ARHGAP11A

Summary

ARHGAP11A (Rho GTPase activating protein 11A, HGNC:15783) is a protein-coding gene on chromosome 15q13.3, encoding Rho GTPase-activating protein 11A (Q6P4F7). GTPase activator for the Rho-type GTPases by converting them to an inactive GDP-bound state. It is a selective cancer dependency (DepMap: 16.1% of cell lines).

This gene encodes a member of the Rho GTPase activating protein family. In response to DNA damage, the encoded protein interacts with the p53 tumor suppressor protein and stimulates its tetramerization, which results in cell-cycle arrest and apoptosis. A chromosomal deletion that includes this gene is one cause of Prader-Willi syndrome, and an intronic variant of this gene may be associated with sleep duration in children. This gene is highly expressed in colon cancers and in a human basal-like breast cancer cell line. This gene also produces a ARHGAP11A-SCG5 readthrough transcript and ARHGAP11A-SCG5 protein.

Source: NCBI Gene 9824 — RefSeq curated summary.

At a glance

• GWAS associations: 2
• Clinical variants (ClinVar): 189 total — 7 pathogenic, 4 likely-pathogenic
• Cancer dependency (DepMap): dependent in 16.1% of screened cell lines
• MANE Select transcript: NM_014783

Identifiers

Gene identifiers

Field	Value
HGNC ID	HGNC:15783
Approved symbol	ARHGAP11A
Name	Rho GTPase activating protein 11A
Location	15q13.3
Locus type	gene with protein product
Status	Approved
Aliases	KIAA0013
Ensembl gene	ENSG00000198826
Ensembl biotype	protein_coding
OMIM	610589
Entrez	9824

Gene structure

Transcript identifiers

Ensembl transcripts: 11 — 9 protein_coding, 1 protein_coding_CDS_not_defined, 1 retained_intron

ENST00000361627, ENST00000543522, ENST00000562481, ENST00000563330, ENST00000563864, ENST00000564918, ENST00000565905, ENST00000567348, ENST00000868567, ENST00000915540, ENST00000915541

RefSeq mRNA: 4 — MANE Select: NM_014783 NM_001286479, NM_001286480, NM_014783, NM_199357

CCDS: CCDS10028, CCDS58349, CCDS66730

Canonical transcript exons

ENST00000361627 — 12 exons

Exon	Start	End
ENSE00001210937	32632979	32633108
ENSE00001210938	32629595	32629762
ENSE00001210956	32636257	32639941
ENSE00001210960	32615504	32616340
ENSE00001611714	32628728	32628802
ENSE00001613612	32625487	32625633
ENSE00003459463	32624173	32624426
ENSE00003498418	32620108	32620178
ENSE00003505044	32635777	32635915
ENSE00003522804	32623492	32623588
ENSE00003523874	32633933	32634041
ENSE00003569328	32625080	32625243

Expression profiles

Bgee: expression breadth ubiquitous, 134 present calls, max score 93.99.

FANTOM5 (CAGE): breadth ubiquitous, TPM avg 6.5672 / max 199.4382, expressed in 1172 samples.

FANTOM5 promoters (1 alternative TSS)

Promoter ID	TPM avg	Samples expressed
145692	6.5672	1172

Top tissues by expression

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

Tissue	Anatomy ID	Expression score	Quality
ganglionic eminence	UBERON:0004023	93.99	gold quality
ventricular zone	UBERON:0003053	93.32	gold quality
primordial germ cell in gonad	CL:0000670 ∩ UBERON:0000991	90.03	gold quality
stromal cell of endometrium	CL:0002255	86.22	gold quality
male germ line stem cell (sensu Vertebrata) in testis	CL:0000089 ∩ UBERON:0000473	85.60	gold quality
bone marrow	UBERON:0002371	84.59	gold quality
vermiform appendix	UBERON:0001154	83.10	gold quality
endometrium	UBERON:0001295	82.67	gold quality
colonic epithelium	UBERON:0000397	81.83	gold quality
rectum	UBERON:0001052	81.55	gold quality
bone marrow cell	CL:0002092	80.55	gold quality
lymph node	UBERON:0000029	80.37	gold quality
adrenal tissue	UBERON:0018303	78.76	gold quality
duodenum	UBERON:0002114	78.46	gold quality
tonsil	UBERON:0002372	77.97	gold quality
placenta	UBERON:0001987	77.78	gold quality
smooth muscle tissue	UBERON:0001135	76.57	gold quality
esophagus mucosa	UBERON:0002469	75.91	gold quality
C1 segment of cervical spinal cord	UBERON:0006469	75.62	gold quality
lower esophagus mucosa	UBERON:0035834	75.34	gold quality
monocyte	CL:0000576	75.11	gold quality
leukocyte	CL:0000738	74.75	gold quality
islet of Langerhans	UBERON:0000006	73.71	gold quality
mucosa of transverse colon	UBERON:0004991	72.88	gold quality
testis	UBERON:0000473	72.21	gold quality
pancreas	UBERON:0001264	71.48	gold quality
right testis	UBERON:0004534	70.18	gold quality
left testis	UBERON:0004533	69.91	gold quality
body of pancreas	UBERON:0001150	69.80	gold quality
calcaneal tendon	UBERON:0003701	69.66	gold quality

Single-cell (SCXA)

Detected in 3 experiment(s), a significant marker in 1.

Experiment	Marker?	Max mean expression
E-GEOD-110499	yes	164.08
E-MTAB-6911	no	222.32
E-ANND-3	no	2.73

Regulation

Is transcription factor: no

miRNA regulators (miRDB)

89 targeting ARHGAP11A, 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-1252-5P	100.00	69.80	2774
HSA-MIR-5692A	100.00	74.40	6850
HSA-MIR-3163	100.00	77.23	8605
HSA-MIR-3646	100.00	73.56	5283
HSA-MIR-548C-3P	99.99	74.01	7587
HSA-MIR-4282	99.99	75.36	6408
HSA-MIR-4534	99.99	66.58	1907
HSA-MIR-4775	99.98	75.00	6394
HSA-MIR-19A-3P	99.98	75.33	2762
HSA-MIR-19B-3P	99.98	75.44	2754
HSA-MIR-3692-3P	99.98	70.27	2139
HSA-MIR-568	99.98	69.86	2084
HSA-MIR-607	99.97	73.62	5593
HSA-MIR-1250-3P	99.96	70.04	4038
HSA-MIR-551B-5P	99.96	71.28	3493
HSA-MIR-3658	99.96	73.87	4379
HSA-MIR-548AT-5P	99.96	70.83	2666
HSA-MIR-493-5P	99.96	72.47	2382
HSA-MIR-548AJ-3P	99.96	73.38	5345
HSA-MIR-548X-3P	99.96	73.38	5345
HSA-LET-7C-3P	99.95	73.42	2862
HSA-MIR-3671	99.90	73.04	3897
HSA-MIR-95-5P	99.89	72.17	3973
HSA-LET-7A-2-3P	99.87	70.53	1921
HSA-MIR-10395-5P	99.86	67.35	676
HSA-LET-7G-3P	99.85	70.43	1929
HSA-MIR-3180-5P	99.82	69.12	2422
HSA-MIR-204-5P	99.79	71.62	2439
HSA-MIR-211-5P	99.79	71.65	2440

Functional genomics

DepMap (CRISPR cell-line fitness): dependent in 16.1% of screened cell lines.

Literature-anchored findings (GeneRIF, showing 6)

• High ARHGAP11A expression is associated with Basal-like Breast Cancers. (PMID:27216196)
• [Rho GTPase-activating protein 11A (ARHGAP11A) is up-regulated in lung adenocarcinoma and positively associated with poor prognosis]. (PMID:34140070)
• Subcellular mRNA localization and local translation of Arhgap11a in radial glial progenitors regulates cortical development. (PMID:36924763)
• ARHGAP11A Is a Novel Prognostic and Predictive Biomarker Correlated with Immunosuppressive Microenvironment in Clear Cell Renal Cell Carcinoma. (PMID:37175461)
• Protooncogenic Role of ARHGAP11A and ARHGAP11B in Invasive Ductal Carcinoma: Two Promising Breast Cancer Biomarkers. (PMID:38046902)
• The hGID[GID4] E3 ubiquitin ligase complex targets ARHGAP11A to regulate cell migration. (PMID:39389782)

Cross-species orthologs

5 orthologs

Organism	Symbol	Gene ID
danio_rerio	arhgap11a	ENSDARG00000100019
mus_musculus	Arhgap11a	ENSMUSG00000041219
rattus_norvegicus	Arhgap11a	ENSRNOG00000008115
caenorhabditis_elegans		WBGENE00019600
caenorhabditis_elegans		WBGENE00022286

Paralogs (1): ARHGAP11B (ENSG00000285077)

Protein

Protein identifiers

Rho GTPase-activating protein 11A — Q6P4F7 (reviewed: Q6P4F7)

Alternative names: Rho-type GTPase-activating protein 11A

All UniProt accessions (3): Q6P4F7, H3BQ41, H3BR51

UniProt curated annotations — full annotation on UniProt →

Function. GTPase activator for the Rho-type GTPases by converting them to an inactive GDP-bound state.

Subcellular location. Nucleus.

Isoforms (3)

UniProt ID	Names	Canonical?
Q6P4F7-1	1	yes
Q6P4F7-2	2
Q6P4F7-3	3

RefSeq proteins (4): NP_001273408, NP_001273409, NP_055598, NP_955389 (=MANE)

Domains & families (InterPro)

ID	Name	Type
IPR000198	RhoGAP_dom	Domain
IPR008936	Rho_GTPase_activation_prot	Homologous_superfamily
IPR042869	ARHGAP11A/B	Family

Pfam: PF00620

UniProt features (46 total): modified residue 16, helix 15, region of interest 3, splice variant 3, strand 3, chain 1, domain 1, sequence variant 1, turn 1, compositionally biased region 1, site 1

Structure

Experimental structures (PDB)

1 structures.

PDB	Method	Resolution (Å)
3EAP	X-RAY DIFFRACTION	2.3

Predicted structure (AlphaFold)

Model	pLDDT	Fraction very-high
AF-Q6P4F7-F1	51.52	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.

Catalytic / active sites (1): 87 (arginine finger; crucial for gtp hydrolysis by stabilizing the transition state)

Post-translational modifications (16): 318, 323, 339, 340, 484, 508, 582, 585, 638, 675, 847, 866, 868, 285, 306, 316

Function

Pathways and Gene Ontology

Reactome pathways

1 pathways

ID	Pathway
R-HSA-8980692	RHOA GTPase cycle

MSigDB gene sets: 232 (showing top): E2F_Q4, E2F_Q4_01, RODRIGUES_THYROID_CARCINOMA_ANAPLASTIC_UP, MULLIGHAN_NPM1_SIGNATURE_3_UP, DORSAM_HOXA9_TARGETS_UP, E2F4DP1_01, MORF_BRCA1, chr15q13, GOBP_REGULATION_OF_GTPASE_ACTIVITY, GOBP_REGULATION_OF_SMALL_GTPASE_MEDIATED_SIGNAL_TRANSDUCTION, PUJANA_CHEK2_PCC_NETWORK, KRASNOSELSKAYA_ILF3_TARGETS_DN, GOBP_POSITIVE_REGULATION_OF_CATALYTIC_ACTIVITY, GOBP_REGULATION_OF_HYDROLASE_ACTIVITY, E2F1DP1_01

GO Biological Process (3): signal transduction (GO:0007165), positive regulation of GTPase activity (GO:0043547), regulation of small GTPase mediated signal transduction (GO:0051056)

GO Molecular Function (1): GTPase activator activity (GO:0005096)

GO Cellular Component (2): nucleus (GO:0005634), cytosol (GO:0005829)

Reactome top-level categories

Rollup of top-1 pathways:

Category	Pathways
RHO GTPase cycle	1

GO top-level categories

Rollup of top GO terms by namespace:

Category	Terms
GTPase activity	2
cell communication	1
cellular process	1
signaling	1
regulation of cellular process	1
cellular response to stimulus	1
regulation of GTPase activity	1
positive regulation of hydrolase activity	1
small GTPase-mediated signal transduction	1
regulation of intracellular signal transduction	1
enzyme activator activity	1
GTPase regulator activity	1
intracellular membrane-bounded organelle	1
cytoplasm	1
cellular anatomical structure	1

Protein interactions and networks

STRING

1382 interactions, top by confidence (×1000):

Protein A	Protein B	Partner UniProt	Score
ARHGAP11A	PIR	O00625	497
ARHGAP11A	TP53	P04637	494
ARHGAP11A	ZNF394	Q53GI3	445
ARHGAP11A	PTPN20	Q4JDL3	435
ARHGAP11A	SCG5	P01164	409
ARHGAP11A	ZNF350	Q9GZX5	405
ARHGAP11A	FIRRM	Q9NSG2	405
ARHGAP11A	GTF2I	P78347	392
ARHGAP11A	BBX	Q8WY36	387
ARHGAP11A	CCDC150	Q8NCX0	387
ARHGAP11A	LXN	Q9BS40	385
ARHGAP11A	HASPIN	Q8TF76	383
ARHGAP11A	NEMP1	O14524	381
ARHGAP11A	CCDC34	Q96HJ3	381
ARHGAP11A	OTUD7A	Q8TE49	377

IntAct

40 interactions, top by confidence:

A	B	Type	Score
DDX21	MED19	psi-mi:“MI:2364”(proximity)	0.480
H3C1	SMCHD1	psi-mi:“MI:2364”(proximity)	0.410
ARHGAP11A	SFN	psi-mi:“MI:0915”(physical association)	0.400
MYH9	PLEKHG3	psi-mi:“MI:0914”(association)	0.350
ANLN	PLEKHG3	psi-mi:“MI:0914”(association)	0.350
Flot2	ACTG1	psi-mi:“MI:0914”(association)	0.350
MYO18A	PLEKHG3	psi-mi:“MI:0914”(association)	0.350
MYO1C	PLEKHG3	psi-mi:“MI:0914”(association)	0.350
MYO19	PLEKHG3	psi-mi:“MI:0914”(association)	0.350
FLNA	PLEKHG3	psi-mi:“MI:0914”(association)	0.350
Actb		psi-mi:“MI:0914”(association)	0.350
Calml3	PLEKHG3	psi-mi:“MI:0914”(association)	0.350
Tpm1	PLEKHG3	psi-mi:“MI:0914”(association)	0.350
Coro1c	PLEKHG3	psi-mi:“MI:0914”(association)	0.350
DBN1	PLEKHG3	psi-mi:“MI:0914”(association)	0.350
SYNPO	LMO7	psi-mi:“MI:0914”(association)	0.350
Myh9	PLEKHG3	psi-mi:“MI:0914”(association)	0.350
Myo1c	PLEKHG3	psi-mi:“MI:0914”(association)	0.350
Kif5b	UNC84A	psi-mi:“MI:0914”(association)	0.350
Myh9	GOSR1	psi-mi:“MI:0914”(association)	0.350
MYH9	NAP1L1	psi-mi:“MI:0914”(association)	0.350
Myh10	NAP1L1	psi-mi:“MI:0914”(association)	0.350
MYO5C	CLIC1	psi-mi:“MI:0914”(association)	0.350
Tmed10	NDUFS8	psi-mi:“MI:0914”(association)	0.350
Vps4b	CNOT1	psi-mi:“MI:0914”(association)	0.350
CAPZA2	PLEKHG3	psi-mi:“MI:0914”(association)	0.350
IQGAP1	PLEKHG3	psi-mi:“MI:0914”(association)	0.350
PPP1CB	PLEKHG3	psi-mi:“MI:0914”(association)	0.350
SCARB2	PLEKHG3	psi-mi:“MI:0914”(association)	0.350

BioGRID (87): ARHGAP11A (Affinity Capture-RNA), ARHGAP11A (Proximity Label-MS), ARHGAP11A (Proximity Label-MS), ARHGAP11A (Affinity Capture-MS), ARHGAP11A (Affinity Capture-MS), ARHGAP11A (Affinity Capture-MS), ARHGAP11A (Affinity Capture-MS), ARHGAP11A (Affinity Capture-MS), ARHGAP11A (Affinity Capture-MS), ARHGAP11A (Affinity Capture-MS), ARHGAP11A (Affinity Capture-MS), ARHGAP11A (Affinity Capture-MS), ARHGAP11A (Affinity Capture-MS), ARHGAP11A (Affinity Capture-MS), ARHGAP11A (Affinity Capture-MS)

ESM2 similar proteins: A0A0R4IYX6, A0A1D5NVS8, A0A1L8H0H2, A0AVK6, A5GFT6, A7XYH5, A7XYJ6, B7ZS37, B8A5Y1, D4A666, E1B7L7, E1BKK0, E1BLP6, F1LMN3, F6YVB9, F8VPJ6, Q12766, Q13029, Q14B70, Q2HNT1, Q2HNT2, Q2KHR2, Q4V9H5, Q58FA4, Q5DTH5, Q5ZIE8, Q5ZIX8, Q5ZJ69, Q5ZM88, Q63679, Q63755, Q68FE9, Q69ZF8, Q6DRC5, Q6P4F7, Q6PCM1, Q6ZSZ6, Q76L83, Q80Y19, Q8BHZ4

Diamond homologs: A1A4S6, A6NI28, A6X8Z5, A7E300, B2RQE8, B5DFQ4, B9VTT2, D3ZFJ3, D3ZZN9, E9Q6X9, F1LQX4, O43182, O60890, P0CAX5, P15882, P30337, P55194, P81128, P83509, P98171, Q07960, Q08DP6, Q13459, Q14CB8, Q17QN0, Q17R89, Q2M1Z3, Q3KRB8, Q54FF4, Q54PG5, Q54TH9, Q54VW7, Q553X3, Q559A0, Q5FWK3, Q5SSM3, Q5TG30, Q5U4T3, Q62172, Q63358

SIGNOR signaling

1 interactions.

A	Effect	B	Mechanism
ARHGAP11A	“down-regulates activity”	RHOA	“gtpase-activating protein”

Enriched among interaction partners

Reactome pathways and GO biological processes over-represented among this gene’s 51 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
Diseases of signal transduction by growth factor receptors and second messengers	5	9.2×	4e-03
Signaling by Rho GTPases, Miro GTPases and RHOBTB3	7	7.6×	2e-03
Dengue Virus-Host Interactions	5	7.4×	7e-03
Membrane Trafficking	6	7.2×	3e-03
Vesicle-mediated transport	6	6.7×	4e-03
Signaling by Rho GTPases	6	6.6×	4e-03

GO biological processes:

GO term	Partners	Fold	FDR
nucleosome assembly	5	18.5×	1e-03
actin filament organization	5	15.6×	1e-03

Disease & clinical

Clinical variants and AI predictions

ClinVar

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

Classification	Count (floor)
Pathogenic	7
Likely pathogenic	4
Uncertain significance	138
Likely benign	12
Benign	9

Top pathogenic / likely-pathogenic (11)

Variant ID	HGVS	Classification
1684562	GRCh37/hg19 15q13.2-13.3(chr15:30783603-32914393)x1	Pathogenic
1703668	GRCh37/hg19 15q13.2-13.3(chr15:31098690-32914240)	Pathogenic
3063358	GRCh37/hg19 15q13.2-13.3(chr15:30913573-32914239)x1	Pathogenic
394946	GRCh37/hg19 15q13.2-13.3(chr15:31115047-32917801)x4	Pathogenic
564180	GRCh37/hg19 15q13.2-13.3(chr15:30913573-32914239)x1	Pathogenic
57845	GRCh38/hg38 15q13.2-13.3(chr15:30361674-32630901)x1	Pathogenic
635876	Single allele	Pathogenic
225089	NM_014783.6(ARHGAP11A):c.2370_2371del (p.Thr790_Cys791insTer)	Likely pathogenic
253353	GRCh37/hg19 15q13.2-13.3(chr15:31115047-32917857)x3	Likely pathogenic
564191	GRCh37/hg19 15q13.3-14(chr15:32446829-34868996)x1	Likely pathogenic
625748	GRCh37/hg19 15q13.2-13.3(chr15:30927362-32929514)	Likely pathogenic

SpliceAI

1689 predictions. Top by Δscore:

Variant	Effect	Δscore
15:32620106:AG:A	acceptor_gain	1.0000
15:32620107:GG:G	acceptor_gain	1.0000
15:32623490:A:AG	acceptor_gain	1.0000
15:32623490:A:G	acceptor_loss	1.0000
15:32623491:G:GC	acceptor_gain	1.0000
15:32623491:GC:G	acceptor_gain	1.0000
15:32623491:GCT:G	acceptor_gain	1.0000
15:32623491:GCTT:G	acceptor_gain	1.0000
15:32623491:GCTTT:G	acceptor_gain	1.0000
15:32623584:TAAAG:T	donor_gain	1.0000
15:32623585:AAAGG:A	donor_loss	1.0000
15:32623586:AAG:A	donor_gain	1.0000
15:32623586:AAGG:A	donor_loss	1.0000
15:32623587:AG:A	donor_gain	1.0000
15:32623587:AGG:A	donor_loss	1.0000
15:32623588:GG:G	donor_gain	1.0000
15:32623588:GGTG:G	donor_loss	1.0000
15:32623589:G:GG	donor_gain	1.0000
15:32624171:A:AG	acceptor_gain	1.0000
15:32624172:G:GG	acceptor_gain	1.0000
15:32625042:C:G	acceptor_gain	1.0000
15:32625057:A:AG	acceptor_gain	1.0000
15:32625077:A:AG	acceptor_gain	1.0000
15:32625078:A:G	acceptor_gain	1.0000
15:32625079:G:GG	acceptor_gain	1.0000
15:32625207:GTA:G	donor_gain	1.0000
15:32625208:T:TA	donor_gain	1.0000
15:32625209:A:AA	donor_gain	1.0000
15:32625241:TTGG:T	donor_loss	1.0000
15:32625242:TGGT:T	donor_loss	1.0000

AlphaMissense

6732 scored. Top likely-pathogenic:

Variant	Protein change	am_pathogenicity
15:32623548:T:C	F86S	0.998
15:32623551:G:C	R87P	0.998
15:32624241:G:C	K122N	0.998
15:32624241:G:T	K122N	0.998
15:32625112:T:C	L195P	0.997
15:32624239:A:G	K122E	0.996
15:32625097:T:C	M190T	0.996
15:32623550:C:G	R87G	0.995
15:32625098:G:A	M190I	0.995
15:32625098:G:C	M190I	0.995
15:32625098:G:T	M190I	0.995
15:32625115:C:A	A196E	0.995
15:32625121:T:A	I198K	0.995
15:32623541:G:A	G84R	0.994
15:32623541:G:C	G84R	0.994
15:32624228:C:A	A118E	0.994
15:32625092:T:A	N188K	0.994
15:32625092:T:G	N188K	0.994
15:32625112:T:A	L195H	0.994
15:32623547:T:C	F86L	0.993
15:32623548:T:G	F86C	0.993
15:32623549:T:A	F86L	0.993
15:32623549:T:G	F86L	0.993
15:32623555:A:C	K88N	0.993
15:32623555:A:T	K88N	0.993
15:32624408:T:C	L178P	0.993
15:32624417:T:A	V181D	0.993
15:32625114:G:C	A196P	0.993
15:32623518:T:C	L76S	0.992
15:32623547:T:A	F86I	0.992

dbSNP variants (sampled 300 via entrez): RS1000020007 (15:32630654 G>A), RS1000028253 (15:32630015 G>A), RS1000087429 (15:32620837 A>G), RS1000139780 (15:32621064 A>C), RS1000158429 (15:32623293 A>C,G), RS1000272450 (15:32628376 T>A,C), RS1000400756 (15:32634510 C>T), RS1000658841 (15:32623966 C>T), RS1000736867 (15:32632821 G>C), RS1001040906 (15:32628510 T>G), RS1001184193 (15:32631200 T>A), RS1001199869 (15:32620426 T>C), RS1001238035 (15:32631039 T>C), RS1001348659 (15:32634861 C>T), RS1001446978 (15:32627843 T>C)

Disease associations

OMIM: gene MIM:610589 | disease phenotypes: MIM:612001

GenCC curated gene-disease

Mondo (3): chromosome 15q13.3 microdeletion syndrome (MONDO:0012774), familial colorectal cancer (MONDO:0023113), neurodevelopmental disorder (MONDO:0700092)

Orphanet (1): 15q13.3 microdeletion syndrome (Orphanet:199318)

HPO phenotypes

0 total (0 of 0 shown, HPO-id order):

GWAS associations

2 associations (top):

Study	Trait	p-value
GCST001762_916	Obesity-related traits	5.000000e-08
GCST005024_86	Pursuit maintenance gain	2.000000e-06

EFO canonical traits (1, from GWAS)

EFO ID	Trait name
EFO:0008433	pursuit maintenance gain measurement

MeSH disease descriptors (2)

Descriptor	Name	Tree numbers
D065886	Neurodevelopmental Disorders	F03.625
C567439	Chromosome 15q13.3 Microdeletion Syndrome (supp.)

Drugs & pharmacology

Drug and pharmacology data

Is drug target: no

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

CTD chemical–gene interactions

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

Chemical	Actions (top 5)	PubMed papers
bisphenol A	increases expression, decreases expression, decreases methylation	2
methylparaben	decreases expression, increases expression	2
sodium arsenite	decreases expression, increases expression	2
Acetaminophen	decreases expression, increases expression	2
Tetrachlorodibenzodioxin	decreases expression	2
Cadmium Chloride	decreases expression, increases expression	2
aristolochic acid I	decreases expression	1
GSK-J4	decreases expression	1
FR900359	decreases phosphorylation	1
TAK-243	increases sumoylation	1
methylmercuric chloride	decreases expression	1
triphenyl phosphate	affects expression	1
propionaldehyde	decreases expression	1
trichostatin A	affects expression	1
2-butenal	decreases expression	1
beta-lapachone	decreases expression	1
arsenite	affects binding, decreases reaction	1
tris(1,3-dichloro-2-propyl)phosphate	decreases expression	1
cobaltous chloride	decreases expression	1
butyraldehyde	decreases expression	1
potassium chromate(VI)	affects cotreatment, decreases expression	1
epigallocatechin gallate	affects cotreatment, decreases expression	1
pentanal	decreases expression	1
phenethyl isothiocyanate	decreases expression	1
perfluorooctane sulfonic acid	decreases expression	1
pentabromodiphenyl ether	decreases expression	1
abrine	decreases expression	1
2,2’,4,4’-tetrabromodiphenyl ether	decreases expression	1
jinfukang	increases expression	1
incobotulinumtoxinA	decreases expression	1

Clinical trials (associated diseases)

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

Trial	Phase	Status	Title
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,
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
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
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
NCT00349817	Not specified	UNKNOWN	Genetics Education: Preparing Physicians for the Future
NCT02645084	Not specified	COMPLETED	Identifying Patients With Hereditary and Familial Colorectal Cancer by Using an Online Risk Tool
NCT03365986	Not specified	UNKNOWN	Systemic Screening for Hereditary Colorectal Cancer in China
NCT04197856	Not specified	ACTIVE_NOT_RECRUITING	Direct Information to At-risk Relatives
NCT04280666	Not specified	UNKNOWN	Next-generation Sequencing of Colorectal Cancer Somatic Cells to Guide Genetic Susceptibility Gene Mutations Screening.
NCT05495776	Not specified	RECRUITING	Prospective Multicenter Registry Study to Assess the Frequency of Lynch Syndrome Among Patients With Colorectal Cancer
NCT07307664	Not specified	RECRUITING	Increasing Germline Genetic Testing for Patients With Cancer
NCT01783041	PHASE2/PHASE3	COMPLETED	Effect of Early L-Carnitine Supplementation on Neurodevelopmental Outcomes in Very Preterm Infants
NCT05767385	PHASE2/PHASE3	RECRUITING	Fetal Cerebrovascular Autoregulation in Congenital Heart Disease and Association With Neonatal Neurobehavior
NCT05675098	EARLY_PHASE1	NOT_YET_RECRUITING	Central Nervous System Stimulants and Physical Function in Children With Cerebral Palsy
NCT00783783	Not specified	COMPLETED	CYP2D6 Pharmacogenetics in Risperidone-Treated Children
NCT01778504	Not specified	RECRUITING	Studying Childhood-onset Behavioral, Psychiatric, and Developmental Disorders
NCT01850784	Not specified	UNKNOWN	High Energy Formula Feeding in Infants With Congenital Heart Disease
NCT01922791	Not specified	COMPLETED	Nutrition and Pregnancy Intervention Study
NCT01942525	Not specified	UNKNOWN	Influence of Intrauterine Growth Restriction on Amplitude-integrated EEG in Preterm Infants
NCT02003170	Not specified	COMPLETED	Etiology and Early Diagnosis of Neurodevelopmental Disorders
NCT02118649	Not specified	ACTIVE_NOT_RECRUITING	Enhancing Behavior and Brain Response to Visual Targets Using a Computer Game
NCT02557191	Not specified	TERMINATED	Biomarkers, Neurodevelopment and Preterm Infants
NCT02690675	Not specified	COMPLETED	Iron Supplement Effect on Child Development
NCT02694003	Not specified	COMPLETED	Better Nights, Better Days for Children With Neurodevelopment Disorders
NCT02792894	Not specified	COMPLETED	Family Networks (FaNs) for Children With Developmental Disorders and Delays
NCT02871674	Not specified	UNKNOWN	Good Night Project: Behavioural Sleep Interventions for Children With ADHD: A Randomised Controlled Trial
NCT02887157	Not specified	COMPLETED	Analyzing Retinal Microanatomy in ROP
NCT02898298	Not specified	COMPLETED	Positive Emotion Regulation Training in Children, Adolescents and Young Adults With and Without Developmental Disorder
NCT02912780	Not specified	UNKNOWN	Introduction of Microsystems in a Level 3 Neonatal Intensive Care Unit
NCT03023293	Not specified	COMPLETED	n-3 PUFAs, Irisin and Maternal Glucose Metabolism From Pregnancy to Postpartum
NCT03023644	Not specified	COMPLETED	Improving Neurodevelopmental Outcomes in Children With Congenital Heart Disease: An Intervention Study
NCT03032991	Not specified	UNKNOWN	Early Biomarkers of Neurodevelopment in Offspring of Diabetic Mothers