SHROOM4

Summary

SHROOM4 (shroom family member 4, HGNC:29215) is a protein-coding gene on chromosome Xp11.22, encoding Protein Shroom4 (Q9ULL8). Probable regulator of cytoskeletal architecture that plays an important role in development.

This gene encodes a member of the APX/Shroom family, which contain an N-terminal PDZ domain and a C-terminal ASD2 motif. The encoded protein may play a role in cytoskeletal architecture. Mutations in this gene have been linked to the X-linked Stocco dos Santos syndrome characterized by cognitive disabilities. Alternatively spliced transcript variants have been described.

Source: NCBI Gene 57477 — RefSeq curated summary.

At a glance

• Gene–disease (curated): idiopathic generalized epilepsy (Strong, GenCC) — +4 more curated relationships
• GWAS associations: 1
• Clinical variants (ClinVar): 419 total — 2 likely-pathogenic
• Phenotypes (HPO): 17
• Dosage sensitivity (ClinGen): haploinsufficiency no evidence, triplosensitivity no evidence
• MANE Select transcript: NM_020717

Identifiers

Gene identifiers

Field	Value
HGNC ID	HGNC:29215
Approved symbol	SHROOM4
Name	shroom family member 4
Location	Xp11.22
Locus type	gene with protein product
Status	Approved
Aliases	KIAA1202, Shrm4, SHAP
Ensembl gene	ENSG00000158352
Ensembl biotype	protein_coding
OMIM	300579
Entrez	57477

Gene structure

Transcript identifiers

Ensembl transcripts: 6 — 4 protein_coding, 2 protein_coding_CDS_not_defined

ENST00000289292, ENST00000376020, ENST00000460112, ENST00000483955, ENST00000484922, ENST00000898514

RefSeq mRNA: 1 — MANE Select: NM_020717 NM_020717

CCDS: CCDS35277

Canonical transcript exons

ENST00000376020 — 9 exons

Exon	Start	End
ENSE00001038485	50598266	50598535
ENSE00001038487	50602633	50602813
ENSE00001038494	50633178	50635668
ENSE00001302283	50607381	50608184
ENSE00001325221	50627614	50627675
ENSE00001525342	50586796	50596964
ENSE00002042413	50813902	50814194
ENSE00003492620	50638174	50638308
ENSE00003688468	50695786	50695937

Expression profiles

Bgee: expression breadth ubiquitous, 190 present calls, max score 89.98.

FANTOM5 (CAGE): breadth broad, TPM avg 3.8268 / max 149.2680, expressed in 775 samples.

FANTOM5 promoters (6 alternative TSS)

Promoter ID	TPM avg	Samples expressed
199297	1.3513	607
199294	1.0799	249
199293	0.6708	244
199296	0.4348	168
199298	0.1973	85
199299	0.0928	40

Top tissues by expression

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

Tissue	Anatomy ID	Expression score	Quality
buccal mucosa cell	CL:0002336	89.98	silver quality
tendon of biceps brachii	UBERON:0008188	87.12	gold quality
left ventricle myocardium	UBERON:0006566	85.64	gold quality
corpus callosum	UBERON:0002336	85.30	gold quality
upper lobe of left lung	UBERON:0008952	84.90	gold quality
C1 segment of cervical spinal cord	UBERON:0006469	84.62	gold quality
sural nerve	UBERON:0015488	84.49	gold quality
right lung	UBERON:0002167	84.29	gold quality
upper lobe of lung	UBERON:0008948	84.09	gold quality
kidney epithelium	UBERON:0004819	83.47	silver quality
spinal cord	UBERON:0002240	83.28	gold quality
apex of heart	UBERON:0002098	82.83	gold quality
lung	UBERON:0002048	82.75	gold quality
male germ line stem cell (sensu Vertebrata) in testis	CL:0000089 ∩ UBERON:0000473	81.35	gold quality
heart left ventricle	UBERON:0002084	79.33	gold quality
cardiac ventricle	UBERON:0002082	79.20	gold quality
medial globus pallidus	UBERON:0002477	79.01	gold quality
subcutaneous adipose tissue	UBERON:0002190	78.03	gold quality
omental fat pad	UBERON:0010414	78.02	gold quality
peritoneum	UBERON:0002358	77.98	gold quality
adipose tissue of abdominal region	UBERON:0007808	77.69	gold quality
globus pallidus	UBERON:0001875	77.55	gold quality
substantia nigra	UBERON:0002038	77.39	gold quality
adipose tissue	UBERON:0001013	77.29	gold quality
heart right ventricle	UBERON:0002080	77.29	gold quality
inferior vagus X ganglion	UBERON:0005363	77.21	gold quality
heart	UBERON:0000948	76.67	gold quality
midbrain	UBERON:0001891	76.58	gold quality
tendon	UBERON:0000043	76.31	gold quality
metanephros cortex	UBERON:0010533	76.13	gold quality

Single-cell (SCXA)

Detected in 3 experiment(s), a significant marker in 3.

Experiment	Marker?	Max mean expression
E-HCAD-35	yes	72.22
E-ANND-3	yes	10.74
E-GEOD-130148	yes	4.38

Regulation

Is transcription factor: no

miRNA regulators (miRDB)

160 targeting SHROOM4, 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-9-5P	100.00	72.28	2361
HSA-MIR-4747-5P	100.00	67.90	2681
HSA-MIR-5196-5P	100.00	67.98	2761
HSA-MIR-5692B	100.00	71.32	2622
HSA-MIR-5692C	100.00	71.32	2622
HSA-MIR-4795-3P	100.00	74.62	4024
HSA-MIR-5692A	100.00	74.40	6850
HSA-MIR-200B-3P	100.00	73.31	2693
HSA-MIR-200C-3P	100.00	73.35	2685
HSA-MIR-429	100.00	73.44	2698
HSA-MIR-1252-5P	100.00	69.80	2774
HSA-MIR-196A-1-3P	99.99	72.15	2772
HSA-MIR-3662	99.99	73.82	5684
HSA-MIR-3667-3P	99.99	67.17	1636
HSA-MIR-4803	99.98	71.99	3117
HSA-MIR-607	99.97	73.62	5593
HSA-MIR-3148	99.97	75.06	6478
HSA-MIR-5688	99.96	73.23	4504
HSA-MIR-495-3P	99.96	72.81	4197
HSA-MIR-651-3P	99.94	73.48	5177
HSA-MIR-6835-3P	99.93	70.49	2904
HSA-MIR-552-5P	99.93	68.56	1583
HSA-MIR-3119	99.92	71.34	2390
HSA-MIR-6508-5P	99.92	70.67	2465
HSA-MIR-10523-5P	99.91	69.22	2038
HSA-MIR-1305	99.91	71.43	3443
HSA-MIR-7-1-3P	99.91	71.53	4384
HSA-MIR-7-2-3P	99.91	71.40	4394
HSA-MIR-4648	99.91	67.00	710
HSA-MIR-3671	99.90	73.04	3897

Functional genomics

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

Literature-anchored findings (GeneRIF, showing 2)

• Shrm4 interaction with GABA-B receptors shapes inhibitory neurotransmission. (PMID:28262662)
• X-linked variations in SHROOM4 are implicated in congenital anomalies of the urinary tract and the anorectal, cardiovascular and central nervous systems. (PMID:36379543)

Cross-species orthologs

4 orthologs

Organism	Symbol	Gene ID
danio_rerio	shroom4	ENSDARG00000079900
mus_musculus	Shroom4	ENSMUSG00000068270
rattus_norvegicus	Shroom4	ENSRNOG00000002959
drosophila_melanogaster	Shrm	FBGN0085408

Paralogs (3): SHROOM3 (ENSG00000138771), SHROOM2 (ENSG00000146950), SHROOM1 (ENSG00000164403)

Protein

Protein identifiers

Protein Shroom4 — Q9ULL8 (reviewed: Q9ULL8)

Alternative names: Second homolog of apical protein

All UniProt accessions (1): Q9ULL8

UniProt curated annotations — full annotation on UniProt →

Function. Probable regulator of cytoskeletal architecture that plays an important role in development. May regulate cellular and cytoskeletal architecture by modulating the spatial distribution of myosin II.

Subunit / interactions. Interacts directly with F-actin.

Subcellular location. Cytoplasm. Cytoskeleton.

Tissue specificity. Expressed in all fetal and adult tissues investigated. Expressed in adult heart, brain, placenta, lung, liver, skeletal muscle, kidney and pancreas. In brain regions detected in cerebellum, cerebral cortex, medulla, spinal cord, occipital pole, frontal lobe, temporal lobe and putamen. The expression is strongest in the medulla and weakest in the cerebral cortex.

Disease relevance. A chromosomal aberration involving SHROOM4 is a cause of X-linked intellectual disability (XLID). Translocation t(X;8)(p11.22;p23.3) with FBXO25. A chromosomal aberration involving SHROOM4 is a cause of X-linked intellectual disability (XLID). Translocation t(X;19).

Similarity. Belongs to the shroom family.

Isoforms (2)

UniProt ID	Names	Canonical?
Q9ULL8-1	1, SHAP-B	yes
Q9ULL8-2	2, SHAP-A

RefSeq proteins (1): NP_065768* (*=MANE)

Domains & families (InterPro)

ID	Name	Type
IPR001478	PDZ	Domain
IPR014799	ASD2_dom	Domain
IPR027685	Shroom_fam	Family
IPR036034	PDZ_sf	Homologous_superfamily

Pfam: PF00595, PF08687

UniProt features (40 total): region of interest 8, compositionally biased region 8, sequence variant 7, strand 5, modified residue 3, helix 3, domain 2, chain 1, coiled-coil region 1, splice variant 1, sequence conflict 1

Structure

Experimental structures (PDB)

1 structures.

PDB	Method	Resolution (Å)
2EDP	SOLUTION NMR

Predicted structure (AlphaFold)

Model	pLDDT	Fraction very-high
AF-Q9ULL8-F1	47.74	0.15

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 (3): 411, 729, 1019

Function

Pathways and Gene Ontology

Reactome pathways

0 pathways

MSigDB gene sets: 146 (showing top): GOBP_COGNITION, MONNIER_POSTRADIATION_TUMOR_ESCAPE_UP, GTGCCTT_MIR506, GOBP_ACTIN_FILAMENT_ORGANIZATION, GOBP_HEAD_DEVELOPMENT, GOCC_APICAL_PLASMA_MEMBRANE, GOMF_ACTIN_BINDING, GOCC_CELL_CELL_JUNCTION, GOCC_CYTOPLASMIC_SIDE_OF_MEMBRANE, GOCC_APICAL_PART_OF_CELL, GOCC_POSTSYNAPSE, GOCC_ACTIN_FILAMENT_BUNDLE, GOCC_ACTOMYOSIN, GOCC_SYNAPSE, GOCC_SIDE_OF_MEMBRANE

GO Biological Process (5): actin filament organization (GO:0007015), brain development (GO:0007420), actin cytoskeleton organization (GO:0030036), cognition (GO:0050890), regulation of postsynaptic membrane neurotransmitter receptor levels (GO:0099072)

GO Molecular Function (4): myosin II binding (GO:0045159), actin filament binding (GO:0051015), actin binding (GO:0003779), protein binding (GO:0005515)

GO Cellular Component (17): stress fiber (GO:0001725), nucleoplasm (GO:0005654), cytoplasm (GO:0005737), actin filament (GO:0005884), adherens junction (GO:0005912), focal adhesion (GO:0005925), cytoplasmic side of plasma membrane (GO:0009898), basal plasma membrane (GO:0009925), apical plasma membrane (GO:0016324), cortical actin cytoskeleton (GO:0030864), apical junction complex (GO:0043296), presynapse (GO:0098793), postsynapse (GO:0098794), glutamatergic synapse (GO:0098978), GABA-ergic synapse (GO:0098982), cytoskeleton (GO:0005856), actin cytoskeleton (GO:0015629)

GO top-level categories

Rollup of top GO terms by namespace:

Category	Terms
cellular anatomical structure	4
synapse	4
actin cytoskeleton	2
cell-cell junction	2
plasma membrane region	2
actin cytoskeleton organization	1
supramolecular fiber organization	1
central nervous system development	1
animal organ development	1
head development	1
cytoskeleton organization	1
actin filament-based process	1
nervous system process	1
regulation of biological quality	1
myosin binding	1
actin binding	1
protein-containing complex binding	1
cytoskeletal protein binding	1
binding	1
actomyosin	1
contractile actin filament bundle	1
nuclear lumen	1
intracellular anatomical structure	1
polymeric cytoskeletal fiber	1
cell-substrate junction	1
plasma membrane	1
cytoplasmic side of membrane	1
basal part of cell	1
apical part of cell	1
cortical cytoskeleton	1
intracellular membraneless organelle	1
cytoskeleton	1

Protein interactions and networks

STRING

1576 interactions, top by confidence (×1000):

Protein A	Protein B	Partner UniProt	Score
SHROOM4	APEX1	P27695	657
SHROOM4	CENPVL1	A0A0U1RR11	507
SHROOM4	LYG1	Q8N1E2	507
SHROOM4	IFT70A	Q86WT1	467
SHROOM4	PBDC1	Q9BVG4	449
SHROOM4	EPM2AIP1	Q7L775	449
SHROOM4	SHROOM1	Q2M3G4	429
SHROOM4	KDM6A	O15550	418
SHROOM4	RTF2	Q9BY42	414
SHROOM4	SHROOM3	Q8TF72	410
SHROOM4	ZSWIM3	Q96MP5	404
SHROOM4	SKIC2	Q15477	401
SHROOM4	IQSEC2	Q5JU85	401
SHROOM4	ZNF674	Q2M3X9	400
SHROOM4	KDM5C	P41229	399

IntAct

156 interactions, top by confidence:

A	B	Type	Score
DGKZ	SHROOM4	psi-mi:“MI:0407”(direct interaction)	0.440
E6	SHROOM4	psi-mi:“MI:0407”(direct interaction)	0.440
ATP2B4	SHROOM4	psi-mi:“MI:0407”(direct interaction)	0.440
SHROOM4	TAMALIN	psi-mi:“MI:0407”(direct interaction)	0.440
ARHGEF16	SHROOM4	psi-mi:“MI:0407”(direct interaction)	0.440
TIAM2	SHROOM4	psi-mi:“MI:0407”(direct interaction)	0.440
APBA3	SHROOM4	psi-mi:“MI:0407”(direct interaction)	0.440
SHROOM4	AHNAK	psi-mi:“MI:0407”(direct interaction)	0.440
SHROOM4	APBA1	psi-mi:“MI:0407”(direct interaction)	0.440
SHROOM4	APBA2	psi-mi:“MI:0407”(direct interaction)	0.440
SHROOM4	ARHGAP21	psi-mi:“MI:0407”(direct interaction)	0.440
SHROOM4	ARHGEF11	psi-mi:“MI:0407”(direct interaction)	0.440
SHROOM4	CARD11	psi-mi:“MI:0407”(direct interaction)	0.440
SHROOM4	CASK	psi-mi:“MI:0407”(direct interaction)	0.440
SHROOM4	WHRN	psi-mi:“MI:0407”(direct interaction)	0.440
SHROOM4	DLG1	psi-mi:“MI:0407”(direct interaction)	0.440
SHROOM4	DLG2	psi-mi:“MI:0407”(direct interaction)	0.440
SHROOM4	DLG3	psi-mi:“MI:0407”(direct interaction)	0.440
SHROOM4	DLG4	psi-mi:“MI:0407”(direct interaction)	0.440
SHROOM4	DLG5	psi-mi:“MI:0407”(direct interaction)	0.440

BioGRID (4): SHROOM4 (Synthetic Lethality), SHROOM4 (Affinity Capture-MS), SHROOM4 (Affinity Capture-RNA), PPIA (Cross-Linking-MS (XL-MS))

ESM2 similar proteins: A0A0A6YY25, A0A5K7RLP0, A6NMK8, A8MVX0, B2RQL2, B2RXH4, C9JSJ3, D2J0Y4, O54824, P97303, Q01954, Q05AH6, Q0VET5, Q14005, Q1W617, Q2YDE2, Q3MHT3, Q3U0P1, Q3ULM6, Q3UXL4, Q4R7L6, Q5RC05, Q5T0L3, Q68CR7, Q6GQV1, Q6NS69, Q6NZK5, Q6P1D7, Q6PG16, Q6ZVT6, Q7Z4V0, Q80W88, Q80XI1, Q811R2, Q86T90, Q86YN6, Q8BHP2, Q8BLK9, Q8BP99, Q8BW86

Diamond homologs: A1Z9P3, Q09JY9, Q13796, Q1W617, Q7TP36, Q8TF72, Q9QXN0, Q9ULL8, A1ZA47, A2ALK8, A2ALU4, D4A702, E9Q9W7, O00151, O70209, O70400, O75112, O88382, P36202, P50479, P52944, P70271, Q3SX40, Q3SYZ8, Q3T005, Q3T0C8, Q3TJD7, Q53GG5, Q5E9E1, Q5F488, Q5RBI7, Q5TCQ9, Q62920, Q66HS7, Q679P3, Q6GLJ6, Q6INU3, Q6P7E4, Q6QGC0, Q86UL8

SIGNOR signaling

0 interactions.

Enriched among interaction partners

Reactome pathways and GO biological processes over-represented among this gene’s 103 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
Ras activation upon Ca2+ influx through NMDA receptor	5	42.6×	6e-06
Unblocking of NMDA receptors, glutamate binding and activation	5	40.6×	6e-06
Negative regulation of NMDA receptor-mediated neuronal transmission	5	40.6×	6e-06
Assembly and cell surface presentation of NMDA receptors	10	37.9×	2e-11
Dopamine Neurotransmitter Release Cycle	5	37.0×	7e-06
Long-term potentiation	5	35.5×	8e-06
Neurexins and neuroligins	10	29.4×	1e-10
Protein-protein interactions at synapses	6	23.8×	7e-06

GO biological processes:

GO term	Partners	Fold	FDR
establishment or maintenance of epithelial cell apical/basal polarity	11	65.9×	3e-15
receptor clustering	7	45.0×	4e-08
protein localization to synapse	5	39.5×	1e-05
regulation of postsynaptic membrane neurotransmitter receptor levels	7	35.8×	2e-07
cell-cell adhesion	10	10.5×	5e-06
protein-containing complex assembly	8	9.4×	1e-04
regulation of small GTPase mediated signal transduction	6	8.9×	2e-03
establishment of localization in cell	5	8.3×	7e-03

Disease & clinical

Clinical variants and AI predictions

ClinVar

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

Classification	Count (floor)
Pathogenic	0
Likely pathogenic	2
Uncertain significance	233
Likely benign	42
Benign	25

Top pathogenic / likely-pathogenic (2)

Variant ID	HGVS	Classification
1321285	NM_020717.5(SHROOM4):c.4212+1G>A	Likely pathogenic
564844	GRCh37/hg19 Xp11.22(chrX:50394843-50659280)x2	Likely pathogenic

SpliceAI

2294 predictions. Top by Δscore:

Variant	Effect	Δscore
X:50596726:T:A	donor_gain	1.0000
X:50596727:C:A	donor_gain	1.0000
X:50596750:T:TA	donor_gain	1.0000
X:50596751:C:A	donor_gain	1.0000
X:50598263:TAC:T	donor_loss	1.0000
X:50598264:A:AT	donor_loss	1.0000
X:50598265:CCTT:C	donor_gain	1.0000
X:50627608:ACTT:A	donor_loss	1.0000
X:50627610:TTA:T	donor_loss	1.0000
X:50627611:TA:T	donor_loss	1.0000
X:50627612:ACCT:A	donor_gain	1.0000
X:50627612:ACCTC:A	donor_gain	1.0000
X:50627613:CCTC:C	donor_gain	1.0000
X:50627613:CCTCC:C	donor_gain	1.0000
X:50627673:TTC:T	acceptor_gain	1.0000
X:50627673:TTCCT:T	acceptor_loss	1.0000
X:50627676:C:CG	acceptor_loss	1.0000
X:50627677:T:A	acceptor_loss	1.0000
X:50695780:CCTTA:C	donor_loss	1.0000
X:50695783:TA:T	donor_loss	1.0000
X:50695784:ACCT:A	donor_gain	1.0000
X:50695785:C:CG	donor_loss	1.0000
X:50695785:CCT:C	donor_gain	1.0000
X:50695785:CCTC:C	donor_gain	1.0000
X:50695787:T:TA	donor_gain	1.0000
X:50695934:CAAT:C	acceptor_gain	1.0000
X:50695937:TC:T	acceptor_loss	1.0000
X:50695938:C:CC	acceptor_gain	1.0000
X:50695940:G:C	acceptor_gain	1.0000
X:50695943:T:C	acceptor_gain	1.0000

AlphaMissense

9822 scored. Top likely-pathogenic:

Variant	Protein change	am_pathogenicity
X:50598345:A:G	L1378P	1.000
X:50695792:A:T	V88D	1.000
X:50695822:T:A	K78I	1.000
X:50695828:A:G	L76P	1.000
X:50695834:A:G	L74P	1.000
X:50813915:A:T	L35H	1.000
X:50813945:A:G	L25P	1.000
X:50813945:A:T	L25H	1.000
X:50813950:G:C	F23L	1.000
X:50813950:G:T	F23L	1.000
X:50813951:A:G	F23S	1.000
X:50813952:A:G	F23L	1.000
X:50813955:C:G	G22R	1.000
X:50813956:C:A	W21C	1.000
X:50813956:C:G	W21C	1.000
X:50813958:A:G	W21R	1.000
X:50813958:A:T	W21R	1.000
X:50596732:A:G	L1482P	0.999
X:50596741:A:G	L1479P	0.999
X:50596795:A:G	L1461P	0.999
X:50596936:A:G	L1414P	0.999
X:50598528:A:G	L1317P	0.999
X:50695804:A:G	L84P	0.999
X:50695821:T:A	K78N	0.999
X:50695821:T:G	K78N	0.999
X:50695825:A:T	I77N	0.999
X:50695838:C:G	A73P	0.999
X:50695847:G:T	R70S	0.999
X:50695882:A:T	L58Q	0.999
X:50695888:T:A	D56V	0.999

dbSNP variants (sampled 300 via entrez): RS1000003339 (X:50620400 T>C,G), RS1000052173 (X:50729534 C>T), RS1000110107 (X:50742688 A>G), RS1000135922 (X:50647078 T>C), RS1000162732 (X:50791730 A>C), RS1000166303 (X:50580656 C>T), RS1000211404 (X:50647649 A>G), RS1000218921 (X:50672644 C>T), RS1000251368 (X:50712496 A>G), RS1000338528 (X:50731291 C>G), RS1000348970 (X:50591749 A>C,G), RS1000382980 (X:50721932 G>T), RS1000393295 (X:50780911 A>G), RS1000435180 (X:50722464 G>A), RS1000519984 (X:50674644 T>C)

Disease associations

OMIM: gene MIM:300579 | disease phenotypes: MIM:300434

GenCC curated gene-disease

Disease	Classification	Inheritance
idiopathic generalized epilepsy	Strong	X-linked
congenital anomaly of kidney and urinary tract	Strong	X-linked
X-linked intellectual disability, Stocco dos Santos type	Supportive	X-linked
complex neurodevelopmental disorder	Limited	X-linked

ClinGen Gene-Disease Validity (1)

Expert-panel classifications — Definitive > Strong > Moderate > Limited > Disputed > Refuted.

Disease	Classification	Inheritance
X-linked complex neurodevelopmental disorder	Disputed	XL

Mondo (5): X-linked intellectual disability, Stocco dos Santos type (MONDO:0010325), intellectual disability (MONDO:0001071), complex neurodevelopmental disorder (MONDO:0100038), idiopathic generalized epilepsy (MONDO:0005579), congenital anomaly of kidney and urinary tract (MONDO:0019719)

Orphanet (2): X-linked intellectual disability, Stocco Dos Santos type (Orphanet:85288), NON RARE IN EUROPE: Unexplained intellectual disability (Orphanet:319658)

HPO phenotypes

17 total (17 of 17 shown, HPO-id order):

HPO	Term
HP:0000286	Epicanthus
HP:0000486	Strabismus
HP:0000518	Cataract
HP:0000750	Delayed speech and language development
HP:0000752	Hyperactivity
HP:0001007	Hirsutism
HP:0001250	Seizure
HP:0001344	Absent speech
HP:0001518	Small for gestational age
HP:0001762	Talipes equinovarus
HP:0002205	Recurrent respiratory infections
HP:0002808	Kyphosis
HP:0003144	Increased serum serotonin
HP:0004322	Short stature
HP:0005280	Depressed nasal bridge
HP:0008780	Congenital bilateral hip dislocation
HP:0010864	Severe intellectual disability

GWAS associations

1 associations (top):

Study	Trait	p-value
GCST008163_462	Height	4.000000e-07

MeSH disease descriptors (4)

Descriptor	Name	Tree numbers
D008607	Intellectual Disability	C10.597.606.360; C23.888.592.604.646; F01.700.687; F03.625.539
C566906	Cakut (supp.)
C562694	Epilepsy, Idiopathic Generalized (supp.)
C537495	Stocco dos Santos syndrome (supp.)

Drugs & pharmacology

Drug and pharmacology data

Is drug target: no

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

CTD chemical–gene interactions

23 total (human), top 23 by PubMed support.

Chemical	Actions (top 5)	PubMed papers
aristolochic acid I	decreases expression	1
FR900359	affects phosphorylation	1
triphenyl phosphate	affects expression	1
bisphenol A	affects cotreatment, decreases methylation	1
erucylphospho-N,N,N-trimethylpropylammonium	increases expression	1
4-(4-((5-(4,5-dimethyl-2-nitrophenyl)-2-furanyl)methylene)-4,5-dihydro-3-methyl-5-oxo-1H-pyrazol-1-yl)benzoic acid	increases expression	1
Resveratrol	affects cotreatment, decreases expression	1
Temozolomide	decreases expression	1
Sunitinib	decreases expression	1
Fulvestrant	affects cotreatment, decreases methylation	1
Acetaminophen	increases expression	1
Benzo(a)pyrene	affects methylation, decreases methylation	1
Doxorubicin	decreases expression	1
Estradiol	affects cotreatment, increases expression	1
Gasoline	affects cotreatment, increases abundance, increases expression	1
Nickel	decreases expression	1
Plant Extracts	affects cotreatment, decreases expression	1
Polycyclic Aromatic Hydrocarbons	affects cotreatment, increases abundance, increases expression	1
Tobacco Smoke Pollution	decreases expression	1
Urethane	decreases expression	1
Valproic Acid	decreases methylation	1
Antirheumatic Agents	increases expression	1
Particulate Matter	affects cotreatment, increases abundance, increases expression	1

Clinical trials (associated diseases)

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

Trial	Phase	Status	Title
NCT03590197	PHASE4	COMPLETED	Effect of Melatonin on Seizure Outcome, Neuronal Damage and Quality of Life in Patients With Generalized Epilepsy
NCT03940326	PHASE4	COMPLETED	Levetiracetam Versus Valproate in Idiopathic Generalized Tonic-clonic Seizures
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
NCT00150735	PHASE3	COMPLETED	Monotherapy With Levetiracetam in Newly Diagnosed Patients Suffering From Epilepsy
NCT00150748	PHASE3	COMPLETED	Long Term Follow up Treatment With Levetiracetam in Subjects of 4 Years and Older With Generalized Epilepsy
NCT03678753	PHASE3	COMPLETED	Randomized, Double-Blind Study to Evaluate Efficacy and Safety of Cenobamate Adjunctive Therapy in PGTC Seizures
NCT05147571	PHASE3	ACTIVE_NOT_RECRUITING	RNS System NAUTILUS Study
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
NCT06908356	PHASE2	RECRUITING	An Open Label Trial to Evaluate the Efficacy and Safety of PRAX-628 in Adults With Focal Onset or Tonic-Clonic Seizures
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
NCT04115345	PHASE1	COMPLETED	A Study of a Renal Autologous Cell Therapy (REACT) in Patients With Chronic Kidney Disease (CKD) From Congenital Anomalies of the Kidney and Urinary Tract (CAKUT).
NCT05694169	PHASE1	TERMINATED	A Study of Participants With Chronic Kidney Disease Previously Treated With REACT
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)
NCT06310681	Not specified	COMPLETED	Pilot Testing of a Co-adapted Group Programme for Parents/Carers of Children With Complex Neurodisability
NCT07303049	Not specified	NOT_YET_RECRUITING	Cognitive Benefit of Intensive Rehabilitation Using Rhythmic Music Training in Children With Complex Neurodevelopmental Disorder
NCT06425159	PHASE2/PHASE3	TERMINATED	A Study to Determine if BHV-7000 is Effective and Safe in Adults With Idiopathic Generalized Epilepsy With Generalized Tonic-clonic Seizures
NCT00001325	Not specified	COMPLETED	Metabolic Abnormalities in Children With Epilepsy
NCT00916903	Not specified	TERMINATED	Genetic Disease Gene Identification
NCT01311440	Not specified	COMPLETED	Modified Atkins Diet Treatment for Adults With Drug-resistant Epilepsy
NCT01432821	Not specified	COMPLETED	Blinking and Yawning in Epilepsy: The Role of Dopamine
NCT03368469	Not specified	WITHDRAWN	Transcranial Direct Current Stimulation (tDCS) in Children and Adolescents With Epilepsy and Depression
NCT03457961	Not specified	UNKNOWN	Post-market Study of AMPA Receptor Antagonists for Epilepsy Patients in Hong Kong
NCT03955432	Not specified	TERMINATED	Long-term Cardiac Monitoring in Epilepsy
NCT04252846	Not specified	COMPLETED	A Study to Investigate Dosage, Effectiveness, and Safety of Perampanel When Used as First Add-on Therapy in Participants >=12 Years With Partial Onset Seizures With or Without Secondary Generalization or With Primary Generalized Tonic-Clonic Seizures Associated With Idiopathic Generalized Epilepsy
NCT04965571	Not specified	COMPLETED	Clinical Features and Outcome of Wilson’s Disease With Generalized Epilepsy in Chinese Patients
NCT05374928	Not specified	ACTIVE_NOT_RECRUITING	Human Epilepsy Project 3
NCT05530109	Not specified	TERMINATED	Study of Attentional Disorders in Patients Suffering From Idiopathic Generalized Epilepsy.
NCT06388174	Not specified	RECRUITING	Idiopathic Generalized Epilepsy Syndromes
NCT06797791	Not specified	COMPLETED	Assessment of Multifocal Continuous Theta Burst Transcranial Magnetic Stimulation (cTBS) Effects in Generalized Epilepsy Patients.
NCT04537364	Not specified	COMPLETED	Prediction of Renal Parenchymal Damage of CAKUT