GTPASE_ACTIVITY, ACEVEDO_NORMAL_TISSUE_ADJACENT_TO_LIVER_TUMOR_DN, GOBP_VESICLE_MEDIATED_TRANSPORT, GOMF_GTPASE_BINDING, GOBP_CELLULAR_RESPONSE_TO_ACID_CHEMICAL, CTATGCA_MIR153, GOBP_PROTEIN_LOCALIZATION_TO_LYSOSOME
GO Biological Process (9): endocytosis (GO:0006897), negative regulation of cell population proliferation (GO:0008285), positive regulation of autophagy (GO:0010508), negative regulation of cell growth (GO:0030308), negative regulation of TOR signaling (GO:0032007), negative regulation of GTPase activity (GO:0034260), regulation of catalytic activity (GO:0050790), protein localization to lysosome (GO:0061462), cellular response to amino acid stimulus (GO:0071230)
GO Molecular Function (4): GDP-dissociation inhibitor activity (GO:0005092), small GTPase binding (GO:0031267), identical protein binding (GO:0042802), protein binding (GO:0005515)
GO Cellular Component (7): nucleus (GO:0005634), cytoplasm (GO:0005737), clathrin-coated pit (GO:0005905), clathrin-coated vesicle (GO:0030136), extracellular exosome (GO:0070062), membrane (GO:0016020), cytoplasmic vesicle (GO:0031410)
Reactome top-level categories
Rollup of top-3 pathways:
| Category | Pathways |
|---|---|
| Cellular response to starvation | 1 |
| Cellular responses to stimuli | 1 |
| Cellular responses to stress | 1 |
GO top-level categories
Rollup of top GO terms by namespace:
| Category | Terms |
|---|---|
| negative regulation of cellular process | 2 |
| cellular anatomical structure | 2 |
| vesicle budding from membrane | 1 |
| membrane invagination | 1 |
| vesicle-mediated transport | 1 |
| import into cell | 1 |
| cell population proliferation | 1 |
| regulation of cell population proliferation | 1 |
| autophagy | 1 |
| positive regulation of catabolic process | 1 |
| regulation of autophagy | 1 |
| regulation of cell growth | 1 |
| cell growth | 1 |
| negative regulation of growth | 1 |
| TOR signaling | 1 |
| regulation of TOR signaling | 1 |
| negative regulation of intracellular signal transduction | 1 |
| GTPase activity | 1 |
| regulation of GTPase activity | 1 |
| negative regulation of biological process | 1 |
| negative regulation of hydrolase activity | 1 |
| catalytic activity | 1 |
| regulation of molecular function | 1 |
| protein localization to vacuole | 1 |
| response to amino acid | 1 |
| cellular response to acid chemical | 1 |
| GDP binding | 1 |
| GTPase regulator activity | 1 |
| GTPase binding | 1 |
| protein binding | 1 |
| binding | 1 |
| intracellular membrane-bounded organelle | 1 |
| intracellular anatomical structure | 1 |
| endomembrane system | 1 |
| membrane | 1 |
| coated vesicle | 1 |
| extracellular vesicle | 1 |
| cytoplasm | 1 |
| intracellular vesicle | 1 |
Protein interactions and networks
STRING
896 interactions, top by confidence (×1000):
| Protein A | Protein B | Partner UniProt | Score |
|---|---|---|---|
| SH3BP4 | EPS15 | P42566 | 799 |
| SH3BP4 | RRAGB | Q5VZM2 | 794 |
| SH3BP4 | NUMB | P49757 | 726 |
| SH3BP4 | NUMBL | Q9Y6R0 | 725 |
| SH3BP4 | EFNA5 | P52803 | 724 |
| SH3BP4 | SRC | P12931 | 562 |
| SH3BP4 | STON2 | Q8WXE9 | 522 |
| SH3BP4 | PDRG1 | Q9NUG6 | 495 |
| SH3BP4 | TMEM82 | A0PJX8 | 492 |
| SH3BP4 | SYNJ1 | O43426 | 480 |
| SH3BP4 | RAB11FIP2 | Q7L804 | 477 |
| SH3BP4 | RRAGC | Q9HB90 | 472 |
| SH3BP4 | SPATA3 | Q8NHX4 | 459 |
| SH3BP4 | SYNJ2 | O15056 | 455 |
| SH3BP4 | MYOF | Q9NZM1 | 451 |
IntAct
152 interactions, top by confidence:
| A | B | Type | Score |
|---|---|---|---|
| SH3BP4 | YWHAG | psi-mi:“MI:0915”(physical association) | 0.910 |
| SH3BP4 | GIPC1 | psi-mi:“MI:0914”(association) | 0.740 |
| GIPC1 | SH3BP4 | psi-mi:“MI:0915”(physical association) | 0.740 |
| ARHGEF12 | GIPC1 | psi-mi:“MI:0914”(association) | 0.720 |
| ARHGEF12 | GIPC1 | psi-mi:“MI:2364”(proximity) | 0.720 |
| CFTR | ESYT2 | psi-mi:“MI:2364”(proximity) | 0.710 |
| SH3BP4 | TFRC | psi-mi:“MI:0915”(physical association) | 0.670 |
| TFRC | SH3BP4 | psi-mi:“MI:0915”(physical association) | 0.670 |
| SH3BP4 | TFRC | psi-mi:“MI:0407”(direct interaction) | 0.670 |
| YWHAZ | SH3BP4 | psi-mi:“MI:0915”(physical association) | 0.650 |
| CETN1 | SFI1 | psi-mi:“MI:0914”(association) | 0.640 |
| YWHAG | BLTP3B | psi-mi:“MI:2364”(proximity) | 0.640 |
| YWHAH | PLEKHG3 | psi-mi:“MI:0914”(association) | 0.610 |
| EPS15 | SH3BP4 | psi-mi:“MI:0407”(direct interaction) | 0.610 |
| YWHAB | BLTP3B | psi-mi:“MI:2364”(proximity) | 0.610 |
| EPS15 | SH3BP4 | psi-mi:“MI:0915”(physical association) | 0.610 |
| SH3BP4 | Dnm2 | psi-mi:“MI:0915”(physical association) | 0.610 |
| Dnm2 | SH3BP4 | psi-mi:“MI:0407”(direct interaction) | 0.610 |
| SH3BP4 | Dnm2 | psi-mi:“MI:0407”(direct interaction) | 0.610 |
| YWHAH | BLTP3B | psi-mi:“MI:2364”(proximity) | 0.570 |
| YWHAG | SHTN1 | psi-mi:“MI:0914”(association) | 0.560 |
BioGRID (199): SH3BP4 (Affinity Capture-MS), SH3BP4 (Affinity Capture-MS), SH3BP4 (Affinity Capture-MS), SH3BP4 (Affinity Capture-MS), SH3BP4 (Affinity Capture-MS), SH3BP4 (Affinity Capture-MS), SH3BP4 (Affinity Capture-MS), SH3BP4 (Affinity Capture-MS), SH3BP4 (Affinity Capture-MS), SH3BP4 (Affinity Capture-MS), SH3BP4 (Affinity Capture-MS), SH3BP4 (Affinity Capture-MS), SH3BP4 (Affinity Capture-MS), SH3BP4 (Affinity Capture-MS), SH3BP4 (Affinity Capture-MS)
ESM2 similar proteins: A0A0R4I9Y1, A0A0R4IBK5, A2ARZ3, A5WUT8, A6NKT7, A7S7F2, E9Q3L2, E9Q555, F1QB81, F5H4B4, H2QII6, O08662, O14715, O15050, O43310, P0DJD0, P0DJD1, P13864, P42356, P49792, Q06190, Q0V9S3, Q0VF22, Q16533, Q1LVQ2, Q24K09, Q2T9I9, Q4R6W9, Q4V847, Q5U228, Q63HN8, Q65Z40, Q6NU22, Q6NU51, Q7TPV2, Q7Z3J3, Q80TA9, Q811D2, Q86Y13, Q921I6
Diamond homologs: A0JNB0, A1A5H8, A1DFN5, A1Y2K1, P00523, P00524, P00525, P00526, P05480, P06241, P09324, P12931, P13115, P13116, P13406, P14084, P14085, P15054, P17713, P25020, P27447, P34109, P39688, P63185, Q05876, Q1JPZ3, Q1LVQ2, Q5RBY8, Q5U228, Q62844, Q6EWH2, Q6NU22, Q6NU51, Q6ZN28, Q8AXQ3, Q921I6, Q9JJS5, Q9P0V3, Q9V9J3, Q9WUD9
SIGNOR signaling
1 interactions.
| A | Effect | B | Mechanism |
|---|---|---|---|
| SH3BP4 | down-regulates | TFRC | binding |
Enriched among interaction partners
Reactome pathways and GO biological processes over-represented among this gene’s 113 IntAct physical interaction partners (hypergeometric vs the genome-wide background, BH-FDR, gene-set size 15–500, ranked by fold). A functional readout of the neighbourhood — distinct from this gene’s own memberships above, and biased toward well-studied / hub proteins, so read it as themes rather than proof.
Reactome pathways:
| Pathway | Partners | Fold | FDR |
|---|---|---|---|
| Activation of BAD and translocation to mitochondria | 7 | 76.1× | 3e-10 |
| Chk1/Chk2(Cds1) mediated inactivation of Cyclin B:Cdk1 complex | 7 | 67.2× | 5e-10 |
| SARS-CoV-1 targets host intracellular signalling and regulatory pathways | 7 | 67.2× | 5e-10 |
| Activation of BH3-only proteins | 7 | 49.6× | 4e-09 |
| RHO GTPases activate PKNs | 7 | 31.7× | 1e-07 |
| Intrinsic Pathway for Apoptosis | 7 | 29.3× | 2e-07 |
| FOXO-mediated transcription | 5 | 24.0× | 4e-05 |
| SARS-CoV-1-host interactions | 7 | 17.6× | 5e-06 |
GO biological processes:
| GO term | Partners | Fold | FDR |
|---|---|---|---|
| protein targeting | 7 | 27.0× | 4e-06 |
| intracellular protein localization | 9 | 9.9× | 1e-04 |
Disease & clinical
Clinical variants and AI predictions
ClinVar
169 variants total. Per-class counts are floors (≥ shown; pagination cap):
| Classification | Count (floor) |
|---|---|
| Pathogenic | 0 |
| Likely pathogenic | 0 |
| Uncertain significance | 133 |
| Likely benign | 15 |
| Benign | 7 |
Top pathogenic / likely-pathogenic (0)
SpliceAI
2095 predictions. Top by Δscore:
| Variant | Effect | Δscore |
|---|---|---|
| 2:234952172:T:G | donor_loss | 1.0000 |
| 2:234995297:TTGCA:T | acceptor_loss | 1.0000 |
| 2:234995298:TGCAG:T | acceptor_loss | 1.0000 |
| 2:234995300:CA:C | acceptor_loss | 1.0000 |
| 2:234995301:A:AG | acceptor_gain | 1.0000 |
| 2:234995301:AGC:A | acceptor_gain | 1.0000 |
| 2:234995302:G:GA | acceptor_gain | 1.0000 |
| 2:234995302:GC:G | acceptor_gain | 1.0000 |
| 2:234995302:GCG:G | acceptor_gain | 1.0000 |
| 2:234995302:GCGT:G | acceptor_gain | 1.0000 |
| 2:234995372:ACCAG:A | donor_loss | 1.0000 |
| 2:234995374:CAGG:C | donor_loss | 1.0000 |
| 2:234995376:GG:G | donor_loss | 1.0000 |
| 2:234995377:GTA:G | donor_loss | 1.0000 |
| 2:234995378:T:G | donor_loss | 1.0000 |
| 2:235035121:G:GA | donor_loss | 1.0000 |
| 2:235035122:T:G | donor_loss | 1.0000 |
| 2:235040884:A:AG | acceptor_gain | 1.0000 |
| 2:235040884:ACAGT:A | acceptor_gain | 1.0000 |
| 2:235040885:C:G | acceptor_gain | 1.0000 |
| 2:235040886:A:AG | acceptor_gain | 1.0000 |
| 2:235040887:G:GT | acceptor_gain | 1.0000 |
| 2:235040887:GT:G | acceptor_gain | 1.0000 |
| 2:235052557:T:TA | acceptor_gain | 1.0000 |
| 2:235052559:CA:C | acceptor_loss | 1.0000 |
| 2:235052560:A:AG | acceptor_gain | 1.0000 |
| 2:235052560:A:C | acceptor_loss | 1.0000 |
| 2:235052560:AG:A | acceptor_gain | 1.0000 |
| 2:235052561:G:GC | acceptor_gain | 1.0000 |
| 2:235052561:GG:G | acceptor_gain | 1.0000 |
AlphaMissense
0 scored. Top likely-pathogenic:
dbSNP variants (sampled 300 via entrez): RS1000006154 (2:234990634 G>A), RS1000024534 (2:235038662 A>C,G), RS1000028771 (2:235002698 C>A,G), RS1000137896 (2:234987031 CA>C), RS1000140993 (2:235033315 C>A,T), RS1000158187 (2:234950935 G>A), RS1000160649 (2:235037472 T>G), RS1000181309 (2:235019975 C>T), RS1000190450 (2:234992646 C>T), RS1000245581 (2:235007396 C>T), RS1000256296 (2:234972042 C>T), RS1000287194 (2:235028009 C>A,T), RS1000375946 (2:235038213 T>A), RS1000399065 (2:234967923 T>C), RS1000406494 (2:234987970 A>G)
Disease associations
OMIM: gene MIM:605611 | disease phenotypes:
GenCC curated gene-disease
Mondo (0):
Orphanet (0):
HPO phenotypes
0 total (0 of 0 shown, HPO-id order):
GWAS associations
12 associations (top):
| Study | Trait | p-value |
|---|---|---|
| GCST001066_25 | Dialysis-related mortality | 9.000000e-06 |
| GCST001442_12 | Orofacial clefts | 7.000000e-07 |
| GCST004227_9 | Obstetric antiphospholipid syndrome | 9.000000e-06 |
| GCST005993_2 | Mean corpuscular hemoglobin | 3.000000e-08 |
| GCST006011_23 | Mean corpuscular volume | 5.000000e-09 |
| GCST006427_30 | Depression in smokers | 2.000000e-06 |
| GCST011742_12 | Triglyceride levels in HIV infection | 2.000000e-07 |
| GCST012308_9 | Schizophrenia | 3.000000e-07 |
| GCST012309_9 | Schizophrenia | 2.000000e-07 |
| GCST012311_19 | Schizophrenia x sex interaction | 3.000000e-06 |
| GCST90002400_348 | Plateletcrit | 3.000000e-12 |
| GCST90002402_294 | Platelet count | 7.000000e-14 |
EFO canonical traits (5, from GWAS)
| EFO ID | Trait name |
|---|---|
| EFO:0004527 | mean corpuscular hemoglobin |
| EFO:0004530 | triglyceride measurement |
| EFO:0008343 | sex interaction measurement |
| EFO:0007985 | platelet crit |
| EFO:0004309 | platelet count |
Drugs & pharmacology
Drug and pharmacology data
Is drug target: no
PharmGKB: 1 entry (VIP=true, CPIC=false)
CTD chemical–gene interactions
50 total (human), top 30 by PubMed support.
| Chemical | Actions (top 5) | PubMed papers |
|---|---|---|
| Valproic Acid | affects expression, decreases methylation, increases expression | 4 |
| Benzo(a)pyrene | affects methylation, increases expression | 3 |
| Tobacco Smoke Pollution | affects expression, decreases expression, increases expression | 3 |
| Silver | increases expression | 2 |
| Aflatoxin B1 | increases expression, increases methylation | 2 |
| 3,19-(2-bromobenzylidene)andrographolide | decreases response to substance, increases expression | 1 |
| FR900359 | affects phosphorylation | 1 |
| dicrotophos | increases expression | 1 |
| methylmercuric chloride | increases expression | 1 |
| alpha-pinene | affects cotreatment, decreases expression, increases abundance | 1 |
| bisphenol A | affects cotreatment, increases methylation | 1 |
| beta-lapachone | increases expression | 1 |
| afimoxifene | decreases expression, decreases reaction | 1 |
| sodium arsenite | increases expression | 1 |
| cobaltous chloride | increases expression | 1 |
| benzo(e)pyrene | increases methylation | 1 |
| 2,3-bis(3’-hydroxybenzyl)butyrolactone | affects cotreatment, decreases expression | 1 |
| coumarin | decreases phosphorylation | 1 |
| methacrylaldehyde | increases abundance, affects cotreatment, decreases expression | 1 |
| perfluorooctane sulfonic acid | decreases expression | 1 |
| CGP 52608 | affects binding, increases reaction | 1 |
| Resveratrol | affects cotreatment, decreases expression | 1 |
| Temozolomide | increases expression | 1 |
| Fulvestrant | affects cotreatment, increases methylation | 1 |
| Leflunomide | increases expression | 1 |
| Acetaminophen | increases expression | 1 |
| Acrolein | affects cotreatment, decreases expression, increases abundance | 1 |
| Air Pollutants | affects cotreatment, decreases expression, increases abundance | 1 |
| Atrazine | decreases expression | 1 |
| Cadmium | increases abundance, decreases expression | 1 |
Cellosaurus cell lines
1 cell lines: 1 transformed cell line
First 10 cell lines (id-ordered, not curated):
| Cellosaurus | Name | Category | Sex |
|---|---|---|---|
| CVCL_D9RJ | Ubigene HEK293 SH3BP4 KO | Transformed cell line | Female |
Clinical trials (associated diseases)
0 trials via MONDO — disease-level, not drug-specific.
Related Atlas pages
- Disease cohort memberships (association, not causation — diseases whose associated-gene cohort lists this gene; a subset are also under Associated diseases): antiphospholipid syndrome, chronic kidney disease, major depressive disorder, orofacial cleft