RAX
gene geneOn this page
Also known as RXRAX1
Summary
RAX (retina and anterior neural fold homeobox, HGNC:18662) is a protein-coding gene on chromosome 18q21.32, encoding Retinal homeobox protein Rx (Q9Y2V3). Plays a critical role in eye formation by regulating the initial specification of retinal cells and/or their subsequent proliferation.
This gene encodes a homeobox-containing transcription factor that functions in eye development. The gene is expressed early in the eye primordia, and is required for retinal cell fate determination and also regulates stem cell proliferation. Mutations in this gene have been reported in patients with defects in ocular development, including microphthalmia, anophthalmia, and coloboma.
Source: NCBI Gene 30062 — RefSeq curated summary.
At a glance
- Gene–disease (curated): isolated microphthalmia 3 (Definitive, GenCC) — +2 more curated relationships
- Clinical variants (ClinVar): 184 total — 6 pathogenic, 4 likely-pathogenic
- MANE Select transcript:
NM_013435
Identifiers
Gene identifiers
| Field | Value |
|---|---|
| HGNC ID | HGNC:18662 |
| Approved symbol | RAX |
| Name | retina and anterior neural fold homeobox |
| Location | 18q21.32 |
| Locus type | gene with protein product |
| Status | Approved |
| Aliases | RX, RAX1 |
| Ensembl gene | ENSG00000134438 |
| Ensembl biotype | protein_coding |
| OMIM | 601881 |
| Entrez | 30062 |
Gene structure
Transcript identifiers
Ensembl transcripts: 4 — 3 protein_coding, 1 retained_intron
ENST00000256852, ENST00000334889, ENST00000555288, ENST00000591550
RefSeq mRNA: 1 — MANE Select: NM_013435
NM_013435
CCDS: CCDS11972
Canonical transcript exons
ENST00000334889 — 3 exons
| Exon | Start | End |
|---|---|---|
| ENSE00000914716 | 59272361 | 59272614 |
| ENSE00000914718 | 59272918 | 59273454 |
| ENSE00003603449 | 59267038 | 59269501 |
Expression profiles
Bgee: expression breadth broad, 29 present calls, max score 75.47.
FANTOM5 (CAGE): breadth tissue_specific, TPM avg 1.2826 / max 123.4061, expressed in 163 samples.
FANTOM5 promoters (3 alternative TSS)
| Promoter ID | TPM avg | Samples expressed |
|---|---|---|
| 172186 | 0.9346 | 132 |
| 172187 | 0.3314 | 93 |
| 172188 | 0.0166 | 6 |
Top tissues by expression
230 total, by Bgee expression score (0-100, higher = more expressed):
| Tissue | Anatomy ID | Expression score | Quality |
|---|---|---|---|
| parotid gland | UBERON:0001831 | 75.47 | gold quality |
| nasal cavity epithelium | UBERON:0005384 | 74.17 | gold quality |
| biceps brachii | UBERON:0001507 | 73.43 | gold quality |
| skeletal muscle tissue of biceps brachii | UBERON:0004502 | 73.37 | gold quality |
| heart right ventricle | UBERON:0002080 | 71.11 | gold quality |
| myocardium | UBERON:0002349 | 71.06 | gold quality |
| secondary oocyte | CL:0000655 | 67.24 | gold quality |
| seminal vesicle | UBERON:0000998 | 67.14 | gold quality |
| skeletal muscle tissue of rectus abdominis | UBERON:0004511 | 66.91 | gold quality |
| lateral nuclear group of thalamus | UBERON:0002736 | 66.77 | gold quality |
| lateral globus pallidus | UBERON:0002476 | 66.35 | gold quality |
| Brodmann (1909) area 46 | UBERON:0006483 | 65.17 | gold quality |
| deltoid | UBERON:0001476 | 65.09 | gold quality |
| entorhinal cortex | UBERON:0002728 | 65.09 | gold quality |
| postcentral gyrus | UBERON:0002581 | 64.46 | gold quality |
| substantia nigra pars reticulata | UBERON:0001966 | 64.39 | gold quality |
| vastus lateralis | UBERON:0001379 | 64.21 | gold quality |
| quadriceps femoris | UBERON:0001377 | 64.04 | gold quality |
| substantia nigra pars compacta | UBERON:0001965 | 63.58 | gold quality |
| parietal lobe | UBERON:0001872 | 63.00 | gold quality |
| neuron projection bundle connecting eye with brain | UBERON:0004904 | 62.49 | silver quality |
| trabecular bone tissue | UBERON:0002483 | 62.47 | gold quality |
| middle temporal gyrus | UBERON:0002771 | 62.15 | gold quality |
| Brodmann (1909) area 23 | UBERON:0013554 | 61.83 | gold quality |
| vena cava | UBERON:0004087 | 61.59 | gold quality |
| tendon of biceps brachii | UBERON:0008188 | 61.56 | gold quality |
| subthalamic nucleus | UBERON:0001906 | 61.19 | gold quality |
| dorsal plus ventral thalamus | UBERON:0001897 | 60.71 | gold quality |
| endothelial cell | CL:0000115 | 60.30 | gold quality |
| adenohypophysis | UBERON:0002196 | 59.48 | gold quality |
Single-cell (SCXA)
Detected in 2 experiment(s), a significant marker in 1.
| Experiment | Marker? | Max mean expression |
|---|---|---|
| E-GEOD-137537 | yes | 37.33 |
| E-ANND-3 | no | 0.00 |
Regulation
Is transcription factor: yes
JASPAR motifs
| Motif | Name | Family |
|---|---|---|
| MA0718.1 | RAX | Paired-related HD factors |
| MA0718.2 | RAX | Paired-related HD factors |
JASPAR matrix evidence (PMIDs): PMID:18585360
miRNA regulators (miRDB)
38 targeting RAX, 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-5193 | 100.00 | 67.26 | 1744 |
| HSA-MIR-6825-5P | 99.96 | 69.81 | 3431 |
| HSA-MIR-106A-5P | 99.90 | 73.94 | 2683 |
| HSA-MIR-17-5P | 99.89 | 73.83 | 2665 |
| HSA-MIR-106B-5P | 99.88 | 74.72 | 2795 |
| HSA-MIR-20A-5P | 99.88 | 74.76 | 2769 |
| HSA-MIR-20B-5P | 99.88 | 74.01 | 2621 |
| HSA-MIR-519D-3P | 99.88 | 73.97 | 2607 |
| HSA-MIR-526B-3P | 99.88 | 74.06 | 2587 |
| HSA-MIR-93-5P | 99.88 | 73.98 | 2606 |
| HSA-MIR-3934-3P | 99.76 | 65.51 | 1351 |
| HSA-MIR-3150A-3P | 99.76 | 64.44 | 1640 |
| HSA-MIR-6763-5P | 99.76 | 64.68 | 1767 |
| HSA-MIR-510-3P | 99.54 | 70.06 | 2965 |
| HSA-MIR-5571-5P | 99.49 | 66.99 | 1764 |
| HSA-MIR-3191-3P | 99.45 | 63.94 | 356 |
| HSA-MIR-372-5P | 99.41 | 69.11 | 2299 |
| HSA-MIR-4279 | 99.19 | 66.70 | 2437 |
| HSA-MIR-4292 | 99.16 | 65.57 | 1767 |
| HSA-MIR-6791-5P | 99.16 | 65.92 | 1844 |
| HSA-MIR-6887-5P | 98.56 | 68.49 | 1295 |
| HSA-MIR-6795-5P | 98.52 | 68.51 | 1277 |
| HSA-MIR-6810-5P | 98.29 | 66.21 | 975 |
| HSA-MIR-4768-3P | 98.16 | 66.02 | 2330 |
| HSA-MIR-7113-5P | 97.88 | 67.33 | 1735 |
| HSA-MIR-3664-3P | 97.85 | 67.62 | 1452 |
| HSA-MIR-3192-5P | 96.98 | 65.76 | 1926 |
| HSA-MIR-4793-5P | 96.88 | 65.90 | 872 |
| HSA-MIR-552-3P | 96.68 | 64.12 | 1026 |
| HSA-MIR-3139 | 96.68 | 66.77 | 652 |
Literature-anchored findings (GeneRIF, showing 7)
- Mutations associated with recessive anophthalmos and sclerocornea. (PMID:14662654)
- A missense mutation in RX was observed in a patient with a small, typical chorioretinal coloboma, and postulate that the mutation is responsible for the patient’s phenotype. (PMID:19158959)
- Mutations in the newly identified RAX regulatory sequence are not a frequent cause of micro/anophthalmia. (PMID:19397404)
- Photosensitive photoreceptor cells can be generated by combinations of transcription factors. The combination of CRX and RX generate immature photoreceptors: and additional NEUROD promotes maturation. (PMID:22558175)
- The three consanguineous Egyptian anophthalmia patients carry a novel homozygous c.543+3A>G mutation (IVS2+3A>G) in RAX. (PMID:22736936)
- combination of WES and homozygosity mapping identified a novel homozygous RAX mutation in a consanguineous family segregating with rarely reported asymmetrical coloboma. Clinical findings and genetic results support that RAX mutation is responsible for eye malformations. (PMID:28831107)
- Construction and characterization of EGFP reporter plasmid harboring putative human RAX promoter for in vitro monitoring of retinal progenitor cells identity. (PMID:34348662)
Cross-species orthologs
2 orthologs
| Organism | Symbol | Gene ID |
|---|---|---|
| mus_musculus | Rax | ENSMUSG00000024518 |
| rattus_norvegicus | Rax | ENSRNOG00000016944 |
Paralogs (50): ARX (ENSG00000004848), PAX6 (ENSG00000007372), PAX7 (ENSG00000009709), ALX4 (ENSG00000052850), GSC2 (ENSG00000063515), PITX1 (ENSG00000069011), PAX2 (ENSG00000075891), RHOXF1 (ENSG00000101883), CRX (ENSG00000105392), EVX1 (ENSG00000106038), PAX4 (ENSG00000106331), NOBOX (ENSG00000106410), PITX3 (ENSG00000107859), PHOX2B (ENSG00000109132), OTX1 (ENSG00000115507), PRRX1 (ENSG00000116132), VSX2 (ENSG00000119614), ESX1 (ENSG00000123576), PAX8 (ENSG00000125618), PAX1 (ENSG00000125813), RHOXF2 (ENSG00000131721), GSC (ENSG00000133937), PAX3 (ENSG00000135903), ALX3 (ENSG00000156150), HESX1 (ENSG00000163666), PITX2 (ENSG00000164093), UNCX (ENSG00000164853), PHOX2A (ENSG00000165462), OTX2 (ENSG00000165588), DRGX (ENSG00000165606), PRRX2 (ENSG00000167157), SHOX2 (ENSG00000168779), OTP (ENSG00000171540), RAX2 (ENSG00000173976), EVX2 (ENSG00000174279), PROP1 (ENSG00000175325), ISX (ENSG00000175329), ALX1 (ENSG00000180318), MIXL1 (ENSG00000185155), SHOX (ENSG00000185960)
Protein
Protein identifiers
Retinal homeobox protein Rx — Q9Y2V3 (reviewed: Q9Y2V3)
Alternative names: Retina and anterior neural fold homeobox protein
All UniProt accessions (2): Q9Y2V3, G3V2C8
UniProt curated annotations — full annotation on UniProt →
Function. Plays a critical role in eye formation by regulating the initial specification of retinal cells and/or their subsequent proliferation. Binds to the photoreceptor conserved element-I (PCE-1/Ret 1) in the photoreceptor cell-specific arrestin promoter.
Subcellular location. Nucleus.
Tissue specificity. Expressed in the developing eye and weakly expressed in the adult retina.
Disease relevance. Microphthalmia, syndromic 16 (MCOPS16) [MIM:611038] An autosomal recessive disorder of eye formation, ranging from small size of a single eye to complete bilateral absence of ocular tissues. Ocular abnormalities like opacities of the cornea and lens, scaring of the retina and choroid, and other abnormalities may also be present. Some patients exhibit developmental delay and intellectual disability or autism. The disease is caused by variants affecting the gene represented in this entry.
Similarity. Belongs to the paired homeobox family. Bicoid subfamily.
Isoforms (2)
| UniProt ID | Names | Canonical? |
|---|---|---|
| Q9Y2V3-1 | 1 | yes |
| Q9Y2V3-2 | 2 |
RefSeq proteins (1): NP_038463* (*=MANE)
Domains & families (InterPro)
| ID | Name | Type |
|---|---|---|
| IPR001356 | HD | Domain |
| IPR003654 | OAR_dom | Domain |
| IPR009057 | Homeodomain-like_sf | Homologous_superfamily |
| IPR017970 | Homeobox_CS | Conserved_site |
| IPR043562 | RAX/RAX2 | Family |
Pfam: PF00046, PF03826
UniProt features (21 total): compositionally biased region 6, sequence variant 5, short sequence motif 3, splice variant 2, region of interest 2, chain 1, DNA-binding region 1, sequence conflict 1
Structure
Experimental structures (PDB)
0 structures.
Predicted structure (AlphaFold)
| Model | pLDDT | Fraction very-high |
|---|---|---|
| AF-Q9Y2V3-F1 | 65.10 | 0.19 |
Function
Pathways and Gene Ontology
Reactome pathways
0 pathways
MSigDB gene sets: 87 (showing top):
GSE45365_CD8A_DC_VS_CD11B_DC_IFNAR_KO_MCMV_INFECTION_UP, BENPORATH_ES_WITH_H3K27ME3, LHX3_01, GOBP_FOREBRAIN_DEVELOPMENT, SHEPARD_BMYB_MORPHOLINO_DN, GOBP_HYPOTHALAMUS_DEVELOPMENT, GOBP_SENSORY_PERCEPTION_OF_LIGHT_STIMULUS, GOBP_APPENDAGE_DEVELOPMENT, GOBP_HEAD_DEVELOPMENT, LYF1_01, GOBP_DIENCEPHALON_DEVELOPMENT, GOBP_SENSORY_PERCEPTION, GOBP_SENSORY_ORGAN_DEVELOPMENT, GOBP_LIMBIC_SYSTEM_DEVELOPMENT, PITX2_Q2
GO Biological Process (9): regulation of transcription by RNA polymerase II (GO:0006357), pattern specification process (GO:0007389), visual perception (GO:0007601), hypothalamus development (GO:0021854), camera-type eye development (GO:0043010), positive regulation of transcription by RNA polymerase II (GO:0045944), limb development (GO:0060173), regulation of DNA-templated transcription (GO:0006355), brain development (GO:0007420)
GO Molecular Function (5): RNA polymerase II cis-regulatory region sequence-specific DNA binding (GO:0000978), DNA-binding transcription factor activity, RNA polymerase II-specific (GO:0000981), DNA-binding transcription activator activity, RNA polymerase II-specific (GO:0001228), sequence-specific double-stranded DNA binding (GO:1990837), DNA binding (GO:0003677)
GO Cellular Component (2): chromatin (GO:0000785), nucleus (GO:0005634)
GO top-level categories
Rollup of top GO terms by namespace:
| Category | Terms |
|---|---|
| RNA polymerase II transcription regulatory region sequence-specific DNA binding | 3 |
| transcription by RNA polymerase II | 2 |
| regulation of transcription by RNA polymerase II | 2 |
| regulation of DNA-templated transcription | 1 |
| multicellular organism development | 1 |
| multicellular organismal process | 1 |
| sensory perception of light stimulus | 1 |
| diencephalon development | 1 |
| limbic system development | 1 |
| anatomical structure development | 1 |
| eye development | 1 |
| positive regulation of DNA-templated transcription | 1 |
| appendage development | 1 |
| DNA-templated transcription | 1 |
| regulation of gene expression | 1 |
| regulation of RNA biosynthetic process | 1 |
| central nervous system development | 1 |
| animal organ development | 1 |
| head development | 1 |
| cis-regulatory region sequence-specific DNA binding | 1 |
| chromatin | 1 |
| DNA-binding transcription factor activity | 1 |
| DNA-binding transcription factor activity, RNA polymerase II-specific | 1 |
| DNA-binding transcription activator activity | 1 |
| positive regulation of transcription by RNA polymerase II | 1 |
| double-stranded DNA binding | 1 |
| sequence-specific DNA binding | 1 |
| nucleic acid binding | 1 |
| chromosome | 1 |
| cellular anatomical structure | 1 |
| intracellular membrane-bounded organelle | 1 |
Protein interactions and networks
STRING
420 interactions, top by confidence (×1000):
| Protein A | Protein B | Partner UniProt | Score |
|---|---|---|---|
| RAX | TTC4 | O95801 | 665 |
| RAX | SOX2 | P48431 | 631 |
| RAX | FIZ1 | Q96SL8 | 528 |
| RAX | SIX3 | O95343 | 504 |
| RAX | NRL | P54845 | 435 |
| RAX | SIX6 | O95475 | 422 |
| RAX | GPR50 | Q13585 | 397 |
| RAX | SH3BP1 | Q9Y3L3 | 396 |
| RAX | SLCO6A1 | Q86UG4 | 392 |
| RAX | OTX2 | P32243 | 353 |
| RAX | FOXE3 | Q13461 | 342 |
| RAX | RPE65 | Q16518 | 296 |
| RAX | SHH | Q15465 | 296 |
| RAX | LMAN1L | Q9HAT1 | 294 |
| RAX | RHO | P08100 | 289 |
| RAX | CPLX4 | Q7Z7G2 | 289 |
IntAct
1 interactions, top by confidence:
| A | B | Type | Score |
|---|---|---|---|
| RAX | SIRT6 | psi-mi:“MI:0915”(physical association) | 0.400 |
BioGRID (4): RAX (Phenotypic Enhancement), RAX (Reconstituted Complex), RAX (Affinity Capture-Western), SIRT6 (Affinity Capture-MS)
ESM2 similar proteins: A0A1W2PQ73, A1YF16, A1YG93, A2RU54, A5PKG8, O02786, O14813, O15353, O35602, O43638, O57601, P13297, P19419, P28360, P35548, P41969, P42580, P43687, P49640, P50223, P50548, P52946, P52950, P63156, P63157, P70459, P78413, Q03358, Q14549, Q2VL78, Q2VL79, Q2VL82, Q2VL83, Q2VL84, Q2VL85, Q2VL86, Q2VL87, Q2VL88, Q5NSW5, Q61575
Diamond homologs: A0A1W2PPK0, A0A1W2PPM1, A1A546, A1YEY5, A1YFI3, A1YG57, A1YGA2, A2T733, A2T777, A2T7P4, A6NFQ7, G5EC89, L8E946, O14813, O15499, O35690, O42250, O42356, O42357, O42477, O70137, O73917, O75360, O95076, O97670, P0DMV5, P26367, P26630, P29454, P41935, P47237, P47238, P53544, P53545, P53546, P54366, P55813, P55864, P56915, P56916
SIGNOR signaling
0 interactions.
Disease & clinical
Clinical variants and AI predictions
ClinVar
184 variants total. Per-class counts are floors (≥ shown; pagination cap):
| Classification | Count (floor) |
|---|---|
| Pathogenic | 6 |
| Likely pathogenic | 4 |
| Uncertain significance | 116 |
| Likely benign | 34 |
| Benign | 14 |
Top pathogenic / likely-pathogenic (10)
| Variant ID | HGVS | Classification |
|---|---|---|
| 1723189 | NM_013435.3(RAX):c.560G>A (p.Arg187Gln) | Pathogenic |
| 1723190 | NM_013435.3(RAX):c.266del (p.Pro89fs) | Pathogenic |
| 1879402 | NM_013435.3(RAX):c.499G>T (p.Glu167Ter) | Pathogenic |
| 7635 | NM_013435.3(RAX):c.439C>T (p.Gln147Ter) | Pathogenic |
| 7636 | NM_013435.3(RAX):c.575G>A (p.Arg192Gln) | Pathogenic |
| 7638 | NM_013435.3(RAX):c.909C>G (p.Tyr303Ter) | Pathogenic |
| 1723188 | NM_013435.3(RAX):c.543+3A>G | Likely pathogenic |
| 3583379 | NM_013435.3(RAX):c.50_53dup (p.Gly19fs) | Likely pathogenic |
| 504029 | NM_013435.3(RAX):c.262_263delinsA (p.Ala88fs) | Likely pathogenic |
| 932556 | NM_013435.3(RAX):c.106G>T (p.Glu36Ter) | Likely pathogenic |
SpliceAI
377 predictions. Top by Δscore:
| Variant | Effect | Δscore |
|---|---|---|
| 18:59272362:TGG:T | donor_gain | 1.0000 |
| 18:59272358:TA:T | donor_loss | 0.9900 |
| 18:59272359:A:C | donor_loss | 0.9900 |
| 18:59272360:CCTGG:C | donor_loss | 0.9900 |
| 18:59269499:CAC:C | acceptor_gain | 0.9800 |
| 18:59269500:ACCT:A | acceptor_loss | 0.9800 |
| 18:59269502:C:T | acceptor_loss | 0.9800 |
| 18:59269503:T:C | acceptor_loss | 0.9800 |
| 18:59270370:G:C | donor_gain | 0.9800 |
| 18:59272384:TG:T | donor_gain | 0.9800 |
| 18:59272913:CTCA:C | donor_loss | 0.9800 |
| 18:59272914:TCAC:T | donor_loss | 0.9800 |
| 18:59272915:CAC:C | donor_loss | 0.9800 |
| 18:59272916:A:AT | donor_loss | 0.9800 |
| 18:59272917:C:A | donor_loss | 0.9800 |
| 18:59269497:CACAC:C | acceptor_gain | 0.9700 |
| 18:59269452:T:TA | donor_gain | 0.9600 |
| 18:59269502:C:CC | acceptor_gain | 0.9600 |
| 18:59270359:CTAAG:C | donor_gain | 0.9600 |
| 18:59270621:TGCA:T | donor_gain | 0.9600 |
| 18:59270624:A:AT | donor_gain | 0.9600 |
| 18:59272385:G:T | donor_gain | 0.9600 |
| 18:59272391:G:A | donor_gain | 0.9600 |
| 18:59272912:ACTC:A | donor_loss | 0.9600 |
| 18:59272911:CACT:C | donor_loss | 0.9500 |
| 18:59270360:TAAG:T | donor_gain | 0.9400 |
| 18:59270361:AAGA:A | donor_gain | 0.9400 |
| 18:59272383:TTG:T | donor_gain | 0.9400 |
| 18:59270358:CCTAA:C | donor_gain | 0.9000 |
| 18:59272361:CTG:C | donor_gain | 0.9000 |
AlphaMissense
2188 scored. Top likely-pathogenic:
| Variant | Protein change | am_pathogenicity |
|---|---|---|
| 18:59269050:G:T | A332D | 1.000 |
| 18:59269062:A:G | L328P | 1.000 |
| 18:59269062:A:T | L328Q | 1.000 |
| 18:59269071:A:T | I325N | 1.000 |
| 18:59269467:C:G | R193P | 1.000 |
| 18:59269470:C:G | R192P | 1.000 |
| 18:59269472:C:A | W191C | 1.000 |
| 18:59269472:C:G | W191C | 1.000 |
| 18:59269474:A:G | W191R | 1.000 |
| 18:59269474:A:T | W191R | 1.000 |
| 18:59269475:C:A | K190N | 1.000 |
| 18:59269475:C:G | K190N | 1.000 |
| 18:59269476:T:A | K190M | 1.000 |
| 18:59269477:T:C | K190E | 1.000 |
| 18:59269477:T:G | K190Q | 1.000 |
| 18:59269479:G:A | A189V | 1.000 |
| 18:59269479:G:T | A189D | 1.000 |
| 18:59269480:C:G | A189P | 1.000 |
| 18:59269482:C:G | R188P | 1.000 |
| 18:59269482:C:T | R188Q | 1.000 |
| 18:59269483:G:A | R188W | 1.000 |
| 18:59269483:G:C | R188G | 1.000 |
| 18:59269485:C:A | R187L | 1.000 |
| 18:59269485:C:G | R187P | 1.000 |
| 18:59269486:G:C | R187G | 1.000 |
| 18:59269487:G:C | N186K | 1.000 |
| 18:59269487:G:T | N186K | 1.000 |
| 18:59269488:T:A | N186I | 1.000 |
| 18:59269488:T:C | N186S | 1.000 |
| 18:59269488:T:G | N186T | 1.000 |
dbSNP variants (sampled 300 via entrez): RS1000290359 (18:59271777 T>A), RS1000590358 (18:59271385 C>A), RS1001130280 (18:59266933 C>A,T), RS1001616686 (18:59267637 C>A,T), RS1001627554 (18:59272686 G>A,T), RS1001773725 (18:59267390 G>A,C), RS1002379426 (18:59270298 G>T), RS1002522362 (18:59267015 A>G,T), RS1002534016 (18:59271262 T>C), RS1002583129 (18:59273432 G>A), RS1002747109 (18:59273243 G>A,C,T), RS1003538642 (18:59269941 C>A,G,T), RS1003667904 (18:59269691 C>T), RS1003942307 (18:59268237 G>A), RS1004149963 (18:59268914 G>A,T)
Disease associations
OMIM: gene MIM:601881 | disease phenotypes: MIM:611038
GenCC curated gene-disease
| Disease | Classification | Inheritance |
|---|---|---|
| isolated microphthalmia 3 | Definitive | Autosomal recessive |
| isolated anophthalmia-microphthalmia syndrome | Supportive | Autosomal dominant |
| coloboma | Limited | Autosomal recessive |
Mondo (3): isolated microphthalmia 3 (MONDO:0012604), isolated anophthalmia-microphthalmia syndrome (MONDO:0016764), coloboma (MONDO:0001476)
Orphanet (1): Isolated microphthalmia-anophthalmia-coloboma (Orphanet:2542)
HPO phenotypes
0 total (0 of 0 shown, HPO-id order):
GWAS associations
0 associations (top):
MeSH disease descriptors (2)
| Descriptor | Name | Tree numbers |
|---|---|---|
| D003103 | Coloboma | C11.250.110; C11.270.147; C16.131.384.282 |
| C567025 | Microphthalmia, Isolated 3 (supp.) |
Drugs & pharmacology
Drug and pharmacology data
Is drug target: no
PharmGKB: 1 entry (VIP=true, CPIC=false)
CTD chemical–gene interactions
20 total (human), top 20 by PubMed support.
| Chemical | Actions (top 5) | PubMed papers |
|---|---|---|
| Valproic Acid | affects cotreatment, decreases expression, decreases methylation | 5 |
| trichostatin A | affects cotreatment, decreases expression | 3 |
| entinostat | decreases expression, affects cotreatment | 2 |
| belinostat | affects cotreatment, decreases expression | 2 |
| Panobinostat | affects cotreatment, decreases expression | 2 |
| Phenylmercuric Acetate | affects cotreatment, decreases expression | 2 |
| Tretinoin | decreases expression, increases expression | 2 |
| methylmercuric chloride | decreases expression | 1 |
| propionaldehyde | decreases expression | 1 |
| bisphenol A | decreases methylation | 1 |
| arsenite | increases methylation | 1 |
| sodium arsenite | 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 |
| dorsomorphin | affects cotreatment, decreases expression | 1 |
| MT19c compound | decreases expression | 1 |
| Vorinostat | affects cotreatment, decreases expression | 1 |
| Acetaminophen | decreases expression | 1 |
| Benzo(a)pyrene | increases methylation | 1 |
| Diazinon | increases methylation | 1 |
| Aflatoxin B1 | decreases methylation | 1 |
Clinical trials (associated diseases)
4 trials via MONDO — disease-level, not drug-specific.
| Trial | Phase | Status | Title |
|---|---|---|---|
| NCT00368004 | Not specified | TERMINATED | Family Studies of Uveal Coloboma |
| NCT01778543 | Not specified | RECRUITING | Pathogenesis and Genetics of Microphthalmia, Anophthalmia and Uveal Coloboma (MAC) |
| NCT04833361 | Not specified | COMPLETED | Potential Environmental Causes of Uveal Coloboma |
| NCT06293560 | Not specified | RECRUITING | Microphthalmia, Anophthalmia, and Coloboma Genetic Epidemiology in Children |
Related Atlas pages
- Associated diseases: isolated microphthalmia 3, isolated anophthalmia-microphthalmia syndrome, coloboma
- Disease cohort memberships (association, not causation — diseases whose associated-gene cohort lists this gene; a subset are also under Associated diseases): coloboma, isolated anophthalmia-microphthalmia syndrome, isolated microphthalmia 3