INTS2
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Also known as INT2
Summary
INTS2 (integrator complex subunit 2, HGNC:29241) is a protein-coding gene on chromosome 17q23.2, encoding Integrator complex subunit 2 (Q9H0H0). Component of the integrator complex, a multiprotein complex that terminates RNA polymerase II (Pol II) transcription in the promoter-proximal region of genes. It is a common-essential gene (DepMap: required in 93.9% of cancer cell lines).
INTS2 is a subunit of the Integrator complex, which associates with the C-terminal domain of RNA polymerase II large subunit (POLR2A; MIM 180660) and mediates 3-prime end processing of small nuclear RNAs U1 (RNU1; MIM 180680) and U2 (RNU2; MIM 180690) (Baillat et al., 2005 [PubMed 16239144]).
Source: NCBI Gene 57508 — RefSeq curated summary.
At a glance
- GWAS associations: 1
- Clinical variants (ClinVar): 159 total — 1 pathogenic
- Cancer dependency (DepMap): dependent in 93.9% of screened cell lines (common-essential)
- MANE Select transcript:
NM_001351695
Identifiers
Gene identifiers
| Field | Value |
|---|---|
| HGNC ID | HGNC:29241 |
| Approved symbol | INTS2 |
| Name | integrator complex subunit 2 |
| Location | 17q23.2 |
| Locus type | gene with protein product |
| Status | Approved |
| Aliases | INT2 |
| Ensembl gene | ENSG00000108506 |
| Ensembl biotype | protein_coding |
| OMIM | 611346 |
| Entrez | 57508 |
Gene structure
Transcript identifiers
Ensembl transcripts: 19 — 15 protein_coding, 3 retained_intron, 1 nonsense_mediated_decay
ENST00000251334, ENST00000444766, ENST00000578805, ENST00000583076, ENST00000583822, ENST00000584967, ENST00000646745, ENST00000646954, ENST00000647009, ENST00000866719, ENST00000866720, ENST00000866721, ENST00000913652, ENST00000913653, ENST00000913654, ENST00000913655, ENST00000913656, ENST00000963385, ENST00000963386
RefSeq mRNA: 3 — MANE Select: NM_001351695
NM_001330417, NM_001351695, NM_020748
CCDS: CCDS45750, CCDS82181
Canonical transcript exons
ENST00000251334 — 25 exons
| Exon | Start | End |
|---|---|---|
| ENSE00000740937 | 61867833 | 61868009 |
| ENSE00000740958 | 61889786 | 61889894 |
| ENSE00000740960 | 61891513 | 61891689 |
| ENSE00000740964 | 61893765 | 61893899 |
| ENSE00000740967 | 61895315 | 61895383 |
| ENSE00000740969 | 61897469 | 61897583 |
| ENSE00000740971 | 61897668 | 61897739 |
| ENSE00000820448 | 61924961 | 61925099 |
| ENSE00000925253 | 61904460 | 61904585 |
| ENSE00000925254 | 61907408 | 61907634 |
| ENSE00000925255 | 61911520 | 61911693 |
| ENSE00000925256 | 61911940 | 61912070 |
| ENSE00000925257 | 61919400 | 61919513 |
| ENSE00000925258 | 61921725 | 61921827 |
| ENSE00001113076 | 61872265 | 61872460 |
| ENSE00001113077 | 61869273 | 61869380 |
| ENSE00001113078 | 61869034 | 61869139 |
| ENSE00001113079 | 61869737 | 61869988 |
| ENSE00003498879 | 61884901 | 61885005 |
| ENSE00003550261 | 61874913 | 61875038 |
| ENSE00003566340 | 61926352 | 61926662 |
| ENSE00003583309 | 61877887 | 61878088 |
| ENSE00003651910 | 61881007 | 61881171 |
| ENSE00003737481 | 61865367 | 61867726 |
| ENSE00003819457 | 61927654 | 61927982 |
Expression profiles
Bgee: expression breadth ubiquitous, 249 present calls, max score 94.39.
FANTOM5 (CAGE): breadth ubiquitous, TPM avg 11.1817 / max 143.5361, expressed in 1733 samples.
FANTOM5 promoters (3 alternative TSS)
| Promoter ID | TPM avg | Samples expressed |
|---|---|---|
| 167408 | 8.8926 | 1688 |
| 167407 | 1.6890 | 941 |
| 167409 | 0.6001 | 319 |
Top tissues by expression
253 total, by Bgee expression score (0-100, higher = more expressed):
| Tissue | Anatomy ID | Expression score | Quality |
|---|---|---|---|
| oviduct epithelium | UBERON:0004804 | 94.39 | gold quality |
| endothelial cell | CL:0000115 | 84.23 | gold quality |
| Brodmann (1909) area 23 | UBERON:0013554 | 83.63 | gold quality |
| middle temporal gyrus | UBERON:0002771 | 82.30 | gold quality |
| male germ line stem cell (sensu Vertebrata) in testis | CL:0000089 ∩ UBERON:0000473 | 82.20 | gold quality |
| primordial germ cell in gonad | CL:0000670 ∩ UBERON:0000991 | 82.17 | gold quality |
| esophagus squamous epithelium | UBERON:0006920 | 81.89 | gold quality |
| calcaneal tendon | UBERON:0003701 | 81.80 | gold quality |
| germinal epithelium of ovary | UBERON:0001304 | 80.56 | gold quality |
| epithelial cell of pancreas | CL:0000083 | 79.96 | gold quality |
| tibia | UBERON:0000979 | 79.96 | gold quality |
| ventricular zone | UBERON:0003053 | 79.81 | gold quality |
| islet of Langerhans | UBERON:0000006 | 79.68 | gold quality |
| caput epididymis | UBERON:0004358 | 79.57 | gold quality |
| adrenal tissue | UBERON:0018303 | 79.37 | gold quality |
| mucosa of paranasal sinus | UBERON:0005030 | 78.87 | gold quality |
| bone marrow cell | CL:0002092 | 78.82 | gold quality |
| colonic epithelium | UBERON:0000397 | 78.60 | gold quality |
| cauda epididymis | UBERON:0004360 | 78.59 | gold quality |
| visceral pleura | UBERON:0002401 | 78.54 | gold quality |
| epithelium of nasopharynx | UBERON:0001951 | 78.53 | gold quality |
| oral cavity | UBERON:0000167 | 78.33 | gold quality |
| fallopian tube | UBERON:0003889 | 78.21 | gold quality |
| gingival epithelium | UBERON:0001949 | 78.08 | gold quality |
| primary visual cortex | UBERON:0002436 | 78.08 | gold quality |
| parietal pleura | UBERON:0002400 | 78.06 | gold quality |
| corpus callosum | UBERON:0002336 | 77.77 | gold quality |
| cerebellar cortex | UBERON:0002129 | 77.67 | gold quality |
| cerebellar hemisphere | UBERON:0002245 | 77.65 | gold quality |
| gingiva | UBERON:0001828 | 77.32 | gold quality |
Single-cell (SCXA)
Detected in 3 experiment(s), a significant marker in 1.
| Experiment | Marker? | Max mean expression |
|---|---|---|
| E-ANND-3 | yes | 5.62 |
| E-CURD-10 | no | 374.81 |
| E-MTAB-6386 | no | 372.10 |
Regulation
Is transcription factor: no
miRNA regulators (miRDB)
114 targeting INTS2, 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-340-5P | 100.00 | 72.50 | 4437 |
| HSA-MIR-4425 | 100.00 | 67.59 | 1049 |
| HSA-MIR-30B-5P | 100.00 | 76.29 | 3248 |
| HSA-MIR-30C-5P | 100.00 | 76.29 | 3248 |
| HSA-MIR-186-5P | 99.99 | 70.83 | 3707 |
| HSA-MIR-4500 | 99.99 | 72.72 | 2367 |
| HSA-MIR-548C-3P | 99.99 | 74.01 | 7587 |
| HSA-MIR-371B-5P | 99.99 | 75.34 | 4759 |
| HSA-MIR-5696 | 99.98 | 72.36 | 4487 |
| HSA-MIR-12136 | 99.98 | 72.81 | 5713 |
| HSA-LET-7A-5P | 99.98 | 72.29 | 1790 |
| HSA-LET-7B-5P | 99.98 | 72.31 | 1790 |
| HSA-LET-7C-5P | 99.98 | 72.29 | 1790 |
| HSA-LET-7E-5P | 99.98 | 72.29 | 1790 |
| HSA-LET-7F-5P | 99.98 | 72.56 | 1784 |
| HSA-LET-7G-5P | 99.98 | 72.37 | 1784 |
| HSA-LET-7I-5P | 99.98 | 72.37 | 1788 |
| HSA-MIR-98-5P | 99.98 | 72.33 | 1787 |
| HSA-MIR-433-3P | 99.98 | 69.37 | 1203 |
| HSA-MIR-520D-5P | 99.98 | 73.34 | 4883 |
| HSA-MIR-524-5P | 99.98 | 73.43 | 4882 |
| HSA-MIR-3617-3P | 99.98 | 67.86 | 918 |
| HSA-MIR-3692-3P | 99.98 | 70.27 | 2139 |
| HSA-MIR-373-5P | 99.98 | 75.36 | 4753 |
| HSA-MIR-616-5P | 99.98 | 75.58 | 4775 |
| HSA-MIR-3148 | 99.97 | 75.06 | 6478 |
| HSA-MIR-3065-5P | 99.97 | 71.56 | 3281 |
| HSA-MIR-302C-5P | 99.97 | 72.56 | 3642 |
| HSA-MIR-548AT-5P | 99.96 | 70.83 | 2666 |
| HSA-MIR-146A-5P | 99.96 | 68.93 | 988 |
Functional genomics
DepMap (CRISPR cell-line fitness): dependent in 93.9% of screened cell lines, common-essential.
Literature-anchored findings (GeneRIF, showing 1)
- Mutation in INTS2 gene is associated with gastric cancer peritoneal carcinomatosis. (PMID:26811494)
Cross-species orthologs
5 orthologs
| Organism | Symbol | Gene ID |
|---|---|---|
| danio_rerio | ints2 | ENSDARG00000069085 |
| mus_musculus | Ints2 | ENSMUSG00000018068 |
| rattus_norvegicus | Brip1 | ENSRNOG00000059997 |
| drosophila_melanogaster | IntS2 | FBGN0030858 |
| caenorhabditis_elegans | WBGENE00013877 |
Protein
Protein identifiers
Integrator complex subunit 2 — Q9H0H0 (reviewed: Q9H0H0)
All UniProt accessions (5): Q9H0H0, A0A2R8Y4Z6, A0A2R8Y7F8, J3KMZ7, J3KRH0
UniProt curated annotations — full annotation on UniProt →
Function. Component of the integrator complex, a multiprotein complex that terminates RNA polymerase II (Pol II) transcription in the promoter-proximal region of genes. The integrator complex provides a quality checkpoint during transcription elongation by driving premature transcription termination of transcripts that are unfavorably configured for transcriptional elongation: the complex terminates transcription by (1) catalyzing dephosphorylation of the C-terminal domain (CTD) of Pol II subunit POLR2A/RPB1 and SUPT5H/SPT5, (2) degrading the exiting nascent RNA transcript via endonuclease activity and (3) promoting the release of Pol II from bound DNA. The integrator complex is also involved in terminating the synthesis of non-coding Pol II transcripts, such as enhancer RNAs (eRNAs), small nuclear RNAs (snRNAs), telomerase RNAs and long non-coding RNAs (lncRNAs). Mediates recruitment of cytoplasmic dynein to the nuclear envelope, probably as component of the integrator complex.
Subunit / interactions. Component of the Integrator complex, composed of core subunits INTS1, INTS2, INTS3, INTS4, INTS5, INTS6, INTS7, INTS8, INTS9/RC74, INTS10, INTS11/CPSF3L, INTS12, INTS13, INTS14 and INTS15. The core complex associates with protein phosphatase 2A subunits PPP2CA and PPP2R1A, to form the Integrator-PP2A (INTAC) complex.
Subcellular location. Nucleus. Nucleus membrane. Cytoplasm.
Similarity. Belongs to the Integrator subunit 2 family.
RefSeq proteins (3): NP_001317346, NP_001338624, NP_065799 (=MANE)
Domains & families (InterPro)
| ID | Name | Type |
|---|---|---|
| IPR026236 | Int2_metazoa | Family |
| IPR029321 | INTS2 | Family |
Pfam: PF14750
UniProt features (93 total): helix 74, strand 9, turn 7, chain 1, transmembrane region 1, sequence variant 1
Structure
Experimental structures (PDB)
8 structures.
| PDB | Method | Resolution (Å) |
|---|---|---|
| 8RC4 | ELECTRON MICROSCOPY | 3.1 |
| 7CUN | ELECTRON MICROSCOPY | 3.5 |
| 7PKS | ELECTRON MICROSCOPY | 3.6 |
| 8RBZ | ELECTRON MICROSCOPY | 3.7 |
| 8RBX | ELECTRON MICROSCOPY | 4.1 |
| 8YJB | ELECTRON MICROSCOPY | 4.1 |
| 7YCX | ELECTRON MICROSCOPY | 4.18 |
| 9VD9 | ELECTRON MICROSCOPY | 4.6 |
Predicted structure (AlphaFold)
| Model | pLDDT | Fraction very-high |
|---|---|---|
| AF-Q9H0H0-F1 | 78.90 | 0.27 |
Function
Pathways and Gene Ontology
Reactome pathways
3 pathways
| ID | Pathway |
|---|---|
| R-HSA-6807505 | RNA polymerase II transcribes snRNA genes |
| R-HSA-73857 | RNA Polymerase II Transcription |
| R-HSA-74160 | Gene expression (Transcription) |
MSigDB gene sets: 134 (showing top):
GOBP_MACROMOLECULE_CATABOLIC_PROCESS, ATGTTAA_MIR302C, MONNIER_POSTRADIATION_TUMOR_ESCAPE_UP, GOBP_RNA_SURVEILLANCE, MODULE_285, TGCTGAY_UNKNOWN, ATTCTTT_MIR186, GOBP_DNA_TEMPLATED_TRANSCRIPTION_INITIATION, GARY_CD5_TARGETS_DN, GOBP_TRANSCRIPTION_INITIATION_AT_RNA_POLYMERASE_II_PROMOTER, ATCATGA_MIR433, ZHANG_BREAST_CANCER_PROGENITORS_UP, GOBP_SNRNA_PROCESSING, NIKOLSKY_BREAST_CANCER_17Q21_Q25_AMPLICON, GOBP_REGULATION_OF_DNA_TEMPLATED_TRANSCRIPTION_ELONGATION
GO Biological Process (4): snRNA processing (GO:0016180), regulation of transcription elongation by RNA polymerase II (GO:0034243), snRNA 3’-end processing (GO:0034472), RNA polymerase II transcription initiation surveillance (GO:0160240)
GO Molecular Function (1): protein binding (GO:0005515)
GO Cellular Component (7): nucleus (GO:0005634), nucleoplasm (GO:0005654), cytoplasm (GO:0005737), membrane (GO:0016020), nuclear membrane (GO:0031965), integrator complex (GO:0032039), INTAC complex (GO:0160232)
Reactome top-level categories
Rollup of top-2 pathways:
| Category | Pathways |
|---|---|
| RNA Polymerase II Transcription | 1 |
| Gene expression (Transcription) | 1 |
GO top-level categories
Rollup of top GO terms by namespace:
| Category | Terms |
|---|---|
| cellular anatomical structure | 3 |
| nuclear protein-containing complex | 2 |
| RNA processing | 1 |
| snRNA metabolic process | 1 |
| transcription elongation by RNA polymerase II | 1 |
| regulation of DNA-templated transcription elongation | 1 |
| snRNA processing | 1 |
| RNA 3’-end processing | 1 |
| transcription initiation at RNA polymerase II promoter | 1 |
| nuclear RNA surveillance | 1 |
| binding | 1 |
| intracellular membrane-bounded organelle | 1 |
| nuclear lumen | 1 |
| intracellular anatomical structure | 1 |
| nucleus | 1 |
| nuclear envelope | 1 |
| organelle membrane | 1 |
| integrator complex | 1 |
Protein interactions and networks
STRING
2024 interactions, top by confidence (×1000):
| Protein A | Protein B | Partner UniProt | Score |
|---|---|---|---|
| INTS2 | INTS11 | Q5TA45 | 913 |
| INTS2 | INTS1 | Q8N201 | 897 |
| INTS2 | INTS5 | Q6P9B9 | 874 |
| INTS2 | INTS4 | Q96HW7 | 831 |
| INTS2 | INTS8 | Q75QN2 | 799 |
| INTS2 | INTS3 | Q68E01 | 775 |
| INTS2 | INTS6 | Q9UL03 | 724 |
| INTS2 | INTS9 | Q9NV88 | 719 |
| INTS2 | INTS7 | Q9NVH2 | 713 |
| INTS2 | INTS12 | Q96CB8 | 665 |
| INTS2 | INTS13 | Q9NVM9 | 664 |
| INTS2 | INTS10 | Q9NVR2 | 606 |
| INTS2 | MED13 | Q9UHV7 | 557 |
| INTS2 | POLR2A | P24928 | 548 |
| INTS2 | CHCT1 | Q86WR6 | 546 |
IntAct
120 interactions, top by confidence:
| A | B | Type | Score |
|---|---|---|---|
| PPP2R1A | STRN | psi-mi:“MI:0914”(association) | 0.880 |
| POLR2C | SUPT5H | psi-mi:“MI:0914”(association) | 0.640 |
| SCN2B | EXOC5 | psi-mi:“MI:0914”(association) | 0.640 |
| VSIG1 | TTI1 | psi-mi:“MI:0914”(association) | 0.640 |
| GYPA | TCAF2 | psi-mi:“MI:0914”(association) | 0.640 |
| CCDC57 | INTS2 | psi-mi:“MI:0915”(physical association) | 0.560 |
| INTS2 | DEF6 | psi-mi:“MI:0915”(physical association) | 0.560 |
| NCK2 | INTS2 | psi-mi:“MI:0915”(physical association) | 0.560 |
| FAM174A | BLTP3B | psi-mi:“MI:0914”(association) | 0.530 |
| APLNR | METTL15 | psi-mi:“MI:0914”(association) | 0.530 |
| SLC15A1 | METTL15 | psi-mi:“MI:0914”(association) | 0.530 |
| CD274 | TTI1 | psi-mi:“MI:0914”(association) | 0.530 |
| SUPT5H | POLR2D | psi-mi:“MI:0914”(association) | 0.530 |
| TMEM9 | ESYT2 | psi-mi:“MI:0914”(association) | 0.530 |
| DPEP1 | ILVBL | psi-mi:“MI:0914”(association) | 0.530 |
| CD70 | METTL15 | psi-mi:“MI:0914”(association) | 0.530 |
| VSIG1 | TNPO2 | psi-mi:“MI:0914”(association) | 0.530 |
| STK16 | UNC119B | psi-mi:“MI:0914”(association) | 0.530 |
| ILVBL | SLC33A1 | psi-mi:“MI:0914”(association) | 0.530 |
| APLNR | SLC33A1 | psi-mi:“MI:0914”(association) | 0.530 |
| CD40 | EXOC5 | psi-mi:“MI:0914”(association) | 0.530 |
| LPAR1 | TMEM223 | psi-mi:“MI:0914”(association) | 0.530 |
| P2RY10 | ATM | psi-mi:“MI:0914”(association) | 0.530 |
| TGOLN2 | DENND11 | psi-mi:“MI:0914”(association) | 0.530 |
BioGRID (141): INTS2 (Affinity Capture-MS), INTS2 (Affinity Capture-MS), INTS2 (Affinity Capture-MS), INTS2 (Affinity Capture-MS), INTS2 (Affinity Capture-MS), ABCF3 (Co-fractionation), C7orf26 (Co-fractionation), INTS1 (Co-fractionation), INTS2 (Co-fractionation), INTS2 (Co-fractionation), INTS2 (Co-fractionation), INTS2 (Co-fractionation), RPP30 (Co-fractionation), INTS2 (Proximity Label-MS), INTS2 (Affinity Capture-MS)
ESM2 similar proteins: A1Z8X3, A1ZAK1, G5ED39, H2QII6, O01510, O08662, O94668, P42173, P42286, P49792, Q00416, Q03280, Q0IEK6, Q10573, Q10669, Q13535, Q18508, Q18892, Q196Z9, Q29L39, Q2U639, Q5EAK6, Q5EB59, Q5RIW8, Q5ZKU4, Q61CW2, Q61WP7, Q6CP76, Q6CT34, Q6V3W0, Q70PP2, Q751J3, Q756G2, Q75DV4, Q80YQ2, Q8IRS9, Q8IRT0, Q9DE14, Q9GNN7, Q9H0H0
Diamond homologs: Q5ZKU4, Q80UK8, Q9H0H0, Q9VX31
SIGNOR signaling
1 interactions.
| A | Effect | B | Mechanism |
|---|---|---|---|
| INTS2 | “form complex” | “Integrator complex” | binding |
Enriched among interaction partners
Reactome pathways and GO biological processes over-represented among this gene’s 142 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 |
|---|---|---|---|
| FGFR2 mutant receptor activation | 6 | 49.1× | 1e-07 |
| Signaling by FGFR2 IIIa TM | 6 | 38.8× | 3e-07 |
| Abortive elongation of HIV-1 transcript in the absence of Tat | 7 | 37.4× | 5e-08 |
| Pausing and recovery of Tat-mediated HIV elongation | 8 | 31.7× | 3e-08 |
| Tat-mediated HIV elongation arrest and recovery | 8 | 31.7× | 3e-08 |
| RNA Pol II CTD phosphorylation and interaction with CE during HIV infection | 7 | 30.7× | 1e-07 |
| Signaling by FGFR2 | 7 | 30.7× | 1e-07 |
| RNA Pol II CTD phosphorylation and interaction with CE | 7 | 30.7× | 1e-07 |
GO biological processes:
| GO term | Partners | Fold | FDR |
|---|---|---|---|
| positive regulation of cytosolic calcium ion concentration | 9 | 8.6× | 5e-04 |
| G protein-coupled receptor signaling pathway | 16 | 4.7× | 2e-04 |
Disease & clinical
Clinical variants and AI predictions
ClinVar
159 variants total. Per-class counts are floors (≥ shown; pagination cap):
| Classification | Count (floor) |
|---|---|
| Pathogenic | 1 |
| Likely pathogenic | 0 |
| Uncertain significance | 126 |
| Likely benign | 5 |
| Benign | 2 |
Top pathogenic / likely-pathogenic (1)
| Variant ID | HGVS | Classification |
|---|---|---|
| 2685605 | GRCh37/hg19 17q23.2(chr17:59960921-60036130)x1 | Pathogenic |
SpliceAI
4450 predictions. Top by Δscore:
| Variant | Effect | Δscore |
|---|---|---|
| 17:61867724:GACC:G | acceptor_loss | 1.0000 |
| 17:61867725:ACC:A | acceptor_loss | 1.0000 |
| 17:61867727:C:CC | acceptor_gain | 1.0000 |
| 17:61867728:T:A | acceptor_loss | 1.0000 |
| 17:61867828:CTTA:C | donor_loss | 1.0000 |
| 17:61867830:TACGT:T | donor_loss | 1.0000 |
| 17:61867831:A:AC | donor_gain | 1.0000 |
| 17:61867831:A:C | donor_loss | 1.0000 |
| 17:61867832:C:CC | donor_gain | 1.0000 |
| 17:61867832:CG:C | donor_gain | 1.0000 |
| 17:61868005:TAAAA:T | acceptor_gain | 1.0000 |
| 17:61868006:AAAA:A | acceptor_gain | 1.0000 |
| 17:61868007:AAA:A | acceptor_gain | 1.0000 |
| 17:61868008:AA:A | acceptor_gain | 1.0000 |
| 17:61868009:AC:A | acceptor_loss | 1.0000 |
| 17:61868010:C:CC | acceptor_gain | 1.0000 |
| 17:61868011:T:G | acceptor_loss | 1.0000 |
| 17:61869756:G:C | donor_gain | 1.0000 |
| 17:61869813:A:C | donor_gain | 1.0000 |
| 17:61869816:T:TA | donor_gain | 1.0000 |
| 17:61869849:T:TA | donor_gain | 1.0000 |
| 17:61869858:C:A | donor_gain | 1.0000 |
| 17:61869890:TTGA:T | donor_gain | 1.0000 |
| 17:61869904:A:C | donor_gain | 1.0000 |
| 17:61869984:CTATC:C | acceptor_gain | 1.0000 |
| 17:61869985:TATC:T | acceptor_gain | 1.0000 |
| 17:61869987:TC:T | acceptor_gain | 1.0000 |
| 17:61869987:TCC:T | acceptor_loss | 1.0000 |
| 17:61869988:CC:C | acceptor_gain | 1.0000 |
| 17:61869988:CCTA:C | acceptor_loss | 1.0000 |
AlphaMissense
7858 scored. Top likely-pathogenic:
| Variant | Protein change | am_pathogenicity |
|---|---|---|
| 17:61869301:A:G | L1045P | 1.000 |
| 17:61869740:A:C | F1017L | 1.000 |
| 17:61869740:A:T | F1017L | 1.000 |
| 17:61869742:A:G | F1017L | 1.000 |
| 17:61869750:A:G | L1014P | 1.000 |
| 17:61869774:A:T | I1006N | 1.000 |
| 17:61869983:A:C | S936R | 1.000 |
| 17:61869983:A:T | S936R | 1.000 |
| 17:61869985:T:G | S936R | 1.000 |
| 17:61877918:A:G | W817R | 1.000 |
| 17:61877918:A:T | W817R | 1.000 |
| 17:61891684:C:A | W576C | 1.000 |
| 17:61891684:C:G | W576C | 1.000 |
| 17:61891686:A:G | W576R | 1.000 |
| 17:61891686:A:T | W576R | 1.000 |
| 17:61893789:A:C | F566L | 1.000 |
| 17:61893789:A:T | F566L | 1.000 |
| 17:61893790:A:G | F566S | 1.000 |
| 17:61893791:A:G | F566L | 1.000 |
| 17:61893805:A:G | L561P | 1.000 |
| 17:61893808:A:G | L560P | 1.000 |
| 17:61893883:G:T | A535E | 1.000 |
| 17:61893884:C:G | A535P | 1.000 |
| 17:61893895:A:T | V531D | 1.000 |
| 17:61895324:A:C | F526L | 1.000 |
| 17:61895324:A:T | F526L | 1.000 |
| 17:61895326:A:G | F526L | 1.000 |
| 17:61897536:G:T | A484D | 1.000 |
| 17:61897708:A:G | W455R | 1.000 |
| 17:61897708:A:T | W455R | 1.000 |
dbSNP variants (sampled 300 via entrez): RS1000107733 (17:61927177 G>A), RS1000109048 (17:61901735 C>A,T), RS1000145604 (17:61908150 C>G), RS1000198683 (17:61907907 C>T), RS1000260376 (17:61895775 C>G,T), RS1000311570 (17:61881631 A>C), RS1000343646 (17:61881363 G>A,C), RS1000526561 (17:61888577 G>A), RS1000536066 (17:61906260 C>T), RS1000599453 (17:61897332 T>A,C), RS1000644056 (17:61883225 C>T), RS1000834763 (17:61920636 G>A), RS1000846445 (17:61918250 T>C), RS1000853646 (17:61877267 G>A,T), RS1000859091 (17:61901570 A>C)
Disease associations
OMIM: gene MIM:611346 | disease phenotypes: MIM:258040
GenCC curated gene-disease
Mondo (1): exstrophy-epispadias complex (MONDO:0017919)
Orphanet (2): Exstrophy-epispadias complex (Orphanet:322), Cloacal exstrophy (Orphanet:93929)
HPO phenotypes
0 total (0 of 0 shown, HPO-id order):
GWAS associations
1 associations (top):
| Study | Trait | p-value |
|---|---|---|
| GCST90002397_582 | Mean spheric corpuscular volume | 4.000000e-12 |
Drugs & pharmacology
Drug and pharmacology data
Is drug target: no
PharmGKB: 1 entry (VIP=true, CPIC=false)
CTD chemical–gene interactions
30 total (human), top 30 by PubMed support.
| Chemical | Actions (top 5) | PubMed papers |
|---|---|---|
| Aflatoxin B1 | affects expression, increases methylation | 3 |
| Hydrogen Peroxide | affects expression | 2 |
| Cyclosporine | decreases expression | 2 |
| triphenyl phosphate | affects expression | 1 |
| bisphenol A | increases expression | 1 |
| salinomycin | decreases expression | 1 |
| manganese chloride | increases abundance, increases expression | 1 |
| nickel sulfate | increases expression | 1 |
| beta-methylcholine | affects expression | 1 |
| cyanoginosin LR | increases expression | 1 |
| di-n-butylphosphoric acid | affects expression | 1 |
| CGP 52608 | affects binding, increases reaction | 1 |
| jinfukang | decreases expression | 1 |
| Resveratrol | affects cotreatment, increases expression | 1 |
| Air Pollutants | increases abundance, decreases expression | 1 |
| Carbamazepine | affects expression | 1 |
| Cisplatin | decreases expression | 1 |
| Doxorubicin | decreases expression | 1 |
| Manganese | increases abundance, increases expression | 1 |
| Ozone | increases expression | 1 |
| Plant Extracts | affects cotreatment, increases expression | 1 |
| Smoke | decreases expression | 1 |
| Tobacco Smoke Pollution | decreases expression | 1 |
| Tretinoin | decreases expression | 1 |
| Valproic Acid | decreases expression | 1 |
| 7,8-Dihydro-7,8-dihydroxybenzo(a)pyrene 9,10-oxide | decreases expression | 1 |
| Copper Sulfate | decreases expression | 1 |
| Lactic Acid | decreases expression | 1 |
| Acrylamide | increases expression | 1 |
| Particulate Matter | decreases expression, increases abundance | 1 |
Clinical trials (associated diseases)
2 trials via MONDO — disease-level, not drug-specific.
| Trial | Phase | Status | Title |
|---|---|---|---|
| NCT04760028 | PHASE4 | COMPLETED | Study on the Influencing Factors of Electroencephalogram Parameters Under Anesthesia |
| NCT06106425 | Not specified | UNKNOWN | Diagnostic and Prognostic Criteria of EEG in Neonatal Convulsions at Assiut University Children Hospital |
Related Atlas pages
- Disease cohort memberships (association, not causation — diseases whose associated-gene cohort lists this gene; a subset are also under Associated diseases): exstrophy-epispadias complex