X-linked syndromic intellectual disability

disease
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Also known as intellectual disability, X-linked syndromicmental retardation, X-linked syndromicsyndromic intellectual disability, X-linkedsyndromic X-linked intellectual disability

Summary

X-linked syndromic intellectual disability (MONDO:0020119) is a disease (an umbrella term covering 81 Mondo subtypes) caused by DDX3X (GenCC Definitive), with 7 cohort genes.

At a glance

  • Causal gene: DDX3X (GenCC Definitive)
  • Umbrella term: 81 Mondo subtypes
  • Cohort genes: 7
  • ClinVar variants: 7

Clinical features

No curated clinical features (Orphanet) for this disease.

Identifiers

Disease identifiers

FieldValue
Canonical nameX-linked syndromic intellectual disability
Mondo IDMONDO:0020119
OMIM309510
Orphanet98464
DOIDDOID:0060309
Is cancer (heuristic)no

Also known as: intellectual disability, X-linked syndromic · mental retardation, X-linked syndromic · syndromic intellectual disability, X-linked · syndromic X-linked intellectual disability · X-linked syndromic intellectual disability

Data availability: 7 ClinVar variants · 2 GenCC gene-disease records.

Disease family

An umbrella term covering 81 Mondo subtypes.

Classification path: disease › human disease › disease by body system or component › nervous system disorderneurodevelopmental disorderintellectual disabilitysyndromic intellectual disabilityX-linked syndromic intellectual disability

Related subtypes (16): Smith-Magenis syndrome, intellectual disability, Buenos-Aires type, intellectual disability, Wolff type, CK syndrome, AHDC1-related intellectual disability - obstructive sleep apnea - mild dysmorphism syndrome, 7p22.1 microduplication syndrome, 9p13 microdeletion syndrome, 3q27.3 microdeletion syndrome, 9q31.1q31.3 microdeletion syndrome, Rubinstein-Taybi syndrome, 9q33.3q34.11 microdeletion syndrome, autosomal recessive syndromic intellectual disability, autosomal dominant syndromic intellectual disability, aplasia cutis-enamel dysplasia syndrome, 2p25.3 microduplication syndrome, dyneinopathy

Subtypes (81): X-linked intellectual disability-psychosis-macroorchidism syndrome, X-linked intellectual disability-plagiocephaly syndrome, intellectual disability, X-linked 49, MEHMO syndrome, syndromic X-linked intellectual disability 7, syndromic X-linked intellectual disability Shashi type, syndromic X-linked intellectual disability Lubs type, syndromic X-linked intellectual disability Abidi type, syndromic X-linked intellectual disability Siderius type, X-linked intellectual disability, Cabezas type, X-linked intellectual disability, Stocco dos Santos type, X-linked intellectual disability-cubitus valgus-dysmorphism syndrome, corpus callosum agenesis-intellectual disability-coloboma-micrognathia syndrome, X-linked intellectual disability-cerebellar hypoplasia syndrome, Allan-Herndon-Dudley syndrome, syndromic X-linked intellectual disability Claes-Jensen type, X-linked intellectual disability-retinitis pigmentosa syndrome, syndromic X-linked intellectual disability 14, syndromic X-linked intellectual disability 94, intellectual disability, X-linked syndromic, Turner type, syndromic X-linked intellectual disability Shrimpton type, X-linked intellectual disability-craniofacioskeletal syndrome, syndromic X-linked intellectual disability Raymond type, syndromic X-linked intellectual disability 17, syndromic X-linked intellectual disability Nascimento type, syndromic X-linked intellectual disability Chudley-Schwartz type, X-linked intellectual disability-cardiomegaly-congestive heart failure syndrome, X-linked intellectual disability, Cantagrel type, X-linked intellectual disability-short stature-overweight syndrome, intellectual disability, X-linked, syndromic 33, syndromic X-linked intellectual disability 34, intellectual disability, X-linked 99, syndromic, female-restricted, intellectual disability, X-linked, syndromic, Bain type, Borjeson-Forssman-Lehmann syndrome, Coffin-Lowry syndrome, syndromic X-linked intellectual disability 5, X-linked intellectual disability-seizures-psoriasis syndrome, Renpenning syndrome, Partington syndrome, syndromic X-linked intellectual disability 12, severe X-linked intellectual disability, Gustavson type, syndromic X-linked intellectual disability Snyder type, Wilson-Turner syndrome, Prieto syndrome, skeletal dysplasia-intellectual disability syndrome, X-linked intellectual disability-spastic quadriparesis syndrome, early-onset parkinsonism-intellectual disability syndrome, X-linked intellectual disability, Schimke type, X-linked intellectual disability, Cilliers type, X-linked intellectual disability, van Esch type, X-linked intellectual disability-epilepsy syndrome, ATR-X-related syndrome, X-linked intellectual disability-hypogonadism-ichthyosis-obesity-short stature syndrome, X-linked intellectual disability, Schutz type, X-linked intellectual disability-hypotonia-movement disorder syndrome, X-linked intellectual disability with isolated growth hormone deficiency, X-linked intellectual disability-hypogammaglobulinemia-progressive neurological deterioration syndrome, X-linked intellectual disability-precocious puberty-obesity syndrome, X-linked intellectual disability-epilepsy-progressive joint contractures-dysmorphism syndrome, X-linked intellectual disability-macrocephaly-macroorchidism syndrome, X-linked intellectual disability, Pai type, X-linked intellectual disability, Seemanova type, X-linked intellectual disability, Stevenson type, X-linked intellectual disability, Stoll type, X-linked intellectual disability-acromegaly-hyperactivity syndrome, X-linked intellectual disability-corpus callosum agenesis-spastic quadriparesis syndrome, fried syndrome, X-linked intellectual disability-ataxia-apraxia syndrome, intellectual developmental disorder, X-linked, syndromic, Pilorge type, Paganini-Miozzo syndrome, intellectual developmental disorder, X-linked, syndromic, Hackmann-Di Donato type, intellectual disability, X-linked, syndromic, 35, intellectual disability, X-linked, syndromic, Houge type, MED12-related intellectual disability syndrome, NAA10-related syndrome, ATP6AP2-related disorder, X-linked intellectual disability with hypopituitarism, SOX3-related X-linked pituitary hormone deficiency with or without intellectual developmental disorder, intellectual developmental disorder, X-linked, syndromic, with pigmentary mosaicism and coarse facies, intellectual developmental disorder, X-linked, syndromic 37, CASK-related intellectual disability

Genetics & variants

GWAS landscape

No GWAS associations recorded — common-variant (GWAS) studies don’t cover this disease (typical for Mendelian / rare diseases). See the curated gene cohort and Mendelian overlap below.

Variant details and genetic-evidence tiers

ClinVar germline variants

7 retrieved; paginated sample, class counts are floors:

2 uncertain significance, 2 pathogenic, 1 conflicting classifications of pathogenicity, 1 not provided, 1 likely pathogenic

ClinVarVariant (HGVS)GeneClassificationReview
1699292NM_001367721.1(CASK):c.2039+1G>ACASKPathogeniccriteria provided, single submitter
375706NM_001291867.2(NHS):c.4448C>G (p.Ser1483Cys)NHSPathogeniccriteria provided, single submitter
4075752NM_001272071.2(AP1S2):c.4C>T (p.Gln2Ter)AP1S2Likely pathogenicno assertion criteria provided
1704169NM_001356.5(DDX3X):c.1106C>G (p.Thr369Ser)DDX3XConflicting classifications of pathogenicitycriteria provided, conflicting classifications
2443366NM_153252.5(BRWD3):c.4057CAA[4] (p.Gln1354_Asp1355insGlnGln)BRWD3Uncertain significancecriteria provided, multiple submitters, no conflicts
1197312NM_004187.5(KDM5C):c.2944C>T (p.Arg982Cys)KDM5CUncertain significancecriteria provided, multiple submitters, no conflicts
1810328NM_001356.5(DDX3X):c.629C>T (p.Ala210Val)DDX3Xnot providedno classification provided

Genes & proteins

Mendelian disease overlap and somatic drivers

GenCC: 10 · Orphanet: 15 · OMIM-shared: 0 · Dual-evidence (GWAS+Mendelian): 0

GenCC gene–disease validity (cohort genes)

the Disease column is the GenCC-asserted condition — a cohort gene’s strongest validity may be for a related predisposition syndrome.

GeneClassificationInheritanceDiseaseRecords
DDX3XDefinitiveX-linkedintellectual disability, X-linked 1027
STEEP1ModerateX-linkedintellectual disability, X-linked 1073

Orphanet rare-disease linkage (cohort genes)

GeneOrphanet IDRare disease
DDX3XOrphanet:3338Toriello-Carey syndrome
DDX3XOrphanet:457260X-linked intellectual disability-hypotonia-movement disorder syndrome
DDX3XOrphanet:99861Precursor T-cell acute lymphoblastic leukemia
STEEP1Orphanet:777X-linked non-syndromic intellectual disability
KDM5COrphanet:85279KDM5C-related syndromic X-linked intellectual disability
CASKOrphanet:163937X-linked intellectual disability, Najm type
CASKOrphanet:1934Early infantile developmental and epileptic encephalopathy
CASKOrphanet:777X-linked non-syndromic intellectual disability
BRWD3Orphanet:528084Non-specific syndromic intellectual disability
AP1S2Orphanet:1568X-linked intellectual disability-Dandy-Walker malformation-basal ganglia disease-seizures syndrome
AP1S2Orphanet:85329X-linked intellectual disability-hypotonia-facial dysmorphism-aggressive behavior syndrome
AP1S2Orphanet:85335Fried syndrome
NHSOrphanet:627Nance-Horan syndrome
NHSOrphanet:98991Early-onset nuclear cataract
NHSOrphanet:98994Total early-onset cataract

Cohort genes → proteins

7 cohort genes, 7 distinct canonical proteins.

Evidence partition

SubsetGenes
multi_evidence7

Cohort genes (full)

SymbolHGNCEnsemblUniProtNameEvidence
DDX3XHGNC:2745ENSG00000215301O00571ATP-dependent RNA helicase DDX3Xgencc,clinvar
STEEP1HGNC:26239ENSG00000018610Q9H5V9STING ER exit proteingencc
KDM5CHGNC:11114ENSG00000126012P41229Lysine-specific demethylase 5Cclinvar
CASKHGNC:1497ENSG00000147044O14936Peripheral plasma membrane protein CASKclinvar
BRWD3HGNC:17342ENSG00000165288Q6RI45Bromodomain and WD repeat-containing protein 3clinvar
AP1S2HGNC:560ENSG00000182287P56377AP-1 complex subunit sigma-2clinvar
NHSHGNC:7820ENSG00000188158Q6T4R5Actin remodeling regulator NHSclinvar

Cohort function summary

Lead sentence per gene, UniProt-curated.

SymbolProtein nameFunction (lead sentence)
DDX3XATP-dependent RNA helicase DDX3XMultifunctional ATP-dependent RNA helicase.
STEEP1STING ER exit proteinMolecular adapter that stimulates membrane curvature formation and subsequent endoplasmic reticulum exit site (ERES) establishment by recruiting PI3K complex I, leading to COPII vesicle-mediated transport.
KDM5CLysine-specific demethylase 5CHistone demethylase that specifically demethylates ‘Lys-4’ of histone H3, thereby playing a central role in histone code.
CASKPeripheral plasma membrane protein CASKMultidomain scaffolding Mg(2+)-independent protein kinase that catalyzes the phosphotransfer from ATP to proteins such as NRXN1, and plays a role in synaptic transmembrane protein anchoring and ion channel trafficking.
BRWD3Bromodomain and WD repeat-containing protein 3Plays a role in the regulation of cell morphology and cytoskeletal organization.
AP1S2AP-1 complex subunit sigma-2Subunit of clathrin-associated adaptor protein complex 1 that plays a role in protein sorting in the late-Golgi/trans-Golgi network (TGN) and/or endosomes.
NHSActin remodeling regulator NHSMay function in cell morphology by maintaining the integrity of the circumferential actin ring and controlling lamellipod formation.

Protein-family classification

Druggable: 2 · Difficult: 2 · Unknown: 3 · Druggable fraction: 0.29

Family distribution

Cohort families vs a genome-wide background (hypergeometric, BH-FDR; fold = observed/expected). Counts kept; sorted by enrichment, so the catch-all Other/Unknown bucket no longer leads.

FamilyGenesFoldFDR
Kinase14.0×0.744
Scaffold/PPI12.5×0.744
Enzyme (other)11.7×0.744
Transcription factor11.2×0.744
Other/Unknown30.8×0.858

Per-gene assignment

SymbolFamilyDruggable?ECInterPro (top 3)
DDX3XEnzyme (other)yes3.6.4.13RNA-helicase_DEAD-box_CS, Helicase_C-like, DEAD/DEAH_box_helicase_dom
STEEP1Other/UnknownnoSTEEP-like, STEEP1_dom
KDM5CTranscription factorno1.14.11.67ARID_dom, Znf_PHD, JmjC_dom
CASKKinaseyes2.7.11.1Prot_kinase_dom, SH3_domain, PDZ
BRWD3Scaffold/PPInoBromodomain, WD40_rpt, WD40/YVTN_repeat-like_dom_sf
AP1S2Other/UnknownnoClathrin_sm-chain_CS, Longin-like_dom_sf, AP_complex_ssu
NHSOther/UnknownnoNHS-like

Expression context

Cohort genes with no expression data: 0.

7 cohort genes are a single-cell marker in ≥1 SCXA experiment.

Breadth distribution (Bgee present_calls)

BucketGenes
narrow (1-5 tissues)0
moderate (6-20)0
broad (>20)7
unknown0

Top tissues across cohort

TissueCohort genes
oocyte2
stromal cell of endometrium2
buccal mucosa cell2
choroid plexus epithelium1
sperm1
secondary oocyte1
right uterine tube1
sural nerve1
cortical plate1
hair follicle1
calcaneal tendon1
epithelial cell of pancreas1
tendon of biceps brachii1
cauda epididymis1
corpus epididymis1
monocyte1
endothelial cell1
oviduct epithelium1

Per-gene tissue summary (top 30)

SymbolBgee breadthFANTOM5 breadthSCXATop tissues
DDX3X294ubiquitousmarkerchoroid plexus epithelium, oocyte, sperm
STEEP1240ubiquitousmarkeroocyte, stromal cell of endometrium, secondary oocyte
KDM5C279ubiquitousmarkersural nerve, stromal cell of endometrium, right uterine tube
CASK284ubiquitousmarkerbuccal mucosa cell, hair follicle, cortical plate
BRWD3223ubiquitousmarkertendon of biceps brachii, epithelial cell of pancreas, calcaneal tendon
AP1S2289ubiquitousmarkercorpus epididymis, cauda epididymis, monocyte
NHS214ubiquitousmarkeroviduct epithelium, buccal mucosa cell, endothelial cell

Protein interactions among cohort

Intra-cohort edges: 1.

Hub genes (top 10 by interactor count)

SymbolInteractor count
DDX3X6,454
CASK4,223
KDM5C4,183
BRWD32,714
AP1S21,346
STEEP11,195
NHS970

Intra-cohort edges

ABSources
DDX3XKDM5Cstring_interaction

Structural data

PDB: 4 · AlphaFold-only: 3 · No structure: 0

Cohort genes with PDB structures (top 30)

SymbolUniProtPDB entries
CASKO1493622
DDX3XO0057117
STEEP1Q9H5V92
KDM5CP412292

AlphaFold-only cohort genes (top 30 by pLDDT)

SymbolUniProtpLDDT
AP1S2P5637794.36
BRWD3Q6RI4565.11
NHSQ6T4R543.65

Function

Pathway analysis

Distinct Reactome pathways touched by cohort: 35. Enrichment computed across 7 evidence-associated genes (6 with Reactome annotation).

Pathways by enrichment

Over-representation of cohort genes vs the genome-wide background (hypergeometric test, Benjamini-Hochberg FDR; fold = observed/expected over 6 annotated cohort genes). Counts and members are kept as ground-truth; sorted by enrichment.

PathwayCohort genesFoldFDRSample cohort genes
Nef mediated downregulation of MHC class I complex cell surface expression1190.3×0.070AP1S2
Nef-mediates down modulation of cell surface receptors by recruiting them to clathrin adapters1105.7×0.070AP1S2
The role of Nef in HIV-1 replication and disease pathogenesis1105.7×0.070AP1S2
Dopamine Neurotransmitter Release Cycle182.8×0.070CASK
Nephrin family interactions179.3×0.070CASK
Syndecan interactions170.5×0.070CASK
Host Interactions of HIV factors156.0×0.070AP1S2
Dengue virus activates/modulates innate and adaptive immune responses156.0×0.070DDX3X
Lysosome Vesicle Biogenesis154.4×0.070AP1S2
trans-Golgi Network Vesicle Budding142.3×0.070AP1S2
Assembly and cell surface presentation of NMDA receptors142.3×0.070CASK
HDMs demethylate histones138.1×0.070KDM5C
Sensory processing of sound by outer hair cells of the cochlea134.0×0.070CASK
Golgi Associated Vesicle Biogenesis133.4×0.070AP1S2
Neurexins and neuroligins132.8×0.070CASK
Sensory processing of sound by inner hair cells of the cochlea127.2×0.079CASK
RAC2 GTPase cycle121.1×0.091NHS
HIV Infection119.8×0.091AP1S2
RAC3 GTPase cycle119.8×0.091NHS
mRNA Splicing118.3×0.093STEEP1
MHC class II antigen presentation114.9×0.109AP1S2
Processing of Capped Intron-Containing Pre-mRNA113.7×0.109STEEP1
Chromatin organization113.6×0.109KDM5C
Chromatin modifying enzymes112.1×0.117KDM5C
RAC1 GTPase cycle110.2×0.132NHS
mRNA Splicing - Major Pathway19.1×0.141STEEP1
Metabolism of RNA17.0×0.176STEEP1
Membrane Trafficking16.2×0.189AP1S2
Vesicle-mediated transport15.8×0.194AP1S2
Viral Infection Pathways15.1×0.209AP1S2

GO biological processes by enrichment

Over-representation of cohort genes vs the genome-wide background (hypergeometric test, Benjamini-Hochberg FDR; fold = observed/expected over 7 annotated cohort genes). Counts and members are kept as ground-truth; sorted by enrichment.

GO termCohort genesFoldFDRSample cohort genes
negative regulation of cellular response to growth factor stimulus11203.7×0.022CASK
positive regulation of toll-like receptor 8 signaling pathway1802.5×0.022DDX3X
positive regulation of translation in response to endoplasmic reticulum stress1601.9×0.022DDX3X
positive regulation of toll-like receptor 7 signaling pathway1481.5×0.022DDX3X
positive regulation of chemokine (C-C motif) ligand 5 production1401.2×0.022DDX3X
cytosolic ribosome assembly1343.9×0.022DDX3X
endoplasmic reticulum membrane organization1343.9×0.022STEEP1
protein exit from endoplasmic reticulum1300.9×0.022STEEP1
cellular response to arsenic-containing substance1300.9×0.022DDX3X
positive regulation of protein K63-linked ubiquitination1300.9×0.022DDX3X
protein localization to cytoplasmic stress granule1300.9×0.022DDX3X
negative regulation of wound healing1185.2×0.029CASK
cellular response to osmotic stress1172.0×0.029DDX3X
positive regulation of mitochondrial translation1160.5×0.029DDX3X
positive regulation of calcium ion import1133.8×0.029CASK
negative regulation of cell-matrix adhesion1126.7×0.029CASK
cytoplasmic pattern recognition receptor signaling pathway1126.7×0.029DDX3X
gamete generation1126.7×0.029DDX3X
melanosome assembly1126.7×0.029AP1S2
positive regulation of translational initiation1120.4×0.029DDX3X
calcium ion import1114.6×0.029CASK
regulation of neurotransmitter secretion1109.4×0.029CASK
negative regulation of intrinsic apoptotic signaling pathway1109.4×0.029DDX3X
negative regulation of keratinocyte proliferation1100.3×0.029CASK
platelet dense granule organization196.3×0.029AP1S2
positive regulation of interferon-alpha production192.6×0.029DDX3X
stress granule assembly186.0×0.029DDX3X
positive regulation of viral genome replication183.0×0.029DDX3X
positive regulation of NLRP3 inflammasome complex assembly183.0×0.029DDX3X
negative regulation of extrinsic apoptotic signaling pathway via death domain receptors183.0×0.029DDX3X

Therapeutics

Drug target analysis

Approved (phase 4): 3 · Phase ≥3: 3 · Phased (≥1): 3 · Undrugged: 4

Druggability breadth: 5 of 7 evidence-associated genes (71%) have a ChEMBL target (buckets above are over the deeply-mined display cohort).

Genes with an approved drug

The molecule shown is one approved compound that hits the gene — not necessarily a drug of choice or one indicated for this disease.

SymbolExample approved molecule
DDX3XIMATINIB
KDM5CDEFERIPRONE
CASKFEDRATINIB

Top cohort targets by molecule count

SymbolMoleculesMax phase
CASK94
DDX3X14
KDM5C14
STEEP100
BRWD300
AP1S200
NHS00

Drugs targeting cohort genes (top 30)

MoleculeMax phaseTargets in cohort
IMATINIB4DDX3X
DEFERIPRONE4KDM5C
FEDRATINIB4CASK
RUXOLITINIB4CASK
BOSUTINIB4CASK
CRIZOTINIB4CASK
LESTAURTINIB3CASK
CYC-0652CASK
RG-5472CASK
AT-75192CASK
BMS-3870321CASK

Bioactivity and enzyme data

Enzyme cohort genes (≥1 EC): 3.

Cohort genes with ChEMBL bioactivity (full, sorted by assay count)

SymbolAssaysType breakdown
CASK92Binding:92
KDM5C49Binding:49
DDX3X32Binding:31, ADMET:1
STEEP16Binding:6
BRWD35Binding:5

Cohort enzymes (BRENDA EC)

SymbolEC numbersNames
DDX3X3.6.4.13RNA helicase
KDM5C1.14.11.67[histone H3]-trimethyl-L-lysine4 demethylase
CASK2.7.11.1, 2.7.4.8non-specific serine/threonine protein kinase, guanylate kinase

Pharmacogenomics

Cohort genes with a PharmGKB record: 7; with CPIC/DPWG dosing guidelines: 0.

No cohort gene has a CPIC/DPWG genotype-guided dosing guideline (PharmGKB).

Chemical tractability of cohort targets

11 approved/phased compounds have measured bioactivity against a cohort gene (and aren’t yet in disease-level trials). This is a research / tractability signal, NOT a therapeutic recommendation — a bioactivity row often reflects off-target or screening binding (e.g. promiscuous kinase inhibitors against a cohort kinase), implying no disease mechanism.

CompoundMax phaseCohort target (bioactivity)
IMATINIB4DDX3X
DEFERIPRONE4KDM5C
FEDRATINIB4CASK
RUXOLITINIB4CASK
BOSUTINIB4CASK
CRIZOTINIB4CASK
LESTAURTINIB3CASK
CYC-0652CASK
RG-5472CASK
AT-75192CASK
BMS-3870321CASK

Druggability pyramid

Cohort genes binned by druggability tier (high → low):

TierDefinitionGenesSymbols
AApproved (phase 4 drug)3DDX3X, KDM5C, CASK
BPhased (≥1) drug, not yet approved0
CDruggable family + PDB, no drug0
DDruggable family + AlphaFold only, no drug0
EDifficult family or no structure, no drug4STEEP1, BRWD3, AP1S2, NHS

Undrugged target profiles

4 cohort genes are undrugged. Ranked by ‘starting-point quality’ (assay depth + drugged-partner adjacency).

SymbolChEMBL assaysDrugged partners (top 3)
STEEP16
BRWD35
AP1S20
NHS0

Clinical trials & evidence

Clinical trials

Clinical trials: 0.