RTCA
gene geneOn this page
Also known as RPCRTC1
Summary
RTCA (RNA 3’-terminal phosphate cyclase, HGNC:17981) is a protein-coding gene on chromosome 1p21.2, encoding RNA 3’-terminal phosphate cyclase (O00442). Catalyzes the conversion of 3’-phosphate to a 2’,3’-cyclic phosphodiester at the end of RNA.
This gene encodes a member of the RNA 3’-phosphate cyclase family. The encoded protein plays a role in RNA metabolism by catalyzing the ATP-dependent conversion of the 3’-phosphate of RNA substrates to a 2’,3’-cyclic phosphodiester. Alternatively spliced transcript variants encoding multiple isoforms have been observed for this gene.
Source: NCBI Gene 8634 — RefSeq curated summary.
At a glance
- GWAS associations: 1
- Clinical variants (ClinVar): 90 total
- MANE Select transcript:
NM_003729
Identifiers
Gene identifiers
| Field | Value |
|---|---|
| HGNC ID | HGNC:17981 |
| Approved symbol | RTCA |
| Name | RNA 3’-terminal phosphate cyclase |
| Location | 1p21.2 |
| Locus type | gene with protein product |
| Status | Approved |
| Aliases | RPC, RTC1 |
| Ensembl gene | ENSG00000137996 |
| Ensembl biotype | protein_coding |
| OMIM | 611286 |
| Entrez | 8634 |
Gene structure
Transcript identifiers
Ensembl transcripts: 12 — 10 protein_coding, 2 protein_coding_CDS_not_defined
ENST00000260563, ENST00000370126, ENST00000370128, ENST00000483474, ENST00000498617, ENST00000881959, ENST00000881960, ENST00000927400, ENST00000927401, ENST00000958304, ENST00000958305, ENST00000958306
RefSeq mRNA: 2 — MANE Select: NM_003729
NM_001130841, NM_003729
CCDS: CCDS44178, CCDS768
Canonical transcript exons
ENST00000370128 — 11 exons
| Exon | Start | End |
|---|---|---|
| ENSE00000831307 | 100274824 | 100274965 |
| ENSE00000831308 | 100275599 | 100275723 |
| ENSE00001166889 | 100287099 | 100287203 |
| ENSE00001166896 | 100285228 | 100285322 |
| ENSE00001166905 | 100277258 | 100277316 |
| ENSE00001167849 | 100266216 | 100266420 |
| ENSE00001196477 | 100291403 | 100292769 |
| ENSE00003514174 | 100268152 | 100268295 |
| ENSE00003537387 | 100266524 | 100266624 |
| ENSE00003607452 | 100273394 | 100273452 |
| ENSE00003618171 | 100270557 | 100270680 |
Expression profiles
Bgee: expression breadth ubiquitous, 296 present calls, max score 96.44.
FANTOM5 (CAGE): breadth ubiquitous, TPM avg 52.2743 / max 487.5155, expressed in 1827 samples.
FANTOM5 promoters (4 alternative TSS)
| Promoter ID | TPM avg | Samples expressed |
|---|---|---|
| 4219 | 48.6806 | 1827 |
| 4220 | 2.3511 | 1161 |
| 4218 | 0.7448 | 488 |
| 4221 | 0.4978 | 276 |
Top tissues by expression
299 total, by Bgee expression score (0-100, higher = more expressed):
| Tissue | Anatomy ID | Expression score | Quality |
|---|---|---|---|
| jejunal mucosa | UBERON:0000399 | 96.44 | gold quality |
| esophagus squamous epithelium | UBERON:0006920 | 94.91 | gold quality |
| duodenum | UBERON:0002114 | 94.40 | gold quality |
| epithelium of esophagus | UBERON:0001976 | 94.16 | gold quality |
| dorsal root ganglion | UBERON:0000044 | 93.59 | gold quality |
| amniotic fluid | UBERON:0000173 | 93.49 | gold quality |
| heart right ventricle | UBERON:0002080 | 92.80 | gold quality |
| jejunum | UBERON:0002115 | 92.75 | gold quality |
| sural nerve | UBERON:0015488 | 92.43 | gold quality |
| mucosa of sigmoid colon | UBERON:0004993 | 92.15 | gold quality |
| colonic mucosa | UBERON:0000317 | 92.14 | gold quality |
| biceps brachii | UBERON:0001507 | 92.11 | gold quality |
| body of pancreas | UBERON:0001150 | 92.03 | gold quality |
| corpus epididymis | UBERON:0004359 | 91.87 | gold quality |
| pons | UBERON:0000988 | 91.80 | gold quality |
| primordial germ cell in gonad | CL:0000670 ∩ UBERON:0000991 | 91.59 | gold quality |
| adrenal tissue | UBERON:0018303 | 91.54 | gold quality |
| gastrocnemius | UBERON:0001388 | 91.45 | gold quality |
| calcaneal tendon | UBERON:0003701 | 91.43 | gold quality |
| nephron tubule | UBERON:0001231 | 91.37 | gold quality |
| muscle of leg | UBERON:0001383 | 91.29 | gold quality |
| oral cavity | UBERON:0000167 | 91.17 | gold quality |
| skeletal muscle tissue of biceps brachii | UBERON:0004502 | 90.97 | gold quality |
| heart left ventricle | UBERON:0002084 | 90.93 | gold quality |
| cardiac ventricle | UBERON:0002082 | 90.84 | gold quality |
| mucosa of transverse colon | UBERON:0004991 | 90.80 | gold quality |
| cortical plate | UBERON:0005343 | 90.72 | gold quality |
| rectum | UBERON:0001052 | 90.70 | gold quality |
| tibia | UBERON:0000979 | 90.68 | gold quality |
| tendon | UBERON:0000043 | 90.64 | gold quality |
Single-cell (SCXA)
Detected in 1 experiment(s), a significant marker in 1.
| Experiment | Marker? | Max mean expression |
|---|---|---|
| E-ANND-3 | yes | 6.73 |
Regulation
Is transcription factor: no
miRNA regulators (miRDB)
62 targeting RTCA, 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-3613-3P | 100.00 | 76.36 | 7965 |
| HSA-MIR-3163 | 100.00 | 77.23 | 8605 |
| HSA-MIR-3646 | 100.00 | 73.56 | 5283 |
| 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-4500 | 99.99 | 72.72 | 2367 |
| HSA-MIR-373-5P | 99.98 | 75.36 | 4753 |
| HSA-MIR-616-5P | 99.98 | 75.58 | 4775 |
| HSA-MIR-5696 | 99.98 | 72.36 | 4487 |
| HSA-MIR-545-3P | 99.95 | 70.74 | 2783 |
| HSA-MIR-3682-5P | 99.93 | 67.97 | 1163 |
| HSA-MIR-454-3P | 99.91 | 74.01 | 1925 |
| HSA-MIR-130A-3P | 99.90 | 73.31 | 1861 |
| HSA-MIR-130B-3P | 99.90 | 73.27 | 1850 |
| HSA-MIR-301A-3P | 99.90 | 73.15 | 1839 |
| HSA-MIR-301B-3P | 99.90 | 73.19 | 1836 |
| HSA-MIR-3666 | 99.90 | 73.24 | 1833 |
| HSA-MIR-4295 | 99.90 | 73.11 | 1838 |
| HSA-MIR-3671 | 99.90 | 73.04 | 3897 |
| HSA-MIR-4671-3P | 99.88 | 72.46 | 1045 |
| HSA-MIR-6780A-5P | 99.88 | 66.69 | 2776 |
| HSA-MIR-202-3P | 99.84 | 71.41 | 1290 |
| HSA-MIR-1273H-5P | 99.77 | 66.32 | 2471 |
| HSA-MIR-3680-3P | 99.75 | 72.51 | 3095 |
| HSA-MIR-4699-3P | 99.71 | 70.15 | 3142 |
| HSA-MIR-30B-3P | 99.70 | 65.76 | 2325 |
| HSA-MIR-3689A-3P | 99.70 | 65.73 | 2306 |
| HSA-MIR-3689B-3P | 99.70 | 65.71 | 2311 |
| HSA-MIR-3689C | 99.70 | 65.71 | 2311 |
Literature-anchored findings (GeneRIF, showing 2)
- Rtc1 forms a stable binary complex with a 3’-phosphate terminated RNA, but not with an identical 3’-OH terminated RNA (PMID:19690099)
- CNP and RtcA fine-tune XBP1 output during ER stress (PMID:30355738)
Cross-species orthologs
4 orthologs
| Organism | Symbol | Gene ID |
|---|---|---|
| danio_rerio | rtca | ENSDARG00000002215 |
| mus_musculus | Rtca | ENSMUSG00000000339 |
| rattus_norvegicus | Rtca | ENSRNOG00000014575 |
| drosophila_melanogaster | Rtca | FBGN0025630 |
Paralogs (1): RCL1 (ENSG00000120158)
Protein
Protein identifiers
RNA 3’-terminal phosphate cyclase — O00442 (reviewed: O00442)
Alternative names: RNA terminal phosphate cyclase domain-containing protein 1
All UniProt accessions (2): A6NIC1, O00442
UniProt curated annotations — full annotation on UniProt →
Function. Catalyzes the conversion of 3’-phosphate to a 2’,3’-cyclic phosphodiester at the end of RNA. The mechanism of action of the enzyme occurs in 3 steps: (A) adenylation of the enzyme by ATP; (B) transfer of adenylate to an RNA-N3’P to produce RNA-N3’PP5’A; (C) and attack of the adjacent 2’-hydroxyl on the 3’-phosphorus in the diester linkage to produce the cyclic end product. Likely functions in some aspects of cellular RNA processing. Function plays an important role in regulating axon regeneration by inhibiting central nervous system (CNS) axon regeneration following optic nerve injury.
Subcellular location. Nucleus. Nucleoplasm.
Tissue specificity. Ubiquitous.
Similarity. Belongs to the RNA 3’-terminal cyclase family. Type 1 subfamily.
Isoforms (2)
| UniProt ID | Names | Canonical? |
|---|---|---|
| O00442-1 | 1 | yes |
| O00442-2 | 2 |
RefSeq proteins (2): NP_001124313, NP_003720* (*=MANE)
Domains & families (InterPro)
| ID | Name | Type |
|---|---|---|
| IPR000228 | RNA3’_term_phos_cyc | Family |
| IPR013791 | RNA3’-term_phos_cycl_insert | Domain |
| IPR013792 | RNA3’P_cycl/enolpyr_Trfase_a/b | Homologous_superfamily |
| IPR017770 | RNA3’_term_phos_cyc_type_1 | Family |
| IPR020719 | RNA3’_term_phos_cycl-like_CS | Conserved_site |
| IPR023797 | RNA3’_phos_cyclase_dom | Domain |
| IPR036553 | RPTC_insert | Homologous_superfamily |
| IPR037136 | RNA3’_phos_cyclase_dom_sf | Homologous_superfamily |
Pfam: PF01137, PF05189
Enzyme classification (BRENDA):
- EC 6.5.1.4 — RNA 3’-terminal-phosphate cyclase (ATP) (BRENDA: 25 organisms, 55 substrates, 8 inhibitors, 9 Km, 1 kcat entries)
Substrate kinetics (BRENDA)
3 substrates with measured Km, best-characterized 3. Km ranges are aggregated across organisms/conditions.
| Substrate | Km (mM) | Measurements |
|---|---|---|
| ATP | 0.0017–0.02 | 5 |
| ATPGAMMAS | 0.006 | 2 |
| GTP | 0.1–0.2 | 2 |
Catalyzed reactions (Rhea), 1 shown:
- a 3’-end 3’-phospho-ribonucleotide-RNA + ATP = a 3’-end 2’,3’-cyclophospho-ribonucleotide-RNA + AMP + diphosphate (RHEA:23976)
UniProt features (10 total): binding site 6, chain 1, active site 1, splice variant 1, sequence conflict 1
Structure
Experimental structures (PDB)
0 structures.
Predicted structure (AlphaFold)
| Model | pLDDT | Fraction very-high |
|---|---|---|
| AF-O00442-F1 | 95.90 | 0.95 |
Functional residue map
Curated UniProt residues grouped by drug-discovery relevance — catalytic, ligand-binding, modification, and mutation-validated positions. Source: UniProtKB sequence features.
Catalytic / active sites (1): 320 (tele-amp-histidine intermediate)
Ligand- & substrate-binding residues (6): 104; 131; 294; 297; 298; 320
Function
Pathways and Gene Ontology
Reactome pathways
0 pathways
MSigDB gene sets: 169 (showing top):
GSE45365_NK_CELL_VS_CD8_TCELL_UP, RODRIGUES_THYROID_CARCINOMA_ANAPLASTIC_UP, RODRIGUES_THYROID_CARCINOMA_POORLY_DIFFERENTIATED_UP, GOBP_REGENERATION, GOBP_NEUROGENESIS, GOBP_RESPONSE_TO_AXON_INJURY, GARGALOVIC_RESPONSE_TO_OXIDIZED_PHOSPHOLIPIDS_BLUE_UP, PATIL_LIVER_CANCER, GOBP_NEGATIVE_REGULATION_OF_CELLULAR_COMPONENT_ORGANIZATION, GOBP_REGULATION_OF_CELL_PROJECTION_ORGANIZATION, GOBP_REGULATION_OF_RESPONSE_TO_WOUNDING, GNF2_XRCC5, GOBP_REGULATION_OF_RESPONSE_TO_STRESS, GOBP_REGULATION_OF_NEURON_PROJECTION_REGENERATION, GOBP_NEGATIVE_REGULATION_OF_CELL_PROJECTION_ORGANIZATION
GO Biological Process (2): RNA processing (GO:0006396), negative regulation of optical nerve axon regeneration (GO:1905592)
GO Molecular Function (7): RNA binding (GO:0003723), RNA-3’-phosphate cyclase activity (GO:0003963), ATP binding (GO:0005524), nucleotide binding (GO:0000166), catalytic activity (GO:0003824), protein binding (GO:0005515), ligase activity (GO:0016874)
GO Cellular Component (2): nucleus (GO:0005634), nucleoplasm (GO:0005654)
GO top-level categories
Rollup of top GO terms by namespace:
| Category | Terms |
|---|---|
| gene expression | 1 |
| RNA biosynthetic process | 1 |
| primary metabolic process | 1 |
| negative regulation of axon regeneration | 1 |
| optical nerve axon regeneration | 1 |
| regulation of optical nerve axon regeneration | 1 |
| nucleic acid binding | 1 |
| cyclase activity | 1 |
| ligase activity, forming phosphoric ester bonds | 1 |
| catalytic activity, acting on RNA | 1 |
| adenyl ribonucleotide binding | 1 |
| purine ribonucleoside triphosphate binding | 1 |
| nucleoside phosphate binding | 1 |
| heterocyclic compound binding | 1 |
| molecular_function | 1 |
| binding | 1 |
| catalytic activity | 1 |
| intracellular membrane-bounded organelle | 1 |
| nuclear lumen | 1 |
| cellular anatomical structure | 1 |
Protein interactions and networks
STRING
2519 interactions, top by confidence (×1000):
| Protein A | Protein B | Partner UniProt | Score |
|---|---|---|---|
| RTCA | BMS1 | Q14692 | 853 |
| RTCA | RTCB | Q9Y3I0 | 851 |
| RTCA | DPH5 | Q9H2P9 | 614 |
| RTCA | LRRC39 | Q96DD0 | 609 |
| RTCA | TRPT1 | Q86TN4 | 605 |
| RTCA | DBT | P11182 | 557 |
| RTCA | ZBTB8OS | Q8IWT0 | 547 |
| RTCA | TRMT13 | Q9NUP7 | 512 |
| RTCA | FCF1 | Q9Y324 | 478 |
| RTCA | SLC35H1 | Q9NQQ7 | 457 |
| RTCA | SLC30A7 | Q8NEW0 | 455 |
| RTCA | RO60 | P10155 | 446 |
| RTCA | FAM98B | Q52LJ0 | 430 |
| RTCA | GGN | Q86UU5 | 425 |
| RTCA | FPGT | O14772 | 423 |
| RTCA | GPR88 | Q9GZN0 | 423 |
IntAct
80 interactions, top by confidence:
| A | B | Type | Score |
|---|---|---|---|
| CFTR | ESYT2 | psi-mi:“MI:2364”(proximity) | 0.710 |
| LAMP3 | METTL15 | psi-mi:“MI:0914”(association) | 0.530 |
| Sass6 | MACF1 | psi-mi:“MI:0914”(association) | 0.350 |
| FOXL2 | RTCA | psi-mi:“MI:0914”(association) | 0.350 |
| FOXQ1 | ARHGAP10 | psi-mi:“MI:0914”(association) | 0.350 |
| FOXS1 | DDX39A | psi-mi:“MI:0914”(association) | 0.350 |
| JUN | psi-mi:“MI:0914”(association) | 0.350 | |
| JUN | TPM3 | psi-mi:“MI:0914”(association) | 0.350 |
| HSCB | RBP5 | psi-mi:“MI:0914”(association) | 0.350 |
| CAND1 | GTPBP10 | psi-mi:“MI:0914”(association) | 0.350 |
| USP45 | RTCA | psi-mi:“MI:0914”(association) | 0.350 |
| PRKD1 | MYO1C | psi-mi:“MI:0914”(association) | 0.350 |
| ZDHHC5 | HACD3 | psi-mi:“MI:0914”(association) | 0.350 |
| TAGLN | LOC392647 | psi-mi:“MI:0914”(association) | 0.350 |
| ARID1B | RTCA | psi-mi:“MI:0914”(association) | 0.350 |
| ITM2B | ILVBL | psi-mi:“MI:0914”(association) | 0.350 |
| OSTM1 | ILVBL | psi-mi:“MI:0914”(association) | 0.350 |
| PRKY | METTL15 | psi-mi:“MI:0914”(association) | 0.350 |
| HOXC5 | PDLIM1 | psi-mi:“MI:0914”(association) | 0.350 |
| GORASP1 | RTCA | psi-mi:“MI:0914”(association) | 0.350 |
| CNTN2 | RTCA | psi-mi:“MI:0914”(association) | 0.350 |
| ZNF695 | RTCA | psi-mi:“MI:0914”(association) | 0.350 |
| PAEP | RTCA | psi-mi:“MI:0914”(association) | 0.350 |
| HNRNPCL2 | SMCHD1 | psi-mi:“MI:0914”(association) | 0.350 |
| RTCA | NDUFA4 | psi-mi:“MI:0914”(association) | 0.350 |
| RTCA | psi-mi:“MI:0914”(association) | 0.350 | |
| POLRMT | psi-mi:“MI:0914”(association) | 0.350 |
BioGRID (146): HNRNPH1 (Co-fractionation), RTCA (Affinity Capture-MS), RTCA (Affinity Capture-MS), RTCA (Affinity Capture-MS), RTCA (Affinity Capture-MS), RTCA (Affinity Capture-MS), RTCA (Affinity Capture-MS), RTCA (Affinity Capture-MS), RTCA (Affinity Capture-MS), RPL21 (Affinity Capture-MS), FBL (Affinity Capture-MS), RPL23A (Affinity Capture-MS), RPL18A (Affinity Capture-MS), DDX21 (Affinity Capture-MS), RTCA (Affinity Capture-MS)
ESM2 similar proteins: A2RVK7, A2X0Q3, A6QLJ3, O00442, O23617, O81147, O81852, P0CT46, P31754, P37142, P48605, P49080, P49368, P80318, Q01415, Q06265, Q14181, Q2HJ88, Q2KHU3, Q3SWZ4, Q3T0K2, Q4QR75, Q4R3J0, Q4R963, Q5NVF9, Q5R6J8, Q5R7P3, Q5RCW2, Q5RGJ5, Q5XJQ5, Q69LE7, Q6P502, Q6STH5, Q6YXZ7, Q7YRA3, Q84T68, Q8C3X4, Q8GZQ3, Q8K1R3, Q8N442
Diamond homologs: A0B532, A1AGU3, A1RSJ7, A2BN21, A3DN24, A3MXQ7, A4XRJ0, A4YEC3, A7ZSU9, A8A5M8, A8A9W2, A8MAV7, B0R414, B1IP46, B1L6E9, B1LI80, B1X765, B1YDJ1, B2IWJ8, B2U3M8, B4TKU5, B5F8N4, B5R378, B5R7J6, B5YTX2, B6YSJ5, B7KCF3, B7L4U9, B7LSC2, B7M2I0, B7MDP5, B7N1J7, B7NE24, B7NMI4, B7UKC4, B7V0C8, B8D680, C0Q0J3, C3MKC1, C3MU91
SIGNOR signaling
0 interactions.
Enriched among interaction partners
Reactome pathways and GO biological processes over-represented among this gene’s 80 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 |
|---|---|---|---|
| Peptide chain elongation | 10 | 23.5× | 1e-09 |
| Viral mRNA Translation | 10 | 23.5× | 1e-09 |
| PELO:HBS1L and ABCE1 dissociate a ribosome on a non-stop mRNA | 10 | 23.2× | 1e-09 |
| Selenocysteine synthesis | 10 | 22.3× | 1e-09 |
| Eukaryotic Translation Termination | 10 | 22.3× | 1e-09 |
| Nonsense Mediated Decay (NMD) independent of the Exon Junction Complex (EJC) | 10 | 21.8× | 1e-09 |
| ZNF598 and the Ribosome-associated Quality Trigger (RQT) complex dissociate a ribosome stalled on a no-go mRNA | 10 | 21.8× | 1e-09 |
| Formation of a pool of free 40S subunits | 10 | 20.7× | 1e-09 |
GO biological processes:
| GO term | Partners | Fold | FDR |
|---|---|---|---|
| cytoplasmic translation | 11 | 28.3× | 6e-11 |
| translation | 10 | 14.3× | 4e-07 |
Disease & clinical
Clinical variants and AI predictions
ClinVar
90 variants total. Per-class counts are floors (≥ shown; pagination cap):
| Classification | Count (floor) |
|---|---|
| Pathogenic | 0 |
| Likely pathogenic | 0 |
| Uncertain significance | 63 |
| Likely benign | 2 |
| Benign | 1 |
Top pathogenic / likely-pathogenic (0)
SpliceAI
1801 predictions. Top by Δscore:
| Variant | Effect | Δscore |
|---|---|---|
| 1:100266417:AGGGG:A | donor_loss | 1.0000 |
| 1:100266418:GGG:G | donor_gain | 1.0000 |
| 1:100266419:GG:G | donor_gain | 1.0000 |
| 1:100266419:GGG:G | donor_gain | 1.0000 |
| 1:100266420:GG:G | donor_gain | 1.0000 |
| 1:100266420:GGT:G | donor_loss | 1.0000 |
| 1:100266421:G:GA | donor_loss | 1.0000 |
| 1:100266421:G:GG | donor_gain | 1.0000 |
| 1:100266422:T:A | donor_loss | 1.0000 |
| 1:100266618:GCC:G | donor_gain | 1.0000 |
| 1:100266621:TGAGG:T | donor_loss | 1.0000 |
| 1:100266623:AGGT:A | donor_loss | 1.0000 |
| 1:100266624:GGTAA:G | donor_loss | 1.0000 |
| 1:100266625:G:A | donor_loss | 1.0000 |
| 1:100266626:T:A | donor_loss | 1.0000 |
| 1:100268135:A:AG | acceptor_gain | 1.0000 |
| 1:100268136:G:GG | acceptor_gain | 1.0000 |
| 1:100268167:T:TA | acceptor_gain | 1.0000 |
| 1:100270556:GGA:G | acceptor_gain | 1.0000 |
| 1:100270556:GGAGT:G | acceptor_gain | 1.0000 |
| 1:100270605:T:A | acceptor_gain | 1.0000 |
| 1:100273388:TTTCA:T | acceptor_loss | 1.0000 |
| 1:100273389:TTCA:T | acceptor_loss | 1.0000 |
| 1:100273391:CA:C | acceptor_loss | 1.0000 |
| 1:100273392:A:AG | acceptor_gain | 1.0000 |
| 1:100273392:A:T | acceptor_loss | 1.0000 |
| 1:100273393:G:GG | acceptor_gain | 1.0000 |
| 1:100274820:ATAGG:A | acceptor_gain | 1.0000 |
| 1:100275592:A:AG | acceptor_gain | 1.0000 |
| 1:100275596:TA:T | acceptor_loss | 1.0000 |
AlphaMissense
2376 scored. Top likely-pathogenic:
| Variant | Protein change | am_pathogenicity |
|---|---|---|
| 1:100274826:G:A | G159E | 0.999 |
| 1:100275623:G:C | A214P | 0.998 |
| 1:100285248:G:A | G274R | 0.998 |
| 1:100285248:G:C | G274R | 0.998 |
| 1:100285249:G:A | G274E | 0.998 |
| 1:100285260:G:C | A278P | 0.998 |
| 1:100285318:A:C | D297A | 0.998 |
| 1:100285318:A:T | D297V | 0.998 |
| 1:100287162:C:G | H320D | 0.998 |
| 1:100268158:A:C | Q51H | 0.997 |
| 1:100268158:A:T | Q51H | 0.997 |
| 1:100268292:C:A | A96E | 0.997 |
| 1:100270558:A:C | S98R | 0.997 |
| 1:100270560:T:A | S98R | 0.997 |
| 1:100270560:T:G | S98R | 0.997 |
| 1:100270568:T:C | L101P | 0.997 |
| 1:100270637:G:A | G124E | 0.997 |
| 1:100270644:T:A | N126K | 0.997 |
| 1:100270644:T:G | N126K | 0.997 |
| 1:100274825:G:A | G159R | 0.997 |
| 1:100274825:G:C | G159R | 0.997 |
| 1:100274847:G:A | G166D | 0.997 |
| 1:100275717:G:A | G245E | 0.997 |
| 1:100277266:C:A | A250D | 0.997 |
| 1:100285261:C:A | A278D | 0.997 |
| 1:100285317:G:C | D297H | 0.997 |
| 1:100287164:T:A | H320Q | 0.997 |
| 1:100287164:T:G | H320Q | 0.997 |
| 1:100266540:G:C | R21T | 0.996 |
| 1:100270633:G:C | G123R | 0.996 |
dbSNP variants (sampled 300 via entrez): RS1000150682 (1:100280849 A>G), RS1000162035 (1:100281423 A>G), RS1000171084 (1:100270214 T>G), RS1000487267 (1:100282517 T>G), RS1000541523 (1:100268926 C>T), RS1000594813 (1:100275143 C>A,T), RS1000912896 (1:100269049 A>C,G), RS1000929471 (1:100287801 T>C), RS1000961809 (1:100264338 T>C), RS1001128756 (1:100270155 C>T), RS1001163737 (1:100279762 A>T), RS1001165586 (1:100281307 G>A), RS1001420737 (1:100276381 T>C), RS1001484497 (1:100281558 A>G), RS1001501670 (1:100265121 T>C)
Disease associations
OMIM: gene MIM:611286 | disease phenotypes:
GenCC curated gene-disease
Mondo (0):
Orphanet (0):
HPO phenotypes
0 total (0 of 0 shown, HPO-id order):
GWAS associations
1 associations (top):
| Study | Trait | p-value |
|---|---|---|
| GCST002337_70 | Amyotrophic lateral sclerosis (sporadic) | 9.000000e-06 |
Drugs & pharmacology
Drug and pharmacology data
Is drug target: no
PharmGKB: 1 entry (VIP=true, CPIC=false)
CTD chemical–gene interactions
37 total (human), top 30 by PubMed support.
| Chemical | Actions (top 5) | PubMed papers |
|---|---|---|
| sodium arsenite | increases expression, decreases expression, increases abundance | 3 |
| Valproic Acid | increases expression, affects expression | 3 |
| cobaltous chloride | increases expression | 2 |
| Air Pollutants | decreases expression, increases abundance, increases expression | 2 |
| Arsenic | affects methylation, increases abundance, increases expression | 2 |
| Cyclosporine | increases expression | 2 |
| Particulate Matter | decreases expression, increases abundance, increases expression | 2 |
| dicrotophos | decreases expression | 1 |
| bisphenol A | affects expression | 1 |
| sodium arsenate | decreases expression | 1 |
| tris(1,3-dichloro-2-propyl)phosphate | increases expression | 1 |
| beta-methylcholine | affects expression | 1 |
| di-n-butylphosphoric acid | affects expression | 1 |
| nutlin 3 | increases secretion, affects cotreatment | 1 |
| ICG 001 | increases expression | 1 |
| bisphenol B | increases expression | 1 |
| abrine | decreases expression | 1 |
| pentabrominated diphenyl ether 100 | decreases expression | 1 |
| hexabrominated diphenyl ether 153 | decreases expression | 1 |
| NSC 689534 | increases expression, affects binding | 1 |
| Resveratrol | affects cotreatment, increases expression | 1 |
| Copper | affects binding, increases expression | 1 |
| Dactinomycin | affects cotreatment, increases secretion | 1 |
| Doxorubicin | decreases expression | 1 |
| Enzyme Inhibitors | decreases activity, increases O-linked glycosylation | 1 |
| Ivermectin | decreases expression | 1 |
| Plant Extracts | affects cotreatment, increases expression | 1 |
| Quercetin | decreases expression | 1 |
| Rotenone | decreases expression | 1 |
| Thiram | increases 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): sporadic amyotrophic lateral sclerosis