ZGRF1
gene geneOn this page
Also known as FLJ11331
Summary
ZGRF1 (zinc finger GRF-type containing 1, HGNC:25654) is a protein-coding gene on chromosome 4q25, encoding 5’-3’ DNA helicase ZGRF1 (Q86YA3). 5’-3’ DNA helicase which is recruited to sites of DNA damage and promotes repair of replication-blocking DNA lesions through stimulation of homologous recombination (HR).
The encoded protein contains GRF zinc finger (zf-GRF) and transmembrane domains. GRF zinc fingers are found in a number of DNA-binding proteins. Alternative splicing results in multiple transcript variants encoding different isoforms.
Source: NCBI Gene 55345 — RefSeq curated summary.
At a glance
- GWAS associations: 5
- Clinical variants (ClinVar): 305 total
- MANE Select transcript:
NM_018392
Identifiers
Gene identifiers
| Field | Value |
|---|---|
| HGNC ID | HGNC:25654 |
| Approved symbol | ZGRF1 |
| Name | zinc finger GRF-type containing 1 |
| Location | 4q25 |
| Locus type | gene with protein product |
| Status | Approved |
| Aliases | FLJ11331 |
| Ensembl gene | ENSG00000138658 |
| Ensembl biotype | protein_coding |
| Entrez | 55345 |
Gene structure
Transcript identifiers
Ensembl transcripts: 16 — 9 protein_coding, 4 nonsense_mediated_decay, 3 retained_intron
ENST00000264370, ENST00000309071, ENST00000445203, ENST00000473015, ENST00000502805, ENST00000503172, ENST00000505019, ENST00000506675, ENST00000512075, ENST00000514770, ENST00000612287, ENST00000925930, ENST00000925931, ENST00000925932, ENST00000925933, ENST00000925934
RefSeq mRNA: 2 — MANE Select: NM_018392
NM_001350397, NM_018392
CCDS: CCDS3700
Canonical transcript exons
ENST00000505019 — 28 exons
| Exon | Start | End |
|---|---|---|
| ENSE00001081365 | 112562371 | 112562485 |
| ENSE00001204701 | 112606008 | 112606091 |
| ENSE00001325774 | 112560733 | 112560995 |
| ENSE00001380072 | 112603524 | 112603697 |
| ENSE00001724813 | 112539339 | 112539689 |
| ENSE00002035425 | 112589724 | 112589874 |
| ENSE00003517792 | 112583978 | 112584174 |
| ENSE00003518149 | 112587280 | 112587929 |
| ENSE00003520121 | 112563131 | 112563274 |
| ENSE00003521632 | 112547285 | 112547408 |
| ENSE00003522575 | 112620002 | 112620190 |
| ENSE00003528262 | 112633156 | 112633242 |
| ENSE00003552898 | 112617440 | 112619690 |
| ENSE00003572627 | 112554705 | 112554782 |
| ENSE00003574344 | 112612524 | 112612588 |
| ENSE00003588602 | 112623817 | 112623876 |
| ENSE00003589797 | 112540821 | 112540955 |
| ENSE00003614880 | 112553835 | 112553982 |
| ENSE00003619087 | 112548253 | 112548380 |
| ENSE00003624003 | 112558150 | 112558309 |
| ENSE00003631664 | 112541092 | 112541268 |
| ENSE00003640570 | 112539863 | 112540124 |
| ENSE00003647426 | 112609379 | 112609429 |
| ENSE00003650375 | 112631930 | 112632010 |
| ENSE00003670892 | 112585541 | 112585725 |
| ENSE00003682378 | 112581663 | 112581802 |
| ENSE00003683265 | 112586445 | 112586583 |
| ENSE00003909986 | 112636851 | 112636909 |
Expression profiles
Bgee: expression breadth ubiquitous, 224 present calls, max score 87.95.
FANTOM5 (CAGE): breadth ubiquitous, TPM avg 3.7271 / max 165.9154, expressed in 1115 samples.
FANTOM5 promoters (3 alternative TSS)
| Promoter ID | TPM avg | Samples expressed |
|---|---|---|
| 53654 | 3.1521 | 996 |
| 53656 | 0.3868 | 207 |
| 53655 | 0.1882 | 82 |
Top tissues by expression
246 total, by Bgee expression score (0-100, higher = more expressed):
| Tissue | Anatomy ID | Expression score | Quality |
|---|---|---|---|
| male germ line stem cell (sensu Vertebrata) in testis | CL:0000089 ∩ UBERON:0000473 | 87.95 | gold quality |
| ventricular zone | UBERON:0003053 | 85.22 | gold quality |
| ganglionic eminence | UBERON:0004023 | 82.77 | gold quality |
| primordial germ cell in gonad | CL:0000670 ∩ UBERON:0000991 | 82.75 | gold quality |
| calcaneal tendon | UBERON:0003701 | 79.41 | gold quality |
| bone marrow cell | CL:0002092 | 79.11 | gold quality |
| oocyte | CL:0000023 | 78.44 | gold quality |
| corpus callosum | UBERON:0002336 | 77.97 | gold quality |
| adrenal tissue | UBERON:0018303 | 77.72 | gold quality |
| vermiform appendix | UBERON:0001154 | 77.59 | gold quality |
| spleen | UBERON:0002106 | 76.19 | gold quality |
| granulocyte | CL:0000094 | 76.18 | gold quality |
| bone marrow | UBERON:0002371 | 76.18 | gold quality |
| cerebellar hemisphere | UBERON:0002245 | 75.14 | gold quality |
| cerebellar cortex | UBERON:0002129 | 75.05 | gold quality |
| lymph node | UBERON:0000029 | 75.00 | gold quality |
| right hemisphere of cerebellum | UBERON:0014890 | 74.91 | gold quality |
| testis | UBERON:0000473 | 74.85 | gold quality |
| right testis | UBERON:0004534 | 74.20 | gold quality |
| C1 segment of cervical spinal cord | UBERON:0006469 | 74.12 | gold quality |
| trabecular bone tissue | UBERON:0002483 | 74.03 | gold quality |
| rectum | UBERON:0001052 | 73.98 | gold quality |
| left testis | UBERON:0004533 | 73.94 | gold quality |
| cerebellum | UBERON:0002037 | 73.93 | gold quality |
| small intestine Peyer’s patch | UBERON:0003454 | 73.86 | gold quality |
| mucosa of stomach | UBERON:0001199 | 73.83 | gold quality |
| tibial nerve | UBERON:0001323 | 73.78 | gold quality |
| secondary oocyte | CL:0000655 | 73.26 | gold quality |
| caecum | UBERON:0001153 | 73.20 | gold quality |
| thymus | UBERON:0002370 | 72.78 | gold quality |
Single-cell (SCXA)
Detected in 1 experiment(s), a significant marker in 0.
| Experiment | Marker? | Max mean expression |
|---|---|---|
| E-ANND-3 | no | 6.55 |
Regulation
Is transcription factor: no
miRNA regulators (miRDB)
14 targeting ZGRF1, 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-4659A-3P | 99.80 | 72.62 | 4248 |
| HSA-MIR-4659B-3P | 99.80 | 72.62 | 4248 |
| HSA-MIR-6516-3P | 99.65 | 68.57 | 1238 |
| HSA-MIR-1290 | 99.59 | 69.90 | 2079 |
| HSA-MIR-21-5P | 99.46 | 70.54 | 1035 |
| HSA-MIR-4666A-5P | 99.41 | 69.72 | 1887 |
| HSA-MIR-590-5P | 99.25 | 70.76 | 930 |
| HSA-MIR-4680-3P | 98.64 | 68.60 | 2093 |
| HSA-MIR-10226 | 98.25 | 66.50 | 811 |
| HSA-MIR-2681-3P | 98.18 | 65.28 | 577 |
| HSA-MIR-1279 | 97.83 | 67.50 | 1898 |
| HSA-MIR-96-3P | 97.47 | 68.03 | 839 |
| HSA-MIR-627-5P | 95.51 | 66.80 | 509 |
Literature-anchored findings (GeneRIF, showing 2)
- Two novel loci IDH1 and ZGRF1 are associated with adiposity. [meta-analysis] (PMID:26599207)
- The ZGRF1 Helicase Promotes Recombinational Repair of Replication-Blocking DNA Damage in Human Cells. (PMID:32640219)
Cross-species orthologs
0 orthologs
Protein
Protein identifiers
5’-3’ DNA helicase ZGRF1 — Q86YA3 (reviewed: Q86YA3)
Alternative names: GRF-type zinc finger domain-containing protein 1
All UniProt accessions (5): D6RB47, D6REN9, D6REQ7, Q86YA3, G3XAL8
UniProt curated annotations — full annotation on UniProt →
Function. 5’-3’ DNA helicase which is recruited to sites of DNA damage and promotes repair of replication-blocking DNA lesions through stimulation of homologous recombination (HR). Promotes HR by directly stimulating RAD51-mediated strand exchange activity. Not required to load RAD51 at sites of DNA damage but promotes recombinational repair after RAD51 recruitment. Also promotes HR by positively regulating EXO1-mediated DNA end resection of double-strand breaks. Required for recruitment of replication protein RPA2 to DNA damage sites. Promotes the initiation of the G2/M checkpoint but not its maintenance. Catalyzes Holliday junction branch migration and dissociation of D-loops and DNA flaps.
Subunit / interactions. Interacts with DNA repair protein RAD51; the interaction promotes RAD51 strand exchange activity. Also interacts with DNA repair proteins EXO1 and BRCA1; the interactions are increased following DNA damage induction.
Subcellular location. Nucleus.
Isoforms (7)
| UniProt ID | Names | Canonical? |
|---|---|---|
| Q86YA3-1 | 1 | yes |
| Q86YA3-2 | 2 | |
| Q86YA3-3 | 3 | |
| Q86YA3-4 | 4 | |
| Q86YA3-5 | 5 | |
| Q86YA3-6 | 6 | |
| Q86YA3-7 | 7 |
RefSeq proteins (2): NP_001337326, NP_060862* (*=MANE)
Domains & families (InterPro)
| ID | Name | Type |
|---|---|---|
| IPR010666 | Znf_GRF | Domain |
| IPR018838 | ZGRF1-like_N | Domain |
| IPR027417 | P-loop_NTPase | Homologous_superfamily |
| IPR041677 | DNA2/NAM7_AAA_11 | Domain |
| IPR041679 | DNA2/NAM7-like_C | Domain |
| IPR047187 | SF1_C_Upf1 | Domain |
| IPR052800 | DNA_Repair_Helicase_ZGRF1 | Family |
Pfam: PF06839, PF10382, PF13086, PF13087
Catalyzed reactions (Rhea), 1 shown:
- ATP + H2O = ADP + phosphate + H(+) (RHEA:13065)
UniProt features (37 total): splice variant 13, sequence variant 6, sequence conflict 4, binding site 4, modified residue 3, region of interest 2, compositionally biased region 2, chain 1, zinc finger region 1, mutagenesis site 1
Structure
Experimental structures (PDB)
0 structures.
Predicted structure (AlphaFold)
| Model | pLDDT | Fraction very-high |
|---|---|---|
| AF-Q86YA3-F1 | 50.08 | 0.18 |
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 (4): 1349; 1351; 1374; 1382
Post-translational modifications (3): 336, 793, 864
Mutagenesis-validated functional residues (1):
| Position | Phenotype |
|---|---|
| 1660 | loss of helicase activity. |
Function
Pathways and Gene Ontology
Reactome pathways
0 pathways
MSigDB gene sets: 110 (showing top):
chr4q25, TGCGCANK_UNKNOWN, MODULE_255, MODULE_317, GOBP_DNA_DAMAGE_RESPONSE, PYEON_CANCER_HEAD_AND_NECK_VS_CERVICAL_UP, DODD_NASOPHARYNGEAL_CARCINOMA_UP, CREB_Q3, FISCHER_DREAM_TARGETS, NOUZOVA_TRETINOIN_AND_H4_ACETYLATION, GOBP_RECOMBINATIONAL_REPAIR, NUYTTEN_EZH2_TARGETS_DN, YGCGYRCGC_UNKNOWN, MODULE_69, GOCC_SITE_OF_DOUBLE_STRAND_BREAK
GO Biological Process (4): recombinational repair (GO:0000725), double-strand break repair (GO:0006302), DNA repair (GO:0006281), DNA damage response (GO:0006974)
GO Molecular Function (9): ATP binding (GO:0005524), zinc ion binding (GO:0008270), hydrolase activity (GO:0016787), 5’-3’ DNA helicase activity (GO:0043139), nucleotide binding (GO:0000166), helicase activity (GO:0004386), protein binding (GO:0005515), isomerase activity (GO:0016853), metal ion binding (GO:0046872)
GO Cellular Component (2): nucleus (GO:0005634), site of double-strand break (GO:0035861)
GO top-level categories
Rollup of top GO terms by namespace:
| Category | Terms |
|---|---|
| DNA repair | 2 |
| catalytic activity | 2 |
| DNA recombination | 1 |
| DNA metabolic process | 1 |
| DNA damage response | 1 |
| cellular response to stress | 1 |
| adenyl ribonucleotide binding | 1 |
| purine ribonucleoside triphosphate binding | 1 |
| transition metal ion binding | 1 |
| DNA helicase activity | 1 |
| nucleoside phosphate binding | 1 |
| heterocyclic compound binding | 1 |
| nucleic acid conformation isomerase activity | 1 |
| catalytic activity, acting on a nucleic acid | 1 |
| ATP-dependent activity | 1 |
| binding | 1 |
| cation binding | 1 |
| intracellular membrane-bounded organelle | 1 |
| site of DNA damage | 1 |
Protein interactions and networks
STRING
1580 interactions, top by confidence (×1000):
| Protein A | Protein B | Partner UniProt | Score |
|---|---|---|---|
| ZGRF1 | SLC71A3P | Q5VZR4 | 542 |
| ZGRF1 | ZNF280D | Q6N043 | 447 |
| ZGRF1 | CCDC184 | Q52MB2 | 441 |
| ZGRF1 | FAM228A | Q86W67 | 431 |
| ZGRF1 | RPUSD3 | Q6P087 | 427 |
| ZGRF1 | CHCHD5 | Q9BSY4 | 417 |
| ZGRF1 | PURG | Q9UJV8 | 400 |
| ZGRF1 | ZC3H6 | P61129 | 384 |
| ZGRF1 | CCDC15 | Q0P6D6 | 374 |
| ZGRF1 | SERP2 | Q8N6R1 | 367 |
| ZGRF1 | RIMKLA | Q8IXN7 | 366 |
| ZGRF1 | DTWD1 | Q8N5C7 | 365 |
| ZGRF1 | FANCM | Q8IYD8 | 365 |
| ZGRF1 | TRMT13 | Q9NUP7 | 364 |
| ZGRF1 | A6NDT3 | A6NDT3 | 359 |
IntAct
26 interactions, top by confidence:
| A | B | Type | Score |
|---|---|---|---|
| ZGRF1 | BRCA1 | psi-mi:“MI:0914”(association) | 0.580 |
| ZGRF1 | BRCA1 | psi-mi:“MI:0915”(physical association) | 0.580 |
| ZGRF1 | BRCA1 | psi-mi:“MI:0403”(colocalization) | 0.580 |
| ZGRF1 | EXO1 | psi-mi:“MI:0915”(physical association) | 0.560 |
| ZGRF1 | RAD51 | psi-mi:“MI:0915”(physical association) | 0.470 |
| RAD51 | ZGRF1 | psi-mi:“MI:2364”(proximity) | 0.470 |
| MMRN1 | ZGRF1 | psi-mi:“MI:0915”(physical association) | 0.400 |
| ZGRF1 | PDIA3 | psi-mi:“MI:0915”(physical association) | 0.400 |
| ZGRF1 | FLNA | psi-mi:“MI:0915”(physical association) | 0.400 |
| ZGRF1 | POLD3 | psi-mi:“MI:0915”(physical association) | 0.400 |
| ZGRF1 | POL32 | psi-mi:“MI:0915”(physical association) | 0.400 |
| ZGRF1 | FANCM | psi-mi:“MI:0915”(physical association) | 0.400 |
| CDKN2A | ZGRF1 | psi-mi:“MI:0915”(physical association) | 0.370 |
| CFTR | ZGRF1 | psi-mi:“MI:0915”(physical association) | 0.370 |
| Ppp2r1a | CCHCR1 | psi-mi:“MI:0914”(association) | 0.350 |
| KIF11 | ILVBL | psi-mi:“MI:0914”(association) | 0.350 |
| VPS18 | DNAJB5 | psi-mi:“MI:0914”(association) | 0.350 |
| PB2 | ESYT2 | psi-mi:“MI:0914”(association) | 0.350 |
| PB1 | ESYT2 | psi-mi:“MI:0914”(association) | 0.350 |
| PB2 | IPO5 | psi-mi:“MI:0914”(association) | 0.350 |
| NEK4 | E2F8 | psi-mi:“MI:0914”(association) | 0.350 |
| HSPA4 | HSPA8 | psi-mi:“MI:0914”(association) | 0.350 |
| PIP | RBM47 | psi-mi:“MI:0914”(association) | 0.350 |
| PTGES3 | SBNO1 | psi-mi:“MI:0914”(association) | 0.350 |
BioGRID (34): ZGRF1 (Affinity Capture-MS), ZGRF1 (Affinity Capture-MS), ZGRF1 (Affinity Capture-MS), ZGRF1 (Two-hybrid), ZGRF1 (Affinity Capture-RNA), ZGRF1 (Proximity Label-MS), ZGRF1 (Proximity Label-MS), ZGRF1 (Proximity Label-MS), ZGRF1 (Proximity Label-MS), ZGRF1 (Proximity Label-MS), ZGRF1 (Proximity Label-MS), ZGRF1 (Proximity Label-MS), ZGRF1 (Affinity Capture-MS), ZGRF1 (Affinity Capture-MS), ZGRF1 (Affinity Capture-MS)
ESM2 similar proteins: A0A140LI88, A4D1E1, D3Z987, D3ZUC6, E5FYH0, E5FYH1, E9Q3S4, F6ULY3, F7DF15, G3S077, G7H7V7, G7NY55, O35923, O54952, O88491, O95405, P38398, P48754, P51587, P97929, Q0VBV7, Q0VGT4, Q2M3C7, Q3V089, Q56UN5, Q5DTT3, Q5F2C3, Q5VWN6, Q61493, Q68DQ2, Q6J6I8, Q6J6I9, Q6J6J0, Q6NSW3, Q6ZP01, Q7TSY8, Q7Z570, Q80U44, Q864S8, Q864U1
Diamond homologs: A0A1L8HU22, A0KEN2, A0L2N2, A1AV29, A1BAN2, A1JHR7, A1RE25, A2C0H4, A3CYP7, A3QJA8, A4J4X3, A4STD1, A4TSD4, A5D0T6, A5UDC3, A5UI87, A5UUN1, A5VG06, A6UFF8, A6WUE9, A7FCT7, A8HA27, A8LNK8, A9BDY5, A9KW47, A9R677, A9WDC2, B0TER7, B0TN04, B0UUX0, B1JQX0, B1WTF7, B1YKA0, B2JYN6, B3Q620, B7K1T1, B7N9V3, B8CVD1, B8EDQ9, B8G9X1
SIGNOR signaling
0 interactions.
Enriched among interaction partners
Reactome pathways and GO biological processes over-represented among this gene’s 29 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.
GO biological processes:
| GO term | Partners | Fold | FDR |
|---|---|---|---|
| protein folding | 5 | 21.5× | 8e-04 |
Disease & clinical
Clinical variants and AI predictions
ClinVar
305 variants total. Per-class counts are floors (≥ shown; pagination cap):
| Classification | Count (floor) |
|---|---|
| Pathogenic | 0 |
| Likely pathogenic | 0 |
| Uncertain significance | 254 |
| Likely benign | 17 |
| Benign | 0 |
Top pathogenic / likely-pathogenic (0)
SpliceAI
4628 predictions. Top by Δscore:
| Variant | Effect | Δscore |
|---|---|---|
| 4:112540120:CAAAG:C | acceptor_gain | 1.0000 |
| 4:112540818:AAC:A | donor_loss | 1.0000 |
| 4:112540819:A:T | donor_loss | 1.0000 |
| 4:112540820:C:T | donor_loss | 1.0000 |
| 4:112540952:CTAT:C | acceptor_gain | 1.0000 |
| 4:112540955:TCTGG:T | acceptor_loss | 1.0000 |
| 4:112540956:C:CA | acceptor_loss | 1.0000 |
| 4:112540956:C:CC | acceptor_gain | 1.0000 |
| 4:112547260:T:TA | donor_gain | 1.0000 |
| 4:112553829:TCTTA:T | donor_loss | 1.0000 |
| 4:112553830:CTTAC:C | donor_loss | 1.0000 |
| 4:112553831:TTA:T | donor_loss | 1.0000 |
| 4:112553832:TACCT:T | donor_loss | 1.0000 |
| 4:112553833:A:AT | donor_loss | 1.0000 |
| 4:112553834:CCTG:C | donor_gain | 1.0000 |
| 4:112562483:CCA:C | acceptor_gain | 1.0000 |
| 4:112562484:CA:C | acceptor_gain | 1.0000 |
| 4:112562484:CAC:C | acceptor_gain | 1.0000 |
| 4:112562486:C:CC | acceptor_gain | 1.0000 |
| 4:112563122:AATAC:A | donor_loss | 1.0000 |
| 4:112563123:ATACT:A | donor_loss | 1.0000 |
| 4:112563124:TACTC:T | donor_loss | 1.0000 |
| 4:112563125:ACTCA:A | donor_loss | 1.0000 |
| 4:112563126:CTCAC:C | donor_loss | 1.0000 |
| 4:112563127:TC:T | donor_loss | 1.0000 |
| 4:112563128:CACTG:C | donor_loss | 1.0000 |
| 4:112563129:A:AC | donor_gain | 1.0000 |
| 4:112563129:A:T | donor_loss | 1.0000 |
| 4:112563130:C:CT | donor_gain | 1.0000 |
| 4:112563130:CT:C | donor_gain | 1.0000 |
AlphaMissense
13972 scored. Top likely-pathogenic:
| Variant | Protein change | am_pathogenicity |
|---|---|---|
| 4:112539890:A:G | W2049R | 0.998 |
| 4:112539890:A:T | W2049R | 0.998 |
| 4:112554749:T:A | R1718S | 0.998 |
| 4:112554749:T:G | R1718S | 0.998 |
| 4:112547298:C:G | R1862P | 0.997 |
| 4:112558165:T:A | D1702V | 0.997 |
| 4:112558166:C:G | D1702H | 0.997 |
| 4:112558171:G:T | A1700D | 0.997 |
| 4:112558287:A:C | S1661R | 0.997 |
| 4:112558287:A:T | S1661R | 0.997 |
| 4:112558289:T:G | S1661R | 0.997 |
| 4:112563266:A:G | W1483R | 0.997 |
| 4:112563266:A:T | W1483R | 0.997 |
| 4:112539987:G:C | F2016L | 0.996 |
| 4:112539987:G:T | F2016L | 0.996 |
| 4:112539989:A:G | F2016L | 0.996 |
| 4:112540047:A:C | F1996L | 0.996 |
| 4:112540047:A:T | F1996L | 0.996 |
| 4:112540049:A:G | F1996L | 0.996 |
| 4:112548291:A:C | S1812R | 0.996 |
| 4:112548291:A:T | S1812R | 0.996 |
| 4:112548293:T:G | S1812R | 0.996 |
| 4:112548298:T:A | E1810V | 0.996 |
| 4:112554750:C:G | R1718T | 0.996 |
| 4:112558156:A:G | L1705P | 0.996 |
| 4:112558165:T:G | D1702A | 0.996 |
| 4:112558176:A:C | N1698K | 0.996 |
| 4:112558176:A:T | N1698K | 0.996 |
| 4:112540052:C:G | A1995P | 0.995 |
| 4:112547364:A:G | L1840P | 0.995 |
dbSNP variants (sampled 300 via entrez): RS1000044420 (4:112559344 G>T), RS1000055225 (4:112582649 G>A), RS1000055279 (4:112576626 T>A,C), RS1000060598 (4:112609635 G>A), RS1000110981 (4:112597226 A>G), RS1000180823 (4:112573839 T>C), RS1000214452 (4:112622316 C>T), RS1000216299 (4:112567087 G>T), RS1000242687 (4:112616314 G>A,C), RS1000245552 (4:112622731 CT>C), RS10002557 (4:112617124 A>G), RS1000269817 (4:112552420 T>C), RS1000290854 (4:112548735 G>C), RS1000370136 (4:112629829 G>A,C,T), RS1000377879 (4:112622411 T>C)
Disease associations
OMIM: gene `` | disease phenotypes: MIM:602081
GenCC curated gene-disease
Mondo (2): autism spectrum disorder (MONDO:0005258), childhood apraxia of speech (MONDO:0011184)
Orphanet (2): Isolated childhood apraxia of speech (Orphanet:209908), NON RARE IN EUROPE: Autism (Orphanet:106)
HPO phenotypes
0 total (0 of 0 shown, HPO-id order):
GWAS associations
5 associations (top):
| Study | Trait | p-value |
|---|---|---|
| GCST002418_1 | Free thyroxine concentration | 5.000000e-06 |
| GCST005951_145 | Body mass index | 4.000000e-08 |
| GCST010701_20 | Cortical surface area (MOSTest) | 1.000000e-242 |
| GCST010702_74 | Subcortical volume (MOSTest) | 2.000000e-11 |
| GCST010703_129 | Brain morphology (MOSTest) | 3.000000e-08 |
EFO canonical traits (2, from GWAS)
| EFO ID | Trait name |
|---|---|
| EFO:0004340 | body mass index |
| EFO:0004346 | neuroimaging measurement |
Drugs & pharmacology
Drug and pharmacology data
Is drug target: no
PharmGKB: 1 entry (VIP=true, CPIC=false)
CTD chemical–gene interactions
38 total (human), top 30 by PubMed support.
| Chemical | Actions (top 5) | PubMed papers |
|---|---|---|
| Valproic Acid | decreases expression, increases expression | 3 |
| perfluorooctanoic acid | decreases expression | 2 |
| Benzo(a)pyrene | decreases methylation, increases expression | 2 |
| Phenylmercuric Acetate | affects cotreatment, decreases expression | 2 |
| aristolochic acid I | decreases expression | 1 |
| TAK-243 | increases sumoylation | 1 |
| triphenyl phosphate | affects expression | 1 |
| propionaldehyde | decreases expression | 1 |
| bisphenol A | decreases expression | 1 |
| beta-lapachone | decreases expression | 1 |
| tris(1,3-dichloro-2-propyl)phosphate | decreases expression | 1 |
| sodium arsenite | decreases expression | 1 |
| butyraldehyde | decreases expression | 1 |
| maleic acid | decreases expression | 1 |
| perfluorooctane sulfonic acid | decreases expression | 1 |
| perfluoro-n-nonanoic acid | decreases expression | 1 |
| 4-(5-benzo(1,3)dioxol-5-yl-4-pyridin-2-yl-1H-imidazol-2-yl)benzamide | affects cotreatment, decreases expression | 1 |
| perfluorohexanesulfonic acid | decreases expression | 1 |
| dorsomorphin | affects cotreatment, decreases expression | 1 |
| Resveratrol | affects cotreatment, increases expression | 1 |
| Sunitinib | increases expression | 1 |
| Acetaminophen | increases expression | 1 |
| Caffeine | affects phosphorylation | 1 |
| Calcitriol | decreases expression, affects cotreatment | 1 |
| Dichlorodiphenyl Dichloroethylene | increases expression | 1 |
| Doxorubicin | decreases expression | 1 |
| Ethyl Methanesulfonate | increases expression | 1 |
| Latex | increases expression | 1 |
| Lead | affects expression | 1 |
| Methyl Methanesulfonate | increases expression | 1 |
Clinical trials (associated diseases)
300 trials via MONDO — disease-level, not drug-specific.
| Trial | Phase | Status | Title |
|---|---|---|---|
| NCT00391261 | PHASE4 | COMPLETED | An Open-label Trial of Metformin for Weight Control of Pediatric Patients on Antipsychotic Medications. |
| NCT01028820 | PHASE4 | COMPLETED | FMRI Brain Activation of Aripiprazole Treatment in Autism Spectrum Disorders |
| NCT01333865 | PHASE4 | COMPLETED | A Study of Memantine Hydrochloride (Namenda®) for Cognitive and Behavioral Impairment in Adults With Autism Spectrum Disorders |
| NCT01337700 | PHASE4 | COMPLETED | Milnacipran in Autism and the Functional Locus Coeruleus and Noradrenergic Model of Autism |
| NCT01695200 | PHASE4 | COMPLETED | Omega-3 Fatty Acids in Autism Spectrum Disorders |
| NCT02096952 | PHASE4 | COMPLETED | Methylphenidate ER Liquid Formulation in Adults With ASD and ADHD |
| NCT02235467 | PHASE4 | COMPLETED | Multisite Study: Parental Training Using Video Modelling to Develop Social Skills in Children With Autism |
| NCT02940574 | PHASE4 | COMPLETED | Neural and Behavioral Effects of Oxytocin in Autism Spectrum Disorders |
| NCT03333629 | PHASE4 | COMPLETED | Promoting Positive Outcomes for Individuals With ASD: Linking Early Detection, Treatment, and Long-term Outcomes |
| NCT03337646 | PHASE4 | COMPLETED | Evaluation of the Effect and Safety of Lisdexamfetamine in Children Aged 6-12 With ADHD and Autism |
| NCT03538431 | PHASE4 | COMPLETED | Improving Driving in Young People With Autism Spectrum Disorders |
| NCT03757585 | PHASE4 | COMPLETED | Natural Treatments for the Management of Emotional Dysregulation in Youth With Non-verbal Learning Disability (NVLD) and/or Autism Spectrum Disorders (ASD) |
| NCT04903353 | PHASE4 | COMPLETED | Pragmatic Trial Comparing Weight Gain in Children With Autism Taking Risperidone Versus Aripiprazole |
| NCT05063656 | PHASE4 | COMPLETED | Biomarker-Driven Pharmacological Treatment of Adolescents With Autism Spectrum Disorder With Gabapentin |
| NCT05146245 | PHASE4 | UNKNOWN | Safety and Pharmacokinetics of Antipsychotics in Children 2: Studying TDM in an RCT |
| NCT05916339 | PHASE4 | RECRUITING | AWARE: Management of ADHD in Autism Spectrum Disorder |
| NCT05954052 | PHASE4 | TERMINATED | A Study of Glutathione in Children With Autism Spectrum Disorder |
| NCT06853665 | PHASE4 | RECRUITING | The TEAM Study - Treatment Efficacy for Autism/Attention Using Mixed Amphetamine |
| NCT07054697 | PHASE4 | COMPLETED | Pilot-RCT With Individualized Homeopathic Treatment in the Children With Autism Spectrum Disorder |
| NCT07161804 | PHASE4 | COMPLETED | Pilot RCT Using Homeopathic Medicines in ASD |
| NCT07439042 | PHASE4 | NOT_YET_RECRUITING | Buspirone for Anxiety in Autistic Youth |
| NCT01302964 | PHASE3 | COMPLETED | Mirtazapine Treatment of Anxiety in Children and Adolescents With Pervasive Developmental Disorders |
| NCT01706523 | PHASE3 | TERMINATED | Open Label Extension Study of STX209 (Arbaclofen) in Autism Spectrum Disorders |
| NCT01825798 | PHASE3 | COMPLETED | Treatment of Overweight Induced by Antipsychotic Medication in Young People With Autism Spectrum Disorders (ASD) |
| NCT01972074 | PHASE3 | COMPLETED | Behavioral and Neural Response to Memantine in Adolescents With Autism Spectrum Disorder |
| NCT02985749 | PHASE3 | COMPLETED | A Study of Oxytocin for the Treatment of Social Impairment in Individuals With High Functioning Autism Spectrum Disorder |
| NCT03197922 | PHASE3 | COMPLETED | Treatment of Encopresis in Children With Autism Spectrum Disorders |
| NCT03504917 | PHASE3 | TERMINATED | A Study of Balovaptan in Adults With Autism Spectrum Disorder With a 2-Year Open-Label Extension |
| NCT03553875 | PHASE3 | TERMINATED | Memantine for the Treatment of Social Deficits in Youth With Disorders of Impaired Social Interactions |
| NCT03640156 | PHASE3 | COMPLETED | Modulating Socially Adaptive Mirror System Functioning in Autism by Oxytocin |
| NCT03715153 | PHASE3 | TERMINATED | Efficacy and Safety of Bumetanide Oral Liquid Formulation in Children Aged From 2 to Less Than 7 Years Old With Autism Spectrum Disorder. |
| NCT03715166 | PHASE3 | TERMINATED | Efficacy and Safety of Bumetanide Oral Liquid Formulation in Children and Adolescents Aged From 7 to Less Than 18 Years Old With Autism Spectrum Disorder |
| NCT04233502 | PHASE3 | WITHDRAWN | Efficacy and Safety of Slenyto for Insomnia in Children With ASD |
| NCT04578756 | PHASE3 | COMPLETED | Open-Label, Flexible-dose Study to Evaluate the Long-Term Safety and Tolerability of Cariprazine in the Treatment of Pediatric Participants With Schizophrenia, Bipolar I Disorder, or Autism Spectrum Disorder |
| NCT04623398 | PHASE3 | COMPLETED | Effect of Lithium in Patients With Autism Spectrum Disorder and Phelan-McDermid Syndrome (SHANK3 Haploinsufficiency) |
| NCT04725383 | PHASE3 | TERMINATED | Amitriptyline for Repetitive Behaviors in Autism Spectrum Disorders |
| NCT05212493 | PHASE3 | COMPLETED | The Effects of Medical Cannabis in Children With Autistic Spectrum Disorder |
| NCT05361707 | PHASE3 | UNKNOWN | Evaluating the Effects of Tasimelteon in Individuals With Autism Spectrum Disorder (ASD) and Sleep Disturbances |
| NCT05439616 | PHASE3 | COMPLETED | Study of Cariprazine Oral Capsules or Solution to Assess Adverse Events and Change in Irritability Due to Autism Spectrum Disorder (ASD) in Participants Aged 5-17 Years With ASD |
| NCT06229210 | PHASE3 | RECRUITING | Safety and Tolerability Trial of Lumateperone in Pediatric Patients With Schizophrenia, Bipolar Disorder or Autism Spectrum Disorder |
Related Atlas pages
- Disease cohort memberships (association, not causation — diseases whose associated-gene cohort lists this gene; a subset are also under Associated diseases): childhood apraxia of speech