RAX

gene
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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

FieldValue
HGNC IDHGNC:18662
Approved symbolRAX
Nameretina and anterior neural fold homeobox
Location18q21.32
Locus typegene with protein product
StatusApproved
AliasesRX, RAX1
Ensembl geneENSG00000134438
Ensembl biotypeprotein_coding
OMIM601881
Entrez30062

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

ExonStartEnd
ENSE000009147165927236159272614
ENSE000009147185927291859273454
ENSE000036034495926703859269501

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 IDTPM avgSamples expressed
1721860.9346132
1721870.331493
1721880.01666

Top tissues by expression

230 total, by Bgee expression score (0-100, higher = more expressed):

TissueAnatomy IDExpression scoreQuality
parotid glandUBERON:000183175.47gold quality
nasal cavity epitheliumUBERON:000538474.17gold quality
biceps brachiiUBERON:000150773.43gold quality
skeletal muscle tissue of biceps brachiiUBERON:000450273.37gold quality
heart right ventricleUBERON:000208071.11gold quality
myocardiumUBERON:000234971.06gold quality
secondary oocyteCL:000065567.24gold quality
seminal vesicleUBERON:000099867.14gold quality
skeletal muscle tissue of rectus abdominisUBERON:000451166.91gold quality
lateral nuclear group of thalamusUBERON:000273666.77gold quality
lateral globus pallidusUBERON:000247666.35gold quality
Brodmann (1909) area 46UBERON:000648365.17gold quality
deltoidUBERON:000147665.09gold quality
entorhinal cortexUBERON:000272865.09gold quality
postcentral gyrusUBERON:000258164.46gold quality
substantia nigra pars reticulataUBERON:000196664.39gold quality
vastus lateralisUBERON:000137964.21gold quality
quadriceps femorisUBERON:000137764.04gold quality
substantia nigra pars compactaUBERON:000196563.58gold quality
parietal lobeUBERON:000187263.00gold quality
neuron projection bundle connecting eye with brainUBERON:000490462.49silver quality
trabecular bone tissueUBERON:000248362.47gold quality
middle temporal gyrusUBERON:000277162.15gold quality
Brodmann (1909) area 23UBERON:001355461.83gold quality
vena cavaUBERON:000408761.59gold quality
tendon of biceps brachiiUBERON:000818861.56gold quality
subthalamic nucleusUBERON:000190661.19gold quality
dorsal plus ventral thalamusUBERON:000189760.71gold quality
endothelial cellCL:000011560.30gold quality
adenohypophysisUBERON:000219659.48gold quality

Single-cell (SCXA)

Detected in 2 experiment(s), a significant marker in 1.

ExperimentMarker?Max mean expression
E-GEOD-137537yes37.33
E-ANND-3no0.00

Regulation

Is transcription factor: yes

JASPAR motifs

MotifNameFamily
MA0718.1RAXPaired-related HD factors
MA0718.2RAXPaired-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):

miRNAMax scoreAvg scoremiRNA target_count
HSA-MIR-5193100.0067.261744
HSA-MIR-6825-5P99.9669.813431
HSA-MIR-106A-5P99.9073.942683
HSA-MIR-17-5P99.8973.832665
HSA-MIR-106B-5P99.8874.722795
HSA-MIR-20A-5P99.8874.762769
HSA-MIR-20B-5P99.8874.012621
HSA-MIR-519D-3P99.8873.972607
HSA-MIR-526B-3P99.8874.062587
HSA-MIR-93-5P99.8873.982606
HSA-MIR-3934-3P99.7665.511351
HSA-MIR-3150A-3P99.7664.441640
HSA-MIR-6763-5P99.7664.681767
HSA-MIR-510-3P99.5470.062965
HSA-MIR-5571-5P99.4966.991764
HSA-MIR-3191-3P99.4563.94356
HSA-MIR-372-5P99.4169.112299
HSA-MIR-427999.1966.702437
HSA-MIR-429299.1665.571767
HSA-MIR-6791-5P99.1665.921844
HSA-MIR-6887-5P98.5668.491295
HSA-MIR-6795-5P98.5268.511277
HSA-MIR-6810-5P98.2966.21975
HSA-MIR-4768-3P98.1666.022330
HSA-MIR-7113-5P97.8867.331735
HSA-MIR-3664-3P97.8567.621452
HSA-MIR-3192-5P96.9865.761926
HSA-MIR-4793-5P96.8865.90872
HSA-MIR-552-3P96.6864.121026
HSA-MIR-313996.6866.77652

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

OrganismSymbolGene ID
mus_musculusRaxENSMUSG00000024518
rattus_norvegicusRaxENSRNOG00000016944

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 RxQ9Y2V3 (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 IDNamesCanonical?
Q9Y2V3-11yes
Q9Y2V3-22

RefSeq proteins (1): NP_038463* (*=MANE)

Domains & families (InterPro)

IDNameType
IPR001356HDDomain
IPR003654OAR_domDomain
IPR009057Homeodomain-like_sfHomologous_superfamily
IPR017970Homeobox_CSConserved_site
IPR043562RAX/RAX2Family

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)

ModelpLDDTFraction very-high
AF-Q9Y2V3-F165.100.19

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:

CategoryTerms
RNA polymerase II transcription regulatory region sequence-specific DNA binding3
transcription by RNA polymerase II2
regulation of transcription by RNA polymerase II2
regulation of DNA-templated transcription1
multicellular organism development1
multicellular organismal process1
sensory perception of light stimulus1
diencephalon development1
limbic system development1
anatomical structure development1
eye development1
positive regulation of DNA-templated transcription1
appendage development1
DNA-templated transcription1
regulation of gene expression1
regulation of RNA biosynthetic process1
central nervous system development1
animal organ development1
head development1
cis-regulatory region sequence-specific DNA binding1
chromatin1
DNA-binding transcription factor activity1
DNA-binding transcription factor activity, RNA polymerase II-specific1
DNA-binding transcription activator activity1
positive regulation of transcription by RNA polymerase II1
double-stranded DNA binding1
sequence-specific DNA binding1
nucleic acid binding1
chromosome1
cellular anatomical structure1
intracellular membrane-bounded organelle1

Protein interactions and networks

STRING

420 interactions, top by confidence (×1000):

Protein AProtein BPartner UniProtScore
RAXTTC4O95801665
RAXSOX2P48431631
RAXFIZ1Q96SL8528
RAXSIX3O95343504
RAXNRLP54845435
RAXSIX6O95475422
RAXGPR50Q13585397
RAXSH3BP1Q9Y3L3396
RAXSLCO6A1Q86UG4392
RAXOTX2P32243353
RAXFOXE3Q13461342
RAXRPE65Q16518296
RAXSHHQ15465296
RAXLMAN1LQ9HAT1294
RAXRHOP08100289
RAXCPLX4Q7Z7G2289

IntAct

1 interactions, top by confidence:

ABTypeScore
RAXSIRT6psi-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):

ClassificationCount (floor)
Pathogenic6
Likely pathogenic4
Uncertain significance116
Likely benign34
Benign14

Top pathogenic / likely-pathogenic (10)

Variant IDHGVSClassification
1723189NM_013435.3(RAX):c.560G>A (p.Arg187Gln)Pathogenic
1723190NM_013435.3(RAX):c.266del (p.Pro89fs)Pathogenic
1879402NM_013435.3(RAX):c.499G>T (p.Glu167Ter)Pathogenic
7635NM_013435.3(RAX):c.439C>T (p.Gln147Ter)Pathogenic
7636NM_013435.3(RAX):c.575G>A (p.Arg192Gln)Pathogenic
7638NM_013435.3(RAX):c.909C>G (p.Tyr303Ter)Pathogenic
1723188NM_013435.3(RAX):c.543+3A>GLikely pathogenic
3583379NM_013435.3(RAX):c.50_53dup (p.Gly19fs)Likely pathogenic
504029NM_013435.3(RAX):c.262_263delinsA (p.Ala88fs)Likely pathogenic
932556NM_013435.3(RAX):c.106G>T (p.Glu36Ter)Likely pathogenic

SpliceAI

377 predictions. Top by Δscore:

VariantEffectΔscore
18:59272362:TGG:Tdonor_gain1.0000
18:59272358:TA:Tdonor_loss0.9900
18:59272359:A:Cdonor_loss0.9900
18:59272360:CCTGG:Cdonor_loss0.9900
18:59269499:CAC:Cacceptor_gain0.9800
18:59269500:ACCT:Aacceptor_loss0.9800
18:59269502:C:Tacceptor_loss0.9800
18:59269503:T:Cacceptor_loss0.9800
18:59270370:G:Cdonor_gain0.9800
18:59272384:TG:Tdonor_gain0.9800
18:59272913:CTCA:Cdonor_loss0.9800
18:59272914:TCAC:Tdonor_loss0.9800
18:59272915:CAC:Cdonor_loss0.9800
18:59272916:A:ATdonor_loss0.9800
18:59272917:C:Adonor_loss0.9800
18:59269497:CACAC:Cacceptor_gain0.9700
18:59269452:T:TAdonor_gain0.9600
18:59269502:C:CCacceptor_gain0.9600
18:59270359:CTAAG:Cdonor_gain0.9600
18:59270621:TGCA:Tdonor_gain0.9600
18:59270624:A:ATdonor_gain0.9600
18:59272385:G:Tdonor_gain0.9600
18:59272391:G:Adonor_gain0.9600
18:59272912:ACTC:Adonor_loss0.9600
18:59272911:CACT:Cdonor_loss0.9500
18:59270360:TAAG:Tdonor_gain0.9400
18:59270361:AAGA:Adonor_gain0.9400
18:59272383:TTG:Tdonor_gain0.9400
18:59270358:CCTAA:Cdonor_gain0.9000
18:59272361:CTG:Cdonor_gain0.9000

AlphaMissense

2188 scored. Top likely-pathogenic:

VariantProtein changeam_pathogenicity
18:59269050:G:TA332D1.000
18:59269062:A:GL328P1.000
18:59269062:A:TL328Q1.000
18:59269071:A:TI325N1.000
18:59269467:C:GR193P1.000
18:59269470:C:GR192P1.000
18:59269472:C:AW191C1.000
18:59269472:C:GW191C1.000
18:59269474:A:GW191R1.000
18:59269474:A:TW191R1.000
18:59269475:C:AK190N1.000
18:59269475:C:GK190N1.000
18:59269476:T:AK190M1.000
18:59269477:T:CK190E1.000
18:59269477:T:GK190Q1.000
18:59269479:G:AA189V1.000
18:59269479:G:TA189D1.000
18:59269480:C:GA189P1.000
18:59269482:C:GR188P1.000
18:59269482:C:TR188Q1.000
18:59269483:G:AR188W1.000
18:59269483:G:CR188G1.000
18:59269485:C:AR187L1.000
18:59269485:C:GR187P1.000
18:59269486:G:CR187G1.000
18:59269487:G:CN186K1.000
18:59269487:G:TN186K1.000
18:59269488:T:AN186I1.000
18:59269488:T:CN186S1.000
18:59269488:T:GN186T1.000

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

DiseaseClassificationInheritance
isolated microphthalmia 3DefinitiveAutosomal recessive
isolated anophthalmia-microphthalmia syndromeSupportiveAutosomal dominant
colobomaLimitedAutosomal 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)

DescriptorNameTree numbers
D003103ColobomaC11.250.110; C11.270.147; C16.131.384.282
C567025Microphthalmia, 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.

ChemicalActions (top 5)PubMed papers
Valproic Acidaffects cotreatment, decreases expression, decreases methylation5
trichostatin Aaffects cotreatment, decreases expression3
entinostatdecreases expression, affects cotreatment2
belinostataffects cotreatment, decreases expression2
Panobinostataffects cotreatment, decreases expression2
Phenylmercuric Acetateaffects cotreatment, decreases expression2
Tretinoindecreases expression, increases expression2
methylmercuric chloridedecreases expression1
propionaldehydedecreases expression1
bisphenol Adecreases methylation1
arseniteincreases methylation1
sodium arseniteincreases expression1
4-(5-benzo(1,3)dioxol-5-yl-4-pyridin-2-yl-1H-imidazol-2-yl)benzamideaffects cotreatment, decreases expression1
dorsomorphinaffects cotreatment, decreases expression1
MT19c compounddecreases expression1
Vorinostataffects cotreatment, decreases expression1
Acetaminophendecreases expression1
Benzo(a)pyreneincreases methylation1
Diazinonincreases methylation1
Aflatoxin B1decreases methylation1

Clinical trials (associated diseases)

4 trials via MONDO — disease-level, not drug-specific.

TrialPhaseStatusTitle
NCT00368004Not specifiedTERMINATEDFamily Studies of Uveal Coloboma
NCT01778543Not specifiedRECRUITINGPathogenesis and Genetics of Microphthalmia, Anophthalmia and Uveal Coloboma (MAC)
NCT04833361Not specifiedCOMPLETEDPotential Environmental Causes of Uveal Coloboma
NCT06293560Not specifiedRECRUITINGMicrophthalmia, Anophthalmia, and Coloboma Genetic Epidemiology in Children