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GeneE
10 sources retrieved Β· Most recent: April 2026 Β· Index updated 14 days ago
β“˜GeneE is for informational purposes only. It is not a substitute for professional medical advice, diagnosis, or treatment.
ARX
aristaless related homeobox
Chromosome X Β· Xp21.3
NCBI Gene: 170302Ensembl: ENSG00000004848.8HGNC: HGNC:18060UniProt: Q96QS3
104PubMed Papers
25Diseases
0Drugs
142Pathogenic Variants
FUNCTIONAL ROLE
Highly ConstrainedTranscription Factor
RESEARCH IMPACT
Variant-Rich
CLINICAL
OMIM Disease Gene
DATA QUALITY
βœ“ Experimental GO Evidenceβœ“ Swiss-Prot Reviewed
DNA-binding transcription repressor activity, RNA polymerase II-specificintestinal type G enteroendocrine cell differentiationintestinal type I enteroendocrine cell differentiationintestinal type L enteroendocrine cell differentiationX-linked lissencephaly with abnormal genitaliaSpasticity - intellectual disability - X-linked epilepsydevelopmental and epileptic encephalopathy, 1Partington syndrome
✦AI Summary

ARX is an X-linked transcription factor essential for neurodevelopment that binds the sequence motif 5'-TAATTA-3' in regulatory elements 12. It positively modulates transcription of target genes including histone demethylase KDM5C, functioning synergistically with PHF8 2. ARX operates as a bifunctional regulator, capable of both activating and repressing RNA polymerase II-dependent transcription 3. During brain development, ARX is critical for neuronal proliferation, interneuronal migration, and differentiation in the embryonic forebrain 4. ARX mutations rank among the most common causes of X-linked intellectual disability, found in approximately 9.5% of X-linked families and 1 in 12,000 male births, second only to Fragile X syndrome 56. Truncating mutations typically cause severe cortical malformations including X-linked lissencephaly with abnormal genitalia, characterized by lissencephaly, corpus callosum agenesis, and intractable seizures 7. In contrast, insertion and missense mutations produce epilepsy and intellectual disability without cortical dysplasia 7. ARX mutations account for up to 5% of infantile spasms cases and are associated with developmental and epileptic encephalopathy, autism spectrum disorder, and Partington syndrome 46. Female carriers with de novo variants show variable penetrance, with 41% manifesting severe phenotypes including intellectual disability 8.

Sources cited
1
ARX binds DNA sequence motif 5'-TAATTA-3' in regulatory elements
PMID: 22194193
2
ARX positively modulates KDM5C transcription and acts synergistically with PHF8
PMID: 31691806
3
ARX functions as bifunctional transcription factor capable of activation and repression
PMID: 35328505
4
ARX is critical for interneuronal migration and neuronal development; accounts for up to 5% of infantile spasms cases
PMID: 38328230
5
ARX mutations found in 9.5% of X-linked intellectual disability families; second most common X-linked cause after Fragile X
PMID: 16650978
6
ARX mutations occur in 1 in 12,000 male births; associated with multiple neurodevelopmental disorders
PMID: 18975239
7
Truncating mutations cause severe cortical malformations including lissencephaly; insertion/missense mutations cause epilepsy without cortical dysplasia
PMID: 14631200
8
Female carriers with de novo ARX variants show 41% severe phenotype including intellectual disability
PMID: 37879892
Disease Associationsβ“˜25
X-linked lissencephaly with abnormal genitaliaOpen Targets
0.81Strong
Spasticity - intellectual disability - X-linked epilepsyOpen Targets
0.80Strong
developmental and epileptic encephalopathy, 1Open Targets
0.79Strong
Partington syndromeOpen Targets
0.78Strong
intellectual disability, X-linked, with or without seizures, ARX-relatedOpen Targets
0.76Strong
corpus callosum agenesis-abnormal genitalia syndromeOpen Targets
0.76Strong
X-linked non-syndromic intellectual disabilityOpen Targets
0.72Strong
infantile spasmsOpen Targets
0.67Moderate
genetic developmental and epileptic encephalopathyOpen Targets
0.67Moderate
infantile epileptic-dyskinetic encephalopathyOpen Targets
0.66Moderate
X-linked spasticity-intellectual disability-epilepsy syndromeOpen Targets
0.62Moderate
genetic disorderOpen Targets
0.52Moderate
developmental and epileptic encephalopathy 91Open Targets
0.49Moderate
X-linked complex neurodevelopmental disorderOpen Targets
0.46Moderate
Intellectual disabilityOpen Targets
0.44Moderate
early-infantile DEEOpen Targets
0.37Weak
non-syndromic X-linked intellectual disabilityOpen Targets
0.37Weak
Aicardi syndromeOpen Targets
0.34Weak
VentriculomegalyOpen Targets
0.34Weak
Abnormal synaptic transmissionOpen Targets
0.33Weak
Agenesis of the corpus callosum, with abnormal genitaliaUniProt
Developmental and epileptic encephalopathy 1UniProt
Intellectual developmental disorder, X-linked 29UniProt
Lissencephaly, X-linked 2UniProt
Partington syndromeUniProt
Pathogenic Variants142
NM_139058.3(ARX):c.426_449dup (p.Gly143_Ala150dup)Pathogenic
Developmental and epileptic encephalopathy, 1;Intellectual disability, X-linked, with or without seizures, ARX-related|Inborn genetic diseases|Intellectual disability, X-linked, with or without seizures, ARX-related
β˜…β˜…β˜†β˜†2026β†’ Residue 143
NM_139058.3(ARX):c.441_464dup (p.Ala148_Ala155dup)Pathogenic
not provided|X-linked lissencephaly with abnormal genitalia|Intellectual disability, X-linked, with or without seizures, ARX-related;Developmental and epileptic encephalopathy, 1|X-linked lissencephaly with abnormal genitalia;Partington syndrome;Intellectual disability, X-linked, with or without seizures, ARX-related;Corpus callosum agenesis-abnormal genitalia syndrome;Developmental and epileptic encephalopathy, 1|Partington syndrome
β˜…β˜…β˜†β˜†2026β†’ Residue 148
NM_139058.3(ARX):c.1111C>T (p.Arg371Ter)Pathogenic
not provided|Developmental and epileptic encephalopathy, 1;Intellectual disability, X-linked, with or without seizures, ARX-related|X-linked ARX-related disorders
β˜…β˜…β˜†β˜†2025β†’ Residue 371
NM_139058.3(ARX):c.590del (p.Gly197fs)Pathogenic
not provided|X-linked ARX-related disorders
β˜…β˜…β˜†β˜†2025β†’ Residue 197
NM_139058.3(ARX):c.306GGC[17] (p.Ala109_Ala115dup)Pathogenic
Developmental and epileptic encephalopathy, 1|X-linked lissencephaly with abnormal genitalia|Developmental and epileptic encephalopathy, 1;Intellectual disability, X-linked, with or without seizures, ARX-related|not provided|Inborn genetic diseases|Intellectual disability, X-linked, with or without seizures, ARX-related|West syndrome|Partington syndrome;X-linked lissencephaly with abnormal genitalia;Developmental and epileptic encephalopathy, 1;Intellectual disability, X-linked, with or without seizures, ARX-related;Corpus callosum agenesis-abnormal genitalia syndrome
β˜…β˜…β˜†β˜†2025β†’ Residue 109
NM_139058.3(ARX):c.1150C>T (p.Arg384Cys)Pathogenic
Developmental and epileptic encephalopathy, 1;Intellectual disability, X-linked, with or without seizures, ARX-related|X-linked ARX-related disorders
β˜…β˜…β˜†β˜†2025β†’ Residue 384
NM_139058.3(ARX):c.922G>T (p.Glu308Ter)Pathogenic
Inborn genetic diseases|not provided
β˜…β˜…β˜†β˜†2025β†’ Residue 308
NM_139058.3(ARX):c.309_341dup (p.Ala105_Ala115dup)Pathogenic
Developmental and epileptic encephalopathy, 1|Intellectual disability, X-linked, with or without seizures, ARX-related;Developmental and epileptic encephalopathy, 1
β˜…β˜…β˜†β˜†2025β†’ Residue 105
NM_139058.3(ARX):c.995G>A (p.Arg332His)Pathogenic
X-linked lissencephaly with abnormal genitalia|not provided|Developmental and epileptic encephalopathy, 1;Intellectual disability, X-linked, with or without seizures, ARX-related|Corpus callosum agenesis-abnormal genitalia syndrome
β˜…β˜…β˜†β˜†2024β†’ Residue 332
NM_139058.3(ARX):c.303_323dup (p.Ala109_Ala115dup)Pathogenic
Intellectual disability, X-linked, with or without seizures, ARX-related;Developmental and epileptic encephalopathy, 1|not provided|Developmental and epileptic encephalopathy, 1
β˜…β˜…β˜†β˜†2024β†’ Residue 109
NM_139058.3(ARX):c.994C>T (p.Arg332Cys)Pathogenic
Arachnoid cyst;Corpus callosum, agenesis of;Periventricular heterotopia|not provided
β˜…β˜…β˜†β˜†2024β†’ Residue 332
NM_139058.3(ARX):c.956C>A (p.Ser319Ter)Pathogenic
Intellectual disability, X-linked, with or without seizures, ARX-related;Developmental and epileptic encephalopathy, 1|X-linked lissencephaly with abnormal genitalia|not provided|ARX-related disorder
β˜…β˜…β˜†β˜†2024β†’ Residue 319
NM_139058.3(ARX):c.1058C>T (p.Pro353Leu)Pathogenic
Developmental and epileptic encephalopathy, 1|Inborn genetic diseases|Partington syndrome;X-linked lissencephaly with abnormal genitalia;Developmental and epileptic encephalopathy, 1;Intellectual disability, X-linked, with or without seizures, ARX-related;Corpus callosum agenesis-abnormal genitalia syndrome
β˜…β˜…β˜†β˜†2024β†’ Residue 353
NM_139058.3(ARX):c.880G>T (p.Glu294Ter)Pathogenic
X-linked lissencephaly with abnormal genitalia|Developmental and epileptic encephalopathy, 1;Intellectual disability, X-linked, with or without seizures, ARX-related
β˜…β˜…β˜†β˜†2024β†’ Residue 294
NM_139058.3(ARX):c.306GGC[18] (p.Ala108_Ala115dup)Pathogenic
X-linked lissencephaly with abnormal genitalia|Developmental and epileptic encephalopathy, 1;Intellectual disability, X-linked, with or without seizures, ARX-related
β˜…β˜…β˜†β˜†2024β†’ Residue 108
NM_139058.3(ARX):c.357_391del (p.Gly120fs)Pathogenic
Inborn genetic diseases|Developmental and epileptic encephalopathy, 1;Intellectual disability, X-linked, with or without seizures, ARX-related
β˜…β˜…β˜†β˜†2024β†’ Residue 120
NM_139058.3(ARX):c.1112G>A (p.Arg371Gln)Likely pathogenic
Intellectual disability, X-linked, with or without seizures, ARX-related|not provided
β˜…β˜…β˜†β˜†2023β†’ Residue 371
NM_139058.3(ARX):c.994C>G (p.Arg332Gly)Pathogenic
Developmental and epileptic encephalopathy, 1;Intellectual disability, X-linked, with or without seizures, ARX-related|Partington syndrome;X-linked lissencephaly with abnormal genitalia;Corpus callosum agenesis-abnormal genitalia syndrome;Developmental and epileptic encephalopathy, 1;Intellectual disability, X-linked, with or without seizures, ARX-related
β˜…β˜…β˜†β˜†2023β†’ Residue 332
NM_139058.3(ARX):c.1471dup (p.Leu491fs)Pathogenic
X-linked lissencephaly with abnormal genitalia|not provided
β˜…β˜…β˜†β˜†2023β†’ Residue 491
NM_139058.3(ARX):c.1472del (p.Leu491fs)Pathogenic
Developmental and epileptic encephalopathy, 1
β˜…β˜…β˜†β˜†2023β†’ Residue 491
View on ClinVar β†—
Related Genes
ALX3Shared pathway100%ISXShared pathway100%DRGXShared pathway100%PNKPProtein interaction78%SCN1AProtein interaction76%SPTAN1Protein interaction76%
Tissue Expression6 tissues
Ovary
100%
Brain
4%
Lung
0%
Bone Marrow
0%
Heart
0%
Liver
0%
Gene Interaction Network
Click a node to explore
ARXALX3ISXDRGXPNKPSCN1ASPTAN1
PROTEIN STRUCTURE
Preparing viewer…
AlphaFoldAI-predicted Β· UniProt Q96QS3
View on AlphaFold β†—
Constraintβ“˜
LOEUFβ“˜
0.21Highly Constrained
pLIβ“˜
1.00Intolerant
Observed/Expected LoF0.04 [0.02–0.21]
RankingsWhere ARX stands among ~20K protein-coding genes
  • #4,570of 20,598
    Most Researched104 Β· top quartile
  • #533of 5,498
    Most Pathogenic Variants142 Β· top 10%
  • #486of 17,882
    Most Constrained (LOEUF)0.21 Β· top 5%
Genes detectedARX
Sources retrieved10 papers
Response timeβ€”
πŸ“„ Sources
10β–Ό
1
X-Linked Epilepsies: A Narrative Review.
PMID: 38612920
Int J Mol Sci Β· 2024
1.00
2
Further characterisation of
PMID: 37879892
J Med Genet Β· 2024
0.90
3
Dual effects of
PMID: 38328230
bioRxiv Β· 2024
0.80
4
[ARX--one gene--many phenotypes].
PMID: 18975239
Neurol Neurochir Pol Β· 2008
0.70
5
Further Delineation of Duplications of
PMID: 35328505
Int J Mol Sci Β· 2022
0.60