UTP25
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Also known as MGC29875DEF
Summary
UTP25 (UTP25 small subunit processome component, HGNC:28440) is a protein-coding gene on chromosome 1q32.2, encoding U3 small nucleolar RNA-associated protein 25 homolog (Q68CQ4). Component of the ribosomal small subunit processome for the biogenesis of ribosomes, functions in pre-ribosomal RNA (pre-rRNA) processing. It is a selective cancer dependency (DepMap: 87.5% of cell lines).
Enables RNA binding activity. Involved in several processes, including protein catabolic process; protein destabilization; and protein localization to nucleolus. Located in nucleolus.
Source: NCBI Gene 27042 — RefSeq curated summary.
At a glance
- GWAS associations: 5
- Clinical variants (ClinVar): 126 total
- Cancer dependency (DepMap): dependent in 87.5% of screened cell lines
- MANE Select transcript:
NM_014388
Identifiers
Gene identifiers
| Field | Value |
|---|---|
| HGNC ID | HGNC:28440 |
| Approved symbol | UTP25 |
| Name | UTP25 small subunit processome component |
| Location | 1q32.2 |
| Locus type | gene with protein product |
| Status | Approved |
| Aliases | MGC29875, DEF |
| Ensembl gene | ENSG00000117597 |
| Ensembl biotype | protein_coding |
| OMIM | 619663 |
| Entrez | 27042 |
Gene structure
Transcript identifiers
Ensembl transcripts: 5 — 5 protein_coding
ENST00000457820, ENST00000491415, ENST00000852869, ENST00000852870, ENST00000915424
RefSeq mRNA: 1 — MANE Select: NM_014388
NM_014388
CCDS: CCDS1493
Canonical transcript exons
ENST00000491415 — 12 exons
| Exon | Start | End |
|---|---|---|
| ENSE00000792137 | 209830108 | 209830147 |
| ENSE00000792138 | 209830803 | 209831043 |
| ENSE00000792139 | 209833185 | 209833358 |
| ENSE00000792140 | 209835075 | 209835163 |
| ENSE00000792141 | 209836801 | 209837211 |
| ENSE00000792142 | 209838909 | 209839128 |
| ENSE00000792143 | 209840853 | 209841055 |
| ENSE00000792144 | 209842265 | 209842447 |
| ENSE00000792145 | 209842583 | 209842695 |
| ENSE00000792146 | 209843451 | 209843696 |
| ENSE00001443261 | 209827972 | 209828170 |
| ENSE00001933838 | 209851204 | 209857565 |
Expression profiles
Bgee: expression breadth ubiquitous, 280 present calls, max score 90.02.
FANTOM5 (CAGE): breadth ubiquitous, TPM avg 20.0498 / max 642.6341, expressed in 1785 samples.
FANTOM5 promoters (1 alternative TSS)
| Promoter ID | TPM avg | Samples expressed |
|---|---|---|
| 8370 | 20.0498 | 1785 |
Top tissues by expression
292 total, by Bgee expression score (0-100, higher = more expressed):
| Tissue | Anatomy ID | Expression score | Quality |
|---|---|---|---|
| endothelial cell | CL:0000115 | 90.02 | gold quality |
| germinal epithelium of ovary | UBERON:0001304 | 82.97 | gold quality |
| epithelium of nasopharynx | UBERON:0001951 | 82.85 | gold quality |
| primordial germ cell in gonad | CL:0000670 ∩ UBERON:0000991 | 82.68 | gold quality |
| cartilage tissue | UBERON:0002418 | 81.79 | gold quality |
| cervix squamous epithelium | UBERON:0006922 | 81.45 | gold quality |
| epithelial cell of pancreas | CL:0000083 | 80.76 | gold quality |
| hair follicle | UBERON:0002073 | 80.49 | gold quality |
| amniotic fluid | UBERON:0000173 | 79.44 | gold quality |
| squamous epithelium | UBERON:0006914 | 78.50 | gold quality |
| stromal cell of endometrium | CL:0002255 | 78.49 | gold quality |
| cortical plate | UBERON:0005343 | 78.29 | gold quality |
| tibia | UBERON:0000979 | 78.10 | gold quality |
| esophagus squamous epithelium | UBERON:0006920 | 78.01 | gold quality |
| cauda epididymis | UBERON:0004360 | 77.86 | gold quality |
| pancreatic ductal cell | CL:0002079 | 77.85 | silver quality |
| caput epididymis | UBERON:0004358 | 77.36 | gold quality |
| oviduct epithelium | UBERON:0004804 | 77.02 | gold quality |
| islet of Langerhans | UBERON:0000006 | 76.80 | gold quality |
| epithelium of esophagus | UBERON:0001976 | 76.72 | gold quality |
| gingival epithelium | UBERON:0001949 | 76.48 | gold quality |
| male germ line stem cell (sensu Vertebrata) in testis | CL:0000089 ∩ UBERON:0000473 | 76.34 | gold quality |
| pericardium | UBERON:0002407 | 76.25 | gold quality |
| ventricular zone | UBERON:0003053 | 76.04 | gold quality |
| adrenal tissue | UBERON:0018303 | 75.56 | gold quality |
| bronchial epithelial cell | CL:0002328 | 75.52 | gold quality |
| tibialis anterior | UBERON:0001385 | 75.31 | gold quality |
| cranial nerve II | UBERON:0000941 | 75.29 | gold quality |
| mucosa of paranasal sinus | UBERON:0005030 | 75.10 | gold quality |
| calcaneal tendon | UBERON:0003701 | 74.99 | gold quality |
Single-cell (SCXA)
Detected in 1 experiment(s), a significant marker in 0.
| Experiment | Marker? | Max mean expression |
|---|---|---|
| E-ANND-3 | no | 5.29 |
Regulation
Is transcription factor: no
Upstream regulators (CollecTRI, top): BRD1
miRNA regulators (miRDB)
205 targeting UTP25, 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-3134 | 100.00 | 66.43 | 777 |
| HSA-MIR-3613-3P | 100.00 | 76.36 | 7965 |
| HSA-MIR-7110-3P | 100.00 | 73.18 | 2486 |
| HSA-MIR-8485 | 100.00 | 77.57 | 4731 |
| HSA-MIR-200B-3P | 100.00 | 73.31 | 2693 |
| HSA-MIR-200C-3P | 100.00 | 73.35 | 2685 |
| HSA-MIR-429 | 100.00 | 73.44 | 2698 |
| HSA-MIR-4795-3P | 100.00 | 74.62 | 4024 |
| HSA-MIR-6833-3P | 100.00 | 70.63 | 3197 |
| HSA-MIR-5011-5P | 100.00 | 83.46 | 5820 |
| HSA-MIR-6867-5P | 100.00 | 82.21 | 3464 |
| HSA-MIR-371B-5P | 99.99 | 75.34 | 4759 |
| HSA-MIR-186-5P | 99.99 | 70.83 | 3707 |
| HSA-MIR-3662 | 99.99 | 73.82 | 5684 |
| HSA-MIR-513B-5P | 99.99 | 69.96 | 2150 |
| HSA-MIR-548C-3P | 99.99 | 74.01 | 7587 |
| HSA-MIR-12136 | 99.98 | 72.81 | 5713 |
| HSA-MIR-616-5P | 99.98 | 75.58 | 4775 |
| HSA-MIR-373-5P | 99.98 | 75.36 | 4753 |
| HSA-MIR-548N | 99.98 | 71.94 | 4170 |
| HSA-MIR-3148 | 99.97 | 75.06 | 6478 |
| HSA-MIR-3688-3P | 99.97 | 72.02 | 2834 |
| HSA-MIR-3065-5P | 99.97 | 71.56 | 3281 |
| HSA-MIR-302C-5P | 99.97 | 72.56 | 3642 |
| HSA-MIR-548AA | 99.96 | 70.64 | 3753 |
| HSA-MIR-548AP-3P | 99.96 | 70.64 | 3753 |
| HSA-MIR-548T-3P | 99.96 | 70.64 | 3753 |
| HSA-MIR-2110 | 99.96 | 66.68 | 1930 |
| HSA-MIR-4267 | 99.96 | 66.53 | 2368 |
| HSA-MIR-3682-5P | 99.93 | 67.97 | 1163 |
Functional genomics
DepMap (CRISPR cell-line fitness): dependent in 87.5% of screened cell lines.
Literature-anchored findings (GeneRIF, showing 4)
- characterization of the related zebrafish protein (PMID:16322560)
- Colonic tissue from patients with Hirschsprung’s disease showed lower expression levels of digestive-organ expansion factor (DIEXF). (PMID:25007945)
- DEF is highly expressed in human neuroblastoma, and its depletion in human neuroblastoma cell lines induces apoptosis. (PMID:28263972)
- Tissue and cancer-specific expression of DIEXF is epigenetically mediated by an Alu repeat. (PMID:32041475)
Cross-species orthologs
5 orthologs
| Organism | Symbol | Gene ID |
|---|---|---|
| danio_rerio | utp25 | ENSDARG00000017696 |
| mus_musculus | Utp25 | ENSMUSG00000016181 |
| rattus_norvegicus | Utp25 | ENSRNOG00000004789 |
| drosophila_melanogaster | CG3735 | FBGN0034933 |
| caenorhabditis_elegans | WBGENE00012756 |
Protein
Protein identifiers
U3 small nucleolar RNA-associated protein 25 homolog — Q68CQ4 (reviewed: Q68CQ4)
Alternative names: Digestive organ expansion factor homolog, UTP25 small subunit processor component
All UniProt accessions (2): H7C2R4, Q68CQ4
UniProt curated annotations — full annotation on UniProt →
Function. Component of the ribosomal small subunit processome for the biogenesis of ribosomes, functions in pre-ribosomal RNA (pre-rRNA) processing. Essential for embryonic development in part through the regulation of p53 pathway. Controls the expansion growth of digestive organs and liver. Also involved in the sympathetic neuronal development. Mediates, with CAPN3, the proteasome-independent degradation of p53/TP53.
Subunit / interactions. Interacts with CAPN3; the interaction is required for CAPN3 translocation to the nucleolus.
Subcellular location. Nucleus. Nucleolus.
Tissue specificity. Expressed in colon.
Post-translational modifications. Phosphorylated. Phosphorylation is required to promote p53/TP53 degradation in the nucleolus which promotes cell cycle progression and liver development.
Induction. Down-regulated by the miRNA MIR195.
Similarity. Belongs to the UTP25 family.
RefSeq proteins (1): NP_055203* (*=MANE)
Domains & families (InterPro)
| ID | Name | Type |
|---|---|---|
| IPR010678 | UTP25 | Family |
| IPR027417 | P-loop_NTPase | Homologous_superfamily |
| IPR053939 | UTP25_C | Domain |
| IPR053940 | UTP25_NTPase-like | Domain |
Pfam: PF06862, PF22916
UniProt features (18 total): modified residue 7, region of interest 4, compositionally biased region 3, sequence variant 2, chain 1, sequence conflict 1
Structure
Experimental structures (PDB)
0 structures.
Predicted structure (AlphaFold)
| Model | pLDDT | Fraction very-high |
|---|---|---|
| AF-Q68CQ4-F1 | 78.78 | 0.54 |
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 (7): 52, 58, 60, 62, 64, 10, 50
Function
Pathways and Gene Ontology
Reactome pathways
2 pathways
| ID | Pathway |
|---|---|
| R-HSA-6790901 | rRNA modification in the nucleus and cytosol |
| R-HSA-6791226 | Major pathway of rRNA processing in the nucleolus and cytosol |
MSigDB gene sets: 227 (showing top):
GOBP_RIBOSOME_BIOGENESIS, BORCZUK_MALIGNANT_MESOTHELIOMA_UP, GOBP_MATURATION_OF_SSU_RRNA, CHUANG_OXIDATIVE_STRESS_RESPONSE_UP, GRAESSMANN_APOPTOSIS_BY_DOXORUBICIN_DN, GRAESSMANN_RESPONSE_TO_MC_AND_DOXORUBICIN_DN, GOBP_MACROMOLECULE_CATABOLIC_PROCESS, WEI_MYCN_TARGETS_WITH_E_BOX, GOBP_PROTEIN_DESTABILIZATION, GOBP_RIBOSOMAL_SMALL_SUBUNIT_BIOGENESIS, GOBP_MATURATION_OF_SSU_RRNA_FROM_TRICISTRONIC_RRNA_TRANSCRIPT_SSU_RRNA_5_8S_RRNA_LSU_RRNA, GOBP_REGULATION_OF_PROTEIN_STABILITY, DODD_NASOPHARYNGEAL_CARCINOMA_UP, FREAC4_01, GOBP_PROTEIN_LOCALIZATION_TO_ORGANELLE
GO Biological Process (7): maturation of SSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) (GO:0000462), protein catabolic process (GO:0030163), protein destabilization (GO:0031648), positive regulation of embryonic development (GO:0040019), embryonic organ development (GO:0048568), protein localization to nucleolus (GO:1902570), rRNA processing (GO:0006364)
GO Molecular Function (4): RNA binding (GO:0003723), rRNA binding (GO:0019843), U3 snoRNA binding (GO:0034511), protein binding (GO:0005515)
GO Cellular Component (4): nucleoplasm (GO:0005654), nucleolus (GO:0005730), small-subunit processome (GO:0032040), nucleus (GO:0005634)
Reactome top-level categories
Rollup of top-1 pathways:
| Category | Pathways |
|---|---|
| rRNA processing in the nucleus and cytosol | 2 |
GO top-level categories
Rollup of top GO terms by namespace:
| Category | Terms |
|---|---|
| embryo development | 2 |
| nuclear lumen | 2 |
| maturation of SSU-rRNA | 1 |
| macromolecule catabolic process | 1 |
| protein metabolic process | 1 |
| regulation of protein stability | 1 |
| regulation of embryonic development | 1 |
| positive regulation of developmental process | 1 |
| positive regulation of multicellular organismal process | 1 |
| animal organ development | 1 |
| protein localization to nucleus | 1 |
| RNA processing | 1 |
| rRNA metabolic process | 1 |
| ribosome biogenesis | 1 |
| nucleic acid binding | 1 |
| RNA binding | 1 |
| snoRNA binding | 1 |
| binding | 1 |
| cellular anatomical structure | 1 |
| intracellular membraneless organelle | 1 |
| nucleolus | 1 |
| preribosome | 1 |
| t-UTP complex | 1 |
| nuclear protein-containing complex | 1 |
| intracellular membrane-bounded organelle | 1 |
Protein interactions and networks
STRING
1546 interactions, top by confidence (×1000):
| Protein A | Protein B | Partner UniProt | Score |
|---|---|---|---|
| UTP25 | UTP3 | Q9NQZ2 | 744 |
| UTP25 | MPHOSPH10 | O00566 | 729 |
| UTP25 | IRF6 | O14896 | 717 |
| UTP25 | DDX49 | Q9Y6V7 | 714 |
| UTP25 | PDCD11 | Q14690 | 680 |
| UTP25 | BYSL | Q13895 | 667 |
| UTP25 | ABT1 | Q9ULW3 | 663 |
| UTP25 | ESF1 | Q9H501 | 639 |
| UTP25 | WDR36 | Q8NI36 | 622 |
| UTP25 | RCL1 | Q9Y2P8 | 606 |
| UTP25 | UTP18 | Q9Y5J1 | 605 |
| UTP25 | DHX8 | Q14562 | 597 |
| UTP25 | NOP14 | P78316 | 579 |
| UTP25 | NOM1 | Q5C9Z4 | 563 |
| UTP25 | PWP2 | Q15269 | 545 |
IntAct
102 interactions, top by confidence:
| A | B | Type | Score |
|---|---|---|---|
| MAPKAPK3 | MAPK11 | psi-mi:“MI:0914”(association) | 0.870 |
| MED17 | MED19 | psi-mi:“MI:0914”(association) | 0.840 |
| CEP70 | UTP25 | psi-mi:“MI:0915”(physical association) | 0.830 |
| UTP25 | CEP70 | psi-mi:“MI:0915”(physical association) | 0.830 |
| UTP25 | RUFY1 | psi-mi:“MI:0915”(physical association) | 0.740 |
| RUFY1 | UTP25 | psi-mi:“MI:0915”(physical association) | 0.740 |
| UTP25 | MIPOL1 | psi-mi:“MI:0915”(physical association) | 0.670 |
| MIPOL1 | UTP25 | psi-mi:“MI:0915”(physical association) | 0.670 |
| UTP25 | RUFY1 | psi-mi:“MI:0915”(physical association) | 0.670 |
| UTP25 | AP2M1 | psi-mi:“MI:0915”(physical association) | 0.670 |
| IMP3 | MPHOSPH10 | psi-mi:“MI:0914”(association) | 0.670 |
| FGL1 | LCMT2 | psi-mi:“MI:0914”(association) | 0.640 |
| MAGEA11 | UTP25 | psi-mi:“MI:0915”(physical association) | 0.560 |
| UTP25 | MID2 | psi-mi:“MI:0915”(physical association) | 0.560 |
| UTP25 | MAGEA11 | psi-mi:“MI:0915”(physical association) | 0.560 |
| MID2 | UTP25 | psi-mi:“MI:0915”(physical association) | 0.560 |
| UTP25 | MEOX2 | psi-mi:“MI:0915”(physical association) | 0.560 |
BioGRID (130): DIEXF (Two-hybrid), DIEXF (Two-hybrid), RUFY1 (Two-hybrid), CEP70 (Two-hybrid), MIPOL1 (Two-hybrid), DIEXF (Affinity Capture-MS), DIEXF (Affinity Capture-MS), DIEXF (Affinity Capture-MS), DIEXF (Two-hybrid), DIEXF (Co-fractionation), DIEXF (Co-fractionation), MYO18A (Co-fractionation), DIEXF (Affinity Capture-MS), DIEXF (Affinity Capture-MS), DIEXF (Affinity Capture-MS)
ESM2 similar proteins: A0AVT1, A4QN59, A6H630, A6QXC6, A7SBF0, A7SKJ3, F4JZC2, O01757, O70467, P49958, P87115, Q09454, Q0J7N5, Q10206, Q17QF2, Q4KLT3, Q58EM4, Q5AWA2, Q5M9G7, Q5TYS0, Q5XI55, Q5ZIE6, Q5ZJM3, Q5ZKI2, Q5ZLG3, Q642T7, Q655R6, Q68CQ4, Q6DE00, Q6DJA3, Q6NTR1, Q6NUA1, Q6PEH4, Q7SXP2, Q8C7R4, Q8GWT4, Q8GXR5, Q8JFW4, Q8K224, Q922H1
Diamond homologs: A1CQH8, A1D3E2, A2QQ09, A3LXV1, A4R0E6, A5DFC2, A5E1F6, A6RT94, A6ZVI6, A7EZP8, A7THH1, B0XQ54, B2B4I8, B2W0B1, B3LTT8, B6H768, B6JX19, B6Q702, B8LVD6, B9WM88, C0NQU6, C0SG20, C1G2D1, C1GPD0, C4JTH6, C4R2K0, C4XWY8, C4YMA4, C5DMP2, C5DPB7, C5G0N1, C5GAH0, C5JMX0, C5M3P0, C5P5Z4, C6HQ17, C7GKL8, C7YRJ1, C8ZAF8, D1Z6B1
SIGNOR signaling
0 interactions.
Enriched among interaction partners
Reactome pathways and GO biological processes over-represented among this gene’s 94 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 |
|---|---|---|---|
| Signaling by NTRK1 (TRKA) | 5 | 16.7× | 3e-03 |
| rRNA modification in the nucleus and cytosol | 5 | 15.9× | 3e-03 |
| Signaling by NTRKs | 5 | 15.4× | 3e-03 |
| Diseases of signal transduction by growth factor receptors and second messengers | 7 | 6.7× | 6e-03 |
GO biological processes:
| GO term | Partners | Fold | FDR |
|---|---|---|---|
| ribosomal small subunit biogenesis | 6 | 15.5× | 1e-03 |
Disease & clinical
Clinical variants and AI predictions
ClinVar
126 variants total. Per-class counts are floors (≥ shown; pagination cap):
| Classification | Count (floor) |
|---|---|
| Pathogenic | 0 |
| Likely pathogenic | 0 |
| Uncertain significance | 108 |
| Likely benign | 2 |
| Benign | 0 |
Top pathogenic / likely-pathogenic (0)
SpliceAI
2194 predictions. Top by Δscore:
| Variant | Effect | Δscore |
|---|---|---|
| 1:209828180:G:T | donor_gain | 1.0000 |
| 1:209830797:TTTTA:T | acceptor_loss | 1.0000 |
| 1:209830799:TTA:T | acceptor_loss | 1.0000 |
| 1:209830800:TA:T | acceptor_loss | 1.0000 |
| 1:209830801:A:AG | acceptor_gain | 1.0000 |
| 1:209830801:A:AT | acceptor_loss | 1.0000 |
| 1:209830802:G:GG | acceptor_gain | 1.0000 |
| 1:209830802:GT:G | acceptor_gain | 1.0000 |
| 1:209830802:GTC:G | acceptor_gain | 1.0000 |
| 1:209830802:GTCA:G | acceptor_gain | 1.0000 |
| 1:209831039:AGAGA:A | donor_gain | 1.0000 |
| 1:209831040:GAGA:G | donor_gain | 1.0000 |
| 1:209831040:GAGAG:G | donor_gain | 1.0000 |
| 1:209831041:AGA:A | donor_gain | 1.0000 |
| 1:209831042:GA:G | donor_gain | 1.0000 |
| 1:209831042:GAG:G | donor_gain | 1.0000 |
| 1:209831044:G:C | donor_loss | 1.0000 |
| 1:209831044:G:GG | donor_gain | 1.0000 |
| 1:209831045:T:G | donor_loss | 1.0000 |
| 1:209833316:G:GT | donor_gain | 1.0000 |
| 1:209833370:GT:G | donor_gain | 1.0000 |
| 1:209835164:G:GG | donor_gain | 1.0000 |
| 1:209836799:A:AG | acceptor_gain | 1.0000 |
| 1:209836799:AGT:A | acceptor_gain | 1.0000 |
| 1:209836800:G:GA | acceptor_gain | 1.0000 |
| 1:209836800:GT:G | acceptor_gain | 1.0000 |
| 1:209836800:GTG:G | acceptor_gain | 1.0000 |
| 1:209837208:CAAGG:C | donor_loss | 1.0000 |
| 1:209837210:AGGTG:A | donor_loss | 1.0000 |
| 1:209837213:T:A | donor_loss | 1.0000 |
AlphaMissense
5042 scored. Top likely-pathogenic:
| Variant | Protein change | am_pathogenicity |
|---|---|---|
| 1:209838931:G:C | R362P | 0.998 |
| 1:209839119:T:C | F425L | 0.998 |
| 1:209839121:C:A | F425L | 0.998 |
| 1:209839121:C:G | F425L | 0.998 |
| 1:209840904:C:G | S445W | 0.998 |
| 1:209840931:G:A | G454D | 0.998 |
| 1:209842323:G:C | R515P | 0.998 |
| 1:209843552:G:C | R628P | 0.998 |
| 1:209839021:T:C | F392S | 0.997 |
| 1:209840853:G:A | G428E | 0.997 |
| 1:209841037:G:C | Q489H | 0.997 |
| 1:209841037:G:T | Q489H | 0.997 |
| 1:209838913:T:C | L356P | 0.996 |
| 1:209839113:G:C | D423H | 0.996 |
| 1:209840907:A:T | D446V | 0.996 |
| 1:209840922:C:T | S451F | 0.996 |
| 1:209841040:C:A | N490K | 0.996 |
| 1:209841040:C:G | N490K | 0.996 |
| 1:209841041:T:A | W491R | 0.996 |
| 1:209841041:T:C | W491R | 0.996 |
| 1:209842365:G:C | R529P | 0.996 |
| 1:209843672:C:T | T668I | 0.996 |
| 1:209837204:G:C | R352T | 0.995 |
| 1:209837204:G:T | R352M | 0.995 |
| 1:209839120:T:C | F425S | 0.995 |
| 1:209840922:C:A | S451Y | 0.995 |
| 1:209843546:G:C | R626P | 0.995 |
| 1:209839114:A:T | D423V | 0.994 |
| 1:209839128:G:A | G428R | 0.994 |
| 1:209839128:G:C | G428R | 0.994 |
dbSNP variants (sampled 300 via entrez): RS1000127283 (1:209845973 C>T), RS1000296113 (1:209835473 A>G), RS1000331843 (1:209855322 G>A), RS1000517735 (1:209842293 C>G), RS1000564380 (1:209844036 GT>G), RS1000745860 (1:209854949 ATCTTCATTACCAAATTTCTACTCCACACT>A), RS1000790681 (1:209848887 T>C), RS1001018397 (1:209844346 T>C), RS1001333845 (1:209855308 T>G), RS1001394189 (1:209855885 G>A), RS1001503288 (1:209849505 G>A,T), RS1001672786 (1:209843089 A>G), RS1001869963 (1:209828969 T>G), RS1001885024 (1:209832325 T>A), RS1001885872 (1:209857686 G>A,C)
Disease associations
OMIM: gene MIM:619663 | disease phenotypes:
GenCC curated gene-disease
Mondo (0):
Orphanet (0):
HPO phenotypes
0 total (0 of 0 shown, HPO-id order):
GWAS associations
5 associations (top):
| Study | Trait | p-value |
|---|---|---|
| GCST003996_12 | Monobrow | 2.000000e-11 |
| GCST004131_1 | Inflammatory bowel disease | 1.000000e-08 |
| GCST004132_85 | Crohn’s disease | 7.000000e-07 |
| GCST004166_10 | Nonsyndromic cleft lip with cleft palate | 9.000000e-19 |
| GCST004866_6 | Alopecia areata | 2.000000e-06 |
EFO canonical traits (2, from GWAS)
| EFO ID | Trait name |
|---|---|
| EFO:0007906 | synophrys measurement |
| EFO:0003959 | cleft lip |
Drugs & pharmacology
Drug and pharmacology data
Is drug target: no
PharmGKB: 1 entry (VIP=true, CPIC=false)
CTD chemical–gene interactions
43 total (human), top 30 by PubMed support.
| Chemical | Actions (top 5) | PubMed papers |
|---|---|---|
| Valproic Acid | affects expression, decreases expression, decreases methylation | 4 |
| Arsenic | increases expression, increases methylation, affects cotreatment, increases abundance | 2 |
| Phenylmercuric Acetate | affects cotreatment, increases expression | 2 |
| Cyclosporine | increases expression | 2 |
| aristolochic acid I | increases expression | 1 |
| triphenyl phosphate | affects expression | 1 |
| bisphenol A | decreases expression | 1 |
| arsenite | increases methylation | 1 |
| tris(1,3-dichloro-2-propyl)phosphate | decreases expression | 1 |
| sodium arsenite | affects cotreatment, increases abundance, increases expression | 1 |
| zinc chromate | increases abundance, increases expression | 1 |
| manganese chloride | affects cotreatment, increases abundance, increases expression | 1 |
| potassium chromate(VI) | decreases expression | 1 |
| chromium hexavalent ion | increases abundance, increases expression | 1 |
| perfluoro-n-nonanoic acid | increases expression | 1 |
| 4-(5-benzo(1,3)dioxol-5-yl-4-pyridin-2-yl-1H-imidazol-2-yl)benzamide | affects cotreatment, increases expression | 1 |
| dorsomorphin | affects cotreatment, increases expression | 1 |
| (+)-JQ1 compound | decreases expression | 1 |
| Sunitinib | increases expression | 1 |
| Leflunomide | increases expression | 1 |
| Acetaminophen | decreases expression | 1 |
| Air Pollutants | decreases expression, increases abundance | 1 |
| Benzo(a)pyrene | affects methylation | 1 |
| Cisplatin | decreases expression | 1 |
| Dichlorodiphenyl Dichloroethylene | increases expression | 1 |
| Doxorubicin | decreases expression | 1 |
| Estradiol | increases expression | 1 |
| Ethyl Methanesulfonate | decreases expression | 1 |
| Hydrogen Peroxide | affects expression | 1 |
| Lead | 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): alopecia areata