ARX

gene
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Also known as ISSXCT121EIEE1

Summary

ARX (aristaless related homeobox, HGNC:18060) is a protein-coding gene on chromosome Xp21.3, encoding Homeobox protein ARX (Q96QS3). Transcription factor. It is haploinsufficient (ClinGen: sufficient evidence).

This gene is a homeobox-containing gene expressed during development. The expressed protein contains two conserved domains, a C-peptide (or aristaless domain) and the prd-like class homeobox domain. It is a member of the group-II aristaless-related protein family whose members are expressed primarily in the central and/or peripheral nervous system. This gene is thought to be involved in CNS development. Expansion of a polyalanine tract and other mutations in this gene cause X-linked cognitive disability and epilepsy.

Source: NCBI Gene 170302 — RefSeq curated summary.

At a glance

  • Gene–disease (curated): genetic developmental and epileptic encephalopathy (Definitive, ClinGen) — +11 more curated relationships
  • Clinical variants (ClinVar): 978 total — 105 pathogenic, 26 likely-pathogenic
  • Phenotypes (HPO): 169
  • Dosage sensitivity (ClinGen): haploinsufficiency sufficient evidence, triplosensitivity no evidence
  • Transcription factor: yes — 30 downstream targets (CollecTRI)
  • MANE Select transcript: NM_139058

Identifiers

Gene identifiers

FieldValue
HGNC IDHGNC:18060
Approved symbolARX
Namearistaless related homeobox
LocationXp21.3
Locus typegene with protein product
StatusApproved
AliasesISSX, CT121, EIEE1
Ensembl geneENSG00000004848
Ensembl biotypeprotein_coding
OMIM300382
Entrez170302

Gene structure

Transcript identifiers

Ensembl transcripts: 5 — 3 protein_coding_CDS_not_defined, 2 protein_coding

ENST00000379044, ENST00000636609, ENST00000636885, ENST00000637394, ENST00000637993

RefSeq mRNA: 1 — MANE Select: NM_139058 NM_139058

CCDS: CCDS14215

Canonical transcript exons

ENST00000379044 — 5 exons

ExonStartEnd
ENSE000012979982500711125007439
ENSE000013048792501292225013798
ENSE000013177882501026025010305
ENSE000014795862500369425004910
ENSE000014796002501554225015965

Expression profiles

Bgee: expression breadth ubiquitous, 162 present calls, max score 97.34.

FANTOM5 (CAGE): breadth broad, TPM avg 11.1592 / max 773.5224, expressed in 277 samples.

FANTOM5 promoters (4 alternative TSS)

Promoter IDTPM avgSamples expressed
19876010.9702274
1987590.131754
2096360.043023
1987610.01434

Top tissues by expression

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

TissueAnatomy IDExpression scoreQuality
left ovaryUBERON:000211997.34gold quality
ovaryUBERON:000099294.28gold quality
right ovaryUBERON:000211893.36gold quality
ventricular zoneUBERON:000305393.33gold quality
vastus lateralisUBERON:000137992.69silver quality
germinal epithelium of ovaryUBERON:000130492.54silver quality
quadriceps femorisUBERON:000137792.20gold quality
endothelial cellCL:000011590.82gold quality
bronchial epithelial cellCL:000232887.08gold quality
Brodmann (1909) area 23UBERON:001355487.07gold quality
biceps brachiiUBERON:000150786.11gold quality
anterior cingulate cortexUBERON:000983585.73gold quality
ganglionic eminenceUBERON:000402385.68gold quality
skeletal muscle tissue of rectus abdominisUBERON:000451185.46gold quality
skeletal muscle tissue of biceps brachiiUBERON:000450285.13gold quality
bronchusUBERON:000218585.00gold quality
middle temporal gyrusUBERON:000277184.41gold quality
skeletal muscle tissueUBERON:000113483.99gold quality
tibialis anteriorUBERON:000138583.89silver quality
dorsolateral prefrontal cortexUBERON:000983483.68gold quality
Brodmann (1909) area 9UBERON:001354083.10gold quality
primary visual cortexUBERON:000243683.08gold quality
male germ line stem cell (sensu Vertebrata) in testisCL:0000089 ∩ UBERON:000047382.52gold quality
Brodmann (1909) area 46UBERON:000648382.52gold quality
right frontal lobeUBERON:000281082.49gold quality
occipital lobeUBERON:000202181.67gold quality
entorhinal cortexUBERON:000272880.67gold quality
deltoidUBERON:000147680.49silver quality
gastrocnemiusUBERON:000138880.36gold quality
right testisUBERON:000453480.32gold quality

Single-cell (SCXA)

Detected in 7 experiment(s), a significant marker in 7.

ExperimentMarker?Max mean expression
E-ENAD-27yes112.60
E-MTAB-5061yes28.15
E-GEOD-81608yes23.27
E-GEOD-83139yes13.18
E-GEOD-93593yes10.93
E-ANND-3yes9.81
E-HCAD-31yes5.16

Regulation

Is transcription factor: yes

Downstream targets (CollecTRI)

30 targets.

TargetRegulation
ACKR3Activation
ARX
CEL
CHGA
DLX1
EBF3Repression
EGR1Activation
ETS2Activation
GAST
GCGActivation
GHRL
HMGN3Repression
IGF1Activation
KDM5CUnknown
LGI1
LMO1Unknown
LMO3Activation
MEIS1Activation
PAX4Unknown
PHLDA1Activation
PLPP1Repression
RASGEF1BRepression
SCT
SHH
SHOX2Unknown
SLC12A5
SLIT2
SST
TGFB3Activation
TPM1

Upstream regulators (CollecTRI, top): ARX, DLX2, ISL1, NKX2-2, NKX6-1, PAX4, SHOX2

miRNA regulators (miRDB)

85 targeting ARX, 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-6870-5P99.9968.552115
HSA-MIR-27A-3P99.9872.132955
HSA-MIR-27B-3P99.9872.132955
HSA-MIR-998599.9872.112939
HSA-MIR-60799.9773.625593
HSA-MIR-7152-3P99.9767.47849
HSA-MIR-4723-5P99.9768.702034
HSA-MIR-569899.9768.492029
HSA-MIR-7111-5P99.9768.482062
HSA-MIR-128-3P99.9571.172484
HSA-MIR-216A-3P99.9571.192505
HSA-MIR-651-3P99.9473.485177
HSA-MIR-454-3P99.9174.011925
HSA-MIR-367199.9073.043897
HSA-MIR-130A-3P99.9073.311861
HSA-MIR-130B-3P99.9073.271850
HSA-MIR-301A-3P99.9073.151839
HSA-MIR-301B-3P99.9073.191836
HSA-MIR-366699.9073.241833
HSA-MIR-429599.9073.111838
HSA-MIR-3529-3P99.9073.553045
HSA-MIR-548D-3P99.8770.674362
HSA-LET-7A-2-3P99.8770.531921
HSA-MIR-612499.8769.783551
HSA-MIR-548BB-3P99.8670.584354
HSA-MIR-394199.8670.542735
HSA-LET-7G-3P99.8570.431929
HSA-MIR-548AC99.8470.774351
HSA-MIR-548H-3P99.8470.804349
HSA-MIR-548Z99.8470.804349

Functional genomics

ClinGen dosage: haploinsufficiency 3 (sufficient evidence), triplosensitivity 0 (no evidence). ClinGen Gene Dosage Map

Literature-anchored findings (GeneRIF, showing 40)

  • Expression is specific to the telencephalon and thalamus. Mutations cause mental retardation without brain malformations. (PMID:11971879)
  • data suggest mutations in the ARX gene are important causes of mental retardation, often associated with diverse neurological manifestations (PMID:12142061)
  • A new syndrome of X-linked myoclonic epilepsy with generalized spasticity and intellectual disability in boys (XMESID) has been described and a novel missense mutation (1058C>T) identified in the ARX open reading frame. (PMID:12177367)
  • The expression pattern suggests that ARX is involved in the differentiation and maintenance of specific neuronal cell types in the central nervous system. (PMID:12359145)
  • ARX plays a role in causing X-linked lissencephaly with abnormal genitalia (PMID:12379852)
  • Disruption of the STK9 gene causes severe X-linked infantile spasms and mental retardation. (PMID:12736870)
  • 2 point mutations (790delC & R332C) in 2 X-linked lissencephaly with abnormal genitalia pedigrees affect the homeodomain of the protein & confirm that ARX is a causative gene for XLAG. (PMID:12874405)
  • A hemizygous 24-bp duplication in exon 2 (441_464dup)results in expansion from 12 to 20 alanine residues (A155_W156insAAAAAAAA) in the second of four polyalanine tracts in the ARX protein, causing West syndrome. (PMID:12874418)
  • Thirteen novel mutations found in ARX gene in 20 males with X-linked lissencephaly with abnormal genitalia. (PMID:14722918)
  • expansions in one of the ARX polyA tracts results in nuclear protein aggregation and an increase in cell death; likely underlying the pathogenesis of the associated infantile spasms and mental retardation (PMID:15533998)
  • Mutations in the ARX gene can result in many different phenotypes, including phenotypes associated with severe brain malformations and less severe phenotypes associated with syndromic or non-syndromic forms of x-linked mental retadation. (PMID:15707237)
  • Familial West syndrome and dystonia caused by an Aristaless related homeobox gene mutation (ARX) (PMID:15726411)
  • Four nonsyndromic XLMR families were found to have a 24 base pair duplication mutation in exon 2 of ARX. (PMID:15850492)
  • Results confirm the significant contribution of ARX mutations in the etiology of X-linked mental retardation (XLMR), and imply that screening for c.428-451 dup (24 bp) mutation should be recommended in all patients with suspected XLMR. (PMID:16523516)
  • These results reinforce the idea that ARX mutations are relevant to mental retardation and are indicative that molecular screening of exon 2 should be considered in males with mental retardation of unknown etiology. (PMID:16845484)
  • Activin A has opposite effects on glucagon and arx gene expression in alpha-cells compared with beta-cells, a finding that may have relevance during pancreatic endocrine lineage specification and physiological function of the adult islets (PMID:16988001)
  • These findings indicate that mutations in the ARX gene are very rare in autism. (PMID:17044103)
  • Features confirm the pleiotropic effect of ARX gene duplication in X-linked mental retardation. (PMID:17082467)
  • study underlines the role of ARXdup24 as a critical mutational site causing mental retardation linked to Xp22 (PMID:17480217)
  • study showed that the c.304ins(GCG)7 mutation causing an increase from 16 to 23 alanines increased the propensity of ARX protein aggregation and a shift from nuclear to cytoplasmic localization (PMID:17490853)
  • Considering genotype-phenotype correlation, we suggest screening of the most common mutation, the c.428_451 dup mutation by PCR, in patients with infantile spasm syndrome, Partington syndrome and non-syndromic X-linked mental retardation. (PMID:17613295)
  • This study reports a novel 24-bp in-frame deletion within exon 2 of the ARX gene in a male child with X-linked mental retardation (PMID:17641262)
  • The phenotype of infantile spasms with severe dyskinetic quadriparesis increases the number of human disorders that result from the pathologic expansion of single alanine repeats of ARX protein. (PMID:17664401)
  • We screened the ARX mutation and found a hemizygous, de novo, 33-bp duplication in exon 2, 298_330dupGCGGCA(GCG)9, in two of three unrelated male patients with EIEE. (PMID:17668384)
  • This study report an case of ombination of infantile spasms, non-epileptic seizures and complex movement disorder on the electroclinical features of a 4-year-old boy with an expansion of the trinucleotide repeat in the ARX gene (PMID:18468866)
  • Although Arx is necessary for the Dlx-dependent promotion of interneuron migration, it is not required for the GABAergic cell fate commitment mediated by Dlx factors. (PMID:18923043)
  • Disorders caused by mutations in the ARX gene include: hydrocephaly, lissencephaly and agenesis of corpus callosum with abnormal genitalia, Partington syndrome S), X-linked infantile spasms , myoclonic epilepsy, and nonspecific mental retardation. (PMID:18975239)
  • Results describe three cases of mental retardation in two different families where the mutation in aristaless-related homeobox (ARX) gene c.428_451 dup24 was found while X-fragile syndrome screening was made. (PMID:19085879)
  • The first viable knock-in mouse model of infantile spasms syndrome spontaneously recapitulates salient phenotypic features of the human triplet repeat expansion mutation. (PMID:19587282)
  • Lissencephaly or mental retardation is caused by ARX mutations without the involvement of other genetic factors. (PMID:19605412)
  • ARX mutations are not responsible for early onset severe myoclonic epilepsy in infancy (PMID:19734009)
  • Findings widen the spectrum of clinical phenotypes because of mutations in the ARX gene, but also emphasize the molecular pathogenetic effect of individual mutations. (PMID:19738637)
  • novel frameshift mutations in the terminal exon of the ARX gene (Ala524fsX534 and E536fsX672) were identified in 2 Ohtahara syndrome patients (2 and 13 years, each) from 2 families (PMID:20384723)
  • This review aims to provide a catalog of the currently known mutations in ARX and associated clinical phenotypes. (PMID:20506206)
  • ARX contributes not only to endocrine development, but also to exocrine development of the human pancreas, and its deficiency may lead to the severe phenotypes of X-linked lissencephaly with abnormal genitalia patients. (PMID:20538404)
  • 2 male individuals, born from monozygotic twin sisters, with Ohtahara syndrome that evolved into West syndrome phenotype and epileptic encephalopathy; previously unreported missense mutation in exon 5 of ARX gene (c.1604T>A) was found in both children (PMID:21108397)
  • ARX polyA expansions are primarily associated with syndromic mental retardation. (PMID:21204215)
  • Contractions in the second polyA tract of ARX are rare, non-pathogenic polymorphisms. (PMID:21204226)
  • study described a novel ARX mutation in a family, leading to Ohtahara syndrome with abnormal genital and psychomotor development (OAGPD) in a male infant, and neurocognitive/psychiatric phenomena in heterozygous, carrier females (PMID:21426321)
  • This study confirmed the pivotal role of the aristaless related homeobox in the pathogenesis of epileptic encephalopathies (PMID:21482751)

Cross-species orthologs

4 orthologs

OrganismSymbolGene ID
danio_rerioarxaENSDARG00000058011
danio_rerioarxbENSDARG00000101523
mus_musculusArxENSMUSG00000035277
rattus_norvegicusArxENSRNOG00000053562

Paralogs (50): 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), RAX (ENSG00000134438), 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

Homeobox protein ARXQ96QS3 (reviewed: Q96QS3)

Alternative names: Aristaless-related homeobox

All UniProt accessions (2): Q96QS3, A0A1B0GUI3

UniProt curated annotations — full annotation on UniProt →

Function. Transcription factor. Binds to specific sequence motif 5’-TAATTA-3’ in regulatory elements of target genes, such as histone demethylase KDM5C. Positively modulates transcription of KDM5C. Activates expression of KDM5C synergistically with histone lysine demethylase PHF8 and perhaps in competition with transcription regulator ZNF711; synergy may be related to enrichment of histone H3K4me3 in regulatory elements. Required for normal brain development. Plays a role in neuronal proliferation, interneuronal migration and differentiation in the embryonic forebrain. May also be involved in axonal guidance in the floor plate.

Subcellular location. Nucleus.

Tissue specificity. Expressed predominantly in fetal and adult brain and skeletal muscle. Expression is specific to the telencephalon and ventral thalamus. There is an absence of expression in the cerebellum throughout development and also in adult.

Disease relevance. Lissencephaly, X-linked 2 (LISX2) [MIM:300215] A classic type lissencephaly associated with abnormal genitalia. Patients have severe congenital or postnatal microcephaly, lissencephaly, agenesis of the corpus callosum, neonatal-onset intractable epilepsy, poor temperature regulation, chronic diarrhea, and ambiguous or underdeveloped genitalia. The disease is caused by variants affecting the gene represented in this entry. Also called X-linked lissencephaly with abnormal genitalia (XLAG). Developmental and epileptic encephalopathy 1 (DEE1) [MIM:308350] A severe form of epilepsy characterized by frequent tonic seizures or spasms beginning in infancy with a specific EEG finding of suppression-burst patterns, characterized by high-voltage bursts alternating with almost flat suppression phases. Patients may progress to West syndrome, which is characterized by tonic spasms with clustering, arrest of psychomotor development, and hypsarrhythmia on EEG. The disease is caused by variants affecting the gene represented in this entry. Partington syndrome (PRTS) [MIM:309510] An X-linked developmental disorder characterized by intellectual disability, episodic dystonic hand movements, lower limb spasticity, and dysarthria. The disease is caused by variants affecting the gene represented in this entry. Intellectual developmental disorder, X-linked 29 (XLID29) [MIM:300419] A disorder characterized by significantly below average general intellectual functioning associated with impairments in adaptive behavior and manifested during the developmental period. Intellectual deficiency is the only primary symptom of non-syndromic X-linked forms, while syndromic intellectual disability presents with associated physical, neurological and/or psychiatric manifestations. The disease is caused by variants affecting the gene represented in this entry. Agenesis of the corpus callosum, with abnormal genitalia (ACCAG) [MIM:300004] An X-linked syndrome with variable expression in females. It is characterized by agenesis of corpus callosum, intellectual disability and seizures. Manifestations in surviving males include severe acquired micrencephaly, intellectual disability, limb contractures, scoliosis, tapered fingers with hyperconvex nails, a characteristic face with large eyes, prominent supraorbital ridges, synophrys, optic atrophy, broad alveolar ridges, and seizures. Urologic anomalies include renal dysplasia, cryptorchidism, and hypospadias. The disease is caused by variants affecting the gene represented in this entry.

Similarity. Belongs to the paired homeobox family. Bicoid subfamily.

RefSeq proteins (1): NP_620689* (*=MANE)

Domains & families (InterPro)

IDNameType
IPR001356HDDomain
IPR003654OAR_domDomain
IPR009057Homeodomain-like_sfHomologous_superfamily
IPR017970Homeobox_CSConserved_site
IPR050649Paired_Homeobox_TFsFamily

Pfam: PF00046, PF03826

UniProt features (25 total): sequence variant 12, compositionally biased region 5, region of interest 3, mutagenesis site 2, chain 1, DNA-binding region 1, short sequence motif 1

Structure

Experimental structures (PDB)

0 structures.

Predicted structure (AlphaFold)

ModelpLDDTFraction very-high
AF-Q96QS3-F156.510.11

Functional residue map

Curated UniProt residues grouped by drug-discovery relevance — catalytic, ligand-binding, modification, and mutation-validated positions. Source: UniProtKB sequence features.

Mutagenesis-validated functional residues (2):

PositionPhenotype
358abolishes sequence-specific dna-binding; reduces transcriptional repression of lmo1 and shox2. abolishes transcriptional
379abolishes sequence-specific dna-binding; reduces transcriptional repression of lmo1 and shox2. abolishes transcriptional

Function

Pathways and Gene Ontology

Reactome pathways

0 pathways

MSigDB gene sets: 523 (showing top): GOBP_FOREBRAIN_NEURON_DEVELOPMENT, GOBP_DIGESTION, GOBP_OLFACTORY_BULB_INTERNEURON_DIFFERENTIATION, GOBP_EPITHELIUM_DEVELOPMENT, TSENG_IRS1_TARGETS_UP, STAEGE_EWING_FAMILY_TUMOR, RORA1_01, GOBP_REGULATION_OF_DEVELOPMENTAL_GROWTH, PEREZ_TP63_TARGETS, GOBP_GROWTH, GOBP_NEUROGENESIS, TGACCTY_ERR1_Q2, AAAYRNCTG_UNKNOWN, USF_C, GOBP_CELL_PROLIFERATION_IN_FOREBRAIN

GO Biological Process (24): negative regulation of transcription by RNA polymerase II (GO:0000122), regulation of transcription by RNA polymerase II (GO:0006357), axon guidance (GO:0007411), positive regulation of gene expression (GO:0010628), globus pallidus development (GO:0021759), cerebral cortex tangential migration (GO:0021800), embryonic olfactory bulb interneuron precursor migration (GO:0021831), cell proliferation in forebrain (GO:0021846), cerebral cortex GABAergic interneuron migration (GO:0021853), organ growth (GO:0035265), lipid digestion (GO:0044241), positive regulation of transcription by RNA polymerase II (GO:0045944), positive regulation of organ growth (GO:0046622), neuron fate commitment (GO:0048663), neuron development (GO:0048666), regulation of epithelial cell proliferation (GO:0050678), epithelial cell fate commitment (GO:0072148), neuron migration (GO:0001764), regulation of DNA-templated transcription (GO:0006355), nervous system development (GO:0007399), olfactory bulb development (GO:0021772), cell differentiation (GO:0030154), forebrain development (GO:0030900), interneuron migration (GO:1904936)

GO Molecular Function (9): RNA polymerase II transcription regulatory region sequence-specific DNA binding (GO:0000977), 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 repressor activity, RNA polymerase II-specific (GO:0001227), DNA-binding transcription activator activity, RNA polymerase II-specific (GO:0001228), chromatin binding (GO:0003682), sequence-specific double-stranded DNA binding (GO:1990837), DNA binding (GO:0003677), protein binding (GO:0005515)

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 binding4
regulation of transcription by RNA polymerase II3
transcription by RNA polymerase II3
regulation of gene expression2
neuron differentiation2
cell fate commitment2
DNA-binding transcription factor activity, RNA polymerase II-specific2
binding2
negative regulation of DNA-templated transcription1
regulation of DNA-templated transcription1
axonogenesis1
neuron projection guidance1
gene expression1
positive regulation of macromolecule biosynthetic process1
diencephalon development1
neural nucleus development1
cerebral cortex cell migration1
substrate-independent telencephalic tangential interneuron migration1
olfactory bulb interneuron development1
tangential migration from the subventricular zone to the olfactory bulb1
forebrain development1
neural precursor cell proliferation1
interneuron migration from the subpallium to the cortex1
cerebral cortex GABAergic interneuron development1
interneuron migration1
multicellular organismal process1
developmental growth1
digestion1
positive regulation of DNA-templated transcription1
organ growth1
regulation of organ growth1
positive regulation of developmental growth1
positive regulation of multicellular organismal process1
cell development1
regulation of cell population proliferation1
epithelial cell proliferation1
epithelial cell differentiation1
cell migration1
generation of neurons1
DNA-templated transcription1

Protein interactions and networks

STRING

710 interactions, top by confidence (×1000):

Protein AProtein BPartner UniProtScore
ARXPCDH19Q8TAB3818
ARXCDKL5O76039804
ARXSTXBP1P61764799
ARXSLC25A22Q9H936781
ARXPNKPQ96T60751
ARXSCN1AP35498750
ARXIPO13O94829730
ARXSPTAN1Q13813722
ARXARHGEF9O43307682
ARXVCX3BQ9H321670
ARXPLCB1Q9NQ66668
ARXPOLA1P09884668
ARXVCXQ9H320648
ARXVCX2Q9H322647
ARXLMO1P25800638

IntAct

19 interactions, top by confidence:

ABTypeScore
PHF8ARXpsi-mi:“MI:0915”(physical association)0.520
ACTN1ARXpsi-mi:“MI:0915”(physical association)0.510
PICK1ARXpsi-mi:“MI:0915”(physical association)0.510
ARXpsi-mi:“MI:0915”(physical association)0.370
ACTN2ARXpsi-mi:“MI:0915”(physical association)0.370
TLE5ARXpsi-mi:“MI:0915”(physical association)0.370
CYTIPARXpsi-mi:“MI:0915”(physical association)0.370
DNM2ARXpsi-mi:“MI:0915”(physical association)0.370
IPO13ARXpsi-mi:“MI:0915”(physical association)0.370
NELL2ARXpsi-mi:“MI:0915”(physical association)0.370
PKMARXpsi-mi:“MI:0915”(physical association)0.370
SETD2ARXpsi-mi:“MI:0915”(physical association)0.370
ARXMIGA1psi-mi:“MI:0914”(association)0.350

BioGRID (29): AP2A1 (Affinity Capture-MS), APOB (Affinity Capture-MS), CLTA (Affinity Capture-MS), CLTB (Affinity Capture-MS), CLTC (Affinity Capture-MS), PIK3C2A (Affinity Capture-MS), RBM4 (Affinity Capture-MS), CLINT1 (Affinity Capture-MS), SEC16A (Affinity Capture-MS), TACC3 (Affinity Capture-MS), CYFIP1 (Affinity Capture-MS), STK39 (Affinity Capture-MS), GTSE1 (Affinity Capture-MS), KLC2 (Affinity Capture-MS), CD99L2 (Affinity Capture-MS)

ESM2 similar proteins: A2A9A2, A6QQ94, A6YP92, A7MB54, B5RHS5, E9PZZ1, M0R6D8, O02786, O08934, O09029, O35085, P13297, P28360, P46153, P50548, P78413, P78414, P78415, P81067, P81068, P84550, P97830, Q12952, Q13207, Q14549, Q14774, Q2VL76, Q2VL77, Q2VL78, Q2VL79, Q2VL80, Q2VL82, Q2VL83, Q2VL84, Q2VL85, Q2VL86, Q2VL87, Q2VL88, Q2VWA4, Q5SQQ9

Diamond homologs: A1A546, A1YEV8, A1YG25, A2T711, A6NJT0, A6NNA5, A6YP92, G5EC89, G5EDS1, L8E946, O08934, O09113, O14813, O15266, O18381, O35085, O35137, O35602, O35690, O35750, O42115, O42201, O42250, O42356, O42357, O42358, O42477, O42567, O60902, O70137, O73917, O95076, O97039, P0DMV5, P23759, P23760, P24610, P26367, P26630, P29506

SIGNOR signaling

3 interactions.

AEffectBMechanism
ARX“down-regulates quantity by repression”EBF3“transcriptional regulation”
DLX2“up-regulates quantity by expression”ARX“transcriptional regulation”
PRKCA“up-regulates activity”ARXphosphorylation

Disease & clinical

Clinical variants and AI predictions

ClinVar

978 variants total. Per-class counts are floors (≥ shown; pagination cap):

ClassificationCount (floor)
Pathogenic105
Likely pathogenic26
Uncertain significance371
Likely benign359
Benign18

Top pathogenic / likely-pathogenic (30)

Variant IDHGVSClassification
1074175NM_139058.3(ARX):c.1443dup (p.Gly482fs)Pathogenic
11188NM_139058.3(ARX):c.1058C>T (p.Pro353Leu)Pathogenic
11189NM_139058.3(ARX):c.1449-816_*460delPathogenic
11192NM_139058.3(ARX):c.995G>A (p.Arg332His)Pathogenic
11193NM_139058.3(ARX):c.1117C>T (p.Gln373Ter)Pathogenic
11195NG_008281.1:g.(?4983)(8028_10643)delPathogenic
11197NM_139058.3(ARX):c.1028T>A (p.Leu343Gln)Pathogenic
11198NM_139058.3(ARX):c.98T>C (p.Leu33Pro)Pathogenic
11200NM_139058.3(ARX):c.998C>A (p.Thr333Asn)Pathogenic
11201NM_139058.3(ARX):c.1105G>T (p.Glu369Ter)Pathogenic
11202NM_139058.3(ARX):c.309_341dup (p.Ala105_Ala115dup)Pathogenic
11205NM_139058.3(ARX):c.232G>T (p.Glu78Ter)Pathogenic
1164076NM_139058.3(ARX):c.1406_1415del (p.Ala469fs)Pathogenic
1172770NM_139058.3(ARX):c.947del (p.Gly316fs)Pathogenic
1299655NM_139058.3(ARX):c.1472del (p.Leu491fs)Pathogenic
1374869NM_139058.3(ARX):c.1125G>A (p.Trp375Ter)Pathogenic
1410535NM_139058.3(ARX):c.642_645del (p.Pro215fs)Pathogenic
1434577NM_139058.3(ARX):c.1120-2A>GPathogenic
1526401NM_139058.3(ARX):c.26dup (p.Cys10fs)Pathogenic
156619NM_139058.3(ARX):c.1141G>A (p.Ala381Thr)Pathogenic
157739NM_139058.3(ARX):c.1111C>T (p.Arg371Ter)Pathogenic
157744NM_139058.3(ARX):c.1372del (p.Ala458fs)Pathogenic
157746NM_139058.3(ARX):c.1414C>T (p.Arg472Ter)Pathogenic
157748NM_139058.3(ARX):c.1465del (p.Ala489fs)Pathogenic
157749NM_139058.3(ARX):c.1544del (p.Gly515fs)Pathogenic
157750NM_139058.3(ARX):c.172del (p.Ala58fs)Pathogenic
157756NM_139058.3(ARX):c.335_368del (p.Ala112fs)Pathogenic
157757NM_139058.3(ARX):c.34G>T (p.Glu12Ter)Pathogenic
157759NM_139058.3(ARX):c.617del (p.Gly206fs)Pathogenic
157765NM_139058.3(ARX):c.995G>T (p.Arg332Leu)Pathogenic

SpliceAI

873 predictions. Top by Δscore:

VariantEffectΔscore
X:25010254:GCTCA:Gdonor_loss1.0000
X:25010256:TCA:Tdonor_loss1.0000
X:25010258:A:Cdonor_loss1.0000
X:25015536:CCTTA:Cdonor_loss1.0000
X:25015537:CTTA:Cdonor_loss1.0000
X:25015538:TTAC:Tdonor_loss1.0000
X:25015539:TA:Tdonor_loss1.0000
X:25015540:A:ACdonor_gain1.0000
X:25015540:A:Tdonor_loss1.0000
X:25015541:C:CCdonor_gain1.0000
X:25015541:C:CGdonor_loss1.0000
X:25007113:G:Adonor_gain0.9900
X:25010301:CCTCC:Cacceptor_gain0.9900
X:25010302:CTCCC:Cacceptor_gain0.9900
X:25010303:TCCCT:Tacceptor_gain0.9900
X:25010304:CC:Cacceptor_gain0.9900
X:25010305:CCTA:Cacceptor_gain0.9900
X:25010306:C:CAacceptor_loss0.9900
X:25010306:C:CCacceptor_gain0.9900
X:25010307:T:Cacceptor_loss0.9900
X:25012917:CATA:Cdonor_loss0.9900
X:25012918:ATACC:Adonor_loss0.9900
X:25012919:TA:Tdonor_loss0.9900
X:25012920:ACCT:Adonor_loss0.9900
X:25014562:T:TAdonor_gain0.9900
X:25014802:T:Adonor_gain0.9900
X:25015540:AC:Adonor_gain0.9900
X:25015541:CC:Cdonor_gain0.9900
X:25015541:CCTTG:Cdonor_gain0.9900
X:25004909:GCCTG:Gacceptor_loss0.9800

AlphaMissense

3585 scored. Top likely-pathogenic:

VariantProtein changeam_pathogenicity
X:25004743:G:TA539D1.000
X:25004744:C:GA539P1.000
X:25004749:A:GL537P1.000
X:25004751:C:AR536S1.000
X:25004751:C:GR536S1.000
X:25004752:C:AR536M1.000
X:25004752:C:GR536T1.000
X:25004755:A:GL535P1.000
X:25004755:A:TL535Q1.000
X:25004764:A:CI532R1.000
X:25004764:A:GI532T1.000
X:25004764:A:TI532K1.000
X:25004766:G:CS531R1.000
X:25004766:G:TS531R1.000
X:25004767:C:AS531I1.000
X:25004768:T:GS531R1.000
X:25007404:C:AK385N1.000
X:25007404:C:GK385N1.000
X:25007405:T:AK385M1.000
X:25007406:T:CK385E1.000
X:25007408:C:GR384P1.000
X:25007409:G:AR384C1.000
X:25007409:G:TR384S1.000
X:25007410:C:AW383C1.000
X:25007410:C:GW383C1.000
X:25007412:A:GW383R1.000
X:25007412:A:TW383R1.000
X:25007413:C:AK382N1.000
X:25007413:C:GK382N1.000
X:25007414:T:AK382M1.000

dbSNP variants (sampled 300 via entrez): RS1000074971 (X:25006584 G>A,T), RS1000106379 (X:25014422 G>A), RS1000498226 (X:25012086 G>A), RS1000954674 (X:25011689 T>C), RS1001362221 (X:25012821 A>G), RS1001384484 (X:25005315 G>A), RS1002214533 (X:25003487 A>C), RS1002515777 (X:25007824 T>C), RS1002648579 (X:25011436 C>T), RS1002662680 (X:25017511 C>T), RS1003146115 (X:25017903 G>A,C), RS1003424363 (X:25011166 G>A), RS1003856468 (X:25005417 C>A), RS1003885772 (X:25015283 T>C), RS1003997021 (X:25011419 T>C)

Disease associations

OMIM: gene MIM:300382 | disease phenotypes: MIM:300419, MIM:308350, MIM:217990, MIM:309510, MIM:300004, MIM:300215, MIM:209850, MIM:613154, MIM:304050

GenCC curated gene-disease

DiseaseClassificationInheritance
intellectual disability, X-linked, with or without seizures, ARX-relatedDefinitiveX-linked
X-linked complex neurodevelopmental disorderDefinitiveX-linked
X-linked lissencephaly with abnormal genitaliaStrongX-linked
neurodevelopmental disorderStrongX-linked
developmental and epileptic encephalopathy, 1StrongX-linked
genetic developmental and epileptic encephalopathySupportiveAutosomal dominant
corpus callosum agenesis-abnormal genitalia syndromeSupportiveX-linked
X-linked spasticity-intellectual disability-epilepsy syndromeSupportiveX-linked
infantile spasmsSupportiveAutosomal dominant
infantile epileptic-dyskinetic encephalopathySupportiveX-linked
non-syndromic X-linked intellectual disabilitySupportiveX-linked
Partington syndromeSupportiveX-linked

ClinGen Gene-Disease Validity (2)

Expert-panel classifications — Definitive > Strong > Moderate > Limited > Disputed > Refuted.

DiseaseClassificationInheritance
genetic developmental and epileptic encephalopathyDefinitiveXL
X-linked complex neurodevelopmental disorderDefinitiveXL

Mondo (18): intellectual disability, X-linked, with or without seizures, ARX-related (MONDO:0010317), developmental and epileptic encephalopathy, 1 (MONDO:0010632), arachnoid cyst (MONDO:0008813), corpus callosum, agenesis of (MONDO:0009022), Partington syndrome (MONDO:0010654), corpus callosum agenesis-abnormal genitalia syndrome (MONDO:0010224), X-linked lissencephaly with abnormal genitalia (MONDO:0010268), X-linked spasticity-intellectual disability-epilepsy syndrome (MONDO:0017856), autism (MONDO:0005260), intellectual disability (MONDO:0001071), muscular dystrophy-dystroglycanopathy (congenital with brain and eye anomalies), type A6 (MONDO:0013158), Aicardi syndrome (MONDO:0010568), X-linked complex neurodevelopmental disorder (MONDO:0100148), genetic developmental and epileptic encephalopathy (MONDO:0100062), infantile spasms (MONDO:0018097)

Orphanet (12): X-linked non-syndromic intellectual disability (Orphanet:777), Isolated corpus callosum agenesis (Orphanet:200), Arachnoid cyst (Orphanet:2356), Partington syndrome (Orphanet:94083), Corpus callosum agenesis-abnormal genitalia syndrome (Orphanet:2508), X-linked lissencephaly with abnormal genitalia (Orphanet:452), X-linked spasticity-intellectual disability-epilepsy syndrome (Orphanet:3175), ARX-related epileptic encephalopathy (Orphanet:182079), Muscle-eye-brain disease (Orphanet:588), Walker-Warburg syndrome (Orphanet:899), Aicardi syndrome (Orphanet:50), NON RARE IN EUROPE: Unexplained intellectual disability (Orphanet:319658)

HPO phenotypes

169 total (30 of 169 shown, HPO-id order):

HPOTerm
HP:0000020Urinary incontinence
HP:0000023Inguinal hernia
HP:0000028Cryptorchidism
HP:0000047Hypospadias
HP:0000053Macroorchidism
HP:0000054Micropenis
HP:0000062Ambiguous genitalia
HP:0000070Ureterocele
HP:0000110Renal dysplasia
HP:0000175Cleft palate
HP:0000187Broad alveolar ridges
HP:0000218High palate
HP:0000219Thin upper lip vermilion
HP:0000252Microcephaly
HP:0000260Wide anterior fontanel
HP:0000280Coarse facial features
HP:0000294Low anterior hairline
HP:0000325Triangular face
HP:0000336Prominent supraorbital ridges
HP:0000340Sloping forehead
HP:0000343Long philtrum
HP:0000347Micrognathia
HP:0000348High forehead
HP:0000369Low-set ears
HP:0000407Sensorineural hearing impairment
HP:0000411Protruding ear
HP:0000426Prominent nasal bridge
HP:0000431Wide nasal bridge
HP:0000463Anteverted nares
HP:0000486Strabismus

GWAS associations

0 associations (top):

MeSH disease descriptors (11)

DescriptorNameTree numbers
D061085Agenesis of Corpus CallosumC10.500.034; C16.131.666.034; C23.300.008
D058540Aicardi SyndromeC10.500.034.687; C11.270.019; C16.131.162; C16.131.666.034.687; C16.320.290.019; C16.320.322.030
D016080Arachnoid CystsC04.182.044; C04.588.614.250.387.100; C10.500.142.100; C10.551.240.375.100; C16.131.666.142.100
D001321Autistic DisorderF03.625.164.113.500
D008607Intellectual DisabilityC10.597.606.360; C23.888.592.604.646; F01.700.687; F03.625.539
D065886Neurodevelopmental DisordersF03.625
C567924Infantile Epileptic-Dyskinetic Encephalopathy (supp.)
C564563Lissencephaly, X-Linked, 2 (supp.)
C564490Mental Retardation, X-Linked Nonsyndromic (supp.)
C563150Mental Retardation, X-Linked, With Or Without Seizures, Arx-Related (supp.)
C563110Proud Syndrome (supp.)

Drugs & pharmacology

Drug and pharmacology data

Is drug target: no

PharmGKB: 1 entry (VIP=true, CPIC=false)

CTD chemical–gene interactions

33 total (human), top 30 by PubMed support.

ChemicalActions (top 5)PubMed papers
Valproic Acidaffects expression, increases expression, increases methylation, affects cotreatment, decreases expression8
trichostatin Aaffects cotreatment, decreases expression3
mercuric bromidedecreases expression, affects cotreatment2
entinostatdecreases expression, affects cotreatment2
Panobinostataffects cotreatment, decreases expression2
Phenylmercuric Acetateaffects cotreatment, decreases expression2
p-Chloromercuribenzoic Aciddecreases expression, affects cotreatment2
aristolochic acid Iincreases expression1
methylmercuric chloridedecreases expression1
propionaldehydedecreases expression1
bisphenol Adecreases methylation1
arseniteincreases methylation1
2,3-bis(3’-hydroxybenzyl)butyrolactoneaffects cotreatment, decreases expression1
4-(5-benzo(1,3)dioxol-5-yl-4-pyridin-2-yl-1H-imidazol-2-yl)benzamideaffects cotreatment, decreases expression1
nutlin 3affects cotreatment, increases expression1
abrinedecreases expression1
dorsomorphinaffects cotreatment, decreases expression1
jinfukangdecreases expression1
Resveratrolaffects cotreatment, decreases expression1
Arbutindecreases expression1
Atrazineincreases expression1
Benzo(a)pyreneaffects methylation1
Caffeineincreases phosphorylation1
Camptothecinincreases expression1
Cisplatindecreases expression1
Coumestrolaffects cotreatment, decreases expression1
Dactinomycinaffects cotreatment, increases expression1
Diethylhexyl Phthalatedecreases expression1
Plant Extractsaffects cotreatment, decreases expression1
Silicon Dioxidedecreases expression1

Cellosaurus cell lines

5 cell lines: 3 induced pluripotent stem cell, 1 transformed cell line, 1 embryonic stem cell

First 10 cell lines (id-ordered, not curated):

CellosaurusNameCategorySex
CVCL_A7IQSHCDNi005-AInduced pluripotent stem cellMale
CVCL_A8MUOGHFUi001-AInduced pluripotent stem cellMale
CVCL_C0CKOGHFUi001-A-1Induced pluripotent stem cellMale
CVCL_C0LFGM28075Transformed cell lineMale
CVCL_C1W6SCSe001-A-4Embryonic stem cellMale

Clinical trials (associated diseases)

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

TrialPhaseStatusTitle
NCT01413711PHASE4WITHDRAWNAn Open-Label, Single and Multiple Oral Dose Pharmacokinetic Study of Vigabatrin in Infants With Infantile Spasms
NCT02092883PHASE4COMPLETEDEvaluation of Neuroinflammation in Children With Infantile Spasms
NCT04586348PHASE4UNKNOWNPrenatal Iodine Supplementation and Early Childhood Neurodevelopment
NCT04873115PHASE4UNKNOWNDouble-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,
NCT00211796PHASE4COMPLETEDDivalproex Sodium ER in Adult Autism
NCT00391261PHASE4COMPLETEDAn Open-label Trial of Metformin for Weight Control of Pediatric Patients on Antipsychotic Medications.
NCT00409747PHASE4COMPLETEDMinocycline to Treat Childhood Regressive Autism
NCT00576732PHASE4COMPLETEDA Study of the Effectiveness and Safety of Two Doses of Risperidone in the Treatment of Children and Adolescents With Autistic Disorder
NCT00844753PHASE4COMPLETEDAtomoxetine, Placebo and Parent Management Training in Autism
NCT01028820PHASE4COMPLETEDFMRI Brain Activation of Aripiprazole Treatment in Autism Spectrum Disorders
NCT01098383PHASE4UNKNOWNTreatment With Acetyl-Choline Esterase Inhibitors in Children With Autism Spectrum Disorders
NCT01333865PHASE4COMPLETEDA Study of Memantine Hydrochloride (Namenda®) for Cognitive and Behavioral Impairment in Adults With Autism Spectrum Disorders
NCT01337700PHASE4COMPLETEDMilnacipran in Autism and the Functional Locus Coeruleus and Noradrenergic Model of Autism
NCT01695200PHASE4COMPLETEDOmega-3 Fatty Acids in Autism Spectrum Disorders
NCT02069977PHASE4UNKNOWNStudy to Evaluate the Efficacy and Safety of Aripiprazole
NCT02096952PHASE4COMPLETEDMethylphenidate ER Liquid Formulation in Adults With ASD and ADHD
NCT02199925PHASE4UNKNOWNAn Open-Label Study to Evaluate the Efficacy of High-Dose Gammaplex in Children on the Autism Spectrum
NCT02235467PHASE4COMPLETEDMultisite Study: Parental Training Using Video Modelling to Develop Social Skills in Children With Autism
NCT02255565PHASE4COMPLETEDDose Response Effects of Quillivant XR in Children With ADHD and Autism: A Pilot Study
NCT02940574PHASE4COMPLETEDNeural and Behavioral Effects of Oxytocin in Autism Spectrum Disorders
NCT03333629PHASE4COMPLETEDPromoting Positive Outcomes for Individuals With ASD: Linking Early Detection, Treatment, and Long-term Outcomes
NCT03337646PHASE4COMPLETEDEvaluation of the Effect and Safety of Lisdexamfetamine in Children Aged 6-12 With ADHD and Autism
NCT03538431PHASE4COMPLETEDImproving Driving in Young People With Autism Spectrum Disorders
NCT03757585PHASE4COMPLETEDNatural Treatments for the Management of Emotional Dysregulation in Youth With Non-verbal Learning Disability (NVLD) and/or Autism Spectrum Disorders (ASD)
NCT04903353PHASE4COMPLETEDPragmatic Trial Comparing Weight Gain in Children With Autism Taking Risperidone Versus Aripiprazole
NCT05063656PHASE4COMPLETEDBiomarker-Driven Pharmacological Treatment of Adolescents With Autism Spectrum Disorder With Gabapentin
NCT05146245PHASE4UNKNOWNSafety and Pharmacokinetics of Antipsychotics in Children 2: Studying TDM in an RCT
NCT05916339PHASE4RECRUITINGAWARE: Management of ADHD in Autism Spectrum Disorder
NCT05954052PHASE4TERMINATEDA Study of Glutathione in Children With Autism Spectrum Disorder
NCT06853665PHASE4RECRUITINGThe TEAM Study - Treatment Efficacy for Autism/Attention Using Mixed Amphetamine
NCT07054697PHASE4COMPLETEDPilot-RCT With Individualized Homeopathic Treatment in the Children With Autism Spectrum Disorder
NCT07161804PHASE4COMPLETEDPilot RCT Using Homeopathic Medicines in ASD
NCT07439042PHASE4NOT_YET_RECRUITINGBuspirone for Anxiety in Autistic Youth
NCT06719141PHASE3RECRUITINGA Study to Investigate LP352 in Children and Adults With Developmental and Epileptic Encephalopathies (DEE)
NCT06908226PHASE3ENROLLING_BY_INVITATIONA Study to Investigate LP352 in Children and Adults With Developmental and Epileptic Encephalopathy (DEE)
NCT01575639PHASE3COMPLETEDPrednisolone in Infantile Spasms- High Dose Versus Usual Dose
NCT01828437PHASE3COMPLETEDAddition of Pyridoxine to Prednisolone in Infantile Spasms
NCT02299115PHASE3WITHDRAWNPrednisolone Versus Vigabatrin in the First-line Treatment of Infantile Spasms
NCT02953548PHASE3COMPLETEDTrial of Cannabidiol (CBD; GWP42003-P) for Infantile Spasms (GWPCARE7)
NCT02954887PHASE3COMPLETEDPhase 3 Trial of Cannabidiol (CBD; GWP42003-P) for Infantile Spasms: Open-label Extension Phase (GWPCARE7)