ZMYM3

Summary

ZMYM3 (zinc finger MYM-type containing 3, HGNC:13054) is a protein-coding gene on chromosome Xq13.1, encoding Zinc finger MYM-type protein 3 (Q14202). Plays a role in the regulation of cell morphology and cytoskeletal organization.

This gene is located on the X chromosome and is subject to X inactivation. It is highly conserved in vertebrates and most abundantly expressed in the brain. The encoded protein is a component of histone deacetylase-containing multiprotein complexes that function through modifying chromatin structure to keep genes silent. A chromosomal translocation (X;13) involving this gene is associated with X-linked cognitive disability. Several alternatively spliced transcript variants have been found for this gene.

Source: NCBI Gene 9203 — RefSeq curated summary.

At a glance

• Gene–disease (curated): intellectual developmental disorder, X-linked 112 (Strong, GenCC) — +2 more curated relationships
• Clinical variants (ClinVar): 222 total — 3 pathogenic, 9 likely-pathogenic
• Phenotypes (HPO): 43
• Cancer driver (intOGen): loss-of-function (tumor-suppressor-like) across 8 cancer types
• Dosage sensitivity (ClinGen): haploinsufficiency no evidence, triplosensitivity no evidence
• MANE Select transcript: NM_201599

Identifiers

Gene identifiers

Field	Value
HGNC ID	HGNC:13054
Approved symbol	ZMYM3
Name	zinc finger MYM-type containing 3
Location	Xq13.1
Locus type	gene with protein product
Status	Approved
Aliases	ZNF198L2, DXS6673E, KIAA0385, MYM
Ensembl gene	ENSG00000147130
Ensembl biotype	protein_coding
OMIM	300061
Entrez	9203

Gene structure

Transcript identifiers

Ensembl transcripts: 21 — 19 protein_coding, 2 protein_coding_CDS_not_defined

ENST00000314425, ENST00000373978, ENST00000373981, ENST00000373982, ENST00000373984, ENST00000373988, ENST00000373998, ENST00000470832, ENST00000489332, ENST00000851900, ENST00000851901, ENST00000851902, ENST00000851903, ENST00000851904, ENST00000851905, ENST00000851906, ENST00000936826, ENST00000936827, ENST00000936828, ENST00000936829, ENST00000936830

RefSeq mRNA: 4 — MANE Select: NM_201599 NM_001171162, NM_001171163, NM_005096, NM_201599

CCDS: CCDS14409, CCDS55443, CCDS55444

Canonical transcript exons

ENST00000314425 — 25 exons

Exon	Start	End
ENSE00001462092	71254029	71254140
ENSE00001672355	71247734	71247906
ENSE00001730345	71247345	71247510
ENSE00001755024	71239624	71241108
ENSE00003464384	71246353	71246512
ENSE00003472120	71244302	71244470
ENSE00003483350	71244790	71244893
ENSE00003485664	71242970	71243084
ENSE00003490974	71243829	71243980
ENSE00003507697	71248162	71248312
ENSE00003512397	71250432	71250726
ENSE00003553367	71248686	71248801
ENSE00003578282	71249019	71249169
ENSE00003587832	71241227	71241344
ENSE00003592360	71245668	71245842
ENSE00003592687	71251558	71251601
ENSE00003596122	71246595	71246692
ENSE00003609245	71245339	71245485
ENSE00003638540	71251178	71251244
ENSE00003639056	71242170	71242424
ENSE00003657615	71245986	71246098
ENSE00003658185	71249461	71249679
ENSE00003661454	71248438	71248524
ENSE00003671079	71250026	71250203
ENSE00003677092	71252589	71253274

Expression profiles

Bgee: expression breadth ubiquitous, 281 present calls, max score 93.00.

FANTOM5 (CAGE): breadth ubiquitous, TPM avg 13.9100 / max 86.6752, expressed in 1765 samples.

FANTOM5 promoters (4 alternative TSS)

Promoter ID	TPM avg	Samples expressed
199552	11.5423	1749
199555	1.1847	587
199554	0.9461	543
199553	0.2369	119

Top tissues by expression

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

Tissue	Anatomy ID	Expression score	Quality
right adrenal gland	UBERON:0001233	93.00	gold quality
right adrenal gland cortex	UBERON:0035827	92.96	gold quality
endothelial cell	CL:0000115	92.79	gold quality
right ovary	UBERON:0002118	92.41	gold quality
left ovary	UBERON:0002119	91.83	gold quality
ovary	UBERON:0000992	91.55	gold quality
left adrenal gland	UBERON:0001234	91.05	gold quality
adrenal cortex	UBERON:0001235	90.96	gold quality
left adrenal gland cortex	UBERON:0035825	90.92	gold quality
right uterine tube	UBERON:0001302	90.86	gold quality
embryo	UBERON:0000922	90.26	gold quality
olfactory bulb	UBERON:0002264	90.14	gold quality
adrenal gland	UBERON:0002369	89.99	gold quality
secondary oocyte	CL:0000655	89.41	gold quality
type B pancreatic cell	CL:0000169	89.36	gold quality
CA1 field of hippocampus	UBERON:0003881	89.10	gold quality
ventricular zone	UBERON:0003053	89.09	gold quality
cortical plate	UBERON:0005343	89.05	gold quality
adrenal tissue	UBERON:0018303	88.96	gold quality
oocyte	CL:0000023	88.89	gold quality
pancreatic ductal cell	CL:0002079	88.52	gold quality
ganglionic eminence	UBERON:0004023	88.29	gold quality
right hemisphere of cerebellum	UBERON:0014890	87.36	gold quality
metanephros cortex	UBERON:0010533	87.34	gold quality
diaphragm	UBERON:0001103	87.28	gold quality
right frontal lobe	UBERON:0002810	87.05	gold quality
Brodmann (1909) area 46	UBERON:0006483	86.90	gold quality
pituitary gland	UBERON:0000007	86.88	gold quality
left uterine tube	UBERON:0001303	86.83	gold quality
right testis	UBERON:0004534	86.82	gold quality

Single-cell (SCXA)

Detected in 1 experiment(s), a significant marker in 1.

Experiment	Marker?	Max mean expression
E-ANND-3	yes	6.28

Regulation

Is transcription factor: no

miRNA regulators (miRDB)

115 targeting ZMYM3, top 30 by miRDB confidence (max_score; target_count = how many genes the miRNA targets in total — lower means more specific):

miRNA	Max score	Avg score	miRNA target_count
HSA-MIR-3134	100.00	66.43	777
HSA-MIR-340-5P	100.00	72.50	4437
HSA-MIR-6077	99.99	68.04	2299
HSA-MIR-23B-5P	99.98	66.07	587
HSA-MIR-548AN	99.97	70.91	2817
HSA-MIR-4725-3P	99.96	69.53	2520
HSA-MIR-6780B-5P	99.96	69.60	2562
HSA-MIR-4666A-3P	99.96	71.71	3434
HSA-MIR-548AJ-3P	99.96	73.38	5345
HSA-MIR-548X-3P	99.96	73.38	5345
HSA-MIR-495-3P	99.96	72.81	4197
HSA-MIR-5688	99.96	73.23	4504
HSA-MIR-590-3P	99.96	74.34	6478
HSA-MIR-23A-5P	99.94	65.39	468
HSA-MIR-548J-3P	99.94	72.61	4881
HSA-MIR-548AE-3P	99.93	72.66	4867
HSA-MIR-548AH-3P	99.93	72.54	4872
HSA-MIR-548AM-3P	99.93	72.54	4872
HSA-MIR-548AQ-3P	99.93	72.66	4867
HSA-MIR-552-5P	99.93	68.56	1583
HSA-MIR-338-5P	99.92	72.34	2951
HSA-MIR-205-3P	99.92	69.92	3165
HSA-MIR-589-3P	99.91	69.62	2088
HSA-MIR-3529-3P	99.90	73.55	3045
HSA-MIR-4731-5P	99.89	67.23	2537
HSA-MIR-6783-3P	99.89	67.92	2059
HSA-MIR-1343-3P	99.89	66.78	1815
HSA-MIR-4271	99.88	68.32	2244
HSA-MIR-6780A-5P	99.88	66.69	2776
HSA-MIR-548D-3P	99.87	70.67	4362

Functional genomics

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

Literature-anchored findings (GeneRIF, showing 5)

• Data found skewing of the genetic architecture at the ZMYM3 short tandem repeats (STR) in schizophrenia. Further, results found a bell-shaped distribution of alleles and selection against alleles at the extreme ends of this STR. (PMID:29332164)
• AGS mutations in this cluster impair the interaction of RNase H2 with several members of the CoREST chromatin-silencing complex that include the histone deacetylase HDAC2 and the demethylase KDM1A, the transcriptional regulators RCOR1 and GTFII-I as well as ZMYM3, an MYM-type zinc finger protein. (PMID:30889214)
• The ZMYM3 “exceptionally long” 5’ UTR STR findings may alter our perspective of disease pathogenesis in psychiatric disorders, and set an example in which the low frequency alleles at the extreme short and long ends of the human STRs are, at least in part, a result of natural selection against these alleles and their unambiguous link to major human disorders. (PMID:30909162)
• Evolving evidence on a link between the ZMYM3 exceptionally long GA-STR and human cognition. (PMID:33173136)
• Deleterious, protein-altering variants in the transcriptional coregulator ZMYM3 in 27 individuals with a neurodevelopmental delay phenotype. (PMID:36586412)

Cross-species orthologs

2 orthologs

Organism	Symbol	Gene ID
mus_musculus	Zmym3	ENSMUSG00000031310
rattus_norvegicus	Zmym3	ENSRNOG00000003707

Paralogs (18): GTF2IRD1 (ENSG00000006704), ZMYM2 (ENSG00000121741), ZMYM5 (ENSG00000132950), THAP12 (ENSG00000137492), ZMYM4 (ENSG00000146463), ZMYM6 (ENSG00000163867), KIAA1958 (ENSG00000165185), GTF2IRD2B (ENSG00000174428), EPM2AIP1 (ENSG00000178567), GTF2IRD2 (ENSG00000196275), ZMYM1 (ENSG00000197056), QRICH1 (ENSG00000198218), FAM200C (ENSG00000221886), FAM200A (ENSG00000221909), SCAND3 (ENSG00000232040), ZBED5 (ENSG00000236287), FAM200B (ENSG00000237765), GTF2I (ENSG00000263001)

Protein

Protein identifiers

Zinc finger MYM-type protein 3 — Q14202 (reviewed: Q14202)

Alternative names: Zinc finger protein 261

All UniProt accessions (5): Q14202, A6NC58, A6NHB5, A6NHN7, A6NL54

UniProt curated annotations — full annotation on UniProt →

Function. Plays a role in the regulation of cell morphology and cytoskeletal organization.

Subunit / interactions. May be a component of a BHC histone deacetylase complex that contains HDAC1, HDAC2, HMG20B/BRAF35, KDM1A, RCOR1/CoREST, PHF21A/BHC80, ZMYM2, ZNF217, ZMYM3, GSE1 and GTF2I.

Subcellular location. Nucleus.

Tissue specificity. Most abundant in brain, moderate in muscle and heart, low in other tissues except placenta.

Disease relevance. Intellectual developmental disorder, X-linked 112 (XLID112) [MIM:301111] A neurodevelopmental disorder characterized by developmental delay, impaired intellectual development, language and motor delay, autism or autistic traits, and variable dysmorphic features. The disease is caused by variants affecting the gene represented in this entry. A chromosomal aberration involving ZMYM3 may be a cause of X-linked intellectual disability in Xq13.1. Translocation t(X;13)(q13.1;q31).

Isoforms (3)

UniProt ID	Names	Canonical?
Q14202-1	1	yes
Q14202-2	2
Q14202-3	3

RefSeq proteins (4): NP_001164633, NP_001164634, NP_005087, NP_963893* (*=MANE)

Domains & families (InterPro)

ID	Name	Type
IPR010507	Znf_MYM	Domain
IPR011017	TRASH_dom	Domain
IPR021893	ZMYM2-like_C	Domain
IPR051284	ZnF_MYMT-QRICH1	Family
IPR057926	QRICH1_dom	Domain

Pfam: PF06467, PF12012, PF25561

UniProt features (61 total): sequence variant 22, cross-link 11, zinc finger region 9, compositionally biased region 6, modified residue 6, region of interest 3, splice variant 3, chain 1

Structure

Experimental structures (PDB)

0 structures.

Predicted structure (AlphaFold)

Model	pLDDT	Fraction very-high
AF-Q14202-F1	63.19	0.20

Functional residue map

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

Post-translational modifications (17): 263, 267, 464, 795, 817, 826, 308, 320, 328, 778, 786, 804, 847, 861, 920, 1275, 786

Function

Pathways and Gene Ontology

Reactome pathways

0 pathways

MSigDB gene sets: 234 (showing top): GGGACCA_MIR133A_MIR133B, RNGTGGGC_UNKNOWN, WANG_CLIM2_TARGETS_UP, BUYTAERT_PHOTODYNAMIC_THERAPY_STRESS_DN, GOBP_REGULATION_OF_CELL_MORPHOGENESIS, GRAESSMANN_APOPTOSIS_BY_DOXORUBICIN_DN, KLEIN_PRIMARY_EFFUSION_LYMPHOMA_UP, ZIC1_01, LIAO_METASTASIS, HOFMANN_MYELODYSPLASTIC_SYNDROM_HIGH_RISK_UP, MODULE_6, IVANOVA_HEMATOPOIESIS_EARLY_PROGENITOR, chrXq13, ZHOU_INFLAMMATORY_RESPONSE_FIMA_DN, ESC_V6.5_UP_LATE.V1_DN

GO Biological Process (2): cytoskeleton organization (GO:0007010), regulation of cell morphogenesis (GO:0022604)

GO Molecular Function (4): DNA binding (GO:0003677), zinc ion binding (GO:0008270), protein binding (GO:0005515), metal ion binding (GO:0046872)

GO Cellular Component (2): nucleus (GO:0005634), nucleoplasm (GO:0005654)

GO top-level categories

Rollup of top GO terms by namespace:

Category	Terms
organelle organization	1
cell morphogenesis	1
regulation of anatomical structure morphogenesis	1
nucleic acid binding	1
transition metal ion binding	1
binding	1
cation binding	1
intracellular membrane-bounded organelle	1
nuclear lumen	1
cellular anatomical structure	1

Protein interactions and networks

STRING

1929 interactions, top by confidence (×1000):

Protein A	Protein B	Partner UniProt	Score
ZMYM3	GTF2I	P78347	859
ZMYM3	UIMC1	Q96RL1	774
ZMYM3	HDAC1	Q13547	744
ZMYM3	KDM1A	O60341	714
ZMYM3	GSE1	Q14687	683
ZMYM3	RCOR1	Q9UKL0	670
ZMYM3	ZMYM2	Q9UBW7	654
ZMYM3	KMT2C	Q8NEZ4	615
ZMYM3	KDM6A	O15550	615
ZMYM3	HDAC2	Q92769	584
ZMYM3	KMT2D	O14686	580
ZMYM3	KLHL6	Q8WZ60	579
ZMYM3	HMG20B	Q9P0W2	570
ZMYM3	KLHL7	Q8IXQ5	567
ZMYM3	ZNF217	O75362	538

IntAct

119 interactions, top by confidence:

A	B	Type	Score
HDAC2	KDM1A	psi-mi:“MI:0914”(association)	0.890
HDAC1	CDK2AP1	psi-mi:“MI:0914”(association)	0.840
HDAC1	TNRC18	psi-mi:“MI:0914”(association)	0.790
DYNLL1	BLTP3B	psi-mi:“MI:0914”(association)	0.730
HDAC1	ZNF609	psi-mi:“MI:0914”(association)	0.730
ATP5PF	ATP5PD	psi-mi:“MI:0914”(association)	0.670
ZNF202	SCAND1	psi-mi:“MI:0914”(association)	0.660
HDAC3	KDM1A	psi-mi:“MI:0914”(association)	0.650
INSRR	INSR	psi-mi:“MI:0914”(association)	0.650
RNASEH2B	RNASEH2A	psi-mi:“MI:0914”(association)	0.640
DYNLL2	BLTP3B	psi-mi:“MI:0914”(association)	0.640
ATP5PB	SLC19A2	psi-mi:“MI:0914”(association)	0.640
PRG2	YPEL5	psi-mi:“MI:0914”(association)	0.640
KPNA1	TCERG1	psi-mi:“MI:0914”(association)	0.640
RNASEH2B	ZMYM3	psi-mi:“MI:0915”(physical association)	0.580
ZMYM3	H2BC21	psi-mi:“MI:0915”(physical association)	0.560
ZMYM3	YWHAG	psi-mi:“MI:0915”(physical association)	0.560
ZMYM3	SETDB1	psi-mi:“MI:0915”(physical association)	0.560
ZMYM3	KAT5	psi-mi:“MI:0915”(physical association)	0.560
LMO3	ZMYM3	psi-mi:“MI:0915”(physical association)	0.560

BioGRID (210): ZMYM3 (Affinity Capture-RNA), ZMYM3 (Affinity Capture-RNA), ZMYM3 (Affinity Capture-MS), ZMYM3 (Affinity Capture-MS), ZMYM3 (Affinity Capture-MS), ZMYM3 (Affinity Capture-MS), ZMYM3 (Affinity Capture-MS), ZMYM3 (Affinity Capture-MS), ZMYM3 (Reconstituted Complex), ZMYM3 (Reconstituted Complex), UBQLN2 (Co-fractionation), ZMYM3 (Co-fractionation), ZMYM3 (Co-fractionation), ZMYM3 (Affinity Capture-MS), ZMYM3 (Affinity Capture-MS)

ESM2 similar proteins: A0A1L8GR68, A2A791, B2GUN4, E1BP74, E1BZ85, F1QLG5, F7AQ22, O00472, O15164, O15550, O70546, O88974, O95789, P49140, P55265, P70365, Q14202, Q14596, Q15047, Q15788, Q4PJW2, Q5R413, Q5RC94, Q5RDJ2, Q5VZL5, Q64127, Q69Z66, Q6H8Q1, Q6KC51, Q6NXK2, Q6P3Y5, Q6PFK1, Q7Z3K3, Q8BJ34, Q8BL65, Q8BZH4, Q8CHY6, Q8IZD4, Q8TEW8, Q8VIG2

Diamond homologs: A2A791, A6QPH9, O95789, Q0P5J0, Q14202, Q2TAL8, Q3U2E2, Q3UA37, Q4R3D6, Q5RDJ2, Q5SVZ6, Q5VZL5, Q9CU65, Q9JLM4, Q9UBW7, Q9UJ78, A4Z943, A4Z944, A4Z945, P0CF97, Q49AG3, Q4R6P1, Q6R2W3, Q8IZ13, Q8TCP9

SIGNOR signaling

0 interactions.

Enriched among interaction partners

Reactome pathways and GO biological processes over-represented among this gene’s 133 IntAct physical interaction partners (hypergeometric vs the genome-wide background, BH-FDR, gene-set size 15–500, ranked by fold). A functional readout of the neighbourhood — distinct from this gene’s own memberships above, and biased toward well-studied / hub proteins, so read it as themes rather than proof.

Reactome pathways:

Pathway	Partners	Fold	FDR
Regulation of PTEN gene transcription	6	13.1×	9e-04
HDACs deacetylate histones	7	10.3×	9e-04
Negative Regulation of CDH1 Gene Transcription	7	10.3×	9e-04
Differentiation of naive CD4+ T cells to T helper 2 cells (Th2 cells)	5	8.9×	1e-02
Potential therapeutics for SARS	6	8.4×	4e-03
Viral Infection Pathways	11	4.1×	4e-03

GO biological processes:

GO term	Partners	Fold	FDR
heterochromatin formation	8	16.7×	8e-06
protein import into nucleus	7	8.3×	2e-03
chromatin remodeling	10	6.0×	1e-03

Disease & clinical

Cancer significance

From intOGen — cancer-driver classification: loss-of-function (tumor-suppressor-like) across 8 cancer types — BRCA, CLLSLL, HNSC, LUAD, MBL, PRAD, PROSTATE, THYM.

Clinical variants and AI predictions

ClinVar

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

Classification	Count (floor)
Pathogenic	3
Likely pathogenic	9
Uncertain significance	165
Likely benign	31
Benign	5

Top pathogenic / likely-pathogenic (12)

Variant ID	HGVS	Classification
2572042	NM_201599.3(ZMYM3):c.1332G>A (p.Lys444=)	Pathogenic
3764646	NM_201599.3(ZMYM3):c.3802+2T>A	Pathogenic
4538546	NM_201599.3(ZMYM3):c.779-1G>C	Pathogenic
1710149	NM_201599.3(ZMYM3):c.1322G>A (p.Arg441Gln)	Likely pathogenic
3255096	NM_201599.3(ZMYM3):c.2609C>A (p.Pro870Gln)	Likely pathogenic
3340748	NM_201599.3(ZMYM3):c.3820C>T (p.Arg1274Trp)	Likely pathogenic
3342365	NM_201599.3(ZMYM3):c.2255A>G (p.Tyr752Cys)	Likely pathogenic
3602248	NM_201599.3(ZMYM3):c.3452G>A (p.Arg1151Gln)	Likely pathogenic
3764655	NM_201599.3(ZMYM3):c.1352G>A (p.Cys451Tyr)	Likely pathogenic
3765597	NM_201599.3(ZMYM3):c.3622C>T (p.Leu1208Phe)	Likely pathogenic
3781048	NM_201599.3(ZMYM3):c.1000T>A (p.Phe334Ile)	Likely pathogenic
4291783	NM_201599.3(ZMYM3):c.3881G>A (p.Arg1294His)	Likely pathogenic

SpliceAI

3504 predictions. Top by Δscore:

Variant	Effect	Δscore
X:71241104:CAGGA:C	acceptor_gain	1.0000
X:71241105:AGGA:A	acceptor_gain	1.0000
X:71241106:GGA:G	acceptor_gain	1.0000
X:71241107:GA:G	acceptor_gain	1.0000
X:71241109:C:CC	acceptor_gain	1.0000
X:71241115:C:CT	acceptor_gain	1.0000
X:71241118:C:CT	acceptor_gain	1.0000
X:71241119:G:T	acceptor_gain	1.0000
X:71241123:G:C	acceptor_gain	1.0000
X:71241123:G:GC	acceptor_gain	1.0000
X:71241129:G:GC	acceptor_gain	1.0000
X:71241222:CTCA:C	donor_loss	1.0000
X:71241223:TCA:T	donor_loss	1.0000
X:71241225:A:T	donor_loss	1.0000
X:71241255:TG:T	donor_gain	1.0000
X:71241340:CGTGT:C	acceptor_gain	1.0000
X:71241341:GTGT:G	acceptor_gain	1.0000
X:71241342:TGT:T	acceptor_gain	1.0000
X:71241343:GT:G	acceptor_gain	1.0000
X:71241343:GTCT:G	acceptor_loss	1.0000
X:71241344:TCTA:T	acceptor_loss	1.0000
X:71241345:C:CA	acceptor_loss	1.0000
X:71241345:C:CC	acceptor_gain	1.0000
X:71241347:A:AC	acceptor_gain	1.0000
X:71241347:A:C	acceptor_gain	1.0000
X:71242164:TCGTA:T	donor_loss	1.0000
X:71242165:CGTA:C	donor_loss	1.0000
X:71242169:C:A	donor_loss	1.0000
X:71242179:T:A	donor_gain	1.0000
X:71242420:CGTAT:C	acceptor_gain	1.0000

AlphaMissense

8977 scored. Top likely-pathogenic:

Variant	Protein change	am_pathogenicity
X:71240981:G:T	R1350S	1.000
X:71240986:A:G	L1348P	1.000
X:71241028:T:C	Y1334C	1.000
X:71241028:T:G	Y1334S	1.000
X:71241029:A:C	Y1334D	1.000
X:71241029:A:G	Y1334H	1.000
X:71241030:C:A	W1333C	1.000
X:71241030:C:G	W1333C	1.000
X:71241031:C:G	W1333S	1.000
X:71241032:A:G	W1333R	1.000
X:71241032:A:T	W1333R	1.000
X:71241064:G:C	P1322R	1.000
X:71241064:G:T	P1322H	1.000
X:71241065:G:A	P1322S	1.000
X:71241070:A:G	L1320P	1.000
X:71241074:A:C	Y1319D	1.000
X:71241074:A:T	Y1319N	1.000
X:71241076:A:G	F1318S	1.000
X:71241108:A:C	C1307W	1.000
X:71241228:A:G	C1307R	1.000
X:71241229:T:A	K1306N	1.000
X:71241229:T:G	K1306N	1.000
X:71241230:T:A	K1306I	1.000
X:71241231:T:C	K1306E	1.000
X:71241234:A:G	S1305P	1.000
X:71241236:A:G	L1304P	1.000
X:71241240:A:C	Y1303D	1.000
X:71241240:A:G	Y1303H	1.000
X:71241240:A:T	Y1303N	1.000
X:71241241:G:C	F1302L	1.000

dbSNP variants (sampled 300 via entrez): RS1000326248 (X:71253387 C>G,T), RS1000666307 (X:71246885 T>C), RS1001401567 (X:71255450 A>G), RS1001848982 (X:71247725 C>T), RS1002306181 (X:71248642 T>C), RS1002607521 (X:71240692 G>C), RS1003003717 (X:71239529 A>C), RS1003486186 (X:71240162 T>C), RS1003573411 (X:71255128 C>A,G), RS1003841742 (X:71254536 A>C), RS1004373073 (X:71242488 C>T), RS1004589415 (X:71246240 T>A,C), RS1004882775 (X:71255195 C>G), RS1005254831 (X:71251371 TAGG>T), RS1005371977 (X:71239233 T>C)

Disease associations

OMIM: gene MIM:300061 | disease phenotypes: MIM:301111

GenCC curated gene-disease

Disease	Classification	Inheritance
intellectual developmental disorder, X-linked 112	Strong	X-linked
intellectual disability	Limited	X-linked
syndromic intellectual disability	No Known Disease Relationship	X-linked

Mondo (4): intellectual developmental disorder, X-linked 112 (MONDO:0957496), neurodevelopmental disorder (MONDO:0700092), intellectual disability (MONDO:0001071), syndromic intellectual disability (MONDO:0000508)

Orphanet (1): NON RARE IN EUROPE: Unexplained intellectual disability (Orphanet:319658)

HPO phenotypes

43 total (30 of 43 shown, HPO-id order):

HPO	Term
HP:0000028	Cryptorchidism
HP:0000047	Hypospadias
HP:0000062	Ambiguous genitalia
HP:0000076	Vesicoureteral reflux
HP:0000085	Horseshoe kidney
HP:0000086	Ectopic kidney
HP:0000107	Renal cyst
HP:0000252	Microcephaly
HP:0000378	Cupped ear
HP:0000488	Retinopathy
HP:0000545	Myopia
HP:0000708	Atypical behavior
HP:0000729	Autistic behavior
HP:0000750	Delayed speech and language development
HP:0000805	Enuresis
HP:0001249	Intellectual disability
HP:0001270	Motor delay
HP:0001382	Joint hypermobility
HP:0001423	X-linked dominant inheritance
HP:0001627	Abnormal heart morphology
HP:0001647	Bicuspid aortic valve
HP:0001737	Pancreatic cysts
HP:0002019	Constipation
HP:0002020	Gastroesophageal reflux
HP:0002046	Heat intolerance
HP:0002342	Moderate intellectual disability
HP:0002360	Sleep disturbance
HP:0002579	Gastrointestinal dysmotility
HP:0002580	Volvulus
HP:0002650	Scoliosis

GWAS associations

0 associations (top):

MeSH disease descriptors (2)

Descriptor	Name	Tree numbers
D008607	Intellectual Disability	C10.597.606.360; C23.888.592.604.646; F01.700.687; F03.625.539
D065886	Neurodevelopmental Disorders	F03.625

Drugs & pharmacology

Drug and pharmacology data

Is drug target: no

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

CTD chemical–gene interactions

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

Chemical	Actions (top 5)	PubMed papers
Valproic Acid	decreases expression, affects expression, affects cotreatment	6
sodium arsenite	decreases expression, affects cotreatment, increases abundance, increases expression	5
Air Pollutants	affects cotreatment, increases abundance, increases oxidation, decreases expression	3
Tobacco Smoke Pollution	decreases expression	2
FR900359	affects phosphorylation	1
bisphenol F	affects cotreatment, decreases expression	1
TAK-243	decreases sumoylation	1
dicrotophos	increases expression	1
triphenyl phosphate	affects expression	1
alpha-pinene	affects cotreatment, increases oxidation, increases abundance	1
bisphenol A	increases expression	1
sodium arsenate	increases abundance, decreases expression	1
terbufos	increases methylation	1
beta-lapachone	decreases expression	1
arsenite	decreases expression, increases abundance	1
o,p’-DDT	increases expression	1
butyraldehyde	decreases expression	1
monomethylarsonic acid	decreases expression	1
manganese chloride	affects cotreatment, decreases expression, increases abundance	1
arsenic acid	decreases expression, increases abundance	1
nickel sulfate	decreases expression	1
coumarin	affects phosphorylation	1
methacrylaldehyde	increases oxidation, increases abundance, affects cotreatment	1
S-(1,2-dichlorovinyl)cysteine	affects response to substance, increases expression	1
monomethylarsonous acid	decreases expression	1
4-(5-benzo(1,3)dioxol-5-yl-4-pyridin-2-yl-1H-imidazol-2-yl)benzamide	affects cotreatment, decreases expression	1
abrine	decreases expression	1
Grape Seed Proanthocyanidins	increases expression, affects cotreatment	1
dorsomorphin	affects cotreatment, decreases expression	1
dimethylmonothioarsinic acid	decreases expression	1

Cellosaurus cell lines

5 cell lines: 5 cancer cell line

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

Cellosaurus	Name	Category	Sex
CVCL_B2LT	Abcam HeLa ZMYM3 KO	Cancer cell line	Female
CVCL_TZ26	HAP1 ZMYM3 (-) 1	Cancer cell line	Male
CVCL_TZ27	HAP1 ZMYM3 (-) 2	Cancer cell line	Male
CVCL_TZ28	HAP1 ZMYM3 (-) 3	Cancer cell line	Male
CVCL_TZ29	HAP1 ZMYM3 (-) 4	Cancer cell line	Male

Clinical trials (associated diseases)

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

Trial	Phase	Status	Title
NCT05657860	PHASE4	COMPLETED	Guanfacine Extended Release for the Reduction of Aggression and Self-injurious Behavior Associated With Prader-Willi Syndrome
NCT05744479	PHASE4	RECRUITING	Metformin for Antipsychotic-induced Weight Gain in Adults With Intellectual Disability
NCT06107829	PHASE4	WITHDRAWN	Valbenazine Treatment of Tardive Dyskinesia in Adults With Intellectual/Developmental Disabilities
NCT06997198	PHASE4	NOT_YET_RECRUITING	Deutetrabenazine Treatment for Tardive Dyskinesia in Intellectual/Developmental Disabilities
NCT04586348	PHASE4	UNKNOWN	Prenatal Iodine Supplementation and Early Childhood Neurodevelopment
NCT04873115	PHASE4	UNKNOWN	Double-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,
NCT02270736	PHASE3	COMPLETED	Clinical Study to Investigate the Efficacy and Safety of NT 201 Compared to Placebo in the Treatment of Chronic Troublesome Drooling Associated With Neurological Disorders and/or Intellectual Disability
NCT02559102	PHASE3	COMPLETED	Dexmedetomidine Sedation Versus General Anaesthesia for Inguinal Hernia Surgery in Infants
NCT02757079	PHASE3	COMPLETED	Study of the Efficacy and Safety of NPC-15 for Sleep Disorders of Children With Neurodevelopmental Disorders
NCT06915480	PHASE3	RECRUITING	Reducing Missed Appointments
NCT07377032	PHASE3	RECRUITING	TAP-GRIN: Interventional Study on Patients With GRIN-related Neurodevelopmental Disorders
NCT02304302	PHASE2	COMPLETED	Down Syndrome Memantine Follow-up Study
NCT03862950	PHASE2	COMPLETED	A Trial of Metformin in Individuals With Fragile X Syndrome (Met)
NCT04529226	PHASE2	UNKNOWN	Study to Compare Clozapine vs Treatment as Usual in People With Intellectual Disability & Treatment-resistant Psychosis
NCT04821856	PHASE2	COMPLETED	Evaluation of the Effectiveness of Cannabidiol in Treating Severe Behavioural Problems in Children and Adolescents With Intellectual Disability
NCT02909959	PHASE2	COMPLETED	Sulforaphane for the Treatment of Young Men With Autism Spectrum Disorder
NCT06081348	PHASE2	RECRUITING	Sertraline vs. Placebo in the Treatment of Anxiety in Children and AdoLescents With NeurodevelopMental Disorders
NCT06352372	PHASE2	COMPLETED	Safety and Efficacy of tPBM for Epileptiform Activity in Autism
NCT05273320	PHASE1	COMPLETED	Clinical Trial of Nabilone for Aggression in Adults With Intellectual and Developmental Disabilities
NCT05301361	PHASE1	ENROLLING_BY_INVITATION	Sensitivity of the NIH Toolbox to Stimulant Treatment in Intellectual Disabilities
NCT06016764	PHASE1	COMPLETED	Use of MRI and cTBS for Catatonia in Autism
NCT06586827	PHASE1	COMPLETED	Impact of Competency-Based Training and Technical Assistance Employment Outcomes of Individuals With ID/DD
NCT07531940	PHASE1	NOT_YET_RECRUITING	Escalating Doses of Memantine in Down Syndrome (MEDS-123)
NCT00503191	PHASE1	COMPLETED	NeuroModulation Technique Treatment of Autism
NCT04475848	PHASE1	COMPLETED	A Study to Investigate the Safety, Tolerability, Pharmacokinetics, Pharmacodynamics and Food Effect of RO6953958 in Healthy Participants
NCT06300398	PHASE1	COMPLETED	IAMA-6 Oral Dose Study in Healthy Adults
NCT03479476	PHASE2/PHASE3	COMPLETED	A Trial of Metformin in Individuals With Fragile X Syndrome
NCT02616796	PHASE1/PHASE2	COMPLETED	Effects of Social Gaze Training on Brain and Behavior in Fragile X Syndrome
NCT06860672	EARLY_PHASE1	RECRUITING	Clinical Trial of the Dual Vector Base Editor for the Treatment of the CHD3-R1025W Mutation
NCT00597948	Not specified	COMPLETED	Healthy Lifestyles for People With Intellectual Disabilities
NCT01087320	Not specified	RECRUITING	Genome Medical Sequencing for Gene Discovery
NCT01652963	Not specified	UNKNOWN	Picture-based Computerised Assessment and Training of Cognitive Behaviour Therapy Skills
NCT01695395	Not specified	COMPLETED	Mental Health Care Provision for Adults With Intellectual Disability and a Mental Disorder
NCT01867554	Not specified	COMPLETED	Research and Characterization of New Genes Involved in Intellectual Disability
NCT01915381	Not specified	COMPLETED	Improving Adherence Healthy Lifestyle With a Smartphone Application Based on Adults With Intellectual Disabilities
NCT01988623	Not specified	COMPLETED	Pivotal Response Treatment for Individuals With Intellectual Disabilities
NCT02099773	Not specified	COMPLETED	Support Staff-client Interactions With Augmentative and Alternative Communication
NCT02136849	Not specified	COMPLETED	Inter-regional Project of the Great Western Exploration Approach for Exome Molecular Causes Severe Intellectual Disability Isolated or Syndromic
NCT02225041	Not specified	COMPLETED	Sedation Strategy and Cognitive Outcome After Critical Illness in Early Childhood
NCT02414438	Not specified	COMPLETED	Establishing the Clinical Utility of First StepDx PLUS and NextStepDx PLUS Study