RNF186
gene geneOn this page
Also known as FLJ20225
Summary
RNF186 (ring finger protein 186, HGNC:25978) is a protein-coding gene on chromosome 1p36.13, encoding E3 ubiquitin-protein ligase RNF186 (Q9NXI6). E3 ubiquitin protein ligase that is part of an apoptotic signaling pathway activated by endoplasmic reticulum stress.
Enables ubiquitin protein ligase activity and ubiquitin protein ligase binding activity. Involved in several processes, including intrinsic apoptotic signaling pathway in response to endoplasmic reticulum stress; proteasome-mediated ubiquitin-dependent protein catabolic process; and protein ubiquitination. Acts upstream of with a positive effect on regulation of autophagosome assembly. Located in endoplasmic reticulum membrane. Is active in endoplasmic reticulum.
Source: NCBI Gene 54546 — RefSeq curated summary.
At a glance
- GWAS associations: 9
- Clinical variants (ClinVar): 55 total — 1 likely-pathogenic
- MANE Select transcript:
NM_019062
Identifiers
Gene identifiers
| Field | Value |
|---|---|
| HGNC ID | HGNC:25978 |
| Approved symbol | RNF186 |
| Name | ring finger protein 186 |
| Location | 1p36.13 |
| Locus type | gene with protein product |
| Status | Approved |
| Aliases | FLJ20225 |
| Ensembl gene | ENSG00000178828 |
| Ensembl biotype | protein_coding |
| OMIM | 617163 |
| Entrez | 54546 |
Gene structure
Transcript identifiers
Ensembl transcripts: 1 — 1 protein_coding
ENST00000375121
RefSeq mRNA: 1 — MANE Select: NM_019062
NM_019062
CCDS: CCDS199
Canonical transcript exons
ENST00000375121 — 1 exons
| Exon | Start | End |
|---|---|---|
| ENSE00001465820 | 19814029 | 19815283 |
Expression profiles
Bgee: expression breadth broad, 76 present calls, max score 96.87.
FANTOM5 (CAGE): breadth tissue_specific, TPM avg 0.4944 / max 156.5897, expressed in 30 samples.
FANTOM5 promoters (5 alternative TSS)
| Promoter ID | TPM avg | Samples expressed |
|---|---|---|
| 10695 | 0.2335 | 22 |
| 10691 | 0.0987 | 17 |
| 10694 | 0.0765 | 15 |
| 10692 | 0.0540 | 11 |
| 10693 | 0.0317 | 12 |
Top tissues by expression
269 total, by Bgee expression score (0-100, higher = more expressed):
| Tissue | Anatomy ID | Expression score | Quality |
|---|---|---|---|
| jejunal mucosa | UBERON:0000399 | 96.87 | gold quality |
| duodenum | UBERON:0002114 | 95.50 | gold quality |
| corpus epididymis | UBERON:0004359 | 92.47 | gold quality |
| nephron tubule | UBERON:0001231 | 91.19 | gold quality |
| body of pancreas | UBERON:0001150 | 90.69 | gold quality |
| mucosa of transverse colon | UBERON:0004991 | 88.47 | gold quality |
| kidney epithelium | UBERON:0004819 | 86.99 | gold quality |
| colonic mucosa | UBERON:0000317 | 85.82 | gold quality |
| renal glomerulus | UBERON:0000074 | 85.45 | gold quality |
| metanephric glomerulus | UBERON:0004736 | 85.31 | gold quality |
| mucosa of sigmoid colon | UBERON:0004993 | 84.67 | gold quality |
| pancreatic ductal cell | CL:0002079 | 84.40 | silver quality |
| adult mammalian kidney | UBERON:0000082 | 84.16 | gold quality |
| rectum | UBERON:0001052 | 83.55 | gold quality |
| pancreas | UBERON:0001264 | 80.06 | gold quality |
| kidney | UBERON:0002113 | 78.53 | gold quality |
| cortex of kidney | UBERON:0001225 | 78.08 | gold quality |
| transverse colon | UBERON:0001157 | 75.84 | gold quality |
| jejunum | UBERON:0002115 | 75.22 | gold quality |
| ileal mucosa | UBERON:0000331 | 73.98 | gold quality |
| vermiform appendix | UBERON:0001154 | 73.67 | gold quality |
| caecum | UBERON:0001153 | 71.95 | gold quality |
| metanephros | UBERON:0000081 | 71.27 | gold quality |
| small intestine | UBERON:0002108 | 70.21 | gold quality |
| oocyte | CL:0000023 | 69.43 | gold quality |
| caput epididymis | UBERON:0004358 | 68.58 | gold quality |
| small intestine Peyer’s patch | UBERON:0003454 | 67.29 | gold quality |
| intestine | UBERON:0000160 | 65.98 | gold quality |
| secondary oocyte | CL:0000655 | 65.67 | gold quality |
| large intestine | UBERON:0000059 | 64.68 | gold quality |
Single-cell (SCXA)
Detected in 2 experiment(s), a significant marker in 2.
| Experiment | Marker? | Max mean expression |
|---|---|---|
| E-GEOD-125970 | yes | 15.67 |
| E-ANND-3 | yes | 11.19 |
Regulation
Is transcription factor: no
miRNA regulators (miRDB)
27 targeting RNF186, top 30 by miRDB confidence (max_score; target_count = how many genes the miRNA targets in total — lower means more specific):
| miRNA | Max score | Avg score | miRNA target_count |
|---|---|---|---|
| HSA-MIR-548AW | 99.99 | 72.57 | 3559 |
| HSA-MIR-4482-3P | 99.98 | 72.50 | 3147 |
| HSA-MIR-145-5P | 99.92 | 71.13 | 1836 |
| HSA-MIR-5195-3P | 99.92 | 70.92 | 1877 |
| HSA-MIR-1297 | 99.91 | 73.41 | 3162 |
| HSA-MIR-26A-5P | 99.78 | 73.52 | 2303 |
| HSA-MIR-26B-5P | 99.78 | 73.51 | 2305 |
| HSA-MIR-6505-5P | 99.73 | 69.25 | 1595 |
| HSA-MIR-26A-1-3P | 99.64 | 66.81 | 788 |
| HSA-MIR-26A-2-3P | 99.64 | 66.82 | 786 |
| HSA-MIR-4328 | 99.57 | 71.06 | 4094 |
| HSA-MIR-5697 | 99.39 | 67.74 | 1249 |
| HSA-MIR-6853-3P | 99.36 | 70.79 | 1558 |
| HSA-MIR-3168 | 99.08 | 67.75 | 1384 |
| HSA-MIR-6814-5P | 99.03 | 66.68 | 1273 |
| HSA-MIR-10A-5P | 98.89 | 69.85 | 712 |
| HSA-MIR-10B-5P | 98.89 | 69.86 | 711 |
| HSA-MIR-6829-5P | 98.86 | 65.12 | 1480 |
| HSA-MIR-4289 | 98.26 | 66.90 | 810 |
| HSA-MIR-4436B-3P | 98.25 | 65.26 | 1494 |
| HSA-MIR-6735-5P | 98.24 | 65.36 | 1488 |
| HSA-MIR-7843-5P | 98.12 | 65.26 | 1421 |
| HSA-MIR-4632-5P | 97.82 | 65.38 | 1470 |
| HSA-MIR-6879-5P | 97.77 | 65.52 | 1521 |
| HSA-MIR-4642 | 97.52 | 67.60 | 916 |
| HSA-MIR-214-5P | 97.34 | 66.50 | 617 |
| HSA-MIR-1266-3P | 96.23 | 66.36 | 778 |
Literature-anchored findings (GeneRIF, showing 10)
- Single-nucleotide polymorphism in RNF186 gene is associated with ulcerative colitis. (PMID:23511034)
- BNip1 functions as a downstream modulator of RNF186 to direct endoplasmic reticulum stress-associated apoptotic signaling. (PMID:23896122)
- Our results confirmed significant association to rare non-synonymous coding variants in both IL23R and CARD9, previously identified from sequencing of CD loci, as well as identified a novel association in RNF186 (PMID:24068945)
- a predicted protein-truncating variant (rs36095412, p.R179X, genotyped in 11,148 ulcerative colitis patients and 295,446 controls, MAF=up to 0.78%) in RNF186, a single-exon ring finger E3 ligase with strong colonic expression, protects against ulcerative colitis. (PMID:27503255)
- RNF186 and Sestrin-2 bind each other through distinct C-terminal motifs and that Lys-13 in Sestrin-2 is a putative ubiquitin acceptor site. RNF186 knockdown increased Sestrin-2 protein levels and decreased mTORC1 activation. (PMID:31586034)
- The Role of Tissue-Specific Ubiquitin Ligases, RNF183, RNF186, RNF182 and RNF152, in Disease and Biological Function. (PMID:32486221)
- The role and mechanism of action of RNF186 in colorectal cancer through negative regulation of NF-kappaB. (PMID:32882406)
- The E3 ubiquitin ligase RNF186 and RNF186 risk variants regulate innate receptor-induced outcomes. (PMID:34353900)
- Ubiquitination of ATF6 by disease-associated RNF186 promotes the innate receptor-induced unfolded protein response. (PMID:34623328)
- Systematic pan-cancer analysis of RNF186 with potential implications in progression and prognosis in human cancer. (PMID:38160786)
Cross-species orthologs
2 orthologs
| Organism | Symbol | Gene ID |
|---|---|---|
| mus_musculus | Rnf186 | ENSMUSG00000070661 |
| rattus_norvegicus | Rnf186 | ENSRNOG00000017244 |
Protein
Protein identifiers
E3 ubiquitin-protein ligase RNF186 — Q9NXI6 (reviewed: Q9NXI6)
Alternative names: RING finger protein 186
All UniProt accessions (1): Q9NXI6
UniProt curated annotations — full annotation on UniProt →
Function. E3 ubiquitin protein ligase that is part of an apoptotic signaling pathway activated by endoplasmic reticulum stress. Stimulates the expression of proteins specific of the unfolded protein response (UPR), ubiquitinates BNIP1 and regulates its localization to the mitochondrion and induces calcium release from the endoplasmic reticulum that ultimately leads to cell apoptosis. Plays a role in the maintenance of intestinal homeostasis and clearance of enteric pathogens. Upon NOD2 stimulation, ubiquitinates the ER stress sensor activating transcription factor 6/ATF6 and promotes the unfolded protein response UPR. Participates in basal level of autophagy maintenance by regulating the ubiquitination of EPHB2 and EPHB3. Upon stimulation by ligand EFNB1, ubiquitinates EPHB2 and further recruits MAP1LC3B for autophagy induction. Controls nutrient sensing by ubiquitinating Sestrin-2/SESN2, which is an intracellular sensor of cytosolic leucine and inhibitor of mTORC1 activity.
Subunit / interactions. Interacts with BNIP1.
Subcellular location. Endoplasmic reticulum membrane.
Post-translational modifications. Polyubiquitinated. ‘Lys-29’-linked autoubiquitination leads to proteasomal degradation.
Domain organisation. The RING-type domain is required for ubiquitination.
Pathway. Protein modification; protein ubiquitination.
RefSeq proteins (1): NP_061935* (*=MANE)
Domains & families (InterPro)
| ID | Name | Type |
|---|---|---|
| IPR001841 | Znf_RING | Domain |
| IPR013083 | Znf_RING/FYVE/PHD | Homologous_superfamily |
| IPR017907 | Znf_RING_CS | Conserved_site |
| IPR051435 | RING_finger_E3_ubiq-ligases | Family |
Enzyme classification (BRENDA):
- EC 2.3.2.27 — RING-type E3 ubiquitin transferase (BRENDA: 28 organisms, 138 substrates, 10 inhibitors, 1 Km, 1 kcat entries)
Substrate kinetics (BRENDA)
1 substrates with measured Km, best-characterized 1. Km ranges are aggregated across organisms/conditions.
| Substrate | Km (mM) | Measurements |
|---|---|---|
| [UBE2W]-S-UBIQUITINYL-L-CYSTEINE | 0.3014 | 1 |
UniProt features (10 total): mutagenesis site 3, transmembrane region 2, sequence variant 2, chain 1, zinc finger region 1, sequence conflict 1
Structure
Experimental structures (PDB)
0 structures.
Predicted structure (AlphaFold)
| Model | pLDDT | Fraction very-high |
|---|---|---|
| AF-Q9NXI6-F1 | 68.89 | 0.22 |
Functional residue map
Curated UniProt residues grouped by drug-discovery relevance — catalytic, ligand-binding, modification, and mutation-validated positions. Source: UniProtKB sequence features.
Mutagenesis-validated functional residues (3):
| Position | Phenotype |
|---|---|
| 58–66 | loss of autoubiquitination; loss of bnip1 polyubiquitination; no effect on interaction with bnip1; decreased effect on c |
| 60 | loss of ability to decrease sesn2 protein. |
| 64 | exhibits a reduced ability to ubiquitinate ephb2 but retained ability to ubiquitinate ephb3. |
Function
Pathways and Gene Ontology
Reactome pathways
0 pathways
MSigDB gene sets: 79 (showing top):
GOBP_RESPONSE_TO_ENDOPLASMIC_RETICULUM_STRESS, GOBP_MACROMOLECULE_CATABOLIC_PROCESS, HNF1_Q6, GOBP_APOPTOTIC_SIGNALING_PATHWAY, RGTTAMWNATT_HNF1_01, GATA6_01, GOBP_PROTEIN_AUTOUBIQUITINATION, TGANTCA_AP1_C, GOBP_POST_TRANSLATIONAL_PROTEIN_MODIFICATION, GOBP_PROTEIN_POLYUBIQUITINATION, GOBP_INTRINSIC_APOPTOTIC_SIGNALING_PATHWAY, HNF1_C, TGGNNNNNNKCCAR_UNKNOWN, GOBP_PROTEIN_LOCALIZATION_TO_ORGANELLE, GOBP_PROTEIN_K63_LINKED_UBIQUITINATION
GO Biological Process (9): protein K29-linked ubiquitination (GO:0035519), proteasome-mediated ubiquitin-dependent protein catabolic process (GO:0043161), protein autoubiquitination (GO:0051865), intrinsic apoptotic signaling pathway in response to endoplasmic reticulum stress (GO:0070059), protein K63-linked ubiquitination (GO:0070534), protein localization to mitochondrion (GO:0070585), protein ubiquitination (GO:0016567), apoptotic process in response to mitochondrial fragmentation (GO:0140208), regulation of autophagosome assembly (GO:2000785)
GO Molecular Function (7): ubiquitin-protein transferase activity (GO:0004842), zinc ion binding (GO:0008270), ubiquitin protein ligase binding (GO:0031625), ubiquitin protein ligase activity (GO:0061630), protein binding (GO:0005515), transferase activity (GO:0016740), metal ion binding (GO:0046872)
GO Cellular Component (3): endoplasmic reticulum (GO:0005783), endoplasmic reticulum membrane (GO:0005789), membrane (GO:0016020)
GO top-level categories
Rollup of top GO terms by namespace:
| Category | Terms |
|---|---|
| protein polyubiquitination | 2 |
| ubiquitin-dependent protein catabolic process | 1 |
| proteasomal protein catabolic process | 1 |
| protein ubiquitination | 1 |
| response to endoplasmic reticulum stress | 1 |
| intrinsic apoptotic signaling pathway | 1 |
| protein localization to organelle | 1 |
| protein modification by small protein conjugation | 1 |
| apoptotic process | 1 |
| autophagosome assembly | 1 |
| regulation of vacuole organization | 1 |
| regulation of organelle assembly | 1 |
| ubiquitin-like protein transferase activity | 1 |
| transition metal ion binding | 1 |
| ubiquitin-like protein ligase binding | 1 |
| ubiquitin-protein transferase activity | 1 |
| ubiquitin-like protein ligase activity | 1 |
| binding | 1 |
| catalytic activity | 1 |
| cation binding | 1 |
| cytoplasm | 1 |
| endomembrane system | 1 |
| intracellular membrane-bounded organelle | 1 |
| organelle membrane | 1 |
| nuclear outer membrane-endoplasmic reticulum membrane network | 1 |
| endoplasmic reticulum subcompartment | 1 |
| cellular anatomical structure | 1 |
Protein interactions and networks
STRING
420 interactions, top by confidence (×1000):
| Protein A | Protein B | Partner UniProt | Score |
|---|---|---|---|
| RNF186 | OTUD3 | Q5T2D3 | 620 |
| RNF186 | RNF183 | Q96D59 | 620 |
| RNF186 | PLA2G2E | Q9NZK7 | 609 |
| RNF186 | RNF182 | Q8N6D2 | 576 |
| RNF186 | CARD9 | Q9H257 | 524 |
| RNF186 | RNF175 | Q8N4F7 | 504 |
| RNF186 | BNIP1 | Q12981 | 469 |
| RNF186 | RNF150 | Q9ULK6 | 454 |
| RNF186 | SVOPL | Q8N434 | 449 |
| RNF186 | ZNRF4 | Q8WWF5 | 447 |
| RNF186 | IL23R | Q5VWK5 | 432 |
| RNF186 | KBTBD3 | Q8NAB2 | 429 |
| RNF186 | SLC25A45 | Q8N413 | 414 |
| RNF186 | BTNL2 | Q9UIR0 | 410 |
| RNF186 | INAVA | Q3KP66 | 403 |
IntAct
13 interactions, top by confidence:
| A | B | Type | Score |
|---|---|---|---|
| RNF186 | psi-mi:“MI:0915”(physical association) | 0.560 | |
| PBX3 | RNF186 | psi-mi:“MI:0915”(physical association) | 0.560 |
| SCAND1 | RNF186 | psi-mi:“MI:0915”(physical association) | 0.560 |
| UBE2D2 | RNF186 | psi-mi:“MI:0915”(physical association) | 0.370 |
| RNF186 | UBE2H | psi-mi:“MI:0915”(physical association) | 0.370 |
| RNF186 | TFRC | psi-mi:“MI:0914”(association) | 0.350 |
| RNF186 | psi-mi:“MI:0915”(physical association) | 0.000 | |
| PBX3 | RNF186 | psi-mi:“MI:0915”(physical association) | 0.000 |
| SCAND1 | RNF186 | psi-mi:“MI:0915”(physical association) | 0.000 |
BioGRID (22): RNF186 (PCA), RNF186 (Two-hybrid), RNF186 (Two-hybrid), RNF186 (Two-hybrid), SESN2 (Reconstituted Complex), RNF186 (Reconstituted Complex), EPHB2 (Affinity Capture-MS), EPHB3 (Affinity Capture-MS), TOLLIP (Affinity Capture-MS), TFRC (Affinity Capture-MS), TRIM21 (Affinity Capture-MS), EPHB2 (Affinity Capture-Western), EPHB3 (Affinity Capture-Western), RNF186 (Affinity Capture-Western), RNF186 (Affinity Capture-Western)
ESM2 similar proteins: A6NCL7, A6NCQ9, A6QP29, A6QQV9, B1AVH7, B5DFA1, D2H0G5, D2H6Z0, D2H788, D3ZBM4, D4A723, E1C2W7, O95153, Q0QWG9, Q3SWY0, Q3T0Y9, Q3U0L2, Q3UV31, Q3V3A7, Q5RF77, Q60943, Q6INB3, Q6PGG2, Q7TNF8, Q7Z465, Q80TI1, Q810L3, Q8BG47, Q8BRJ3, Q8BXP5, Q8C0R7, Q8C432, Q8CEF8, Q8HYZ0, Q8N0U2, Q8N6D2, Q8N8N0, Q8NC24, Q8QZS5, Q8TED9
Diamond homologs: A0A7I2V3R4, A6NIN4, D2H788, D3ZBM4, O70277, O75382, Q13049, Q3T0Y9, Q6IMG5, Q6INB3, Q8C432, Q8CH72, Q8K0W3, Q8N6D2, Q9DCB3, Q9FY48, Q9H0X6, Q9NXI6, Q9R1R2, Q58EC8, Q9D241, Q9VE61, D2H6Z0, D4A723, E1C2W7, P36406, P36407, Q3SWY0, Q68EV7, Q6GND7, Q6NRD3, Q8BG47, Q8BGX0, Q8N8N0, Q8QZS5, E7ERA6, P33288, Q3UV31, Q96D59
SIGNOR signaling
1 interactions.
| A | Effect | B | Mechanism |
|---|---|---|---|
| Ub:E2 | “up-regulates activity” | RNF186 | ubiquitination |
Disease & clinical
Clinical variants and AI predictions
ClinVar
55 variants total. Per-class counts are floors (≥ shown; pagination cap):
| Classification | Count (floor) |
|---|---|
| Pathogenic | 0 |
| Likely pathogenic | 1 |
| Uncertain significance | 50 |
| Likely benign | 4 |
| Benign | 0 |
Top pathogenic / likely-pathogenic (1)
| Variant ID | HGVS | Classification |
|---|---|---|
| 3767281 | NC_000001.11:g.19676448_19875998del | Likely pathogenic |
SpliceAI
141 predictions. Top by Δscore:
| Variant | Effect | Δscore |
|---|---|---|
| 1:19814668:A:AC | donor_gain | 0.8600 |
| 1:19814669:C:CC | donor_gain | 0.8600 |
| 1:19814838:G:T | donor_gain | 0.8500 |
| 1:19814834:CGG:C | donor_gain | 0.7600 |
| 1:19814669:CTT:C | donor_gain | 0.7300 |
| 1:19814837:TG:T | donor_gain | 0.7000 |
| 1:19814836:G:GC | donor_gain | 0.6500 |
| 1:19814497:GTGCT:G | acceptor_loss | 0.6300 |
| 1:19814499:GCTGG:G | acceptor_loss | 0.6300 |
| 1:19814566:C:CT | acceptor_gain | 0.6300 |
| 1:19814500:C:CC | acceptor_gain | 0.6100 |
| 1:19814662:GCACT:G | donor_loss | 0.6100 |
| 1:19814663:CACT:C | donor_loss | 0.6100 |
| 1:19814664:ACTTA:A | donor_loss | 0.6100 |
| 1:19814665:CT:C | donor_loss | 0.6100 |
| 1:19814666:T:TC | donor_loss | 0.6100 |
| 1:19814667:TAC:T | donor_loss | 0.6100 |
| 1:19814668:ACTTC:A | donor_loss | 0.6100 |
| 1:19814669:C:CA | donor_loss | 0.6100 |
| 1:19814661:TGCAC:T | donor_loss | 0.6000 |
| 1:19814786:C:CT | donor_gain | 0.5900 |
| 1:19814498:TG:T | acceptor_gain | 0.5700 |
| 1:19814878:T:TA | donor_gain | 0.5700 |
| 1:19814493:CCGGG:C | acceptor_gain | 0.5500 |
| 1:19814577:C:T | acceptor_gain | 0.5500 |
| 1:19814787:C:CT | donor_gain | 0.5500 |
| 1:19814512:C:CT | acceptor_gain | 0.5400 |
| 1:19814578:G:T | acceptor_gain | 0.5400 |
| 1:19814669:CT:C | donor_gain | 0.5300 |
| 1:19814576:CCGGG:C | acceptor_gain | 0.5200 |
AlphaMissense
1443 scored. Top likely-pathogenic:
| Variant | Protein change | am_pathogenicity |
|---|---|---|
| 1:19814916:G:C | F62L | 0.993 |
| 1:19814916:G:T | F62L | 0.993 |
| 1:19814918:A:G | F62L | 0.993 |
| 1:19814940:C:A | K54N | 0.989 |
| 1:19814940:C:G | K54N | 0.989 |
| 1:19814904:G:C | C66W | 0.984 |
| 1:19814858:A:G | C82R | 0.983 |
| 1:19814984:A:G | C40R | 0.981 |
| 1:19814906:A:G | C66R | 0.980 |
| 1:19814913:G:C | C63W | 0.979 |
| 1:19814914:C:T | C63Y | 0.978 |
| 1:19814856:G:C | C82W | 0.975 |
| 1:19814905:C:T | C66Y | 0.974 |
| 1:19814915:A:G | C63R | 0.974 |
| 1:19814917:A:G | F62S | 0.974 |
| 1:19814975:A:G | C43R | 0.973 |
| 1:19814974:C:G | C43S | 0.972 |
| 1:19814975:A:T | C43S | 0.972 |
| 1:19814917:A:C | F62C | 0.969 |
| 1:19814846:G:T | R86S | 0.968 |
| 1:19814930:A:G | C58R | 0.968 |
| 1:19814830:A:T | V91D | 0.967 |
| 1:19814849:A:G | C85R | 0.967 |
| 1:19814922:A:C | H60Q | 0.966 |
| 1:19814922:A:T | H60Q | 0.966 |
| 1:19814983:C:G | C40S | 0.966 |
| 1:19814984:A:T | C40S | 0.966 |
| 1:19814848:C:G | C85S | 0.965 |
| 1:19814849:A:T | C85S | 0.965 |
| 1:19814847:G:C | C85W | 0.963 |
dbSNP variants (sampled 300 via entrez): RS1002502163 (1:19813623 A>C), RS1003768412 (1:19814664 A>C), RS1003816950 (1:19816070 G>A), RS1003982515 (1:19816371 G>T), RS1004311936 (1:19816657 C>T), RS1004417911 (1:19816166 C>T), RS1005826765 (1:19813982 C>T), RS1006288097 (1:19816093 G>A), RS1006322648 (1:19815493 A>C), RS1007717131 (1:19816706 T>C), RS1008250187 (1:19814114 C>A,T), RS1008602260 (1:19814335 C>G,T), RS1009763148 (1:19815846 A>C), RS1010249420 (1:19815572 G>A,C), RS1011180434 (1:19817096 C>G,T)
Disease associations
OMIM: gene MIM:617163 | disease phenotypes: MIM:300310
GenCC curated gene-disease
Mondo (1): immunodeficiency 61 (MONDO:0010296)
Orphanet (3): Non-syndromic agammaglobulinemia (Orphanet:229717), X-linked agammaglobulinemia (Orphanet:47), X-linked common variable immunodeficiency phenotype due to SH3KBP1 deficiency (Orphanet:696945)
HPO phenotypes
0 total (0 of 0 shown, HPO-id order):
GWAS associations
9 associations (top):
| Study | Trait | p-value |
|---|---|---|
| GCST000311_7 | Ulcerative colitis | 7.000000e-09 |
| GCST000624_1 | Ulcerative colitis | 3.000000e-08 |
| GCST000624_11 | Ulcerative colitis | 2.000000e-10 |
| GCST000624_21 | Ulcerative colitis | 2.000000e-21 |
| GCST001938_4 | Ulcerative colitis | 7.000000e-09 |
| GCST004131_40 | Inflammatory bowel disease | 1.000000e-19 |
| GCST004133_1 | Ulcerative colitis | 3.000000e-42 |
| GCST005537_152 | Chronic inflammatory diseases (ankylosing spondylitis, Crohn’s disease, psoriasis, primary sclerosing cholangitis, ulcerative colitis) (pleiotropy) | 1.000000e-24 |
| GCST005537_153 | Chronic inflammatory diseases (ankylosing spondylitis, Crohn’s disease, psoriasis, primary sclerosing cholangitis, ulcerative colitis) (pleiotropy) | 8.000000e-20 |
MeSH disease descriptors (1)
| Descriptor | Name | Tree numbers |
|---|---|---|
| C538057 | Agammaglobulinemia, X-linked, type 2 (supp.) |
Drugs & pharmacology
Drug and pharmacology data
Is drug target: no
PharmGKB: 1 entry (VIP=true, CPIC=false)
CTD chemical–gene interactions
14 total (human), top 14 by PubMed support.
| Chemical | Actions (top 5) | PubMed papers |
|---|---|---|
| Benzo(a)pyrene | affects methylation, decreases expression | 2 |
| pirinixic acid | affects binding, decreases expression, increases activity | 1 |
| terbufos | increases methylation | 1 |
| 2-amino-3,8-dimethylimidazo(4,5-f)quinoxaline | decreases expression | 1 |
| 2-amino-1-methyl-6-phenylimidazo(4,5-b)pyridine | decreases expression | 1 |
| CGP 52608 | affects binding, increases reaction | 1 |
| Arsenic | affects methylation | 1 |
| Fonofos | increases methylation | 1 |
| Parathion | increases methylation | 1 |
| Rotenone | decreases expression | 1 |
| Valproic Acid | increases methylation | 1 |
| Aflatoxin B1 | increases expression | 1 |
| Okadaic Acid | increases expression | 1 |
| Copper Sulfate | decreases expression | 1 |
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): immunodeficiency 61