ARHGEF39
gene geneOn this page
Also known as FLJ14642
Summary
ARHGEF39 (Rho guanine nucleotide exchange factor 39, HGNC:25909) is a protein-coding gene on chromosome 9p13.3, encoding Rho guanine nucleotide exchange factor 39 (Q8N4T4). Promotes cell proliferation.
Predicted to enable guanyl-nucleotide exchange factor activity. Involved in positive regulation of cell migration. Located in plasma membrane.
Source: NCBI Gene 84904 — RefSeq curated summary.
At a glance
- GWAS associations: 1
- Clinical variants (ClinVar): 116 total — 1 pathogenic
- MANE Select transcript:
NM_032818
Identifiers
Gene identifiers
| Field | Value |
|---|---|
| HGNC ID | HGNC:25909 |
| Approved symbol | ARHGEF39 |
| Name | Rho guanine nucleotide exchange factor 39 |
| Location | 9p13.3 |
| Locus type | gene with protein product |
| Status | Approved |
| Aliases | FLJ14642 |
| Ensembl gene | ENSG00000137135 |
| Ensembl biotype | protein_coding |
| OMIM | 621172 |
| Entrez | 84904 |
Gene structure
Transcript identifiers
Ensembl transcripts: 9 — 4 protein_coding, 3 protein_coding_CDS_not_defined, 2 nonsense_mediated_decay
ENST00000378387, ENST00000468876, ENST00000475323, ENST00000488918, ENST00000490638, ENST00000490970, ENST00000935482, ENST00000935483, ENST00000935484
RefSeq mRNA: 1 — MANE Select: NM_032818
NM_032818
CCDS: CCDS6584
Canonical transcript exons
ENST00000378387 — 9 exons
| Exon | Start | End |
|---|---|---|
| ENSE00000928216 | 35664756 | 35664850 |
| ENSE00001252962 | 35662946 | 35663074 |
| ENSE00001903032 | 35665032 | 35665195 |
| ENSE00003502920 | 35662512 | 35662741 |
| ENSE00003512786 | 35663322 | 35663392 |
| ENSE00003524401 | 35664372 | 35664492 |
| ENSE00003535301 | 35664008 | 35664126 |
| ENSE00003576503 | 35662179 | 35662267 |
| ENSE00003625725 | 35659343 | 35662002 |
Expression profiles
Bgee: expression breadth ubiquitous, 162 present calls, max score 86.36.
FANTOM5 (CAGE): breadth ubiquitous, TPM avg 5.9922 / max 100.7118, expressed in 1045 samples.
FANTOM5 promoters (1 alternative TSS)
| Promoter ID | TPM avg | Samples expressed |
|---|---|---|
| 100599 | 5.9922 | 1045 |
Top tissues by expression
254 total, by Bgee expression score (0-100, higher = more expressed):
| Tissue | Anatomy ID | Expression score | Quality |
|---|---|---|---|
| primordial germ cell in gonad | CL:0000670 ∩ UBERON:0000991 | 86.36 | gold quality |
| tibial artery | UBERON:0007610 | 85.13 | gold quality |
| popliteal artery | UBERON:0002250 | 85.11 | gold quality |
| ventricular zone | UBERON:0003053 | 84.77 | gold quality |
| aorta | UBERON:0000947 | 82.25 | gold quality |
| mucosa of transverse colon | UBERON:0004991 | 82.00 | gold quality |
| ascending aorta | UBERON:0001496 | 79.32 | gold quality |
| thoracic aorta | UBERON:0001515 | 79.01 | gold quality |
| body of stomach | UBERON:0001161 | 78.95 | gold quality |
| rectum | UBERON:0001052 | 78.37 | gold quality |
| mucosa of stomach | UBERON:0001199 | 77.87 | gold quality |
| lower esophagus muscularis layer | UBERON:0035833 | 77.70 | gold quality |
| lower esophagus | UBERON:0013473 | 77.66 | gold quality |
| male germ line stem cell (sensu Vertebrata) in testis | CL:0000089 ∩ UBERON:0000473 | 77.62 | gold quality |
| muscle layer of sigmoid colon | UBERON:0035805 | 77.41 | gold quality |
| esophagogastric junction muscularis propria | UBERON:0035841 | 77.23 | gold quality |
| left coronary artery | UBERON:0001626 | 77.15 | gold quality |
| transverse colon | UBERON:0001157 | 77.04 | gold quality |
| descending thoracic aorta | UBERON:0002345 | 76.98 | gold quality |
| right coronary artery | UBERON:0001625 | 76.22 | gold quality |
| stomach | UBERON:0000945 | 75.62 | gold quality |
| lower esophagus mucosa | UBERON:0035834 | 75.59 | gold quality |
| coronary artery | UBERON:0001621 | 75.08 | gold quality |
| ganglionic eminence | UBERON:0004023 | 74.66 | gold quality |
| granulocyte | CL:0000094 | 74.64 | gold quality |
| small intestine Peyer’s patch | UBERON:0003454 | 73.57 | gold quality |
| esophagus | UBERON:0001043 | 73.54 | gold quality |
| bone marrow cell | CL:0002092 | 73.39 | gold quality |
| colon | UBERON:0001155 | 73.39 | gold quality |
| large intestine | UBERON:0000059 | 72.38 | gold quality |
Single-cell (SCXA)
Detected in 1 experiment(s), a significant marker in 1.
| Experiment | Marker? | Max mean expression |
|---|---|---|
| E-ANND-3 | yes | 3.36 |
Regulation
Is transcription factor: no
miRNA regulators (miRDB)
118 targeting ARHGEF39, 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-4510 | 100.00 | 66.60 | 2050 |
| HSA-MIR-6127 | 100.00 | 66.76 | 2188 |
| HSA-MIR-6129 | 100.00 | 66.46 | 2080 |
| HSA-MIR-6130 | 100.00 | 66.69 | 2012 |
| HSA-MIR-6133 | 100.00 | 66.48 | 2064 |
| HSA-MIR-4673 | 100.00 | 66.64 | 1490 |
| HSA-MIR-4534 | 99.99 | 66.58 | 1907 |
| HSA-MIR-4282 | 99.99 | 75.36 | 6408 |
| HSA-MIR-10401-5P | 99.99 | 65.79 | 948 |
| HSA-MIR-4500 | 99.99 | 72.72 | 2367 |
| HSA-MIR-520D-5P | 99.98 | 73.34 | 4883 |
| HSA-MIR-524-5P | 99.98 | 73.43 | 4882 |
| HSA-MIR-4645-5P | 99.98 | 65.81 | 1284 |
| HSA-MIR-433-3P | 99.98 | 69.37 | 1203 |
| HSA-MIR-3148 | 99.97 | 75.06 | 6478 |
| HSA-MIR-6793-5P | 99.97 | 65.95 | 758 |
| HSA-MIR-3688-3P | 99.97 | 72.02 | 2834 |
| HSA-MIR-8082 | 99.95 | 67.27 | 1170 |
| HSA-MIR-4648 | 99.91 | 67.00 | 710 |
| HSA-MIR-7162-3P | 99.89 | 68.16 | 1682 |
| HSA-MIR-4731-5P | 99.89 | 67.23 | 2537 |
| HSA-MIR-6783-3P | 99.89 | 67.92 | 2059 |
| HSA-MIR-4302 | 99.89 | 67.94 | 1187 |
| HSA-MIR-1343-3P | 99.89 | 66.78 | 1815 |
| HSA-MIR-4492 | 99.87 | 68.25 | 3611 |
| HSA-MIR-579-3P | 99.86 | 71.66 | 3628 |
| HSA-MIR-765 | 99.84 | 68.24 | 2442 |
| HSA-MIR-202-3P | 99.84 | 71.41 | 1290 |
| HSA-MIR-664B-3P | 99.84 | 71.65 | 3590 |
| HSA-MIR-8080 | 99.82 | 67.52 | 1342 |
Literature-anchored findings (GeneRIF, showing 6)
- C9orf100 plays a potential oncogenic role in the development and metastasis of HCC. (PMID:22327280)
- findings suggest that ARHGEF39 may contribute to cell proliferation and migration in gastric cancer via a possible mechanism involving Akt signaling. (PMID:28871449)
- ARHGEF39 promotes tumor growth and invasion by activating the Rac1-P38-ATF2 signaling pathway, as well as increasing the expression of Cyclin A2, Cyclin D1, and MMP2 in NSCLC cells. (PMID:29382922)
- FARP1, ARHGEF39, and TIAM2 are essential receptor tyrosine kinase effectors for Rac1-dependent cell motility in human lung adenocarcinoma. (PMID:34731623)
- Genome-wide admixture and association analysis identifies African ancestry-specific risk loci of eosinophilic esophagitis in African Americans. (PMID:36400179)
- ARHGEF39 targeted by E2F1 fosters hepatocellular carcinoma metastasis by mediating fatty acid metabolism. (PMID:39128592)
Cross-species orthologs
5 orthologs
| Organism | Symbol | Gene ID |
|---|---|---|
| danio_rerio | arhgef39 | ENSDARG00000013476 |
| mus_musculus | Arhgef39 | ENSMUSG00000051517 |
| rattus_norvegicus | Arhgef39 | ENSRNOG00000021433 |
| caenorhabditis_elegans | WBGENE00001366 | |
| caenorhabditis_elegans | WBGENE00001490 |
Paralogs (10): FARP2 (ENSG00000006607), FGD1 (ENSG00000102302), FGD3 (ENSG00000127084), FGD4 (ENSG00000139132), FGD2 (ENSG00000146192), FARP1 (ENSG00000152767), FGD5 (ENSG00000154783), FRMD7 (ENSG00000165694), FGD6 (ENSG00000180263), ECT2L (ENSG00000203734)
Protein
Protein identifiers
Rho guanine nucleotide exchange factor 39 — Q8N4T4 (reviewed: Q8N4T4)
All UniProt accessions (1): Q8N4T4
UniProt curated annotations — full annotation on UniProt →
Function. Promotes cell proliferation.
Subcellular location. Cell membrane.
Tissue specificity. Strongly expressed in hepatocellular carcinoma (HCC) compared with their non-cancerous counterparts.
Isoforms (4)
| UniProt ID | Names | Canonical? |
|---|---|---|
| Q8N4T4-1 | 1 | yes |
| Q8N4T4-2 | 2 | |
| Q8N4T4-3 | 3 | |
| Q8N4T4-4 | 4 |
RefSeq proteins (1): NP_116207* (*=MANE)
Domains & families (InterPro)
| ID | Name | Type |
|---|---|---|
| IPR000219 | DH_dom | Domain |
| IPR001849 | PH_domain | Domain |
| IPR011993 | PH-like_dom_sf | Homologous_superfamily |
| IPR035899 | DBL_dom_sf | Homologous_superfamily |
| IPR042987 | ARHGEF39 | Family |
Pfam: PF00169, PF00621
UniProt features (12 total): splice variant 6, domain 2, sequence variant 2, chain 1, sequence conflict 1
Structure
Experimental structures (PDB)
0 structures.
Predicted structure (AlphaFold)
| Model | pLDDT | Fraction very-high |
|---|---|---|
| AF-Q8N4T4-F1 | 92.99 | 0.84 |
Function
Pathways and Gene Ontology
Reactome pathways
12 pathways
| ID | Pathway |
|---|---|
| R-HSA-193648 | NRAGE signals death through JNK |
| R-HSA-416482 | G alpha (12/13) signalling events |
| R-HSA-9013149 | RAC1 GTPase cycle |
| R-HSA-162582 | Signal Transduction |
| R-HSA-193704 | p75 NTR receptor-mediated signalling |
| R-HSA-194315 | Signaling by Rho GTPases |
| R-HSA-204998 | Cell death signalling via NRAGE, NRIF and NADE |
| R-HSA-372790 | Signaling by GPCR |
| R-HSA-388396 | GPCR downstream signalling |
| R-HSA-73887 | Death Receptor Signaling |
| R-HSA-9012999 | RHO GTPase cycle |
| R-HSA-9716542 | Signaling by Rho GTPases, Miro GTPases and RHOBTB3 |
MSigDB gene sets: 103 (showing top):
WANG_CLIM2_TARGETS_UP, REACTOME_NRAGE_SIGNALS_DEATH_THROUGH_JNK, AREB6_01, FISCHER_G2_M_CELL_CYCLE, chr9p13, TGACATY_UNKNOWN, FISCHER_DREAM_TARGETS, YNGTTNNNATT_UNKNOWN, NUYTTEN_EZH2_TARGETS_DN, GOMF_GUANYL_NUCLEOTIDE_EXCHANGE_FACTOR_ACTIVITY, STAT5A_01, GOMF_NUCLEOSIDE_TRIPHOSPHATASE_REGULATOR_ACTIVITY, GOMF_ENZYME_REGULATOR_ACTIVITY, MEISSNER_BRAIN_HCP_WITH_H3K4ME3_AND_H3K27ME3, REACTOME_CELL_DEATH_SIGNALLING_VIA_NRAGE_NRIF_AND_NADE
GO Biological Process (1): positive regulation of cell migration (GO:0030335)
GO Molecular Function (2): guanyl-nucleotide exchange factor activity (GO:0005085), protein binding (GO:0005515)
GO Cellular Component (2): plasma membrane (GO:0005886), membrane (GO:0016020)
Reactome top-level categories
Rollup of top-9 pathways:
| Category | Pathways |
|---|---|
| Signal Transduction | 3 |
| Cell death signalling via NRAGE, NRIF and NADE | 1 |
| GPCR downstream signalling | 1 |
| RHO GTPase cycle | 1 |
| Death Receptor Signaling | 1 |
| Signaling by Rho GTPases, Miro GTPases and RHOBTB3 | 1 |
| p75 NTR receptor-mediated signalling | 1 |
| Signaling by GPCR | 1 |
| Signaling by Rho GTPases | 1 |
GO top-level categories
Rollup of top GO terms by namespace:
| Category | Terms |
|---|---|
| cell migration | 1 |
| regulation of cell migration | 1 |
| positive regulation of cell motility | 1 |
| GTP binding | 1 |
| GDP binding | 1 |
| GTPase regulator activity | 1 |
| binding | 1 |
| membrane | 1 |
| cell periphery | 1 |
| cellular anatomical structure | 1 |
Protein interactions and networks
STRING
856 interactions, top by confidence (×1000):
| Protein A | Protein B | Partner UniProt | Score |
|---|---|---|---|
| ARHGEF39 | GALNT1 | Q10472 | 550 |
| ARHGEF39 | ARHGEF9 | O43307 | 491 |
| ARHGEF39 | CERS2 | Q96G23 | 479 |
| ARHGEF39 | ARHGEF37 | A1IGU5 | 468 |
| ARHGEF39 | RNLS | Q5VYX0 | 432 |
| ARHGEF39 | MCF2 | P10911 | 432 |
| ARHGEF39 | CCDC107 | Q8WV48 | 403 |
| ARHGEF39 | ARHGAP36 | Q6ZRI8 | 397 |
| ARHGEF39 | HAUS6 | Q7Z4H7 | 380 |
| ARHGEF39 | ABLIM2 | Q6H8Q1 | 375 |
| ARHGEF39 | EPS8L1 | Q8TE68 | 360 |
| ARHGEF39 | MPP3 | Q13368 | 357 |
| ARHGEF39 | ABLIM3 | O94929 | 352 |
| ARHGEF39 | CBFA2T3 | O75081 | 351 |
| ARHGEF39 | EPS8L2 | Q9H6S3 | 345 |
IntAct
30 interactions, top by confidence:
| A | B | Type | Score |
|---|---|---|---|
| ARHGEF39 | CALCOCO2 | psi-mi:“MI:0915”(physical association) | 0.670 |
| TIFA | ARHGEF39 | psi-mi:“MI:0915”(physical association) | 0.670 |
| CALCOCO2 | ARHGEF39 | psi-mi:“MI:0915”(physical association) | 0.670 |
| SLC31A1 | C2orf72 | psi-mi:“MI:0914”(association) | 0.530 |
| CACNG5 | ZNF316 | psi-mi:“MI:0914”(association) | 0.530 |
| IMPDH1 | BCAT2 | psi-mi:“MI:0914”(association) | 0.530 |
| ZNRD2 | CCDC85C | psi-mi:“MI:0914”(association) | 0.530 |
| ARHGEF39 | TYSND1 | psi-mi:“MI:0915”(physical association) | 0.500 |
| DVL2 | ARHGEF39 | psi-mi:“MI:0915”(physical association) | 0.370 |
| RBPMS | ARHGEF39 | psi-mi:“MI:0915”(physical association) | 0.370 |
| ARHGEF10 | S100A8 | psi-mi:“MI:0914”(association) | 0.350 |
| Tagap | PPIH | psi-mi:“MI:0914”(association) | 0.350 |
| PIPSL | C1orf226 | psi-mi:“MI:0914”(association) | 0.350 |
| FTL | SH3PXD2B | psi-mi:“MI:0914”(association) | 0.350 |
| PTGES3 | SBNO1 | psi-mi:“MI:0914”(association) | 0.350 |
| ZNRD2 | KRBA1 | psi-mi:“MI:0914”(association) | 0.350 |
| CAMK2A | SMCHD1 | psi-mi:“MI:0914”(association) | 0.350 |
| ARHGEF39 | ACAA1 | psi-mi:“MI:0914”(association) | 0.350 |
| IMPDH1 | MGST3 | psi-mi:“MI:0914”(association) | 0.350 |
| FTL | psi-mi:“MI:0914”(association) | 0.350 | |
| KCTD12 | CYTH3 | psi-mi:“MI:0914”(association) | 0.350 |
BioGRID (61): ARHGEF39 (Two-hybrid), TIFA (Two-hybrid), ARHGEF39 (Two-hybrid), ARHGEF39 (Two-hybrid), ARHGEF39 (Two-hybrid), ARHGEF39 (Affinity Capture-MS), ARHGEF39 (Affinity Capture-MS), ARHGEF39 (Affinity Capture-MS), ARHGEF39 (Affinity Capture-MS), ARHGEF39 (Affinity Capture-MS), BCR (Affinity Capture-Western), ARHGEF39 (Affinity Capture-MS), BCR (Affinity Capture-MS), CSDE1 (Affinity Capture-MS), CSTA (Affinity Capture-MS)
ESM2 similar proteins: A1IGU3, A1IGU4, A1IGU5, A6QP75, B2RUP2, D3ZI76, G1T469, P00530, P00542, P07332, P14238, P16879, Q0P5E3, Q14451, Q14DK4, Q1LZ97, Q3B7L1, Q3MIN7, Q3U5C8, Q3UYI5, Q53B87, Q53B88, Q58EX7, Q5VV41, Q5W0U4, Q60I26, Q60I27, Q66JY6, Q6DT37, Q6E804, Q6NUI2, Q6P5Z2, Q6PFY1, Q6PJ69, Q70J99, Q7Z6J4, Q80UW5, Q86WN1, Q8BTM9, Q8BY35
Diamond homologs: Q0P5E3, Q66JY6, Q69ZL1, Q8N4T4, A0A0D1E015, A0JMD2, A3LX75, A8QCE4, A8XJZ8, B0G126, B0WAQ0, B3MT31, B3P851, B4G2G5, B4IC49, B4JHI7, B4K982, B4M140, B4NFJ7, B4PRU6, D2H5P6, D3ZVP7, D4A8G9, E1BLZ4, F1P065, O13821, O14964, O59722, O76902, O88387, O95405, P0CS26, P0CS27, P34657, P40343, P52734, P98174, Q05B78, Q0P4S0, Q0V8S0
SIGNOR signaling
0 interactions.
Disease & clinical
Clinical variants and AI predictions
ClinVar
116 variants total. Per-class counts are floors (≥ shown; pagination cap):
| Classification | Count (floor) |
|---|---|
| Pathogenic | 1 |
| Likely pathogenic | 0 |
| Uncertain significance | 90 |
| Likely benign | 8 |
| Benign | 1 |
Top pathogenic / likely-pathogenic (1)
| Variant ID | HGVS | Classification |
|---|---|---|
| 1210154 | GRCh37/hg19 9p13.3-13.2(chr9:35059633-37660586)x1 | Pathogenic |
SpliceAI
2121 predictions. Top by Δscore:
| Variant | Effect | Δscore |
|---|---|---|
| 9:35660396:A:AG | acceptor_gain | 1.0000 |
| 9:35660396:AACAG:A | acceptor_gain | 1.0000 |
| 9:35660397:A:G | acceptor_gain | 1.0000 |
| 9:35660398:CAGG:C | acceptor_loss | 1.0000 |
| 9:35660399:A:AG | acceptor_gain | 1.0000 |
| 9:35660399:A:C | acceptor_loss | 1.0000 |
| 9:35660399:AG:A | acceptor_gain | 1.0000 |
| 9:35660399:AGG:A | acceptor_gain | 1.0000 |
| 9:35660399:AGGG:A | acceptor_gain | 1.0000 |
| 9:35660400:G:GC | acceptor_loss | 1.0000 |
| 9:35660400:G:GG | acceptor_gain | 1.0000 |
| 9:35660400:GG:G | acceptor_gain | 1.0000 |
| 9:35660400:GGG:G | acceptor_gain | 1.0000 |
| 9:35660400:GGGG:G | acceptor_gain | 1.0000 |
| 9:35660457:GTCAG:G | donor_gain | 1.0000 |
| 9:35660461:GG:G | donor_loss | 1.0000 |
| 9:35660462:G:A | donor_loss | 1.0000 |
| 9:35660549:A:AG | acceptor_gain | 1.0000 |
| 9:35660550:T:G | acceptor_gain | 1.0000 |
| 9:35660553:CCA:C | acceptor_loss | 1.0000 |
| 9:35660554:CA:C | acceptor_loss | 1.0000 |
| 9:35660555:A:AC | acceptor_loss | 1.0000 |
| 9:35660555:A:AG | acceptor_gain | 1.0000 |
| 9:35660556:G:GC | acceptor_gain | 1.0000 |
| 9:35660556:GA:G | acceptor_gain | 1.0000 |
| 9:35660556:GAGC:G | acceptor_gain | 1.0000 |
| 9:35660556:GAGCA:G | acceptor_gain | 1.0000 |
| 9:35660643:GAGCG:G | donor_gain | 1.0000 |
| 9:35660645:GCG:G | donor_gain | 1.0000 |
| 9:35660646:CGG:C | donor_loss | 1.0000 |
AlphaMissense
2141 scored. Top likely-pathogenic:
| Variant | Protein change | am_pathogenicity |
|---|---|---|
| 9:35662207:A:G | W322R | 0.982 |
| 9:35662207:A:T | W322R | 0.982 |
| 9:35664091:A:C | F130L | 0.977 |
| 9:35664091:A:T | F130L | 0.977 |
| 9:35664093:A:G | F130L | 0.977 |
| 9:35664758:G:C | S77R | 0.973 |
| 9:35664758:G:T | S77R | 0.973 |
| 9:35664760:T:G | S77R | 0.973 |
| 9:35664845:A:C | F48L | 0.969 |
| 9:35664845:A:T | F48L | 0.969 |
| 9:35664847:A:G | F48L | 0.969 |
| 9:35664017:C:G | R155P | 0.963 |
| 9:35664101:A:G | F127S | 0.963 |
| 9:35662259:G:C | F304L | 0.961 |
| 9:35662259:G:T | F304L | 0.961 |
| 9:35662261:A:G | F304L | 0.961 |
| 9:35665081:A:G | L30P | 0.961 |
| 9:35662205:C:A | W322C | 0.960 |
| 9:35662205:C:G | W322C | 0.960 |
| 9:35665069:T:A | E34V | 0.958 |
| 9:35662239:A:T | L311H | 0.957 |
| 9:35665113:C:A | W19C | 0.956 |
| 9:35665113:C:G | W19C | 0.956 |
| 9:35662651:A:T | L255H | 0.955 |
| 9:35664788:A:C | F67L | 0.955 |
| 9:35664788:A:T | F67L | 0.955 |
| 9:35664790:A:G | F67L | 0.955 |
| 9:35662651:A:G | L255P | 0.954 |
| 9:35664781:A:G | W70R | 0.954 |
| 9:35664781:A:T | W70R | 0.954 |
dbSNP variants (sampled 300 via entrez): RS1000308916 (9:35661853 G>A,T), RS1000462230 (9:35662211 T>A), RS1000727643 (9:35661483 A>G,T), RS1000968517 (9:35666862 G>A,T), RS1001076608 (9:35661759 C>G), RS1001970786 (9:35665336 C>A,G,T), RS1001978453 (9:35659803 A>G), RS1002003254 (9:35665196 G>A), RS1002023911 (9:35667170 C>T), RS1002317041 (9:35659007 C>T), RS1002466740 (9:35659249 G>A,C), RS1002637570 (9:35664702 G>A,C), RS1003004942 (9:35663635 T>C), RS1003959520 (9:35667093 T>G), RS1004412779 (9:35666750 C>A)
Disease associations
OMIM: gene MIM:621172 | disease phenotypes:
GenCC curated gene-disease
Mondo (1): neurodevelopmental disorder (MONDO:0700092)
Orphanet (0):
HPO phenotypes
0 total (0 of 0 shown, HPO-id order):
GWAS associations
1 associations (top):
| Study | Trait | p-value |
|---|---|---|
| GCST90026413_8 | Severe insulin-deficient type 2 diabetes | 7.000000e-06 |
MeSH disease descriptors (1)
| Descriptor | Name | Tree numbers |
|---|---|---|
| D065886 | Neurodevelopmental Disorders | F03.625 |
Drugs & pharmacology
Drug and pharmacology data
Is drug target: no
PharmGKB: 1 entry (VIP=true, CPIC=false)
CTD chemical–gene interactions
52 total (human), top 30 by PubMed support.
| Chemical | Actions (top 5) | PubMed papers |
|---|---|---|
| sodium arsenite | affects expression, decreases expression, affects cotreatment, increases abundance, increases expression | 4 |
| Air Pollutants | affects expression, increases abundance, decreases expression | 2 |
| Tobacco Smoke Pollution | decreases expression | 2 |
| aristolochic acid I | decreases expression | 1 |
| methylmercuric chloride | decreases expression | 1 |
| bisphenol A | affects cotreatment, decreases methylation | 1 |
| trichostatin A | affects expression | 1 |
| beta-lapachone | decreases expression | 1 |
| sulforaphane | increases expression | 1 |
| manganese chloride | affects cotreatment, decreases expression, increases abundance | 1 |
| rutecarpine | decreases expression | 1 |
| di-n-butylphosphoric acid | affects expression | 1 |
| pentabromodiphenyl ether | decreases expression | 1 |
| perfluoro-n-nonanoic acid | decreases expression | 1 |
| 2,2’,4,4’-tetrabromodiphenyl ether | decreases expression | 1 |
| 2-methyl-2H-pyrazole-3-carboxylic acid (2-methyl-4-o-tolylazophenyl)amide | affects cotreatment, decreases expression | 1 |
| (+)-JQ1 compound | decreases expression | 1 |
| NSC668394 | decreases expression | 1 |
| Irinotecan | decreases expression | 1 |
| Resveratrol | affects cotreatment, decreases expression | 1 |
| Sunitinib | decreases expression | 1 |
| Fulvestrant | affects cotreatment, decreases methylation | 1 |
| Leflunomide | decreases expression | 1 |
| Acetaminophen | decreases expression | 1 |
| Arsenic | affects cotreatment, decreases expression, increases abundance | 1 |
| Benzo(a)pyrene | decreases expression | 1 |
| Calcitriol | decreases expression, affects cotreatment | 1 |
| Coumestrol | increases expression | 1 |
| Dichlorodiphenyl Dichloroethylene | increases expression | 1 |
| Drugs, Chinese Herbal | decreases expression | 1 |
Cellosaurus cell lines
3 cell lines: 3 cancer cell line
First 10 cell lines (id-ordered, not curated):
| Cellosaurus | Name | Category | Sex |
|---|---|---|---|
| CVCL_XL47 | HAP1 ARHGEF39 (-) 1 | Cancer cell line | Male |
| CVCL_XL48 | HAP1 ARHGEF39 (-) 2 | Cancer cell line | Male |
| CVCL_XL49 | HAP1 ARHGEF39 (-) 3 | Cancer cell line | Male |
Clinical trials (associated diseases)
202 trials via MONDO — disease-level, not drug-specific.
| Trial | Phase | Status | Title |
|---|---|---|---|
| NCT04586348 | PHASE4 | UNKNOWN | Prenatal Iodine Supplementation and Early Childhood Neurodevelopment |
| NCT04873115 | PHASE4 | UNKNOWN | Double-blind, Placebo-controlled, Randomized Clinical Trial Comparing the Efficacy and Safety of Sialanar Plus orAl rehabiLitation Against Placebo Plus Oral Rehabilitation for chIldren and Adolescents With seVere Sialorrhoea and Neurodisabilties, |
| NCT02559102 | PHASE3 | COMPLETED | Dexmedetomidine Sedation Versus General Anaesthesia for Inguinal Hernia Surgery in Infants |
| NCT02757079 | PHASE3 | COMPLETED | Study of the Efficacy and Safety of NPC-15 for Sleep Disorders of Children With Neurodevelopmental Disorders |
| NCT06915480 | PHASE3 | RECRUITING | Reducing Missed Appointments |
| NCT07377032 | PHASE3 | RECRUITING | TAP-GRIN: Interventional Study on Patients With GRIN-related Neurodevelopmental Disorders |
| NCT02909959 | PHASE2 | COMPLETED | Sulforaphane for the Treatment of Young Men With Autism Spectrum Disorder |
| NCT06081348 | PHASE2 | RECRUITING | Sertraline vs. Placebo in the Treatment of Anxiety in Children and AdoLescents With NeurodevelopMental Disorders |
| NCT06352372 | PHASE2 | COMPLETED | Safety and Efficacy of tPBM for Epileptiform Activity in Autism |
| NCT00503191 | PHASE1 | COMPLETED | NeuroModulation Technique Treatment of Autism |
| NCT04475848 | PHASE1 | COMPLETED | A Study to Investigate the Safety, Tolerability, Pharmacokinetics, Pharmacodynamics and Food Effect of RO6953958 in Healthy Participants |
| NCT06300398 | PHASE1 | COMPLETED | IAMA-6 Oral Dose Study in Healthy Adults |
| NCT01783041 | PHASE2/PHASE3 | COMPLETED | Effect of Early L-Carnitine Supplementation on Neurodevelopmental Outcomes in Very Preterm Infants |
| NCT05767385 | PHASE2/PHASE3 | RECRUITING | Fetal Cerebrovascular Autoregulation in Congenital Heart Disease and Association With Neonatal Neurobehavior |
| NCT05675098 | EARLY_PHASE1 | NOT_YET_RECRUITING | Central Nervous System Stimulants and Physical Function in Children With Cerebral Palsy |
| NCT00783783 | Not specified | COMPLETED | CYP2D6 Pharmacogenetics in Risperidone-Treated Children |
| NCT01778504 | Not specified | RECRUITING | Studying Childhood-onset Behavioral, Psychiatric, and Developmental Disorders |
| NCT01850784 | Not specified | UNKNOWN | High Energy Formula Feeding in Infants With Congenital Heart Disease |
| NCT01922791 | Not specified | COMPLETED | Nutrition and Pregnancy Intervention Study |
| NCT01942525 | Not specified | UNKNOWN | Influence of Intrauterine Growth Restriction on Amplitude-integrated EEG in Preterm Infants |
| NCT02003170 | Not specified | COMPLETED | Etiology and Early Diagnosis of Neurodevelopmental Disorders |
| NCT02118649 | Not specified | ACTIVE_NOT_RECRUITING | Enhancing Behavior and Brain Response to Visual Targets Using a Computer Game |
| NCT02557191 | Not specified | TERMINATED | Biomarkers, Neurodevelopment and Preterm Infants |
| NCT02690675 | Not specified | COMPLETED | Iron Supplement Effect on Child Development |
| NCT02694003 | Not specified | COMPLETED | Better Nights, Better Days for Children With Neurodevelopment Disorders |
| NCT02792894 | Not specified | COMPLETED | Family Networks (FaNs) for Children With Developmental Disorders and Delays |
| NCT02871674 | Not specified | UNKNOWN | Good Night Project: Behavioural Sleep Interventions for Children With ADHD: A Randomised Controlled Trial |
| NCT02887157 | Not specified | COMPLETED | Analyzing Retinal Microanatomy in ROP |
| NCT02898298 | Not specified | COMPLETED | Positive Emotion Regulation Training in Children, Adolescents and Young Adults With and Without Developmental Disorder |
| NCT02912780 | Not specified | UNKNOWN | Introduction of Microsystems in a Level 3 Neonatal Intensive Care Unit |
| NCT03023293 | Not specified | COMPLETED | n-3 PUFAs, Irisin and Maternal Glucose Metabolism From Pregnancy to Postpartum |
| NCT03023644 | Not specified | COMPLETED | Improving Neurodevelopmental Outcomes in Children With Congenital Heart Disease: An Intervention Study |
| NCT03032991 | Not specified | UNKNOWN | Early Biomarkers of Neurodevelopment in Offspring of Diabetic Mothers |
| NCT03088189 | Not specified | TERMINATED | Effect of Parental Peri-conceptional Vitamin B12 Supplementation on Infant Neurocognitive Development in Offspring |
| NCT03096028 | Not specified | COMPLETED | Developmental Origins of Mental Health Disorders |
| NCT03148782 | Not specified | COMPLETED | Brain Plasticity Underlying Acquisition of New Organizational Skills in Children-R61 Phase |
| NCT03172104 | Not specified | COMPLETED | Neurobehavioural Development of Infants Born <30 Weeks Gestational Age Between Birth and Five Years of Age |
| NCT03222375 | Not specified | RECRUITING | SQUED™ Series 28.1 Home-use and Treatment of Autowave Reverberator of Autism |
| NCT03229928 | Not specified | COMPLETED | Clinical Testing of a Real-Time Behavior Measurement Tool: Measuring Outcomes for CHAnge |
| NCT03232489 | Not specified | UNKNOWN | Study for the Evaluation of the Feasibility of Applying Advanced MRI Scanning in Pediatric Clinical Practice |
Related Atlas pages
No linked Atlas pages yet — the cross-entity mesh grows as the corpus expands.