intellectual developmental disorder, X-linked 112

Summary

intellectual developmental disorder, X-linked 112 (MONDO:0957496) is a disease caused by ZMYM3 (GenCC Strong), with 1 cohort gene.

At a glance

• Causal gene: ZMYM3 (GenCC Strong)
• Cohort genes: 1
• ClinVar variants: 13

Clinical features

No curated clinical features (Orphanet) for this disease.

Identifiers

Disease identifiers

Field	Value
Canonical name	intellectual developmental disorder, X-linked 112
Mondo ID	MONDO:0957496
OMIM	301111
UMLS	C5829589
MedGen	1840225
GARD	0026854
Is cancer (heuristic)	no

Data availability: 13 ClinVar variants · 2 GenCC gene-disease records.

Disease family

Classification path: disease › human disease › disease by body system or component › nervous system disorder › neurodevelopmental disorder › intellectual disability › non-syndromic intellectual disability › non-syndromic X-linked intellectual disability › intellectual developmental disorder, X-linked 112

Related subtypes (51): intellectual disability, X-linked 23, intellectual disability, X-linked 20, intellectual disability, X-linked 14, intellectual disability, X-linked 50, intellectual disability, X-linked 21, intellectual disability, X-linked 58, intellectual disability, X-linked 72, intellectual disability, X-linked 53, intellectual disability, X-linked 73, intellectual disability, X-linked 42, intellectual disability, X-linked 63, intellectual disability, X-linked, with or without seizures, ARX-related, intellectual disability, X-linked 2, intellectual disability, X-linked 81, intellectual disability, X-linked 46, intellectual disability, X-linked 77, intellectual disability, X-linked 45, intellectual disability, X-linked 84, intellectual disability, X-linked 82, intellectual disability, X-linked 30, intellectual disability, X-linked 91, intellectual disability, X-linked 93, chromosome Xp11.22 duplication syndrome, intellectual disability, X-linked 95, intellectual disability, X-linked 96, intellectual disability, X-linked 97, intellectual disability, X-linked 19, intellectual disability, X-linked 89, intellectual disability, X-linked 41, intellectual disability, X-linked 90, intellectual disability, X-linked 92, intellectual disability, X-linked 88, intellectual disability, X-linked 99, intellectual disability, X-linked 100, intellectual disability, X-linked 101, intellectual disability, X-linked 102, intellectual disability, X-linked 61, intellectual disability, X-linked 103, intellectual disability, X-linked 104, intellectual disability, X-linked 105, intellectual disability, X-linked 1, methylmalonic acidemia with homocystinuria, type cblX, FRAXE intellectual disability, intellectual disability, X-linked 9, intellectual developmental disorder, X-linked 108, intellectual disability, X-linked 106, intellectual disability, X-linked 107, intellectual developmental disorder, X-linked 110, intellectual developmental disorder, X-linked 111, intellectual developmental disorder, X-linked 113, intellectual developmental disorder, X-linked 114

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

13 retrieved; paginated sample, class counts are floors:

4 likely pathogenic, 4 uncertain significance, 3 pathogenic, 2 conflicting classifications of pathogenicity

ClinVar	Variant (HGVS)	Gene	Classification	Review
2572042	NM_201599.3(ZMYM3):c.1332G>A (p.Lys444=)	ZMYM3	Pathogenic	no assertion criteria provided
3764646	NM_201599.3(ZMYM3):c.3802+2T>A	ZMYM3	Pathogenic	criteria provided, single submitter
4538546	NM_201599.3(ZMYM3):c.779-1G>C	ZMYM3	Pathogenic	criteria provided, single submitter
3255096	NM_201599.3(ZMYM3):c.2609C>A (p.Pro870Gln)	ZMYM3	Likely pathogenic	criteria provided, single submitter
3764655	NM_201599.3(ZMYM3):c.1352G>A (p.Cys451Tyr)	ZMYM3	Likely pathogenic	criteria provided, single submitter
3765597	NM_201599.3(ZMYM3):c.3622C>T (p.Leu1208Phe)	ZMYM3	Likely pathogenic	criteria provided, single submitter
4291783	NM_201599.3(ZMYM3):c.3881G>A (p.Arg1294His)	ZMYM3	Likely pathogenic	criteria provided, single submitter
127192	NM_201599.3(ZMYM3):c.1321C>T (p.Arg441Trp)	ZMYM3	Conflicting classifications of pathogenicity	no assertion criteria provided
252553	NM_201599.3(ZMYM3):c.3880C>T (p.Arg1294Cys)	ZMYM3	Conflicting classifications of pathogenicity	criteria provided, conflicting classifications
3338305	NM_201599.3(ZMYM3):c.4029G>T (p.Met1343Ile)	ZMYM3	Uncertain significance	criteria provided, single submitter
4076345	NM_201599.3(ZMYM3):c.2633C>T (p.Pro878Leu)	ZMYM3	Uncertain significance	criteria provided, single submitter
4081986	NM_201599.3(ZMYM3):c.2584C>G (p.Pro862Ala)	ZMYM3	Uncertain significance	no assertion criteria provided
4294395	NM_201599.3(ZMYM3):c.2296C>T (p.Pro766Ser)	ZMYM3	Uncertain significance	criteria provided, single submitter

Genes & proteins

Mendelian disease overlap and somatic drivers

GenCC: 4 · Orphanet: 0 · 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.

Gene	Classification	Inheritance	Disease	Records
ZMYM3	Strong	X-linked	intellectual developmental disorder, X-linked 112	4

Cohort genes → proteins

1 cohort genes, 1 distinct canonical proteins.

Evidence partition

Subset	Genes
multi_evidence	1

Cohort genes (full)

Symbol	HGNC	Ensembl	UniProt	Name	Evidence
ZMYM3	HGNC:13054	ENSG00000147130	Q14202	Zinc finger MYM-type protein 3	gencc,clinvar

Cohort function summary

Lead sentence per gene, UniProt-curated.

Symbol	Protein name	Function (lead sentence)
ZMYM3	Zinc finger MYM-type protein 3	Plays a role in the regulation of cell morphology and cytoskeletal organization.

Protein-family classification

Druggable: 0 · Difficult: 1 · 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.

Family	Genes	Fold	FDR
Transcription factor	1	8.3×	0.121

Per-gene assignment

Symbol	Family	Druggable?	EC	InterPro (top 3)
ZMYM3	Transcription factor	no		Znf_MYM, TRASH_dom, ZMYM2-like_C

Expression context

Cohort genes with no expression data: 0.

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

Breadth distribution (Bgee present_calls)

Bucket	Genes
narrow (1-5 tissues)	0
moderate (6-20)	0
broad (>20)	1
unknown	0

Top tissues across cohort

Tissue	Cohort genes
endothelial cell	1
right adrenal gland	1
right adrenal gland cortex	1

Per-gene tissue summary (top 30)

Symbol	Bgee breadth	FANTOM5 breadth	SCXA	Top tissues
ZMYM3	281	ubiquitous	marker	right adrenal gland, right adrenal gland cortex, endothelial cell

Protein interactions among cohort

Intra-cohort edges: 0.

Hub genes (top 10 by interactor count)

Symbol	Interactor count
ZMYM3	2,258

Structural data

PDB: 0 · AlphaFold-only: 1 · No structure: 0

AlphaFold-only cohort genes (top 30 by pLDDT)

Symbol	UniProt	pLDDT
ZMYM3	Q14202	63.19

Function

Pathway analysis

Distinct Reactome pathways touched by cohort: 0. Enrichment computed across 1 evidence-associated genes (0 with Reactome annotation).

GO biological processes 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.

GO term	Cohort genes	Fold	FDR	Sample cohort genes
regulation of cell morphogenesis	1	624.1×	0.003	ZMYM3
cytoskeleton organization	1	132.7×	0.008	ZMYM3

Therapeutics

Drug target analysis

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

Druggability breadth: 0 of 1 evidence-associated genes (0%) have a ChEMBL target (buckets above are over the deeply-mined display cohort).

Top cohort targets by molecule count

Symbol	Molecules	Max phase
ZMYM3	0	0

Bioactivity and enzyme data

Enzyme cohort genes (≥1 EC): 0.

Pharmacogenomics

Cohort genes with a PharmGKB record: 1; 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):

Tier	Definition	Genes	Symbols
A	Approved (phase 4 drug)	0
B	Phased (≥1) drug, not yet approved	0
C	Druggable family + PDB, no drug	0
D	Druggable family + AlphaFold only, no drug	0
E	Difficult family or no structure, no drug	1	ZMYM3

Undrugged target profiles

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

Symbol	ChEMBL assays	Drugged partners (top 3)
ZMYM3	0	—

Clinical trials & evidence

Clinical trials

Clinical trials: 0.