Intellectual disability, autosomal dominant 30

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Also known as autosomal dominant intellectual disability 30intellectual disability, autosomal dominant type 30intellectual disability-expressive aphasia-facial dysmorphism syndrome caused by mutation in ZMYND11mental retardation, autosomal dominant 30mental retardation, autosomal dominant type 30MRD30ZMYND11 intellectual disability-expressive aphasia-facial dysmorphism syndrome

Summary

Intellectual disability, autosomal dominant 30 (MONDO:0014486) is a disease caused by ZMYND11 (GenCC Strong), with 2 cohort genes.

At a glance

  • Causal gene: ZMYND11 (GenCC Strong)
  • Cohort genes: 2
  • ClinVar variants: 91

Clinical features

No curated clinical features (Orphanet) for this disease.

Identifiers

Disease identifiers

FieldValue
Canonical nameintellectual disability, autosomal dominant 30
Mondo IDMONDO:0014486
OMIM616083
Orphanet694304, 694308
DOIDDOID:0070060
UMLSC4015167
MedGen863604
GARD0013136
Is cancer (heuristic)no

Also known as: autosomal dominant intellectual disability 30 · intellectual disability, autosomal dominant 30 · intellectual disability, autosomal dominant type 30 · intellectual disability-expressive aphasia-facial dysmorphism syndrome caused by mutation in ZMYND11 · mental retardation, autosomal dominant 30 · mental retardation, autosomal dominant type 30 · MRD30 · ZMYND11 intellectual disability-expressive aphasia-facial dysmorphism syndrome

Data availability: 91 ClinVar variants · 4 GenCC gene-disease records.

Disease family

Classification path: disease › human disease › disease by etiologic mechanism › disease of genetic or genomic mechanism › hereditary disease › autosomal genetic disease › autosomal dominant disease › intellectual disability, autosomal dominant 30

Related subtypes (191): autosomal dominant polycystic liver disease, cerebral arteriopathy, autosomal dominant, with subcortical infarcts and leukoencephalopathy, type 1, tuberous sclerosis, Treacher-Collins syndrome, hereditary breast ovarian cancer syndrome, autosomal dominant polycystic kidney disease, Lynch syndrome, branchio-oto-renal syndrome, autosomal dominant Aarskog syndrome, acroosteolysis dominant type, ADULT syndrome, autosomal dominant Alport syndrome, amelogenesis imperfecta type 1B, Townes-Brocks syndrome, nevoid basal cell carcinoma syndrome, blepharophimosis, ptosis, and epicanthus inversus syndrome, autosomal dominant brachyolmia, branchiooculofacial syndrome, pheochromocytoma/paraganglioma syndrome 4, cataract-aberrant oral frenula-growth delay syndrome, cherubism, autosomal dominant chondrodysplasia punctata, autosomal dominant popliteal pterygium syndrome, blepharocheilodontic syndrome, cochleosaccular degeneration-cataract syndrome, renal coloboma syndrome, Beare-Stevenson cutis gyrata syndrome, autosomal dominant vibratory urticaria, neurohypophyseal diabetes insipidus, autosomal dominant Kenny-Caffey syndrome, Rapp-Hodgkin syndrome, Ehlers-Danlos syndrome, classic type, autosomal dominant Ehlers-Danlos syndrome, vascular type, multiple endocrine neoplasia type 1, Coffin-Siris syndrome 1, isolated congenital adermatoglyphia, Flynn-Aird syndrome, Frasier syndrome, hand-foot-genital syndrome, Holt-Oram syndrome, hyperkeratosis-hyperpigmentation syndrome, autosomal dominant ichthyosis vulgaris, hyper-IgE recurrent infection syndrome 1, autosomal dominant, autosomal dominant keratitis, autosomal dominant keratitis-ichthyosis-hearing loss syndrome, LADD syndrome, trichorhinophalangeal syndrome type II, Noonan syndrome with multiple lentigines, microcephaly with or without chorioretinopathy, lymphedema, or intellectual disability, Marfan syndrome, melanoma, cutaneous malignant, susceptibility to, 2, autosomal dominant primary microcephaly, autosomal dominant progressive external ophthalmoplegia, monilethrix, Muir-Torre syndrome, autosomal dominant myoglobinuria, autosomal dominant centronuclear myopathy, nail-patella syndrome, multiple endocrine neoplasia type 2B, autosomal dominant omodysplasia, pheochromocytoma/paraganglioma syndrome 1, Pelger-Huet anomaly, multiple endocrine neoplasia type 2A, piebaldism, autosomal dominant medullary cystic kidney disease with or without hyperuricemia, generalized juvenile polyposis/juvenile polyposis coli, juvenile polyposis/hereditary hemorrhagic telangiectasia syndrome, Peutz-Jeghers syndrome, contractures, pterygia, and spondylocarpotarsal fusion syndrome 1A, autosomal dominant distal renal tubular acidosis, retinoschisis, autosomal dominant, autosomal dominant Robinow syndrome, scapuloperoneal spinal muscular atrophy, autosomal dominant, autosomal dominant sideroblastic anemia, spondyloepiphyseal dysplasia tarda, autosomal dominant, proximal symphalangism, calcaneonavicular coalition, thanatophoric dysplasia type 1, trichorhinophalangeal syndrome type I, Muckle-Wells syndrome, autosomal dominant hypophosphatemic rickets, von Hippel-Lindau disease, Denys-Drash syndrome, autosomal dominant severe congenital neutropenia, Costello syndrome, EEC syndrome, multiple cutaneous and mucosal venous malformations, diffuse nonepidermolytic palmoplantar keratoderma, Timothy syndrome, pheochromocytoma/paraganglioma syndrome 2, spondyloepimetaphyseal dysplasia with multiple dislocations, Brooke-Spiegler syndrome, macrocephaly-autism syndrome, pheochromocytoma/paraganglioma syndrome 3, Duane-radial ray syndrome, PCWH syndrome, heart-hand syndrome, Slovenian type, congenital stationary night blindness autosomal dominant 3, mandibulofacial dysostosis-microcephaly syndrome, multiple endocrine neoplasia type 4, juvenile cataract-microcornea-renal glucosuria syndrome, Crouzon syndrome-acanthosis nigricans syndrome, Birk-Barel syndrome, thrombophilia due to protein S deficiency, autosomal dominant, dyskeratosis congenita, autosomal dominant 2, dyskeratosis congenita, autosomal dominant 3, colorectal cancer, hereditary nonpolyposis, type 6, colorectal cancer, hereditary nonpolyposis, type 7, brain small vessel disease 2A, autosomal dominant, intellectual disability, autosomal dominant 14, intellectual disability, autosomal dominant 15, intellectual disability, autosomal dominant 16, hypopigmentation-punctate palmoplantar keratoderma syndrome, intellectual disability-facial dysmorphism syndrome due to SETD5 haploinsufficiency, postaxial polydactyly-anterior pituitary anomalies-facial dysmorphism syndrome, intellectual developmental disorder with microcephaly and with or without ocular malformations or hypogonadotropic hypogonadism, intellectual disability, autosomal dominant 29, Houge-Janssens syndrome 2, severe achondroplasia-developmental delay-acanthosis nigricans syndrome, dyskeratosis congenita, autosomal dominant 6, epidermolysis bullosa simplex 6, generalized, with scarring and hair loss, autosomal dominant complex spastic paraplegia, early-onset autosomal dominant Alzheimer disease, muscular dystrophy, limb-girdle, autosomal dominant, Feingold syndrome, Carney complex, neuronopathy, distal hereditary motor, autosomal dominant, autosomal dominant coarctation of aorta, autosomal dominant spondylocostal dysostosis, autosomal dominant hypohidrotic ectodermal dysplasia, Cowden disease, autosomal dominant distal myopathy, autosomal dominant rhegmatogenous retinal detachment, palmoplantar keratoderma-spastic paralysis syndrome, Alagille syndrome due to a JAG1 point mutation, PTEN hamartoma tumor syndrome, gastric adenocarcinoma and proximal polyposis of the stomach, autosomal dominant proximal renal tubular acidosis, autosomal dominant spastic ataxia, Waardenburg syndrome, hereditary retinoblastoma, autosomal dominant hypocalcemia, Li-Fraumeni syndrome, Loeys-Dietz syndrome, hereditary hemorrhagic telangiectasia, hereditary inclusion body myopathy-joint contractures-ophthalmoplegia syndrome, microcephalic osteodysplastic dysplasia, Saul-Wilson type, autosomal dominant intermediate Charcot-Marie-Tooth disease, autosomal dominant cutis laxa, autosomal dominant nonsyndromic hearing loss, autosomal dominant optic atrophy, autosomal dominant Emery-Dreifuss muscular dystrophy, autosomal dominant cerebellar ataxia, autosomal dominant osteopetrosis, autosomal dominant epidermolytic ichthyosis, ventricular arrhythmias due to cardiac ryanodine receptor calcium release deficiency syndrome, distal arthrogryposis type 2B1, neurofibromatosis, autosomal dominant cataract, arthrogryposis, distal, type 2B2, arthrogryposis, distal, type 2B3, Charcot-Marie-Tooth disease, demyelinating, type 1G, Delpire-McNeill syndrome, LAMA5-related multisystemic syndrome, autosomal dominant oculocutaneous albinism, Charcot-Marie-tooth disease, axonal, type 2DD, Pilarowski-Bjornsson syndrome, intellectual disability, autosomal dominant, fatty acyl-CoA reductase 1 upregulation, GUCY2D-related dominant retinopathy, RPE65-related dominant retinopathy, autosomal dominant titinopathy, NOG-related symphalangism spectrum disorder, ALPL-related autosomal dominant hypophosphatasia, MYH10-related neurodevelopmental disorder with congenital anomalies, spastic paraplegia 30A, autosomal dominant, TMEM127-related tumor predisposition, MAX-related tumor predisposition, BMPR1A-related juvenile polyposis syndrome, RP1-related dominant retinopathy, Birt-Hogg-Dube syndrome, inclusion body myopathy and brain white matter abnormalities, KINSSHIP syndrome, autosomal dominant nebulin-related myopathy, IMPG1-related dominant retinopathy, PROM1-related dominant retinopathy, PURA-related severe neonatal hypotonia-seizures-encephalopathy syndrome, ALG8-related autosomal dominant polycystic kidney and/or liver disease, NOTCH1-related AOS spectrum disorder, FLNB-associated autosomal dominant filamin related bone disorder, familial antiphospholipid syndrome

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

91 retrieved; paginated sample, class counts are floors:

31 uncertain significance, 24 likely pathogenic, 22 pathogenic, 5 benign, 5 pathogenic/likely pathogenic, 2 conflicting classifications of pathogenicity, 1 benign/likely benign, 1 not provided

ClinVarVariant (HGVS)GeneClassificationReview
4819222Single alleleLOC111589206Pathogeniccriteria provided, single submitter
157553NM_001370100.5(ZMYND11):c.1246_1247del (p.Glu416fs)LOC126860802Pathogenicno assertion criteria provided
1704323NM_001370100.5(ZMYND11):c.1573dup (p.Asp525fs)LOC126860802Pathogenicno assertion criteria provided
3068340NM_001370100.5(ZMYND11):c.1483C>T (p.Arg495Ter)LOC126860802Pathogeniccriteria provided, single submitter
871341NM_001370100.5(ZMYND11):c.1317_1320del (p.Thr440fs)LOC126860802Pathogeniccriteria provided, multiple submitters, no conflicts
1064579NM_001370100.5(ZMYND11):c.1687-1G>AZMYND11Pathogeniccriteria provided, single submitter
1064584NM_001370100.5(ZMYND11):c.1129del (p.Ser377fs)ZMYND11Pathogeniccriteria provided, single submitter
1064646NM_001370100.5(ZMYND11):c.709C>T (p.Gln237Ter)ZMYND11Pathogeniccriteria provided, single submitter
1209429NM_001370100.5(ZMYND11):c.744_745del (p.Cys249fs)ZMYND11Pathogeniccriteria provided, multiple submitters, no conflicts
1335032NM_001370100.5(ZMYND11):c.1769G>A (p.Trp590Ter)ZMYND11Pathogeniccriteria provided, multiple submitters, no conflicts
157551NM_001370100.5(ZMYND11):c.206dup (p.Thr70fs)ZMYND11Pathogeniccriteria provided, single submitter
157552NM_001370100.5(ZMYND11):c.976C>T (p.Gln326Ter)ZMYND11Pathogenicno assertion criteria provided
157554NM_001370100.5(ZMYND11):c.561del (p.Met187fs)ZMYND11Pathogenicno assertion criteria provided
1704321NM_001370100.5(ZMYND11):c.630C>G (p.Tyr210Ter)ZMYND11Pathogeniccriteria provided, single submitter
1704322NM_001370100.5(ZMYND11):c.1089G>A (p.Trp363Ter)ZMYND11Pathogenicno assertion criteria provided
1704324NM_001370100.5(ZMYND11):c.1756C>T (p.Gln586Ter)ZMYND11Pathogenicno assertion criteria provided
208648NM_001370100.5(ZMYND11):c.1798C>T (p.Arg600Trp)ZMYND11Pathogenic/Likely pathogeniccriteria provided, multiple submitters, no conflicts
2503414NM_001370100.5(ZMYND11):c.876_882del (p.Phe293fs)ZMYND11Pathogenic/Likely pathogeniccriteria provided, multiple submitters, no conflicts
3369996NM_001370100.5(ZMYND11):c.912_915del (p.Asn304fs)ZMYND11Pathogenic/Likely pathogeniccriteria provided, multiple submitters, no conflicts
3773685NM_001370100.5(ZMYND11):c.121_122del (p.Met41fs)ZMYND11Pathogeniccriteria provided, single submitter
3897871NM_001370100.5(ZMYND11):c.127C>T (p.Arg43Ter)ZMYND11Pathogeniccriteria provided, multiple submitters, no conflicts
393552NM_001370100.5(ZMYND11):c.22C>T (p.Arg8Ter)ZMYND11Pathogeniccriteria provided, multiple submitters, no conflicts
431092NM_001370100.5(ZMYND11):c.383del (p.Ser128fs)ZMYND11Pathogeniccriteria provided, single submitter
431123NM_001370100.5(ZMYND11):c.76C>T (p.Arg26Trp)ZMYND11Pathogenic/Likely pathogeniccriteria provided, multiple submitters, no conflicts
451936NM_001370100.5(ZMYND11):c.82C>T (p.Gln28Ter)ZMYND11Pathogeniccriteria provided, multiple submitters, no conflicts
504175NM_001370100.5(ZMYND11):c.737_738del (p.Lys246fs)ZMYND11Pathogenic/Likely pathogeniccriteria provided, multiple submitters, no conflicts
520843NM_001370100.5(ZMYND11):c.1072C>T (p.Arg358Ter)ZMYND11Pathogeniccriteria provided, multiple submitters, no conflicts
2580931NM_001366521.1(ATP2B1):c.2959G>T (p.Glu987Ter)ATP2B1Likely pathogeniccriteria provided, single submitter
1029064NM_001370100.5(ZMYND11):c.1255A>C (p.Ser419Arg)LOC126860802Likely pathogeniccriteria provided, single submitter
1064578NM_001370100.5(ZMYND11):c.1581dup (p.Cys528fs)LOC126860802Likely pathogeniccriteria provided, single submitter

Genes & proteins

Mendelian disease overlap and somatic drivers

GenCC: 5 · Orphanet: 3 · 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
ZMYND11StrongAutosomal dominantintellectual disability, autosomal dominant 305

Orphanet rare-disease linkage (cohort genes)

GeneOrphanet IDRare disease
ZMYND11Orphanet:687424ZMYND11-related developmental delay-speech delay-seizures-behavioral abnormalities-craniofacial dysmorphism syndrome due to 10p15.3 microdeletion
ZMYND11Orphanet:694308ZMYND11-related developmental delay-speech delay-seizures-behavioral abnormalities-craniofacial dysmorphism syndrome due to a point mutation
ATP2B1Orphanet:528084Non-specific syndromic intellectual disability

Cohort genes → proteins

2 cohort genes, 2 distinct canonical proteins.

Evidence partition

SubsetGenes
multi_evidence2

Cohort genes (full)

SymbolHGNCEnsemblUniProtNameEvidence
ZMYND11HGNC:16966ENSG00000015171Q15326Zinc finger MYND domain-containing protein 11gencc,clinvar
ATP2B1HGNC:814ENSG00000070961P20020Plasma membrane calcium-transporting ATPase 1clinvar

Cohort function summary

Lead sentence per gene, UniProt-curated.

SymbolProtein nameFunction (lead sentence)
ZMYND11Zinc finger MYND domain-containing protein 11Chromatin reader that specifically recognizes and binds histone H3.3 trimethylated at ‘Lys-36’ (H3.3K36me3) and regulates RNA polymerase II elongation.
ATP2B1Plasma membrane calcium-transporting ATPase 1Catalyzes the hydrolysis of ATP coupled with the transport of calcium from the cytoplasm to the extracellular space thereby maintaining intracellular calcium homeostasis.

Protein-family classification

Druggable: 0 · Difficult: 2 · Unknown: 0 · Druggable fraction: 0.0

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
Transcription factor28.3×0.015

Per-gene assignment

SymbolFamilyDruggable?ECInterPro (top 3)
ZMYND11Transcription factornoPWWP_dom, Bromodomain, Znf_PHD
ATP2B1Transcription factorno7.2.2.10P_typ_ATPase, ATPase_P-typ_cation-transptr_N, ATPase_P-typ_cation-transptr_C

Expression context

Cohort genes with no expression data: 0.

2 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)2
unknown0

Top tissues across cohort

TissueCohort genes
caput epididymis1
cauda epididymis1
cranial nerve II1
Brodmann (1909) area 231
frontal pole1
lateral nuclear group of thalamus1

Per-gene tissue summary (top 30)

SymbolBgee breadthFANTOM5 breadthSCXATop tissues
ZMYND11301ubiquitousmarkercranial nerve II, caput epididymis, cauda epididymis
ATP2B1296ubiquitousmarkerfrontal pole, Brodmann (1909) area 23, lateral nuclear group of thalamus

Protein interactions among cohort

Intra-cohort edges: 0.

Hub genes (top 10 by interactor count)

SymbolInteractor count
ATP2B13,055
ZMYND111,264

Structural data

PDB: 2 · AlphaFold-only: 0 · No structure: 0

Cohort genes with PDB structures (top 30)

SymbolUniProtPDB entries
ZMYND11Q153268
ATP2B1P200201

Function

Pathway analysis

Distinct Reactome pathways touched by cohort: 13. Enrichment computed across 2 evidence-associated genes (1 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 1 annotated cohort genes). Counts and members are kept as ground-truth; sorted by enrichment.

PathwayCohort genesFoldFDRSample cohort genes
Reduction of cytosolic Ca++ levels1951.7×0.009ATP2B1
Platelet calcium homeostasis1713.8×0.009ATP2B1
Sensory processing of sound1308.6×0.011ATP2B1
Platelet homeostasis1278.5×0.011ATP2B1
Ion transport by P-type ATPases1207.6×0.011ATP2B1
Ion homeostasis1203.9×0.011ATP2B1
Sensory processing of sound by inner hair cells of the cochlea1163.1×0.011ATP2B1
Cardiac conduction1108.8×0.014ATP2B1
Ion channel transport196.0×0.014ATP2B1
Sensory Perception195.2×0.014ATP2B1
Muscle contraction177.2×0.015ATP2B1
Hemostasis136.0×0.030ATP2B1
Transport of small molecules125.1×0.040ATP2B1

GO biological processes by enrichment

Over-representation of cohort genes vs the genome-wide background (hypergeometric test, Benjamini-Hochberg FDR; fold = observed/expected over 2 annotated cohort genes). Counts and members are kept as ground-truth; sorted by enrichment.

GO termCohort genesFoldFDRSample cohort genes
regulation of vascular associated smooth muscle contraction11685.2×0.006ATP2B1
calcium ion export across plasma membrane11404.3×0.006ATP2B1
regulation of cellular response to insulin stimulus1766.0×0.007ATP2B1
negative regulation of cytosolic calcium ion concentration1648.1×0.007ATP2B1
regulation of cardiac conduction1421.3×0.007ATP2B1
regulation of transcription elongation by RNA polymerase II1401.2×0.007ZMYND11
positive regulation of calcium ion transport1290.6×0.008ATP2B1
negative regulation of JNK cascade1280.9×0.008ZMYND11
negative regulation of cytokine production1255.3×0.008ATP2B1
negative regulation of extrinsic apoptotic signaling pathway1210.7×0.008ZMYND11
positive regulation of bone mineralization1195.9×0.008ATP2B1
regulation of cytosolic calcium ion concentration1191.5×0.008ATP2B1
regulation of signal transduction1133.8×0.010ZMYND11
regulation of blood pressure1110.9×0.012ATP2B1
monoatomic ion transmembrane transport1104.0×0.012ATP2B1
negative regulation of canonical NF-kappaB signal transduction186.0×0.013ZMYND11
defense response to virus134.7×0.030ZMYND11
negative regulation of DNA-templated transcription115.8×0.062ZMYND11

Therapeutics

Drug target analysis

Approved (phase 4): 0 · Phase ≥3: 0 · Phased (≥1): 0 · Undrugged: 2

Druggability breadth: 1 of 2 evidence-associated genes (50%) have a ChEMBL target (buckets above are over the deeply-mined display cohort).

Top cohort targets by molecule count

SymbolMoleculesMax phase
ZMYND1100
ATP2B100

Bioactivity and enzyme data

Enzyme cohort genes (≥1 EC): 1.

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

SymbolAssaysType breakdown
ZMYND111Binding:1

Cohort enzymes (BRENDA EC)

SymbolEC numbersNames
ATP2B17.2.2.10P-type Ca2+ transporter

Pharmacogenomics

Cohort genes with a PharmGKB record: 2; with CPIC/DPWG dosing guidelines: 0.

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

Chemical tractability of cohort targets

0 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.

Druggability pyramid

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

TierDefinitionGenesSymbols
AApproved (phase 4 drug)0
BPhased (≥1) drug, not yet approved0
CDruggable family + PDB, no drug0
DDruggable family + AlphaFold only, no drug0
EDifficult family or no structure, no drug2ZMYND11, ATP2B1

Undrugged target profiles

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

SymbolChEMBL assaysDrugged partners (top 3)
ZMYND111
ATP2B10

Clinical trials & evidence

Clinical trials

Clinical trials: 0.