ZNF407
geneOn this page
Also known as FLJ20307FLJ13839KIAA1703
Summary
ZNF407 (zinc finger protein 407, HGNC:19904) is a protein-coding gene on chromosome 18q23, encoding Zinc finger protein 407 (Q9C0G0). May be involved in transcriptional regulation. It is a selective cancer dependency (DepMap: 83.7% of cell lines).
This gene encodes a zinc finger protein whose exact function is not known. It may be involved in transcriptional regulation. Several alternatively spliced transcript variants encoding different isoforms have been found for this gene.
Source: NCBI Gene 55628 — RefSeq curated summary.
At a glance
- Gene–disease (curated): short stature, impaired intellectual development, microcephaly, hypotonia, and ocular anomalies (Strong, GenCC) — +3 more curated relationships
- GWAS associations: 2
- Clinical variants (ClinVar): 468 total — 1 pathogenic
- Phenotypes (HPO): 27
- Cancer dependency (DepMap): dependent in 83.7% of screened cell lines
- Dosage sensitivity (ClinGen): haploinsufficiency no evidence, triplosensitivity no evidence
- MANE Select transcript:
NM_017757
Identifiers
Gene identifiers
| Field | Value |
|---|---|
| HGNC ID | HGNC:19904 |
| Approved symbol | ZNF407 |
| Name | zinc finger protein 407 |
| Location | 18q23 |
| Locus type | gene with protein product |
| Status | Approved |
| Aliases | FLJ20307, FLJ13839, KIAA1703 |
| Ensembl gene | ENSG00000215421 |
| Ensembl biotype | protein_coding |
| OMIM | 615894 |
| Entrez | 55628 |
Gene structure
Transcript identifiers
Ensembl transcripts: 10 — 8 protein_coding, 1 retained_intron, 1 protein_coding_CDS_not_defined
ENST00000299687, ENST00000309902, ENST00000577538, ENST00000579200, ENST00000581829, ENST00000582214, ENST00000582337, ENST00000584235, ENST00000949101, ENST00000949102
RefSeq mRNA: 4 — MANE Select: NM_017757
NM_001146189, NM_001146190, NM_001384475, NM_017757
CCDS: CCDS45885, CCDS54191, CCDS58634
Canonical transcript exons
ENST00000299687 — 9 exons
| Exon | Start | End |
|---|---|---|
| ENSE00001104019 | 74641008 | 74641122 |
| ENSE00001104029 | 74781428 | 74781502 |
| ENSE00001179660 | 74920514 | 74920692 |
| ENSE00001179669 | 74877197 | 74877363 |
| ENSE00001179690 | 75063150 | 75065671 |
| ENSE00002710413 | 74630967 | 74635706 |
| ENSE00002723372 | 74597870 | 74597937 |
| ENSE00003715156 | 74889918 | 74890038 |
| ENSE00003716268 | 74881036 | 74881119 |
Expression profiles
Bgee: expression breadth ubiquitous, 265 present calls, max score 99.16.
FANTOM5 (CAGE): breadth ubiquitous, TPM avg 7.3593 / max 229.6578, expressed in 1622 samples.
FANTOM5 promoters (1 alternative TSS)
| Promoter ID | TPM avg | Samples expressed |
|---|---|---|
| 170768 | 7.3593 | 1622 |
Top tissues by expression
291 total, by Bgee expression score (0-100, higher = more expressed):
| Tissue | Anatomy ID | Expression score | Quality |
|---|---|---|---|
| secondary oocyte | CL:0000655 | 99.16 | gold quality |
| oocyte | CL:0000023 | 97.35 | gold quality |
| tibia | UBERON:0000979 | 91.25 | gold quality |
| visceral pleura | UBERON:0002401 | 87.88 | gold quality |
| parietal pleura | UBERON:0002400 | 87.62 | gold quality |
| middle temporal gyrus | UBERON:0002771 | 87.57 | gold quality |
| male germ line stem cell (sensu Vertebrata) in testis | CL:0000089 ∩ UBERON:0000473 | 86.95 | gold quality |
| pleura | UBERON:0000977 | 86.46 | gold quality |
| esophagus squamous epithelium | UBERON:0006920 | 86.19 | gold quality |
| Brodmann (1909) area 23 | UBERON:0013554 | 85.31 | gold quality |
| germinal epithelium of ovary | UBERON:0001304 | 84.83 | gold quality |
| calcaneal tendon | UBERON:0003701 | 84.34 | gold quality |
| primordial germ cell in gonad | CL:0000670 ∩ UBERON:0000991 | 83.55 | gold quality |
| pigmented layer of retina | UBERON:0001782 | 82.87 | gold quality |
| retina | UBERON:0000966 | 82.85 | gold quality |
| sural nerve | UBERON:0015488 | 82.67 | gold quality |
| endothelial cell | CL:0000115 | 81.89 | gold quality |
| tendon | UBERON:0000043 | 80.34 | gold quality |
| epithelium of esophagus | UBERON:0001976 | 80.32 | gold quality |
| skin of hip | UBERON:0001554 | 79.81 | gold quality |
| eye | UBERON:0000970 | 79.59 | gold quality |
| skeletal muscle tissue of rectus abdominis | UBERON:0004511 | 79.53 | gold quality |
| amniotic fluid | UBERON:0000173 | 79.38 | gold quality |
| adrenal tissue | UBERON:0018303 | 79.12 | gold quality |
| palpebral conjunctiva | UBERON:0001812 | 78.51 | gold quality |
| upper leg skin | UBERON:0004262 | 78.23 | gold quality |
| skeletal muscle tissue of biceps brachii | UBERON:0004502 | 78.08 | gold quality |
| tonsil | UBERON:0002372 | 78.04 | gold quality |
| epithelium of nasopharynx | UBERON:0001951 | 78.01 | gold quality |
| ventricular zone | UBERON:0003053 | 77.94 | gold quality |
Single-cell (SCXA)
Detected in 1 experiment(s), a significant marker in 0.
| Experiment | Marker? | Max mean expression |
|---|---|---|
| E-ANND-3 | no | 5.41 |
Regulation
Is transcription factor: yes
JASPAR motifs
| Motif | Name | Family |
|---|---|---|
| MA2553.1 | ZNF407 | Factors with multiple dispersed zinc fingers |
JASPAR matrix evidence (PMIDs): PMID:39605320
miRNA regulators (miRDB)
62 targeting ZNF407, 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-9-5P | 100.00 | 72.28 | 2361 |
| HSA-MIR-4775 | 99.98 | 75.00 | 6394 |
| HSA-MIR-548P | 99.98 | 72.25 | 3784 |
| HSA-MIR-607 | 99.97 | 73.62 | 5593 |
| HSA-MIR-1468-3P | 99.96 | 72.74 | 3797 |
| HSA-MIR-590-3P | 99.96 | 74.34 | 6478 |
| HSA-MIR-570-3P | 99.96 | 72.41 | 4910 |
| HSA-MIR-23A-3P | 99.95 | 74.24 | 3163 |
| HSA-MIR-23B-3P | 99.95 | 74.24 | 3163 |
| HSA-MIR-23C | 99.95 | 73.92 | 3192 |
| HSA-MIR-22-3P | 99.93 | 68.13 | 917 |
| HSA-MIR-205-3P | 99.92 | 69.92 | 3165 |
| HSA-MIR-3119 | 99.92 | 71.34 | 2390 |
| HSA-MIR-10527-5P | 99.91 | 72.28 | 3754 |
| HSA-MIR-627-3P | 99.90 | 71.42 | 3316 |
| HSA-MIR-548E-5P | 99.89 | 72.73 | 4486 |
| HSA-MIR-4496 | 99.88 | 68.89 | 2236 |
| HSA-MIR-6124 | 99.87 | 69.78 | 3551 |
| HSA-MIR-6739-5P | 99.80 | 67.87 | 2806 |
| HSA-MIR-4668-5P | 99.79 | 70.58 | 3782 |
| HSA-MIR-6733-5P | 99.74 | 67.94 | 2759 |
| HSA-MIR-33A-3P | 99.70 | 70.27 | 3362 |
| HSA-MIR-1208 | 99.70 | 68.28 | 1533 |
| HSA-MIR-7157-5P | 99.66 | 69.33 | 1829 |
| HSA-MIR-4261 | 99.59 | 70.30 | 3415 |
Functional genomics
ClinGen dosage: haploinsufficiency 0 (no evidence), triplosensitivity 0 (no evidence). ClinGen Gene Dosage Map
DepMap (CRISPR cell-line fitness): dependent in 83.7% of screened cell lines.
Literature-anchored findings (GeneRIF, showing 3)
- Data indicate that mutations in the ZNF407 gene contribute to the pathogenesis of a group of intellectual disability (ID) patients with autism. (PMID:23195952)
- WDR5 shows a direct binding to the ZNF407 promoter. (PMID:28300833)
- Biallelic ZNF407 mutations in a neurodevelopmental disorder with ID, short stature and variable microcephaly, hypotonia, ocular anomalies and facial dysmorphism. (PMID:32737394)
Cross-species orthologs
3 orthologs
| Organism | Symbol | Gene ID |
|---|---|---|
| danio_rerio | znf407 | ENSDARG00000087536 |
| mus_musculus | Zfp407 | ENSMUSG00000048410 |
| rattus_norvegicus | Zfp407 | ENSRNOG00000043357 |
Paralogs (51): WIZ (ENSG00000011451), ZNF416 (ENSG00000083817), MYNN (ENSG00000085274), PRDM4 (ENSG00000110851), PRDM2 (ENSG00000116731), ZBTB17 (ENSG00000116809), ZNF644 (ENSG00000122482), GZF1 (ENSG00000125812), ZNF426 (ENSG00000130818), ZNF287 (ENSG00000141040), ZNF697 (ENSG00000143067), ZNF687 (ENSG00000143373), ZNF214 (ENSG00000149050), ZNF547 (ENSG00000152433), ZNF776 (ENSG00000152443), ZNF230 (ENSG00000159882), ZNF222 (ENSG00000159885), ZNF233 (ENSG00000159915), ZNF333 (ENSG00000160961), ZNF319 (ENSG00000166188), ZNF592 (ENSG00000166716), ZNF646 (ENSG00000167395), ZNF507 (ENSG00000168813), ZNF768 (ENSG00000169957), ZNF417 (ENSG00000173480), ZNF408 (ENSG00000175213), ZBTB41 (ENSG00000177888), ZNF223 (ENSG00000178386), ZNF852 (ENSG00000178917), ZNF784 (ENSG00000179922), ZNF572 (ENSG00000180938), ZNF707 (ENSG00000181135), ZNF746 (ENSG00000181220), ZNF467 (ENSG00000181444), ZNF530 (ENSG00000183647), ZNF17 (ENSG00000186272), ZNF527 (ENSG00000189164), ZKSCAN7 (ENSG00000196345), ZNF34 (ENSG00000196378), ZNF774 (ENSG00000196391)
Protein
Protein identifiers
Zinc finger protein 407 — Q9C0G0 (reviewed: Q9C0G0)
All UniProt accessions (3): A0A087WV78, A0A087WYH1, Q9C0G0
UniProt curated annotations — full annotation on UniProt →
Function. May be involved in transcriptional regulation.
Subcellular location. Nucleus.
Disease relevance. Short stature, impaired intellectual development, microcephaly, hypotonia, and ocular anomalies (SIMHA) [MIM:619557] An autosomal recessive syndrome characterized by short stature, impaired intellectual development, microcephaly, hypotonia, and ocular anomalies. The disease is caused by variants affecting the gene represented in this entry.
Isoforms (3)
| UniProt ID | Names | Canonical? |
|---|---|---|
| Q9C0G0-1 | 1 | yes |
| Q9C0G0-2 | 2 | |
| Q9C0G0-3 | 3 |
RefSeq proteins (4): NP_001139661, NP_001139662, NP_001371404, NP_060227* (*=MANE)
Domains & families (InterPro)
| ID | Name | Type |
|---|---|---|
| IPR003604 | Matrin/U1-like-C_Znf_C2H2 | Domain |
| IPR013087 | Znf_C2H2_type | Domain |
| IPR036236 | Znf_C2H2_sf | Homologous_superfamily |
| IPR050688 | Zinc_finger/UBP_domain | Family |
Pfam: PF00096
UniProt features (54 total): zinc finger region 22, sequence variant 10, sequence conflict 7, region of interest 6, splice variant 4, compositionally biased region 3, chain 1, modified residue 1
Structure
Experimental structures (PDB)
0 structures.
Predicted structure (AlphaFold)
| Model | pLDDT | Fraction very-high |
|---|---|---|
| AF-Q9C0G0-F1 | 46.31 | 0.00 |
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 (1): 1262
Function
Pathways and Gene Ontology
Reactome pathways
0 pathways
MSigDB gene sets: 156 (showing top):
EFC_Q6, WANG_LMO4_TARGETS_DN, AML_Q6, WTGAAAT_UNKNOWN, GARY_CD5_TARGETS_DN, NKX22_01, chr18q22, GATA1_02, FOXJ2_02, TGGAAA_NFAT_Q4_01, WGTTNNNNNAAA_UNKNOWN, HAMAI_APOPTOSIS_VIA_TRAIL_UP, GOMF_SEQUENCE_SPECIFIC_DNA_BINDING, TEF_Q6, STAMBOLSKY_TARGETS_OF_MUTATED_TP53_UP
GO Biological Process (1): positive regulation of transcription by RNA polymerase II (GO:0045944)
GO Molecular Function (4): DNA binding (GO:0003677), zinc ion binding (GO:0008270), nucleic acid binding (GO:0003676), metal ion binding (GO:0046872)
GO Cellular Component (1): nucleus (GO:0005634)
GO top-level categories
Rollup of top GO terms by namespace:
| Category | Terms |
|---|---|
| regulation of transcription by RNA polymerase II | 1 |
| transcription by RNA polymerase II | 1 |
| positive regulation of DNA-templated transcription | 1 |
| nucleic acid binding | 1 |
| transition metal ion binding | 1 |
| binding | 1 |
| cation binding | 1 |
| intracellular membrane-bounded organelle | 1 |
Protein interactions and networks
STRING
784 interactions, top by confidence (×1000):
| Protein A | Protein B | Partner UniProt | Score |
|---|---|---|---|
| ZNF407 | PTGR3 | Q8N4Q0 | 577 |
| ZNF407 | SUSD4 | Q5VX71 | 551 |
| ZNF407 | ADNP2 | Q6IQ32 | 528 |
| ZNF407 | SLC66A2 | Q8N2U9 | 505 |
| ZNF407 | FHAD1 | B1AJZ9 | 499 |
| ZNF407 | SMIM21 | Q3B7S5 | 480 |
| ZNF407 | RIBC1 | Q8N443 | 475 |
| ZNF407 | ZNF385B | Q569K4 | 462 |
| ZNF407 | SEL1L3 | Q68CR1 | 460 |
| ZNF407 | BCAS3 | Q9H6U6 | 423 |
| ZNF407 | TSHZ3 | Q63HK5 | 418 |
| ZNF407 | GNA12 | Q03113 | 413 |
| ZNF407 | ZNF559 | Q9BR84 | 409 |
| ZNF407 | TXNL4A | P83876 | 407 |
| ZNF407 | TSHZ1 | Q6ZSZ6 | 400 |
IntAct
11 interactions, top by confidence:
| A | B | Type | Score |
|---|---|---|---|
| NOTCH2 | ZNF316 | psi-mi:“MI:0914”(association) | 0.530 |
| ZNF407 | ZBTB9 | psi-mi:“MI:0915”(physical association) | 0.370 |
| ZNF407 | ZSCAN1 | psi-mi:“MI:0915”(physical association) | 0.370 |
| STAT6 | ZNF407 | psi-mi:“MI:0915”(physical association) | 0.370 |
| CAND1 | GTPBP10 | psi-mi:“MI:0914”(association) | 0.350 |
| CUL4A | HAX1 | psi-mi:“MI:0914”(association) | 0.350 |
| FBLN5 | ZNF320 | psi-mi:“MI:0914”(association) | 0.350 |
| NOTCH2 | ZNF320 | psi-mi:“MI:0914”(association) | 0.350 |
| AFG2B | MMP24OS | psi-mi:“MI:0914”(association) | 0.350 |
| ZNF407 | C1QTNF9 | psi-mi:“MI:0915”(physical association) | 0.000 |
BioGRID (21): ZNF407 (Affinity Capture-MS), ZNF407 (Affinity Capture-RNA), ZNF407 (Two-hybrid), ZNF407 (Affinity Capture-MS), ZNF407 (Affinity Capture-MS), ZNF407 (Proximity Label-MS), STMN1 (Cross-Linking-MS (XL-MS)), ZNF407 (Cross-Linking-MS (XL-MS)), ZNF407 (Affinity Capture-MS), ZNF407 (Affinity Capture-RNA), ZNF407 (Proximity Label-MS), ZNF407 (Proximity Label-MS), ZNF407 (Proximity Label-MS), ZNF407 (Proximity Label-MS), ZNF407 (Proximity Label-MS)
ESM2 similar proteins: A0A5K7RLP0, A1YEX3, A7YWH3, B1WBU4, O15151, O35618, O43298, O88850, P24278, P97303, Q01954, Q0V8G8, Q15916, Q17RG1, Q562E2, Q5RC05, Q5RDQ6, Q5SXH7, Q5TC79, Q5VYS8, Q5W0Q7, Q5XIN1, Q6ZPY5, Q6ZSB9, Q6ZU67, Q7ZUW7, Q7ZYI3, Q8BLK9, Q8BSV3, Q8IW35, Q8K088, Q8N680, Q8N7W2, Q8TCN5, Q8VHI4, Q8WW38, Q90W33, Q96BR9, Q96S38, Q99ME3
Diamond homologs: O75362, Q9C0G0
SIGNOR signaling
0 interactions.
Disease & clinical
Clinical variants and AI predictions
ClinVar
468 variants total. Per-class counts are floors (≥ shown; pagination cap):
| Classification | Count (floor) |
|---|---|
| Pathogenic | 1 |
| Likely pathogenic | 0 |
| Uncertain significance | 335 |
| Likely benign | 74 |
| Benign | 21 |
Top pathogenic / likely-pathogenic (1)
| Variant ID | HGVS | Classification |
|---|---|---|
| 1298357 | NM_017757.3(ZNF407):c.5054C>G (p.Ser1685Trp) | Pathogenic |
SpliceAI
4659 predictions. Top by Δscore:
| Variant | Effect | Δscore |
|---|---|---|
| 18:74781422:TTTTA:T | acceptor_loss | 1.0000 |
| 18:74781423:TTTA:T | acceptor_loss | 1.0000 |
| 18:74781424:TTA:T | acceptor_loss | 1.0000 |
| 18:74781425:TAG:T | acceptor_loss | 1.0000 |
| 18:74781426:A:AG | acceptor_gain | 1.0000 |
| 18:74781426:AG:A | acceptor_gain | 1.0000 |
| 18:74781426:AGG:A | acceptor_gain | 1.0000 |
| 18:74781426:AGGGT:A | acceptor_loss | 1.0000 |
| 18:74781427:G:A | acceptor_gain | 1.0000 |
| 18:74781427:G:GA | acceptor_gain | 1.0000 |
| 18:74781427:GGG:G | acceptor_gain | 1.0000 |
| 18:74781427:GGGT:G | acceptor_gain | 1.0000 |
| 18:74781427:GGGTT:G | acceptor_gain | 1.0000 |
| 18:74781498:GAAAG:G | donor_gain | 1.0000 |
| 18:74781503:G:GA | donor_loss | 1.0000 |
| 18:74781504:T:G | donor_loss | 1.0000 |
| 18:74898192:GCA:G | donor_gain | 1.0000 |
| 18:74920505:ACTT:A | acceptor_gain | 1.0000 |
| 18:74920506:C:G | acceptor_gain | 1.0000 |
| 18:74920508:T:A | acceptor_gain | 1.0000 |
| 18:74920508:TGGTA:T | acceptor_loss | 1.0000 |
| 18:74920509:GGTAG:G | acceptor_loss | 1.0000 |
| 18:74920510:GTA:G | acceptor_loss | 1.0000 |
| 18:74920511:TAG:T | acceptor_loss | 1.0000 |
| 18:74920512:A:AG | acceptor_gain | 1.0000 |
| 18:74920512:AG:A | acceptor_gain | 1.0000 |
| 18:74920513:G:GA | acceptor_gain | 1.0000 |
| 18:74920513:GG:G | acceptor_gain | 1.0000 |
| 18:74920513:GGT:G | acceptor_gain | 1.0000 |
| 18:74920513:GGTC:G | acceptor_gain | 1.0000 |
AlphaMissense
14937 scored. Top likely-pathogenic:
| Variant | Protein change | am_pathogenicity |
|---|---|---|
| 18:74633138:T:C | C707R | 1.000 |
| 18:74633147:T:C | C710R | 1.000 |
| 18:74633225:T:A | C736S | 1.000 |
| 18:74633225:T:C | C736R | 1.000 |
| 18:74633226:G:A | C736Y | 1.000 |
| 18:74633226:G:C | C736S | 1.000 |
| 18:74633227:T:G | C736W | 1.000 |
| 18:74633234:T:C | C739R | 1.000 |
| 18:74633235:G:A | C739Y | 1.000 |
| 18:74633236:T:G | C739W | 1.000 |
| 18:74633573:T:C | C852R | 1.000 |
| 18:74633575:T:G | C852W | 1.000 |
| 18:74633582:T:C | C855R | 1.000 |
| 18:74633583:G:A | C855Y | 1.000 |
| 18:74633584:T:G | C855W | 1.000 |
| 18:74633660:T:C | C881R | 1.000 |
| 18:74633662:C:G | C881W | 1.000 |
| 18:74633669:T:C | C884R | 1.000 |
| 18:74634161:T:C | C1048R | 1.000 |
| 18:74634163:C:G | C1048W | 1.000 |
| 18:74635265:T:A | C1416S | 1.000 |
| 18:74635265:T:C | C1416R | 1.000 |
| 18:74635266:G:A | C1416Y | 1.000 |
| 18:74635266:G:C | C1416S | 1.000 |
| 18:74635267:T:G | C1416W | 1.000 |
| 18:74635274:T:C | C1419R | 1.000 |
| 18:74635275:G:A | C1419Y | 1.000 |
| 18:74635276:T:G | C1419W | 1.000 |
| 18:74635305:T:C | L1429P | 1.000 |
| 18:74635355:T:C | C1446R | 1.000 |
dbSNP variants (sampled 300 via entrez): RS1000000318 (18:74825482 A>G), RS1000004433 (18:74682922 G>A), RS1000006963 (18:74987408 C>T), RS1000010615 (18:74763359 A>G), RS1000022357 (18:74654595 C>A), RS1000050364 (18:75038686 C>T), RS1000053242 (18:74867781 C>G), RS1000064235 (18:75035575 T>C), RS1000076970 (18:74756704 G>A), RS1000097827 (18:74655979 A>C), RS1000100055 (18:74735825 T>G), RS1000106903 (18:74629202 A>G), RS1000116820 (18:74654901 T>G), RS1000124746 (18:74985213 T>G), RS1000142496 (18:74618159 T>C)
Disease associations
OMIM: gene MIM:615894 | disease phenotypes: MIM:619557, MIM:603438
GenCC curated gene-disease
| Disease | Classification | Inheritance |
|---|---|---|
| short stature, impaired intellectual development, microcephaly, hypotonia, and ocular anomalies | Strong | Autosomal recessive |
| intellectual disability | Limited | Autosomal dominant |
| complex neurodevelopmental disorder | Limited | Autosomal recessive |
| neurodevelopmental disorder | Limited | Autosomal dominant |
Mondo (5): short stature, impaired intellectual development, microcephaly, hypotonia, and ocular anomalies (MONDO:0859198), radioulnar synostosis-microcephaly-scoliosis syndrome (MONDO:0011320), intellectual disability (MONDO:0001071), complex neurodevelopmental disorder (MONDO:0100038), neurodevelopmental disorder (MONDO:0700092)
Orphanet (1): Radioulnar synostosis-microcephaly-scoliosis syndrome (Orphanet:3268)
HPO phenotypes
27 total (27 of 27 shown, HPO-id order):
| HPO | Term |
|---|---|
| HP:0000007 | Autosomal recessive inheritance |
| HP:0000219 | Thin upper lip vermilion |
| HP:0000286 | Epicanthus |
| HP:0000365 | Hearing impairment |
| HP:0000387 | Absent earlobe |
| HP:0000411 | Protruding ear |
| HP:0000486 | Strabismus |
| HP:0000664 | Synophrys |
| HP:0000750 | Delayed speech and language development |
| HP:0001212 | Prominent fingertip pads |
| HP:0001252 | Hypotonia |
| HP:0001263 | Global developmental delay |
| HP:0001488 | Bilateral ptosis |
| HP:0001510 | Growth delay |
| HP:0001845 | Overlapping toe |
| HP:0002650 | Scoliosis |
| HP:0002714 | Downturned corners of mouth |
| HP:0002808 | Kyphosis |
| HP:0003593 | Infantile onset |
| HP:0004322 | Short stature |
| HP:0004689 | Short fourth metatarsal |
| HP:0005617 | Bilateral camptodactyly |
| HP:0010864 | Severe intellectual disability |
| HP:0011800 | Midface retrusion |
| HP:0025335 | Delayed ability to stand |
| HP:0030043 | Hip subluxation |
| HP:0031936 | Delayed ability to walk |
GWAS associations
2 associations (top):
| Study | Trait | p-value |
|---|---|---|
| GCST001553_8 | Estradiol levels | 4.000000e-06 |
| GCST007327_108 | Smoking status (ever vs never smokers) | 2.000000e-09 |
EFO canonical traits (2, from GWAS)
| EFO ID | Trait name |
|---|---|
| EFO:0004697 | estradiol measurement |
| EFO:0004318 | smoking behavior |
MeSH disease descriptors (2)
| Descriptor | Name | Tree numbers |
|---|---|---|
| D008607 | Intellectual Disability | C10.597.606.360; C23.888.592.604.646; F01.700.687; F03.625.539 |
| 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
25 total (human), top 25 by PubMed support.
| Chemical | Actions (top 5) | PubMed papers |
|---|---|---|
| Benzo(a)pyrene | affects methylation, decreases expression, increases expression | 5 |
| Valproic Acid | affects expression, decreases expression | 2 |
| 7,8-Dihydro-7,8-dihydroxybenzo(a)pyrene 9,10-oxide | decreases expression, affects expression | 2 |
| aristolochic acid I | decreases expression | 1 |
| FR900359 | increases phosphorylation | 1 |
| triphenyl phosphate | affects expression | 1 |
| bisphenol A | decreases methylation | 1 |
| arsenite | affects binding, decreases reaction | 1 |
| tris(1,3-dichloro-2-propyl)phosphate | decreases expression | 1 |
| benzo(e)pyrene | increases methylation | 1 |
| aflatoxin B2 | increases methylation | 1 |
| coumarin | decreases phosphorylation | 1 |
| beta-methylcholine | affects expression | 1 |
| perfluorooctane sulfonic acid | decreases expression | 1 |
| CGP 52608 | affects binding, increases reaction | 1 |
| MT19c compound | increases expression | 1 |
| Air Pollutants | affects expression, increases abundance | 1 |
| Caffeine | decreases phosphorylation | 1 |
| Cisplatin | decreases expression | 1 |
| Methapyrilene | increases methylation | 1 |
| Methotrexate | increases expression | 1 |
| Ozone | affects expression, increases abundance | 1 |
| Aflatoxin B1 | increases methylation | 1 |
| Cadmium Chloride | increases expression | 1 |
| Copper Sulfate | increases expression | 1 |
Clinical trials (associated diseases)
298 trials via MONDO — disease-level, not drug-specific.
| Trial | Phase | Status | Title |
|---|---|---|---|
| NCT05657860 | PHASE4 | COMPLETED | Guanfacine Extended Release for the Reduction of Aggression and Self-injurious Behavior Associated With Prader-Willi Syndrome |
| NCT05744479 | PHASE4 | RECRUITING | Metformin for Antipsychotic-induced Weight Gain in Adults With Intellectual Disability |
| NCT06107829 | PHASE4 | WITHDRAWN | Valbenazine Treatment of Tardive Dyskinesia in Adults With Intellectual/Developmental Disabilities |
| NCT06997198 | PHASE4 | NOT_YET_RECRUITING | Deutetrabenazine Treatment for Tardive Dyskinesia in Intellectual/Developmental Disabilities |
| 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, |
| NCT02270736 | PHASE3 | COMPLETED | Clinical Study to Investigate the Efficacy and Safety of NT 201 Compared to Placebo in the Treatment of Chronic Troublesome Drooling Associated With Neurological Disorders and/or Intellectual Disability |
| 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 |
| NCT02304302 | PHASE2 | COMPLETED | Down Syndrome Memantine Follow-up Study |
| NCT03862950 | PHASE2 | COMPLETED | A Trial of Metformin in Individuals With Fragile X Syndrome (Met) |
| NCT04529226 | PHASE2 | UNKNOWN | Study to Compare Clozapine vs Treatment as Usual in People With Intellectual Disability & Treatment-resistant Psychosis |
| NCT04821856 | PHASE2 | COMPLETED | Evaluation of the Effectiveness of Cannabidiol in Treating Severe Behavioural Problems in Children and Adolescents With Intellectual Disability |
| 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 |
| NCT05273320 | PHASE1 | COMPLETED | Clinical Trial of Nabilone for Aggression in Adults With Intellectual and Developmental Disabilities |
| NCT05301361 | PHASE1 | ENROLLING_BY_INVITATION | Sensitivity of the NIH Toolbox to Stimulant Treatment in Intellectual Disabilities |
| NCT06016764 | PHASE1 | COMPLETED | Use of MRI and cTBS for Catatonia in Autism |
| NCT06586827 | PHASE1 | COMPLETED | Impact of Competency-Based Training and Technical Assistance Employment Outcomes of Individuals With ID/DD |
| NCT07531940 | PHASE1 | NOT_YET_RECRUITING | Escalating Doses of Memantine in Down Syndrome (MEDS-123) |
| 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 |
| NCT03479476 | PHASE2/PHASE3 | COMPLETED | A Trial of Metformin in Individuals With Fragile X Syndrome |
| NCT02616796 | PHASE1/PHASE2 | COMPLETED | Effects of Social Gaze Training on Brain and Behavior in Fragile X Syndrome |
| NCT06860672 | EARLY_PHASE1 | RECRUITING | Clinical Trial of the Dual Vector Base Editor for the Treatment of the CHD3-R1025W Mutation |
| NCT00597948 | Not specified | COMPLETED | Healthy Lifestyles for People With Intellectual Disabilities |
| NCT01087320 | Not specified | RECRUITING | Genome Medical Sequencing for Gene Discovery |
| NCT01652963 | Not specified | UNKNOWN | Picture-based Computerised Assessment and Training of Cognitive Behaviour Therapy Skills |
| NCT01695395 | Not specified | COMPLETED | Mental Health Care Provision for Adults With Intellectual Disability and a Mental Disorder |
| NCT01867554 | Not specified | COMPLETED | Research and Characterization of New Genes Involved in Intellectual Disability |
| NCT01915381 | Not specified | COMPLETED | Improving Adherence Healthy Lifestyle With a Smartphone Application Based on Adults With Intellectual Disabilities |
| NCT01988623 | Not specified | COMPLETED | Pivotal Response Treatment for Individuals With Intellectual Disabilities |
| NCT02099773 | Not specified | COMPLETED | Support Staff-client Interactions With Augmentative and Alternative Communication |
| NCT02136849 | Not specified | COMPLETED | Inter-regional Project of the Great Western Exploration Approach for Exome Molecular Causes Severe Intellectual Disability Isolated or Syndromic |
| NCT02225041 | Not specified | COMPLETED | Sedation Strategy and Cognitive Outcome After Critical Illness in Early Childhood |
| NCT02414438 | Not specified | COMPLETED | Establishing the Clinical Utility of First StepDx PLUS and NextStepDx PLUS Study |
Related Atlas pages
- Associated diseases: intellectual disability, complex neurodevelopmental disorder, neurodevelopmental disorder, short stature, impaired intellectual development, microcephaly, hypotonia, and ocular anomalies
- Disease cohort memberships (association, not causation — diseases whose associated-gene cohort lists this gene; a subset are also under Associated diseases): complex neurodevelopmental disorder, radioulnar synostosis-microcephaly-scoliosis syndrome, short stature, impaired intellectual development, microcephaly, hypotonia, and ocular anomalies