ARFGEF3
geneOn this page
Also known as dJ171N11.1BIG3PPP1R33
Summary
ARFGEF3 (ARFGEF family member 3, HGNC:21213) is a protein-coding gene on chromosome 6q23.3-q24.1, encoding Brefeldin A-inhibited guanine nucleotide-exchange protein 3 (Q5TH69). Participates in the regulation of systemic glucose homeostasis, where it negatively regulates insulin granule biogenesis in pancreatic islet beta cells.
Predicted to enable guanyl-nucleotide exchange factor activity. Predicted to be involved in regulation of ARF protein signal transduction. Predicted to be located in transport vesicle membrane.
Source: NCBI Gene 57221 — RefSeq curated summary.
At a glance
- Gene–disease (curated): inherited dystonia (Strong, GenCC)
- GWAS associations: 1
- Clinical variants (ClinVar): 373 total — 1 pathogenic
- Phenotypes (HPO): 1
- MANE Select transcript:
NM_020340
Identifiers
Gene identifiers
| Field | Value |
|---|---|
| HGNC ID | HGNC:21213 |
| Approved symbol | ARFGEF3 |
| Name | ARFGEF family member 3 |
| Location | 6q23.3-q24.1 |
| Locus type | gene with protein product |
| Status | Approved |
| Aliases | dJ171N11.1, BIG3, PPP1R33 |
| Ensembl gene | ENSG00000112379 |
| Ensembl biotype | protein_coding |
| OMIM | 617411 |
| Entrez | 57221 |
Gene structure
Transcript identifiers
Ensembl transcripts: 2 — 2 protein_coding
ENST00000251691, ENST00000895851
RefSeq mRNA: 1 — MANE Select: NM_020340
NM_020340
CCDS: CCDS5189
Canonical transcript exons
ENST00000251691 — 34 exons
| Exon | Start | End |
|---|---|---|
| ENSE00000764592 | 138278451 | 138278617 |
| ENSE00000764602 | 138279999 | 138280164 |
| ENSE00000764604 | 138286701 | 138286916 |
| ENSE00000764612 | 138287074 | 138287184 |
| ENSE00000764626 | 138289818 | 138289968 |
| ENSE00000764631 | 138296810 | 138296955 |
| ENSE00000764638 | 138308739 | 138308861 |
| ENSE00000764639 | 138311407 | 138311510 |
| ENSE00000764643 | 138319703 | 138319879 |
| ENSE00000764647 | 138324023 | 138324154 |
| ENSE00000798933 | 138262701 | 138263611 |
| ENSE00000798934 | 138285946 | 138286053 |
| ENSE00000798935 | 138291733 | 138292053 |
| ENSE00000798936 | 138293993 | 138294126 |
| ENSE00000798937 | 138298606 | 138298785 |
| ENSE00000798938 | 138307253 | 138307397 |
| ENSE00000798939 | 138313795 | 138313939 |
| ENSE00000798940 | 138317251 | 138317379 |
| ENSE00000798941 | 138321111 | 138321225 |
| ENSE00000798942 | 138323671 | 138323773 |
| ENSE00000798943 | 138328021 | 138328142 |
| ENSE00000798944 | 138333970 | 138335188 |
| ENSE00001363571 | 138261527 | 138261639 |
| ENSE00001363579 | 138255436 | 138255769 |
| ENSE00001364931 | 138245513 | 138245591 |
| ENSE00001367198 | 138242952 | 138242994 |
| ENSE00001373287 | 138238509 | 138238631 |
| ENSE00001381692 | 138253880 | 138253984 |
| ENSE00001386605 | 138209910 | 138210041 |
| ENSE00001389298 | 138229784 | 138229852 |
| ENSE00001813154 | 138161939 | 138162171 |
| ENSE00001841691 | 138336295 | 138344663 |
| ENSE00002215616 | 138170662 | 138170713 |
| ENSE00002313548 | 138207042 | 138207123 |
Expression profiles
Bgee: expression breadth ubiquitous, 223 present calls, max score 98.37.
FANTOM5 (CAGE): breadth broad, TPM avg 6.0519 / max 180.4164, expressed in 868 samples.
FANTOM5 promoters (3 alternative TSS)
| Promoter ID | TPM avg | Samples expressed |
|---|---|---|
| 70106 | 5.2777 | 815 |
| 70105 | 0.6163 | 278 |
| 70104 | 0.1579 | 78 |
Top tissues by expression
253 total, by Bgee expression score (0-100, higher = more expressed):
| Tissue | Anatomy ID | Expression score | Quality |
|---|---|---|---|
| parotid gland | UBERON:0001831 | 98.37 | gold quality |
| cerebellar vermis | UBERON:0004720 | 97.39 | gold quality |
| substantia nigra pars reticulata | UBERON:0001966 | 95.79 | gold quality |
| lateral nuclear group of thalamus | UBERON:0002736 | 95.24 | gold quality |
| substantia nigra pars compacta | UBERON:0001965 | 95.03 | gold quality |
| lateral globus pallidus | UBERON:0002476 | 94.83 | gold quality |
| globus pallidus | UBERON:0001875 | 94.63 | gold quality |
| medial globus pallidus | UBERON:0002477 | 94.60 | gold quality |
| Brodmann (1909) area 46 | UBERON:0006483 | 94.52 | gold quality |
| endothelial cell | CL:0000115 | 94.37 | gold quality |
| bronchial epithelial cell | CL:0002328 | 94.36 | gold quality |
| nasal cavity epithelium | UBERON:0005384 | 93.83 | silver quality |
| bronchus | UBERON:0002185 | 93.81 | gold quality |
| middle temporal gyrus | UBERON:0002771 | 93.73 | gold quality |
| subthalamic nucleus | UBERON:0001906 | 93.37 | gold quality |
| dorsal plus ventral thalamus | UBERON:0001897 | 93.12 | gold quality |
| inferior vagus X ganglion | UBERON:0005363 | 92.69 | gold quality |
| Brodmann (1909) area 23 | UBERON:0013554 | 92.32 | gold quality |
| pons | UBERON:0000988 | 92.02 | gold quality |
| entorhinal cortex | UBERON:0002728 | 91.01 | gold quality |
| corpus callosum | UBERON:0002336 | 90.99 | gold quality |
| superior vestibular nucleus | UBERON:0007227 | 90.98 | gold quality |
| parietal lobe | UBERON:0001872 | 90.95 | gold quality |
| islet of Langerhans | UBERON:0000006 | 90.94 | gold quality |
| medulla oblongata | UBERON:0001896 | 90.59 | gold quality |
| postcentral gyrus | UBERON:0002581 | 90.52 | gold quality |
| ventral tegmental area | UBERON:0002691 | 90.48 | gold quality |
| epithelial cell of pancreas | CL:0000083 | 89.91 | silver quality |
| superior frontal gyrus | UBERON:0002661 | 89.78 | gold quality |
| ileal mucosa | UBERON:0000331 | 89.31 | gold quality |
Single-cell (SCXA)
Detected in 8 experiment(s), a significant marker in 5.
| Experiment | Marker? | Max mean expression |
|---|---|---|
| E-MTAB-5061 | yes | 780.53 |
| E-CURD-114 | yes | 45.60 |
| E-GEOD-81547 | yes | 27.40 |
| E-ANND-3 | yes | 22.37 |
| E-GEOD-83139 | yes | 9.81 |
| E-GEOD-99795 | no | 287.90 |
| E-GEOD-81608 | no | 13.97 |
| E-ENAD-27 | no | 9.65 |
Regulation
Is transcription factor: no
miRNA regulators (miRDB)
355 targeting ARFGEF3, 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-3163 | 100.00 | 77.23 | 8605 |
| HSA-MIR-190A-3P | 100.00 | 80.35 | 5520 |
| HSA-MIR-5011-5P | 100.00 | 83.46 | 5820 |
| HSA-MIR-4481 | 100.00 | 66.42 | 1669 |
| HSA-MIR-3646 | 100.00 | 73.56 | 5283 |
| HSA-MIR-5692A | 100.00 | 74.40 | 6850 |
| HSA-MIR-4262 | 100.00 | 73.26 | 3931 |
| HSA-MIR-4682 | 100.00 | 68.89 | 1258 |
| HSA-MIR-340-5P | 100.00 | 72.50 | 4437 |
| HSA-MIR-3134 | 100.00 | 66.43 | 777 |
| HSA-MIR-200B-3P | 100.00 | 73.31 | 2693 |
| HSA-MIR-200C-3P | 100.00 | 73.35 | 2685 |
| HSA-MIR-429 | 100.00 | 73.44 | 2698 |
| HSA-MIR-3924 | 100.00 | 72.09 | 2394 |
| HSA-MIR-4283 | 100.00 | 66.42 | 2097 |
| HSA-MIR-9-5P | 100.00 | 72.28 | 2361 |
| HSA-MIR-4668-3P | 100.00 | 68.74 | 2635 |
| HSA-MIR-4533 | 100.00 | 69.48 | 2758 |
| HSA-MIR-4747-5P | 100.00 | 67.90 | 2681 |
| HSA-MIR-5196-5P | 100.00 | 67.98 | 2761 |
| HSA-MIR-3662 | 99.99 | 73.82 | 5684 |
| HSA-MIR-511-3P | 99.99 | 68.85 | 1467 |
| HSA-MIR-181A-5P | 99.99 | 72.96 | 2995 |
| HSA-MIR-181B-5P | 99.99 | 72.97 | 2996 |
| HSA-MIR-181C-5P | 99.99 | 72.95 | 2996 |
| HSA-MIR-181D-5P | 99.99 | 73.04 | 2997 |
| HSA-MIR-4534 | 99.99 | 66.58 | 1907 |
| HSA-MIR-186-5P | 99.99 | 70.83 | 3707 |
| HSA-MIR-371B-5P | 99.99 | 75.34 | 4759 |
| HSA-MIR-4775 | 99.98 | 75.00 | 6394 |
Literature-anchored findings (GeneRIF, showing 3)
- BIG3 (ARFGEF3) is predicted to interact with its partner PHB2 through an ARM-type alpha-helical structure. (PMID:24997568)
- These results establish a model for the BIG3-PHB2 interaction and an entry for drug discovery for breast cancer. (PMID:31421830)
- The survival and proliferation of osteosarcoma cells are dependent on the mitochondrial BIG3-PHB2 complex formation. (PMID:34363714)
Cross-species orthologs
3 orthologs
| Organism | Symbol | Gene ID |
|---|---|---|
| danio_rerio | arfgef3 | ENSDARG00000077656 |
| mus_musculus | Arfgef3 | ENSMUSG00000019852 |
| rattus_norvegicus | Arfgef3 | ENSRNOG00000011460 |
Protein
Protein identifiers
Brefeldin A-inhibited guanine nucleotide-exchange protein 3 — Q5TH69 (reviewed: Q5TH69)
Alternative names: ARFGEF family member 3
All UniProt accessions (1): Q5TH69
UniProt curated annotations — full annotation on UniProt →
Function. Participates in the regulation of systemic glucose homeostasis, where it negatively regulates insulin granule biogenesis in pancreatic islet beta cells. Also regulates glucagon granule production in pancreatic alpha cells. Inhibits nuclear translocation of the transcriptional coregulator PHB2 and may enhance estrogen receptor alpha (ESR1) transcriptional activity in breast cancer cells.
Subunit / interactions. Interacts with PHB2.
Subcellular location. Cytoplasm. Cytoplasmic vesicle. Secretory vesicle. Secretory vesicle membrane.
Tissue specificity. Expressed in breast cancer cell lines. Not expressed in normal tissues such as duct, mammary gland, lung, heart, liver, kidnay, bone marrow.
RefSeq proteins (1): NP_065073* (*=MANE)
Domains & families (InterPro)
| ID | Name | Type |
|---|---|---|
| IPR000904 | Sec7_dom | Domain |
| IPR015403 | Mon2/Sec7/BIG1-like_HDS | Domain |
| IPR016024 | ARM-type_fold | Homologous_superfamily |
| IPR032629 | DCB_dom | Domain |
| IPR046455 | Sec7/BIG1-like_C | Domain |
Pfam: PF09324, PF16213, PF20252
UniProt features (34 total): modified residue 10, region of interest 8, compositionally biased region 7, sequence variant 4, sequence conflict 2, chain 1, transmembrane region 1, domain 1
Structure
Experimental structures (PDB)
0 structures.
Predicted structure (AlphaFold)
| Model | pLDDT | Fraction very-high |
|---|---|---|
| AF-Q5TH69-F1 | 65.15 | 0.08 |
Functional residue map
Curated UniProt residues grouped by drug-discovery relevance — catalytic, ligand-binding, modification, and mutation-validated positions. Source: UniProtKB sequence features.
Post-translational modifications (10): 471, 632, 636, 1049, 1991, 2079, 2081, 2095, 2101, 2103
Function
Pathways and Gene Ontology
Reactome pathways
0 pathways
MSigDB gene sets: 156 (showing top):
PEREZ_TP63_TARGETS, GOZGIT_ESR1_TARGETS_DN, GOBP_REGULATION_OF_SMALL_GTPASE_MEDIATED_SIGNAL_TRANSDUCTION, GOBP_VESICLE_MEDIATED_TRANSPORT, RODWELL_AGING_KIDNEY_NO_BLOOD_DN, GTGCCTT_MIR506, KOYAMA_SEMA3B_TARGETS_UP, BILD_E2F3_ONCOGENIC_SIGNATURE, CREIGHTON_ENDOCRINE_THERAPY_RESISTANCE_5, COATES_MACROPHAGE_M1_VS_M2_UP, LIAO_METASTASIS, CUI_TCF21_TARGETS_2_DN, GOBP_SMALL_GTPASE_MEDIATED_SIGNAL_TRANSDUCTION, TGCCTTA_MIR124A, LIU_SOX4_TARGETS_DN
GO Biological Process (1): regulation of ARF protein signal transduction (GO:0032012)
GO Molecular Function (1): guanyl-nucleotide exchange factor activity (GO:0005085)
GO Cellular Component (5): transport vesicle membrane (GO:0030658), cytoplasm (GO:0005737), membrane (GO:0016020), transport vesicle (GO:0030133), cytoplasmic vesicle (GO:0031410)
GO top-level categories
Rollup of top GO terms by namespace:
| Category | Terms |
|---|---|
| cellular anatomical structure | 2 |
| ARF protein signal transduction | 1 |
| regulation of small GTPase mediated signal transduction | 1 |
| GTP binding | 1 |
| GDP binding | 1 |
| GTPase regulator activity | 1 |
| transport vesicle | 1 |
| cytoplasmic vesicle membrane | 1 |
| bounding membrane of organelle | 1 |
| intracellular anatomical structure | 1 |
| endomembrane system | 1 |
| cytoplasmic vesicle | 1 |
| cytoplasm | 1 |
| intracellular vesicle | 1 |
Protein interactions and networks
STRING
568 interactions, top by confidence (×1000):
| Protein A | Protein B | Partner UniProt | Score |
|---|---|---|---|
| ARFGEF3 | PHB2 | Q99623 | 863 |
| ARFGEF3 | TMEM253 | P0C7T8 | 541 |
| ARFGEF3 | CCDC167 | Q9P0B6 | 508 |
| ARFGEF3 | LRRTM4 | Q86VH4 | 479 |
| ARFGEF3 | DRG2 | P55039 | 449 |
| ARFGEF3 | ORC5 | O43913 | 429 |
| ARFGEF3 | CHMP7 | Q8WUX9 | 424 |
| ARFGEF3 | KCNH7 | Q9NS40 | 423 |
| ARFGEF3 | EAPP | Q56P03 | 414 |
| ARFGEF3 | PKIA | P04541 | 407 |
| ARFGEF3 | PHACTR2 | O75167 | 393 |
| ARFGEF3 | ASB14 | A6NK59 | 391 |
| ARFGEF3 | SERPINI2 | O75830 | 389 |
| ARFGEF3 | PSIP1 | O75475 | 362 |
| ARFGEF3 | PITPNC1 | Q9UKF7 | 354 |
IntAct
64 interactions, top by confidence:
| A | B | Type | Score |
|---|---|---|---|
| LPAR4 | POTEF | psi-mi:“MI:0914”(association) | 0.530 |
| NPY2R | RTL8C | psi-mi:“MI:0914”(association) | 0.530 |
| ARRDC4 | WWP2 | psi-mi:“MI:0914”(association) | 0.530 |
| AP4E1 | AP4M1 | psi-mi:“MI:0914”(association) | 0.530 |
| ILVBL | SLC33A1 | psi-mi:“MI:0914”(association) | 0.530 |
| PPP1CA | ARFGEF3 | psi-mi:“MI:0407”(direct interaction) | 0.440 |
| TNFSF13B | HEATR1 | psi-mi:“MI:0914”(association) | 0.350 |
| CLEC2D | TMEM120B | psi-mi:“MI:0914”(association) | 0.350 |
| SIGLECL1 | KIAA1324L | psi-mi:“MI:0914”(association) | 0.350 |
| PACC1 | DEGS1 | psi-mi:“MI:0914”(association) | 0.350 |
| PNKD | EXOC5 | psi-mi:“MI:0914”(association) | 0.350 |
| VIPR1 | GPR89A | psi-mi:“MI:0914”(association) | 0.350 |
| ST6GAL1 | HLA-C | psi-mi:“MI:0914”(association) | 0.350 |
| CTDP1 | ESYT2 | psi-mi:“MI:0914”(association) | 0.350 |
| GPR17 | TMEM120B | psi-mi:“MI:0914”(association) | 0.350 |
| KLK15 | DENND11 | psi-mi:“MI:0914”(association) | 0.350 |
| P2RY10 | POTEF | psi-mi:“MI:0914”(association) | 0.350 |
| TACSTD2 | RIMOC1 | psi-mi:“MI:0914”(association) | 0.350 |
| SIGLECL1 | RBFOX3 | psi-mi:“MI:0914”(association) | 0.350 |
| GPR182 | METTL15 | psi-mi:“MI:0914”(association) | 0.350 |
| NPTN | RTL8C | psi-mi:“MI:0914”(association) | 0.350 |
| FPR1 | GPR89A | psi-mi:“MI:0914”(association) | 0.350 |
| FIS1 | QSOX1 | psi-mi:“MI:0914”(association) | 0.350 |
| TACR3 | TCAF2 | psi-mi:“MI:0914”(association) | 0.350 |
| CD40 | NHERF1 | psi-mi:“MI:0914”(association) | 0.350 |
BioGRID (123): KIAA1244 (Affinity Capture-MS), KIAA1244 (Affinity Capture-MS), KIAA1244 (Affinity Capture-MS), KIAA1244 (Affinity Capture-MS), KIAA1244 (Biochemical Activity), KIAA1244 (Proximity Label-MS), KIAA1244 (Proximity Label-MS), KIAA1244 (Proximity Label-MS), PHB2 (Affinity Capture-Western), KIAA1244 (Affinity Capture-MS), KIAA1244 (Affinity Capture-MS), KIAA1244 (Affinity Capture-MS), KIAA1244 (Affinity Capture-MS), KIAA1244 (Affinity Capture-MS), KIAA1244 (Affinity Capture-MS)
ESM2 similar proteins: A0A571BF63, A0A8M9QN10, A0JMA8, A1A535, A1A5P5, A1L1K1, A2AVJ5, A7YDW0, B3MJV4, B4MV81, O00443, O08576, O17237, Q0V9V7, Q12923, Q14D04, Q17QK1, Q1LYM3, Q2NKQ1, Q3UGY8, Q59EK9, Q5EB20, Q5JWR5, Q5PQS3, Q5R565, Q5RAY1, Q5TH69, Q5U245, Q5U3W3, Q5XHG1, Q61194, Q61QK6, Q64512, Q6ING4, Q6MZQ0, Q6ZUJ8, Q7Z3E5, Q803Q4, Q80U12, Q8BPQ7
Diamond homologs: Q3UGY8, Q5TH69
SIGNOR signaling
0 interactions.
Disease & clinical
Clinical variants and AI predictions
ClinVar
373 variants total. Per-class counts are floors (≥ shown; pagination cap):
| Classification | Count (floor) |
|---|---|
| Pathogenic | 1 |
| Likely pathogenic | 0 |
| Uncertain significance | 281 |
| Likely benign | 35 |
| Benign | 29 |
Top pathogenic / likely-pathogenic (1)
| Variant ID | HGVS | Classification |
|---|---|---|
| 830783 | NC_000006.12:g.(?137871228)(138263611_?)del | Pathogenic |
SpliceAI
4866 predictions. Top by Δscore:
| Variant | Effect | Δscore |
|---|---|---|
| 6:138162151:A:T | donor_gain | 1.0000 |
| 6:138162169:TGGG:T | donor_loss | 1.0000 |
| 6:138162170:GG:G | donor_gain | 1.0000 |
| 6:138162170:GGGT:G | donor_loss | 1.0000 |
| 6:138162171:GG:G | donor_gain | 1.0000 |
| 6:138162171:GGTA:G | donor_loss | 1.0000 |
| 6:138162172:G:C | donor_loss | 1.0000 |
| 6:138162172:G:GG | donor_gain | 1.0000 |
| 6:138162173:T:G | donor_loss | 1.0000 |
| 6:138207037:GCCAG:G | acceptor_loss | 1.0000 |
| 6:138207040:A:AG | acceptor_gain | 1.0000 |
| 6:138207040:A:T | acceptor_loss | 1.0000 |
| 6:138207040:AG:A | acceptor_gain | 1.0000 |
| 6:138207041:G:GC | acceptor_gain | 1.0000 |
| 6:138207041:GG:G | acceptor_gain | 1.0000 |
| 6:138207041:GGGA:G | acceptor_gain | 1.0000 |
| 6:138207121:CAGGT:C | donor_loss | 1.0000 |
| 6:138207122:AGG:A | donor_loss | 1.0000 |
| 6:138207123:GGTAT:G | donor_loss | 1.0000 |
| 6:138207124:G:A | donor_loss | 1.0000 |
| 6:138207125:T:G | donor_loss | 1.0000 |
| 6:138209904:TTACA:T | acceptor_loss | 1.0000 |
| 6:138209905:TACA:T | acceptor_loss | 1.0000 |
| 6:138209908:A:AG | acceptor_gain | 1.0000 |
| 6:138209908:AG:A | acceptor_loss | 1.0000 |
| 6:138209909:G:A | acceptor_loss | 1.0000 |
| 6:138209909:G:GG | acceptor_gain | 1.0000 |
| 6:138209909:GA:G | acceptor_gain | 1.0000 |
| 6:138209909:GAA:G | acceptor_gain | 1.0000 |
| 6:138210030:G:GT | donor_gain | 1.0000 |
AlphaMissense
14323 scored. Top likely-pathogenic:
| Variant | Protein change | am_pathogenicity |
|---|---|---|
| 6:138238561:C:A | A158D | 0.999 |
| 6:138238576:T:C | L163P | 0.999 |
| 6:138255651:T:C | L329P | 0.999 |
| 6:138280056:T:A | W785R | 0.999 |
| 6:138280056:T:C | W785R | 0.999 |
| 6:138286871:A:C | S914R | 0.999 |
| 6:138286873:C:A | S914R | 0.999 |
| 6:138286873:C:G | S914R | 0.999 |
| 6:138289952:T:A | W1011R | 0.999 |
| 6:138289952:T:C | W1011R | 0.999 |
| 6:138289954:G:C | W1011C | 0.999 |
| 6:138289954:G:T | W1011C | 0.999 |
| 6:138307310:T:A | W1296R | 0.999 |
| 6:138307310:T:C | W1296R | 0.999 |
| 6:138317265:T:A | W1454R | 0.999 |
| 6:138317265:T:C | W1454R | 0.999 |
| 6:138317287:T:C | L1461P | 0.999 |
| 6:138319759:T:A | W1511R | 0.999 |
| 6:138319759:T:C | W1511R | 0.999 |
| 6:138319818:G:C | K1530N | 0.999 |
| 6:138319818:G:T | K1530N | 0.999 |
| 6:138319829:G:A | G1534D | 0.999 |
| 6:138319844:T:C | L1539P | 0.999 |
| 6:138321209:G:C | G1584R | 0.999 |
| 6:138323714:T:A | W1604R | 0.999 |
| 6:138323714:T:C | W1604R | 0.999 |
| 6:138323716:G:C | W1604C | 0.999 |
| 6:138323716:G:T | W1604C | 0.999 |
| 6:138328025:T:C | F1669S | 0.999 |
| 6:138333999:T:C | L1718P | 0.999 |
dbSNP variants (sampled 300 via entrez): RS1000025222 (6:138163096 C>T), RS1000031538 (6:138175747 G>A), RS1000063871 (6:138287572 G>A), RS1000072328 (6:138225075 C>A,T), RS1000082163 (6:138293431 T>A), RS1000087118 (6:138306093 G>A), RS1000102856 (6:138240756 T>C), RS1000115036 (6:138306434 G>T), RS1000120929 (6:138322489 A>G), RS1000132014 (6:138182838 G>C), RS1000162495 (6:138269929 C>T), RS1000169917 (6:138334740 A>G), RS1000171293 (6:138289714 C>G), RS1000175119 (6:138330672 A>G), RS1000179057 (6:138250272 G>A)
Disease associations
OMIM: gene MIM:617411 | disease phenotypes:
GenCC curated gene-disease
| Disease | Classification | Inheritance |
|---|---|---|
| inherited dystonia | Strong | Autosomal dominant |
Mondo (3): dystonic disorder (MONDO:0003441), neurodevelopmental disorder (MONDO:0700092), inherited dystonia (MONDO:0044807)
Orphanet (0):
HPO phenotypes
1 total (1 of 1 shown, HPO-id order):
| HPO | Term |
|---|---|
| HP:0001332 | Dystonia |
GWAS associations
1 associations (top):
| Study | Trait | p-value |
|---|---|---|
| GCST009391_1745 | Metabolite levels | 9.000000e-06 |
EFO canonical traits (1, from GWAS)
| EFO ID | Trait name |
|---|---|
| EFO:0010348 | cholesteryl ester 20:4 measurement |
MeSH disease descriptors (2)
| Descriptor | Name | Tree numbers |
|---|---|---|
| D020821 | Dystonic Disorders | C10.228.662.300 |
| D065886 | Neurodevelopmental Disorders | F03.625 |
Drugs & pharmacology
Drug and pharmacology data
Is drug target: no
PharmGKB: 1 entry (VIP=true, CPIC=false)
PharmGKB variants
1 variants.
| Variant | Genes | Level | Score | #Clin annots | Drugs |
|---|---|---|---|---|---|
| rs143276236 | ARFGEF3 | 0.00 | 0 |
CTD chemical–gene interactions
43 total (human), top 30 by PubMed support.
| Chemical | Actions (top 5) | PubMed papers |
|---|---|---|
| Cyclosporine | increases expression | 4 |
| Panobinostat | affects cotreatment, decreases expression | 2 |
| Nickel | decreases expression | 2 |
| Phenylmercuric Acetate | affects cotreatment, decreases expression | 2 |
| Valproic Acid | decreases expression, increases expression | 2 |
| aristolochic acid I | decreases expression | 1 |
| sotorasib | affects cotreatment, decreases expression | 1 |
| trichostatin A | decreases expression | 1 |
| sodium arsenite | increases expression | 1 |
| potassium chromate(VI) | increases expression | 1 |
| 2,3-bis(3’-hydroxybenzyl)butyrolactone | decreases expression, affects cotreatment | 1 |
| perfluorooctane sulfonic acid | increases expression | 1 |
| 2-palmitoylglycerol | increases expression | 1 |
| 4-(5-benzo(1,3)dioxol-5-yl-4-pyridin-2-yl-1H-imidazol-2-yl)benzamide | affects cotreatment, decreases expression | 1 |
| abrine | decreases expression | 1 |
| Grape Seed Proanthocyanidins | affects cotreatment, increases expression | 1 |
| dorsomorphin | affects cotreatment, decreases expression | 1 |
| bisphenol S | decreases methylation | 1 |
| trametinib | affects cotreatment, decreases expression | 1 |
| NVP-BKM120 | decreases expression, affects cotreatment | 1 |
| Resveratrol | affects cotreatment, decreases expression | 1 |
| Sunitinib | increases expression | 1 |
| Vorinostat | decreases expression | 1 |
| Air Pollutants | increases abundance, increases expression | 1 |
| Arsenic | affects methylation | 1 |
| Benzo(a)pyrene | decreases expression | 1 |
| Caffeine | affects phosphorylation | 1 |
| Calcitriol | increases expression | 1 |
| Catechin | affects cotreatment, increases expression | 1 |
| Cisplatin | decreases expression | 1 |
Cellosaurus cell lines
2 cell lines: 2 cancer cell line
First 10 cell lines (id-ordered, not curated):
| Cellosaurus | Name | Category | Sex |
|---|---|---|---|
| CVCL_SU63 | HAP1 KIAA1244 (-) 1 | Cancer cell line | Male |
| CVCL_SU64 | HAP1 KIAA1244 (-) 2 | Cancer cell line | Male |
Clinical trials (associated diseases)
300 trials via MONDO — disease-level, not drug-specific.
| Trial | Phase | Status | Title |
|---|---|---|---|
| NCT00142259 | PHASE4 | UNKNOWN | Efficacy and Safety of DBS of the GPi in Patients With Primary Generalized and Segmental Dystonia |
| NCT00950196 | PHASE4 | COMPLETED | Amantadine for Improving Neurologic Symptoms in Ataxia-Telangiectasia |
| NCT00998660 | PHASE4 | COMPLETED | RECHARGE Sub-Study to the Implantable Systems Performance Registry (ISPR) |
| NCT02263417 | PHASE4 | COMPLETED | A Randomized Controlled Trail Comparing Subthalamic and Pallidal Deep Brain Stimulation for Dystonia |
| 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, |
| NCT00169403 | PHASE3 | UNKNOWN | Pallidal Stimulation in Patients With Idiopathic Generalised Dystonia |
| NCT03232320 | PHASE3 | COMPLETED | Meditoxin® Treatment in Patients With Cervical Dystonia |
| 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 |
| NCT00001784 | PHASE2 | COMPLETED | Mexiletine for the Treatment of Focal Dystonia |
| NCT00105430 | PHASE2 | COMPLETED | Deep Brain Stimulation for Cervical Dystonia |
| NCT00106782 | PHASE2 | COMPLETED | Transcranial Electrical Polarization to Treat Focal Hand Dystonia |
| NCT00122044 | PHASE2 | COMPLETED | Childhood Hypertonia of Central Origin: A Trial of Anticholinergic Treatment Effects |
| NCT00169338 | PHASE2 | COMPLETED | Pallidal Stimulation in Patients With Post-anoxic and Idiopathic Dystonia |
| NCT00331669 | PHASE2 | UNKNOWN | Efficacy and Safety of Deep Brain Stimulation (DBS) of the Pallidal (GPi) in Patients With Tardive Dystonia |
| NCT02107261 | PHASE2 | COMPLETED | Incobotulinum Toxin A (Xeomin®) As A Treatment For Focal Task-Specific Dystonia Of The Musician’s Hand |
| NCT02470325 | PHASE2 | UNKNOWN | The Effects of Cannabis on Dystonia and Spasticity on Pediatric Patients |
| NCT05027997 | PHASE2 | COMPLETED | Exploratory Study of Dipraglurant (ADX48621) for the Treatment of Patients With Blepharospasm |
| NCT06412653 | PHASE2 | COMPLETED | Prospective Pilot Trial to Address Feasibility and Safety of Oral Zinc in GNAO1 Associated Disorders |
| NCT07304089 | PHASE2 | RECRUITING | A Study to Evaluate the Efficacy, Safety, and Tolerability of VIM0423 in Individuals With Isolated Dystonia |
| 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 |
| NCT01433757 | PHASE1 | COMPLETED | Ampicillin for DYT-1 Dystonia Motor Symptoms |
| NCT01698450 | PHASE1 | COMPLETED | Magnetic Resonance (MR) Guided Functional Ultrasound-Neurosurgery for Movement Disorders |
| NCT02982304 | PHASE1 | UNKNOWN | Multi-Target Pallidal and Thalamic Deep Brain Stimulation for Hemi-Dystonia |
| NCT06117020 | PHASE1 | COMPLETED | Single and Multiple Ascending Dose Study of MTR-601 in Healthy Individuals |
| NCT06554288 | PHASE1 | RECRUITING | Pharmacogenomic Contributions to Trihexyphenidyl Biotransformation and Response in Children With Dystonic Cerebral Palsy |
| 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 |
| NCT00004421 | PHASE2/PHASE3 | COMPLETED | Deep Brain Stimulation in Treating Patients With Dystonia |
| NCT00272246 | PHASE2/PHASE3 | UNKNOWN | Bilateral Internal Pallidum Stimulation in Primary Generalized Dystonia |
| NCT00608231 | PHASE2/PHASE3 | WITHDRAWN | Dexmedetomidine Effects on Microelectrode Recording in Deep Brain Stimulation |
| NCT04277247 | PHASE2/PHASE3 | UNKNOWN | Botulinum Toxin Type A for Foot Dystonia-associated Pain in Parkinson’s Disease |
| NCT02015039 | PHASE1/PHASE2 | COMPLETED | Pilot Trial of Botulinum Toxin and Occupational Therapy for Writer’s Cramp |
| NCT02911103 | PHASE1/PHASE2 | ACTIVE_NOT_RECRUITING | Deep Brain Stimulation Surgery for Focal Hand Dystonia |
Related Atlas pages
- Associated diseases: inherited dystonia
- Disease cohort memberships (association, not causation — diseases whose associated-gene cohort lists this gene; a subset are also under Associated diseases): dystonic disorder, inherited dystonia