GNL2
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Also known as Ngp-1HUMAUANTIGNog2Nug2
Summary
GNL2 (G protein nucleolar 2, HGNC:29925) is a protein-coding gene on chromosome 1p34.3, encoding Nucleolar GTP-binding protein 2 (Q13823). GTPase that associates with pre-60S ribosomal subunits in the nucleolus and is required for their nuclear export and maturation. It is a common-essential gene (DepMap: required in 99.3% of cancer cell lines).
Enables RNA binding activity. Predicted to be involved in ribosome biogenesis. Located in nucleolus.
Source: NCBI Gene 29889 — RefSeq curated summary.
At a glance
- GWAS associations: 4
- Clinical variants (ClinVar): 119 total
- Cancer dependency (DepMap): dependent in 99.3% of screened cell lines (common-essential)
- MANE Select transcript:
NM_013285
Identifiers
Gene identifiers
| Field | Value |
|---|---|
| HGNC ID | HGNC:29925 |
| Approved symbol | GNL2 |
| Name | G protein nucleolar 2 |
| Location | 1p34.3 |
| Locus type | gene with protein product |
| Status | Approved |
| Aliases | Ngp-1, HUMAUANTIG, Nog2, Nug2 |
| Ensembl gene | ENSG00000134697 |
| Ensembl biotype | protein_coding |
| OMIM | 609365 |
| Entrez | 29889 |
Gene structure
Transcript identifiers
Ensembl transcripts: 15 — 8 protein_coding, 7 protein_coding_CDS_not_defined
ENST00000373062, ENST00000462812, ENST00000463351, ENST00000469191, ENST00000479255, ENST00000488496, ENST00000489146, ENST00000490029, ENST00000538069, ENST00000852774, ENST00000918214, ENST00000965152, ENST00000965153, ENST00000965154, ENST00000965155
RefSeq mRNA: 3 — MANE Select: NM_013285
NM_001323623, NM_001323624, NM_013285
CCDS: CCDS421
Canonical transcript exons
ENST00000373062 — 16 exons
| Exon | Start | End |
|---|---|---|
| ENSE00001079250 | 37574665 | 37574823 |
| ENSE00001079259 | 37574343 | 37574456 |
| ENSE00001079260 | 37568851 | 37569302 |
| ENSE00001079261 | 37576428 | 37576556 |
| ENSE00001156082 | 37593762 | 37593846 |
| ENSE00001459441 | 37595759 | 37595937 |
| ENSE00003460459 | 37587311 | 37587495 |
| ENSE00003479534 | 37583867 | 37583933 |
| ENSE00003524106 | 37582778 | 37582936 |
| ENSE00003569383 | 37582223 | 37582336 |
| ENSE00003600297 | 37567673 | 37567764 |
| ENSE00003603852 | 37592712 | 37592806 |
| ENSE00003623459 | 37568275 | 37568357 |
| ENSE00003645971 | 37590706 | 37590845 |
| ENSE00003661261 | 37566816 | 37567007 |
| ENSE00003791286 | 37575595 | 37575699 |
Expression profiles
Bgee: expression breadth ubiquitous, 292 present calls, max score 96.62.
FANTOM5 (CAGE): breadth ubiquitous, TPM avg 26.5413 / max 223.8749, expressed in 1814 samples.
FANTOM5 promoters (1 alternative TSS)
| Promoter ID | TPM avg | Samples expressed |
|---|---|---|
| 11786 | 26.5413 | 1814 |
Top tissues by expression
295 total, by Bgee expression score (0-100, higher = more expressed):
| Tissue | Anatomy ID | Expression score | Quality |
|---|---|---|---|
| tendon of biceps brachii | UBERON:0008188 | 96.62 | gold quality |
| gingival epithelium | UBERON:0001949 | 95.21 | gold quality |
| tendon | UBERON:0000043 | 95.06 | gold quality |
| sural nerve | UBERON:0015488 | 94.77 | gold quality |
| calcaneal tendon | UBERON:0003701 | 94.71 | gold quality |
| primordial germ cell in gonad | CL:0000670 ∩ UBERON:0000991 | 94.44 | gold quality |
| amniotic fluid | UBERON:0000173 | 93.87 | gold quality |
| gingiva | UBERON:0001828 | 93.51 | gold quality |
| cervix squamous epithelium | UBERON:0006922 | 93.41 | gold quality |
| lower esophagus mucosa | UBERON:0035834 | 93.40 | gold quality |
| olfactory segment of nasal mucosa | UBERON:0005386 | 93.36 | gold quality |
| gastrocnemius | UBERON:0001388 | 93.13 | gold quality |
| epithelium of nasopharynx | UBERON:0001951 | 93.11 | gold quality |
| adenohypophysis | UBERON:0002196 | 93.09 | gold quality |
| islet of Langerhans | UBERON:0000006 | 93.06 | gold quality |
| left testis | UBERON:0004533 | 93.03 | gold quality |
| cartilage tissue | UBERON:0002418 | 92.98 | gold quality |
| right testis | UBERON:0004534 | 92.96 | gold quality |
| skin of abdomen | UBERON:0001416 | 92.86 | gold quality |
| skin of leg | UBERON:0001511 | 92.49 | gold quality |
| testis | UBERON:0000473 | 92.47 | gold quality |
| stromal cell of endometrium | CL:0002255 | 92.43 | gold quality |
| muscle of leg | UBERON:0001383 | 92.41 | gold quality |
| esophagus mucosa | UBERON:0002469 | 92.31 | gold quality |
| minor salivary gland | UBERON:0001830 | 92.29 | gold quality |
| mucosa of transverse colon | UBERON:0004991 | 92.26 | gold quality |
| peritoneum | UBERON:0002358 | 92.23 | gold quality |
| omental fat pad | UBERON:0010414 | 92.23 | gold quality |
| mouth mucosa | UBERON:0003729 | 92.14 | gold quality |
| rectum | UBERON:0001052 | 92.11 | gold quality |
Single-cell (SCXA)
Detected in 1 experiment(s), a significant marker in 1.
| Experiment | Marker? | Max mean expression |
|---|---|---|
| E-ANND-3 | no | 0.00 |
Regulation
Is transcription factor: no
Functional genomics
DepMap (CRISPR cell-line fitness): dependent in 99.3% of screened cell lines, common-essential.
Literature-anchored findings (GeneRIF, showing 4)
- GNL2 and SEC13 are required for nonsense-mediated mRNA decay pathway in human cells. (PMID:25452588)
- NGP-1 promotes cell cycle progression through the activation of the p53/p21(Cip-1/Waf1) pathway. (PMID:26203195)
- Study of the G Protein Nucleolar 2 Value in Liver Hepatocellular Carcinoma Treatment and Prognosis. (PMID:34337013)
- Functional analysis of the 1p34.3 risk locus implicates GNL2 in high-grade serous ovarian cancer. (PMID:34965383)
Cross-species orthologs
5 orthologs
| Organism | Symbol | Gene ID |
|---|---|---|
| danio_rerio | gnl2 | ENSDARG00000098080 |
| mus_musculus | Gnl2 | ENSMUSG00000028869 |
| rattus_norvegicus | Gnl2 | ENSRNOG00000009430 |
| drosophila_melanogaster | Ns2 | FBGN0034243 |
| caenorhabditis_elegans | ngp-1 | WBGENE00003596 |
Paralogs (6): LSG1 (ENSG00000041802), NOA1 (ENSG00000084092), GNL3L (ENSG00000130119), MTG1 (ENSG00000148824), GNL3 (ENSG00000163938), GNL1 (ENSG00000204590)
Protein
Protein identifiers
Nucleolar GTP-binding protein 2 — Q13823 (reviewed: Q13823)
Alternative names: Autoantigen NGP-1
All UniProt accessions (3): Q13823, H0YG10, Q5T0F3
UniProt curated annotations — full annotation on UniProt →
Function. GTPase that associates with pre-60S ribosomal subunits in the nucleolus and is required for their nuclear export and maturation. May promote cell proliferation possibly by increasing p53/TP53 protein levels, and consequently those of its downstream product CDKN1A/p21, and decreasing RPL23A protein levels.
Subunit / interactions. Interacts with LYAR and RPL23A. Interacts with the nuclear importin-beta receptor and, at a lower extent, with importin-alpha.
Subcellular location. Nucleus. Nucleolus.
Tissue specificity. Widely expressed, with the highest expression level in testis.
Similarity. Belongs to the TRAFAC class YlqF/YawG GTPase family. NOG2 subfamily.
RefSeq proteins (3): NP_001310552, NP_001310553, NP_037417* (*=MANE)
Domains & families (InterPro)
| ID | Name | Type |
|---|---|---|
| IPR006073 | GTP-bd | Domain |
| IPR012971 | NOG2_N_dom | Domain |
| IPR023179 | GTP-bd_ortho_bundle_sf | Homologous_superfamily |
| IPR024929 | GNL2_CP_dom | Domain |
| IPR027417 | P-loop_NTPase | Homologous_superfamily |
| IPR030378 | G_CP_dom | Domain |
| IPR050755 | TRAFAC_YlqF/YawG_RiboMat | Family |
Pfam: PF01926, PF08153
UniProt features (34 total): mutagenesis site 16, compositionally biased region 6, region of interest 4, binding site 2, modified residue 2, chain 1, domain 1, sequence variant 1, sequence conflict 1
Structure
Experimental structures (PDB)
23 structures.
| PDB | Method | Resolution (Å) |
|---|---|---|
| 8FL3 | ELECTRON MICROSCOPY | 2.53 |
| 8FL7 | ELECTRON MICROSCOPY | 2.55 |
| 8FL6 | ELECTRON MICROSCOPY | 2.62 |
| 8FL2 | ELECTRON MICROSCOPY | 2.67 |
| 8FL9 | ELECTRON MICROSCOPY | 2.75 |
| 8IDT | ELECTRON MICROSCOPY | 2.8 |
| 8RL2 | ELECTRON MICROSCOPY | 2.84 |
| 8FL4 | ELECTRON MICROSCOPY | 2.89 |
| 8FL0 | ELECTRON MICROSCOPY | 2.91 |
| 8IDY | ELECTRON MICROSCOPY | 3 |
| 8INF | ELECTRON MICROSCOPY | 3 |
| 8FKZ | ELECTRON MICROSCOPY | 3.04 |
| 9QIW | ELECTRON MICROSCOPY | 3.04 |
| 6LU8 | ELECTRON MICROSCOPY | 3.13 |
| 8INE | ELECTRON MICROSCOPY | 3.2 |
| 8INK | ELECTRON MICROSCOPY | 3.2 |
| 8IPD | ELECTRON MICROSCOPY | 3.2 |
| 8IPY | ELECTRON MICROSCOPY | 3.2 |
| 6LSS | ELECTRON MICROSCOPY | 3.23 |
| 8IE3 | ELECTRON MICROSCOPY | 3.3 |
| 8IR1 | ELECTRON MICROSCOPY | 3.3 |
| 8IR3 | ELECTRON MICROSCOPY | 3.5 |
| 8IPX | ELECTRON MICROSCOPY | 4.3 |
Predicted structure (AlphaFold)
| Model | pLDDT | Fraction very-high |
|---|---|---|
| AF-Q13823-F1 | 73.37 | 0.40 |
Functional residue map
Curated UniProt residues grouped by drug-discovery relevance — catalytic, ligand-binding, modification, and mutation-validated positions. Source: UniProtKB sequence features.
Ligand- & substrate-binding residues (2): 317–324; 361–365
Post-translational modifications (2): 1, 504
Mutagenesis-validated functional residues (16):
| Position | Phenotype |
|---|---|
| 33–35 | diffused nuclear localization, loss of nucleolar localization. |
| 39–40 | diffused nuclear localization, loss of nucleolar localization. |
| 39–40 | no effect on nucleolar localization. |
| 49–50 | diffused nuclear localization, loss of nucleolar localization. |
| 227–229 | loss of gtp-binding. efficient localization to the nucleus, but excluded from nucleoli. |
| 258 | loss of gtp-binding. punctate pattern throughout the nucleus, including nucleoli. |
| 323 | no effect on gtp-binding, nor on nucleolar localization. |
| 324 | no effect on gtp-binding, nor on nucleolar localization. |
| 325 | no effect on gtp-binding, nor on nucleolar localization. |
| 343–345 | no effect on gtp-binding, nor on nucleolar localization. |
| 363–364 | no effect on gtp-binding, nor on nucleolar localization. |
| 463 | no effect on nucleolar localization; when associated with a-475. |
| 475 | no effect on nucleolar localization; when associated with a-463. |
| 682–684 | no effect on nucleolar localization. predominantly cytoplasmic, with some nucleolar staining; when associated with 711-a |
| 711–713 | no effect on nucleolar localization predominantly cytoplasmic, with some nucleolar staining; when associated with 682-aa |
| 724–726 | no effect on nucleolar localization. strong nucleolar localization, with some cytoplasmic staining; when associated with |
Function
Pathways and Gene Ontology
Reactome pathways
0 pathways
MSigDB gene sets: 161 (showing top):
GOBP_RIBOSOME_BIOGENESIS, RODRIGUES_THYROID_CARCINOMA_ANAPLASTIC_UP, RODRIGUES_THYROID_CARCINOMA_POORLY_DIFFERENTIATED_UP, GRAESSMANN_APOPTOSIS_BY_DOXORUBICIN_UP, BROWNE_HCMV_INFECTION_16HR_UP, MORF_HDAC2, PUJANA_CHEK2_PCC_NETWORK, WEI_MYCN_TARGETS_WITH_E_BOX, MILI_PSEUDOPODIA_HAPTOTAXIS_UP, chr1p34, MORF_PRKDC, GARY_CD5_TARGETS_DN, MODULE_86, RYTTCCTG_ETS2_B, SPIELMAN_LYMPHOBLAST_EUROPEAN_VS_ASIAN_UP
GO Biological Process (1): ribosome biogenesis (GO:0042254)
GO Molecular Function (4): RNA binding (GO:0003723), GTPase activity (GO:0003924), GTP binding (GO:0005525), nucleotide binding (GO:0000166)
GO Cellular Component (3): nucleus (GO:0005634), nucleolus (GO:0005730), membrane (GO:0016020)
GO top-level categories
Rollup of top GO terms by namespace:
| Category | Terms |
|---|---|
| ribonucleoprotein complex biogenesis | 1 |
| nucleic acid binding | 1 |
| ribonucleoside triphosphate phosphatase activity | 1 |
| guanyl ribonucleotide binding | 1 |
| purine ribonucleoside triphosphate binding | 1 |
| nucleoside phosphate binding | 1 |
| heterocyclic compound binding | 1 |
| intracellular membrane-bounded organelle | 1 |
| nuclear lumen | 1 |
| intracellular membraneless organelle | 1 |
| cellular anatomical structure | 1 |
Protein interactions and networks
STRING
3651 interactions, top by confidence (×1000):
| Protein A | Protein B | Partner UniProt | Score |
|---|---|---|---|
| GNL2 | GTPBP4 | Q9BZE4 | 910 |
| GNL2 | NSA2 | O95478 | 904 |
| GNL2 | RPF2 | Q9H7B2 | 899 |
| GNL2 | RPL37A | P12751 | 852 |
| GNL2 | SENP5 | Q96HI0 | 850 |
| GNL2 | RSL24D1 | Q9UHA3 | 843 |
| GNL2 | NMD3 | Q96D46 | 842 |
| GNL2 | MDN1 | Q9NU22 | 809 |
| GNL2 | SENP3 | Q9H4L4 | 799 |
| GNL2 | WDR12 | Q9GZL7 | 773 |
| GNL2 | NPM1 | P06748 | 771 |
| GNL2 | WDR74 | Q6RFH5 | 766 |
| GNL2 | MRTO4 | Q9UKD2 | 760 |
| GNL2 | RCC1 | P18754 | 736 |
| GNL2 | NOP2 | P46087 | 736 |
IntAct
301 interactions, top by confidence:
| A | B | Type | Score |
|---|---|---|---|
| CDK8 | MED19 | psi-mi:“MI:2364”(proximity) | 0.850 |
| TUBG1 | TUBG1 | psi-mi:“MI:2364”(proximity) | 0.760 |
| N | HNRNPR | psi-mi:“MI:0914”(association) | 0.730 |
| CFTR | ESYT2 | psi-mi:“MI:2364”(proximity) | 0.710 |
| RANBP6 | SLC27A2 | psi-mi:“MI:0914”(association) | 0.640 |
| RPL14 | RRP8 | psi-mi:“MI:0914”(association) | 0.640 |
| H1-1 | RRP8 | psi-mi:“MI:0914”(association) | 0.640 |
| NOP53 | RRP8 | psi-mi:“MI:0914”(association) | 0.640 |
| NOL12 | RRP8 | psi-mi:“MI:0914”(association) | 0.640 |
| NSA2 | TYW5 | psi-mi:“MI:0914”(association) | 0.530 |
| FGF3 | GTPBP10 | psi-mi:“MI:0914”(association) | 0.530 |
| MECP2 | GTPBP10 | psi-mi:“MI:0914”(association) | 0.530 |
| H1-6 | ZNF724 | psi-mi:“MI:0914”(association) | 0.530 |
| ZNF512 | ZNF724 | psi-mi:“MI:0914”(association) | 0.530 |
| RBM34 | NVL | psi-mi:“MI:0914”(association) | 0.530 |
| RRP8 | NVL | psi-mi:“MI:0914”(association) | 0.530 |
| H1-4 | IGF2BP3 | psi-mi:“MI:0914”(association) | 0.530 |
| RPL37A | MPHOSPH10 | psi-mi:“MI:0914”(association) | 0.530 |
| ZNF2 | MPHOSPH10 | psi-mi:“MI:0914”(association) | 0.530 |
| RPL18 | NOP56 | psi-mi:“MI:0914”(association) | 0.530 |
| PRR11 | NVL | psi-mi:“MI:0914”(association) | 0.530 |
| KNOP1 | DHX15 | psi-mi:“MI:0914”(association) | 0.530 |
| RPL30 | RRP8 | psi-mi:“MI:0914”(association) | 0.530 |
| RPL8 | RRP8 | psi-mi:“MI:0914”(association) | 0.530 |
| RPL18A | RRP8 | psi-mi:“MI:0914”(association) | 0.530 |
| ZBTB48 | ZBTB24 | psi-mi:“MI:0914”(association) | 0.530 |
| PDGFB | DKC1 | psi-mi:“MI:0914”(association) | 0.530 |
BioGRID (468): GNL2 (Affinity Capture-MS), GNL2 (Affinity Capture-MS), GNL2 (Affinity Capture-MS), GNL2 (Affinity Capture-MS), GNL2 (Affinity Capture-MS), GNL2 (Affinity Capture-MS), GNL2 (Affinity Capture-MS), GNL2 (Affinity Capture-MS), GNL2 (Affinity Capture-MS), GNL2 (Affinity Capture-MS), GNL2 (Affinity Capture-MS), GNL2 (Affinity Capture-MS), GNL2 (Affinity Capture-MS), GNL2 (Co-fractionation), GNL2 (Co-fractionation)
ESM2 similar proteins: A2XGQ1, G0S8F1, J9VQ03, O14236, O44411, O94659, P0CS94, P36776, P53145, P53742, Q02892, Q10190, Q10LF7, Q13823, Q21086, Q2YDM7, Q3UM18, Q4R8L2, Q54N72, Q59HJ6, Q5BJT6, Q5E9R3, Q5ZJD3, Q6C036, Q6CM00, Q6CSP9, Q6FRV0, Q6FWS1, Q6NY89, Q74ZK6, Q75DA4, Q7SHR8, Q8MT06, Q99LH1, Q99ME9, Q99P77, Q9BZE4, Q9C3Z4, Q9C6I8, Q9C923
Diamond homologs: A2XGQ1, A4SDB8, A5GR60, A5IMB8, A5N2K5, A5VWQ6, A6LT31, A8EXG4, A8GM60, A8GQS1, A8GUK6, A9KFU3, A9NDV6, B0JFL6, B0KG04, B1JFJ3, B1LBK5, B1X0B0, B2TPB6, B2UX10, B3EGV8, B3PN57, B3QQY9, B3WE42, B4S596, B6J7Q3, B7K1S0, B8GAY7, B8I8N7, B9K8C0, C3PMD9, C4K1B9, J9VQ03, O14236, O67679, O74791, P0CS94, P36915, P36916, P40010
SIGNOR signaling
0 interactions.
Enriched among interaction partners
Reactome pathways and GO biological processes over-represented among this gene’s 220 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 | 24 | 21.9× | 4e-24 |
| Viral mRNA Translation | 24 | 21.9× | 4e-24 |
| PELO:HBS1L and ABCE1 dissociate a ribosome on a non-stop mRNA | 24 | 21.7× | 5e-24 |
| SRP-dependent cotranslational protein targeting to membrane | 29 | 20.9× | 3e-28 |
| Selenocysteine synthesis | 24 | 20.8× | 1e-23 |
| Eukaryotic Translation Termination | 24 | 20.8× | 1e-23 |
| Nonsense Mediated Decay (NMD) independent of the Exon Junction Complex (EJC) | 24 | 20.3× | 1e-23 |
| ZNF598 and the Ribosome-associated Quality Trigger (RQT) complex dissociate a ribosome stalled on a no-go mRNA | 24 | 20.3× | 1e-23 |
GO biological processes:
| GO term | Partners | Fold | FDR |
|---|---|---|---|
| negative regulation of DNA recombination | 5 | 28.8× | 6e-05 |
| chromosome condensation | 6 | 25.9× | 1e-05 |
| cytoplasmic translation | 27 | 25.6× | 4e-28 |
| negative regulation of mRNA splicing, via spliceosome | 5 | 19.6× | 3e-04 |
| ribosome biogenesis | 5 | 16.0× | 7e-04 |
| ribosomal large subunit biogenesis | 7 | 15.9× | 3e-05 |
| translation | 28 | 14.8× | 3e-22 |
| rRNA processing | 19 | 13.8× | 4e-14 |
Disease & clinical
Clinical variants and AI predictions
ClinVar
119 variants total. Per-class counts are floors (≥ shown; pagination cap):
| Classification | Count (floor) |
|---|---|
| Pathogenic | 0 |
| Likely pathogenic | 0 |
| Uncertain significance | 99 |
| Likely benign | 5 |
| Benign | 0 |
Top pathogenic / likely-pathogenic (0)
SpliceAI
2326 predictions. Top by Δscore:
| Variant | Effect | Δscore |
|---|---|---|
| 1:37567003:CTCCG:C | acceptor_gain | 1.0000 |
| 1:37568268:A:C | donor_gain | 1.0000 |
| 1:37568270:TTCAC:T | donor_loss | 1.0000 |
| 1:37568271:T:TA | donor_gain | 1.0000 |
| 1:37568271:TCACC:T | donor_loss | 1.0000 |
| 1:37568272:CACCT:C | donor_loss | 1.0000 |
| 1:37568274:C:CG | donor_loss | 1.0000 |
| 1:37568274:CCT:C | donor_gain | 1.0000 |
| 1:37568353:ATATT:A | acceptor_gain | 1.0000 |
| 1:37568354:TATT:T | acceptor_gain | 1.0000 |
| 1:37568355:ATT:A | acceptor_gain | 1.0000 |
| 1:37568356:TT:T | acceptor_gain | 1.0000 |
| 1:37568357:TCT:T | acceptor_loss | 1.0000 |
| 1:37568358:C:CA | acceptor_loss | 1.0000 |
| 1:37568358:C:CC | acceptor_gain | 1.0000 |
| 1:37568359:T:G | acceptor_loss | 1.0000 |
| 1:37568845:TATTA:T | donor_loss | 1.0000 |
| 1:37568847:TTACC:T | donor_loss | 1.0000 |
| 1:37568848:TACC:T | donor_loss | 1.0000 |
| 1:37568849:A:T | donor_loss | 1.0000 |
| 1:37568850:C:CA | donor_loss | 1.0000 |
| 1:37568850:CCTGA:C | donor_gain | 1.0000 |
| 1:37569303:C:CC | acceptor_gain | 1.0000 |
| 1:37569306:T:TC | acceptor_gain | 1.0000 |
| 1:37574337:TCTTA:T | donor_loss | 1.0000 |
| 1:37574338:CTTAC:C | donor_loss | 1.0000 |
| 1:37574339:TTACC:T | donor_loss | 1.0000 |
| 1:37574340:TACCT:T | donor_loss | 1.0000 |
| 1:37574341:A:C | donor_loss | 1.0000 |
| 1:37574452:CCACC:C | acceptor_gain | 1.0000 |
AlphaMissense
4827 scored. Top likely-pathogenic:
| Variant | Protein change | am_pathogenicity |
|---|---|---|
| 1:37575647:C:T | G364D | 1.000 |
| 1:37575648:C:G | G364R | 1.000 |
| 1:37575652:A:C | C362W | 1.000 |
| 1:37575653:C:T | C362Y | 1.000 |
| 1:37575654:A:G | C362R | 1.000 |
| 1:37575662:A:G | L359P | 1.000 |
| 1:37575696:A:G | W348R | 1.000 |
| 1:37575696:A:T | W348R | 1.000 |
| 1:37576438:C:T | G343D | 1.000 |
| 1:37576501:C:T | G322D | 1.000 |
| 1:37576502:C:G | G322R | 1.000 |
| 1:37576525:C:T | G314E | 1.000 |
| 1:37576526:C:A | G314W | 1.000 |
| 1:37576528:A:T | V313D | 1.000 |
| 1:37582263:C:T | G290D | 1.000 |
| 1:37582797:A:G | L259P | 1.000 |
| 1:37582806:T:A | K256I | 1.000 |
| 1:37574416:A:G | L448P | 0.999 |
| 1:37574822:A:T | V382D | 0.999 |
| 1:37575605:A:G | L378P | 0.999 |
| 1:37575648:C:A | G364C | 0.999 |
| 1:37575650:G:T | P363Q | 0.999 |
| 1:37575655:G:C | D361E | 0.999 |
| 1:37575655:G:T | D361E | 0.999 |
| 1:37575656:T:A | D361V | 0.999 |
| 1:37575656:T:C | D361G | 0.999 |
| 1:37575656:T:G | D361A | 0.999 |
| 1:37575657:C:G | D361H | 0.999 |
| 1:37575659:A:T | I360N | 0.999 |
| 1:37575668:A:T | I357K | 0.999 |
dbSNP variants (sampled 300 via entrez): RS1000007899 (1:37591416 G>A), RS1000085217 (1:37592673 T>C), RS1000150854 (1:37595646 T>C), RS1000218777 (1:37596913 C>T), RS1000230444 (1:37589554 C>T), RS1000269390 (1:37573849 G>A,C), RS1000288291 (1:37566749 A>C), RS1000411046 (1:37572166 T>C), RS1000463555 (1:37572373 C>A), RS1000469391 (1:37594159 T>C), RS1000580522 (1:37573466 A>T), RS1000636444 (1:37587894 T>C), RS1000780324 (1:37581208 G>A,T), RS1000791982 (1:37571064 G>A,T), RS1000906963 (1:37570687 T>C)
Disease associations
OMIM: gene MIM:609365 | disease phenotypes:
GenCC curated gene-disease
Mondo (0):
Orphanet (0):
HPO phenotypes
0 total (0 of 0 shown, HPO-id order):
GWAS associations
4 associations (top):
| Study | Trait | p-value |
|---|---|---|
| GCST002115_4 | Axial length | 4.000000e-13 |
| GCST003476_2 | Eyebrow thickness | 7.000000e-06 |
| GCST006464_2 | Endometrial cancer | 4.000000e-08 |
| GCST006465_9 | Endometrial cancer (endometrioid histology) | 3.000000e-08 |
EFO canonical traits (1, from GWAS)
| EFO ID | Trait name |
|---|---|
| EFO:0005318 | axial length measurement |
Drugs & pharmacology
Drug and pharmacology data
Is drug target: no
PharmGKB: 1 entry (VIP=true, CPIC=false)
CTD chemical–gene interactions
40 total (human), top 30 by PubMed support.
| Chemical | Actions (top 5) | PubMed papers |
|---|---|---|
| Estradiol | increases expression, affects expression, affects cotreatment, decreases expression | 3 |
| Cyclosporine | increases expression | 2 |
| Aflatoxin B1 | increases methylation, affects cotreatment, decreases expression | 2 |
| dicrotophos | decreases expression | 1 |
| alpha-pinene | decreases expression, increases abundance, affects cotreatment | 1 |
| bisphenol A | affects expression | 1 |
| deoxynivalenol | increases expression | 1 |
| tris(1,3-dichloro-2-propyl)phosphate | increases expression | 1 |
| sodium arsenite | affects cotreatment, increases abundance, increases expression | 1 |
| cobaltous chloride | decreases expression | 1 |
| manganese chloride | increases abundance, increases expression, affects cotreatment | 1 |
| methacrylaldehyde | affects cotreatment, decreases expression, increases abundance | 1 |
| di-n-butylphosphoric acid | affects expression | 1 |
| K 7174 | increases expression | 1 |
| 4-(5-benzo(1,3)dioxol-5-yl-4-pyridin-2-yl-1H-imidazol-2-yl)benzamide | decreases expression, affects cotreatment | 1 |
| abrine | increases expression | 1 |
| (4-amino-1,4-dihydro-3-(2-pyridyl)-5-thioxo-1,2,4-triazole)copper(II) | increases expression | 1 |
| LDN 193189 | affects cotreatment, decreases expression | 1 |
| Acrolein | affects cotreatment, decreases expression, increases abundance | 1 |
| Air Pollutants | affects cotreatment, decreases expression, increases abundance | 1 |
| Air Pollutants, Occupational | affects expression | 1 |
| Arbutin | increases expression | 1 |
| Arsenic | affects cotreatment, increases abundance, increases expression | 1 |
| Benzo(a)pyrene | affects methylation | 1 |
| Dichlorodiphenyl Dichloroethylene | increases expression | 1 |
| Hydrogen Peroxide | affects expression | 1 |
| Manganese | increases abundance, increases expression, affects cotreatment | 1 |
| Ozone | decreases expression, increases abundance, affects cotreatment | 1 |
| Progesterone | decreases expression, affects cotreatment | 1 |
| Ribonucleotides | affects binding | 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): endometrial carcinoma