SRGAP3

Summary

SRGAP3 (SLIT-ROBO Rho GTPase activating protein 3, HGNC:19744) is a protein-coding gene on chromosome 3p25.3, encoding SLIT-ROBO Rho GTPase-activating protein 3 (O43295). GTPase-activating protein for RAC1 and perhaps Cdc42, but not for RhoA small GTPase.

Predicted to enable GTPase activator activity. Predicted to be involved in negative regulation of cell migration and regulation of postsynapse assembly. Is active in postsynapse.

Source: NCBI Gene 9901 — RefSeq curated summary.

At a glance

• GWAS associations: 4
• Clinical variants (ClinVar): 203 total — 2 pathogenic, 1 likely-pathogenic
• Cancer driver (intOGen): activating (oncogene-like) across 1 cancer types
• MANE Select transcript: NM_014850

Identifiers

Gene identifiers

Field	Value
HGNC ID	HGNC:19744
Approved symbol	SRGAP3
Name	SLIT-ROBO Rho GTPase activating protein 3
Location	3p25.3
Locus type	gene with protein product
Status	Approved
Aliases	KIAA0411, MEGAP, WRP, ARHGAP14
Ensembl gene	ENSG00000196220
Ensembl biotype	protein_coding
OMIM	606525
Entrez	9901

Gene structure

Transcript identifiers

Ensembl transcripts: 12 — 7 protein_coding_CDS_not_defined, 3 retained_intron, 2 protein_coding

ENST00000360413, ENST00000383836, ENST00000433332, ENST00000470951, ENST00000475560, ENST00000480750, ENST00000485983, ENST00000490348, ENST00000490889, ENST00000491467, ENST00000518265, ENST00000520860

RefSeq mRNA: 2 — MANE Select: NM_014850 NM_001033117, NM_014850

CCDS: CCDS2572, CCDS33689

Canonical transcript exons

ENST00000383836 — 22 exons

Exon	Start	End
ENSE00000965652	8992906	8993055
ENSE00000965653	8990512	8990839
ENSE00001874561	9248885	9249646
ENSE00002117802	8980591	8985932
ENSE00003465294	9060231	9060359
ENSE00003485856	9047391	9047475
ENSE00003503743	9080025	9080087
ENSE00003547190	9032650	9032752
ENSE00003553198	9010308	9010387
ENSE00003557009	9015597	9015731
ENSE00003579060	9026935	9026995
ENSE00003592493	9025261	9025338
ENSE00003593447	9104680	9104842
ENSE00003607227	9013737	9013842
ENSE00003631604	9124725	9124917
ENSE00003654306	9058251	9058472
ENSE00003660628	9053027	9053224
ENSE00003671452	9013308	9013535
ENSE00003677735	9064396	9064581
ENSE00003682836	8994343	8994523
ENSE00003687042	9038063	9038090
ENSE00003694578	9056233	9056334

Expression profiles

Bgee: expression breadth ubiquitous, 226 present calls, max score 98.77.

FANTOM5 (CAGE): breadth broad, TPM avg 8.1079 / max 660.2663, expressed in 870 samples.

FANTOM5 promoters (5 alternative TSS)

Promoter ID	TPM avg	Samples expressed
40964	6.7267	810
40965	1.1378	356
40961	0.1213	29
40963	0.0819	41
40962	0.0402	10

Top tissues by expression

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

Tissue	Anatomy ID	Expression score	Quality
middle temporal gyrus	UBERON:0002771	98.77	gold quality
Brodmann (1909) area 23	UBERON:0013554	98.64	gold quality
paraflocculus	UBERON:0005351	97.09	gold quality
Brodmann (1909) area 10	UBERON:0013541	96.36	gold quality
frontal pole	UBERON:0002795	96.06	gold quality
right uterine tube	UBERON:0001302	95.83	gold quality
endothelial cell	CL:0000115	95.38	silver quality
CA1 field of hippocampus	UBERON:0003881	95.15	gold quality
Brodmann (1909) area 46	UBERON:0006483	94.98	gold quality
postcentral gyrus	UBERON:0002581	94.67	gold quality
cerebellar vermis	UBERON:0004720	94.54	gold quality
ventricular zone	UBERON:0003053	94.42	gold quality
superior frontal gyrus	UBERON:0002661	94.25	gold quality
primary visual cortex	UBERON:0002436	94.05	gold quality
orbitofrontal cortex	UBERON:0004167	93.77	gold quality
entorhinal cortex	UBERON:0002728	93.71	gold quality
parietal lobe	UBERON:0001872	93.29	gold quality
cerebellum	UBERON:0002037	92.92	gold quality
right hemisphere of cerebellum	UBERON:0014890	92.78	gold quality
ganglionic eminence	UBERON:0004023	92.76	gold quality
cerebellar cortex	UBERON:0002129	92.61	gold quality
cerebellar hemisphere	UBERON:0002245	92.59	gold quality
occipital lobe	UBERON:0002021	91.32	gold quality
dorsal motor nucleus of vagus nerve	UBERON:0002870	90.33	gold quality
epithelium of bronchus	UBERON:0002031	90.04	gold quality
bronchus	UBERON:0002185	89.63	gold quality
frontal cortex	UBERON:0001870	89.56	gold quality
bronchial epithelial cell	CL:0002328	89.31	gold quality
neocortex	UBERON:0001950	89.18	gold quality
cerebral cortex	UBERON:0000956	89.02	gold quality

Single-cell (SCXA)

Detected in 4 experiment(s), a significant marker in 4.

Experiment	Marker?	Max mean expression
E-GEOD-75140	yes	1384.95
E-GEOD-137537	yes	1028.58
E-MTAB-6678	yes	24.79
E-ANND-3	yes	9.51

Regulation

Is transcription factor: no

miRNA regulators (miRDB)

268 targeting SRGAP3, 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-5011-5P	100.00	83.46	5820
HSA-MIR-8485	100.00	77.57	4731
HSA-MIR-4533	100.00	69.48	2758
HSA-MIR-4476	100.00	68.18	2030
HSA-MIR-6876-5P	100.00	67.68	2126
HSA-MIR-513A-5P	100.00	69.77	2465
HSA-MIR-30B-5P	100.00	76.29	3248
HSA-MIR-30C-5P	100.00	76.29	3248
HSA-MIR-3924	100.00	72.09	2394
HSA-MIR-30A-5P	100.00	76.31	3233
HSA-MIR-30D-5P	100.00	76.32	3233
HSA-MIR-30E-5P	100.00	76.32	3242
HSA-MIR-4481	100.00	66.42	1669
HSA-MIR-190A-3P	100.00	80.35	5520
HSA-MIR-4283	100.00	66.42	2097
HSA-MIR-9-5P	100.00	72.28	2361
HSA-MIR-3646	100.00	73.56	5283
HSA-MIR-1277-5P	100.00	73.95	5056
HSA-MIR-1252-5P	100.00	69.80	2774
HSA-MIR-4692	100.00	67.32	2066
HSA-MIR-6758-5P	100.00	66.21	1470
HSA-MIR-6856-5P	100.00	65.47	1298
HSA-MIR-4789-3P	99.99	70.75	2484
HSA-MIR-150-5P	99.99	66.69	1976
HSA-MIR-3662	99.99	73.82	5684
HSA-MIR-1184	99.99	68.19	1458
HSA-MIR-4500	99.99	72.72	2367
HSA-MIR-4514	99.99	67.10	1870
HSA-MIR-4789-5P	99.98	70.76	2721
HSA-MIR-12136	99.98	72.81	5713

Literature-anchored findings (GeneRIF, showing 10)

• putative role in severe mental retardation (PMID:12195014)
• FNBP2, ARHGAP13, ARHGAP14 and ARHGAP4 constitute the FNBP2 family characterized by FCH, RhoGAP and SH3 domains. (PMID:12736724)
• Data suggest that MEGAP negatively regulates cell migration by perturbing the actin and microtubule cytoskeleton and by hindering the formation of focal complexes. (PMID:16730001)
• We found no association between SRGAP3/MEGAP haploinsufficiency and mental retardation. (PMID:19433673)
• Current evidence suggests that SRGAP3 is the major determinant of mental retardation in distal 3p deletions. (PMID:19760623)
• conclude that srGAP3 has tumor suppressor-like activity in HMECs, likely through its activity as a negative regulator of Rac1 (PMID:23108406)
• deletion of SRGAP3 provides the most convincing explanation for our patient’s phenotype, and our observations lend further weight to a causative role of SRGAP3 haploinsufficiency in mental retardation. (PMID:24300292)
• Nuclear-localized srGAP3 interacts with Brg1. This interaction is mediated by the C-terminal of srGAP3 and the ATPase motif of Brg1. (PMID:24561795)
• A single PXXP motif in the C-terminal region of srGAP3 mediates binding to multiple SH3 domains. (PMID:25819436)
• C5 and SRGAP3 Polymorphisms Are Linked to Paediatric Allergic Asthma in the Italian Population. (PMID:35205259)

Cross-species orthologs

4 orthologs

Organism	Symbol	Gene ID
danio_rerio	srgap3	ENSDARG00000060309
mus_musculus	Srgap3	ENSMUSG00000030257
rattus_norvegicus	Srgap3	ENSRNOG00000006509
caenorhabditis_elegans		WBGENE00006406

Paralogs (5): ARHGAP4 (ENSG00000089820), SRGAP2C (ENSG00000171943), SRGAP2B (ENSG00000196369), SRGAP1 (ENSG00000196935), SRGAP2 (ENSG00000266028)

Protein

Protein identifiers

SLIT-ROBO Rho GTPase-activating protein 3 — O43295 (reviewed: O43295)

Alternative names: Mental disorder-associated GAP, Rho GTPase-activating protein 14, WAVE-associated Rac GTPase-activating protein

All UniProt accessions (1): O43295

UniProt curated annotations — full annotation on UniProt →

Function. GTPase-activating protein for RAC1 and perhaps Cdc42, but not for RhoA small GTPase. May attenuate RAC1 signaling in neurons.

Subunit / interactions. Homodimer. Forms a heterooligomer with SRGAP1 and SRGAP2 through its F-BAR domain. Interacts with WASF1. Probably interacts with ROBO1. Interacts with FASLG.

Tissue specificity. Highly expressed in adult and fetal brain. Expressed at low levels in kidney. Isoform 3 is expressed in the kidney but is absent in the brain.

Disease relevance. A chromosomal aberration involving SRGAP3 is found in a patient with severe idiopathic intellectual disability. Translocation t(X;3)(p11.2;p25).

Domain organisation. The F-BAR domain mediates oligomerization, binds membranes, and induces plasma membrane protrusions.

Isoforms (3)

UniProt ID	Names	Canonical?
O43295-1	1, MEGAPa, srGAP3a	yes
O43295-2	2, MEGAPb, srGAP3b
O43295-3	3, MEGAPc, srGAP3c

RefSeq proteins (2): NP_001028289, NP_055665* (*=MANE)

Domains & families (InterPro)

ID	Name	Type
IPR000198	RhoGAP_dom	Domain
IPR001060	FCH_dom	Domain
IPR001452	SH3_domain	Domain
IPR008936	Rho_GTPase_activation_prot	Homologous_superfamily
IPR027267	AH/BAR_dom_sf	Homologous_superfamily
IPR031160	F_BAR_dom	Domain
IPR035648	srGAP1/2/3_SH3	Domain
IPR036028	SH3-like_dom_sf	Homologous_superfamily
IPR049581	SrGAP3_F-BAR	Domain
IPR051627	SLIT-ROBO_RhoGAP	Family

Pfam: PF00018, PF00611, PF00620

UniProt features (30 total): compositionally biased region 6, modified residue 6, region of interest 6, domain 3, splice variant 3, coiled-coil region 2, sequence variant 2, chain 1, site 1

Structure

Experimental structures (PDB)

0 structures.

Predicted structure (AlphaFold)

Model	pLDDT	Fraction very-high
AF-O43295-F1	72.65	0.45

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): 542 (arginine finger; crucial for gtp hydrolysis by stabilizing the transition state)

Post-translational modifications (6): 817, 820, 821, 837, 858, 954

Function

Pathways and Gene Ontology

Reactome pathways

11 pathways

ID	Pathway
R-HSA-428543	Inactivation of CDC42 and RAC1
R-HSA-9013148	CDC42 GTPase cycle
R-HSA-9013149	RAC1 GTPase cycle
R-HSA-1266738	Developmental Biology
R-HSA-162582	Signal Transduction
R-HSA-194315	Signaling by Rho GTPases
R-HSA-376176	Signaling by ROBO receptors
R-HSA-422475	Axon guidance
R-HSA-9012999	RHO GTPase cycle
R-HSA-9675108	Nervous system development
R-HSA-9716542	Signaling by Rho GTPases, Miro GTPases and RHOBTB3

MSigDB gene sets: 527 (showing top): GSE45365_NK_CELL_VS_CD8_TCELL_UP, GSE45365_CTRL_VS_MCMV_INFECTION_NK_CELL_UP, GSE45365_NK_CELL_VS_CD11B_DC_UP, WAMUNYOKOLI_OVARIAN_CANCER_LMP_DN, GOBP_DENDRITE_DEVELOPMENT, TGGTGCT_MIR29A_MIR29B_MIR29C, GNF2_RTN1, RODRIGUES_THYROID_CARCINOMA_ANAPLASTIC_UP, AAGCAAT_MIR137, BROWNE_HCMV_INFECTION_6HR_DN, GGTGTGT_MIR329, RODRIGUES_THYROID_CARCINOMA_POORLY_DIFFERENTIATED_UP, GOBP_SYNAPSE_ASSEMBLY, TGCACTT_MIR519C_MIR519B_MIR519A, ATACCTC_MIR202

GO Biological Process (5): signal transduction (GO:0007165), nervous system development (GO:0007399), negative regulation of cell migration (GO:0030336), regulation of small GTPase mediated signal transduction (GO:0051056), regulation of synapse assembly (GO:0051963)

GO Molecular Function (2): GTPase activator activity (GO:0005096), protein binding (GO:0005515)

GO Cellular Component (3): cytosol (GO:0005829), postsynapse (GO:0098794), synapse (GO:0045202)

Reactome top-level categories

Rollup of top-8 pathways:

Category	Pathways
RHO GTPase cycle	2
Signaling by ROBO receptors	1
Signaling by Rho GTPases, Miro GTPases and RHOBTB3	1
Axon guidance	1
Nervous system development	1
Signaling by Rho GTPases	1
Developmental Biology	1
Signal Transduction	1

GO top-level categories

Rollup of top GO terms by namespace:

Category	Terms
cellular anatomical structure	2
cell communication	1
cellular process	1
signaling	1
regulation of cellular process	1
cellular response to stimulus	1
system development	1
cell migration	1
regulation of cell migration	1
negative regulation of cell motility	1
small GTPase-mediated signal transduction	1
regulation of intracellular signal transduction	1
synapse assembly	1
regulation of synapse organization	1
regulation of cell junction assembly	1
GTPase activity	1
enzyme activator activity	1
GTPase regulator activity	1
binding	1
cytoplasm	1
synapse	1
cell junction	1

Protein interactions and networks

STRING

1538 interactions, top by confidence (×1000):

Protein A	Protein B	Partner UniProt	Score
SRGAP3	WASF1	Q92558	922
SRGAP3	FMNL1	O95466	865
SRGAP3	HYDIN	Q4G0P3	864
SRGAP3	GPRIN2	O60269	850
SRGAP3	NBPF1	Q3BBV0	839
SRGAP3	NPEPPS	P55786	810
SRGAP3	UGT2B17	O75795	810
SRGAP3	WASL	O00401	791
SRGAP3	TRIP10	Q15642	785
SRGAP3	ROBO1	Q9Y6N7	784
SRGAP3	GTF2I	P78347	775
SRGAP3	DRD5	P21918	770
SRGAP3	ABI2	Q9NYB9	754
SRGAP3	SLIT3	O75094	727
SRGAP3	SLIT1	O75093	704

IntAct

39 interactions, top by confidence:

A	B	Type	Score
SMARCA4	ARID1A	psi-mi:“MI:0914”(association)	0.940
SRGAP3	Amph	psi-mi:“MI:0915”(physical association)	0.600
SRGAP3	Amph	psi-mi:“MI:0407”(direct interaction)	0.600
SRGAP3	GRB2	psi-mi:“MI:0915”(physical association)	0.540
SRGAP3	Sh3gl2	psi-mi:“MI:0407”(direct interaction)	0.540
SRGAP3	Sh3gl1	psi-mi:“MI:0407”(direct interaction)	0.540
SRGAP3	GRB2	psi-mi:“MI:0407”(direct interaction)	0.540
YWHAZ	BLTP3B	psi-mi:“MI:0914”(association)	0.530
SRGAP3	FASLG	psi-mi:“MI:0407”(direct interaction)	0.440
SRGAP3	Dlg4	psi-mi:“MI:0407”(direct interaction)	0.440
	SRGAP3	psi-mi:“MI:0407”(direct interaction)	0.440
SRGAP3	SH3GL2	psi-mi:“MI:0915”(physical association)	0.400
SRGAP3	SH3GL1	psi-mi:“MI:0915”(physical association)	0.400
SRGAP3	SRGAP3	psi-mi:“MI:0915”(physical association)	0.400
SRGAP3	H1-2	psi-mi:“MI:0915”(physical association)	0.400
SRGAP3	S100A10	psi-mi:“MI:0915”(physical association)	0.400
SRGAP3	SUV39H1	psi-mi:“MI:0915”(physical association)	0.370
SRGAP3	KDM1A	psi-mi:“MI:0915”(physical association)	0.370
PRMT6	SRGAP3	psi-mi:“MI:0915”(physical association)	0.370
SRGAP3	HTT	psi-mi:“MI:0915”(physical association)	0.370
HTT	SRGAP3	psi-mi:“MI:0915”(physical association)	0.370
BMI1	MEIS3P1	psi-mi:“MI:0914”(association)	0.350
DYRK1A	TEX13D	psi-mi:“MI:0914”(association)	0.350
HCN1	POTEF	psi-mi:“MI:0914”(association)	0.350

BioGRID (65): SRGAP2 (Affinity Capture-MS), ACAD8 (Affinity Capture-MS), CLOCK (Affinity Capture-MS), SPAG5 (Affinity Capture-MS), CCDC85C (Affinity Capture-MS), PPP1R13B (Affinity Capture-MS), TP53BP2 (Affinity Capture-MS), CCDC22 (Affinity Capture-MS), PGGT1B (Affinity Capture-MS), SRGAP3 (Affinity Capture-MS), SRGAP3 (Affinity Capture-MS), SRGAP3 (Affinity Capture-MS), SRGAP3 (Affinity Capture-MS), SRGAP3 (Affinity Capture-MS), SRGAP2 (Affinity Capture-MS)

ESM2 similar proteins: A1XBS5, B0S6J3, D4A208, O35180, O35964, O43295, O75044, P0DJJ0, P0DMP2, P25343, Q08DK5, Q15057, Q1LU86, Q1RMK1, Q2VR06, Q32LM0, Q3SZG6, Q3V2J0, Q5AFE4, Q5FVC7, Q5PPJ9, Q5PPZ5, Q5R8P5, Q5ZIR1, Q5ZJ81, Q5ZK62, Q62419, Q62421, Q68FW8, Q6AYE2, Q6GN09, Q6IVG4, Q6ZQK5, Q6ZTR7, Q7Z6B7, Q812A2, Q8AXU9, Q8BP22, Q8I190, Q8I1C0

Diamond homologs: A0A0G2JTR4, A1A4S6, A2RUV4, A4II46, A6NI28, A6QNS3, A6X8Z5, A8WRJ2, B2RQE8, B5DFQ4, D3ZZN9, E7EZG2, E7F3F0, F1LQX4, F1LXF1, O14014, O14559, O43182, O43295, O54834, O60890, O94466, P0CAX5, P11274, P15882, P30337, P34288, P38339, P39960, P46941, P52757, P81128, P83509, P97393, Q03070, Q08DP6, Q12979, Q13017, Q17QN0, Q17R89

SIGNOR signaling

5 interactions.

A	Effect	B	Mechanism
SRGAP3	“down-regulates activity”	RAC1	“gtpase-activating protein”
SRGAP3	down-regulates	RAC1
SRGAP3	down-regulates	RAC2
SRGAP3	down-regulates	RAC3
SRGAP3	up-regulates	WASF1	binding

Enriched among interaction partners

Reactome pathways and GO biological processes over-represented among this gene’s 32 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
Chromatin organization	5	20.4×	5e-04
Chromatin modifying enzymes	5	18.1×	5e-04
Signaling by Rho GTPases	5	8.6×	7e-03
Signaling by Rho GTPases, Miro GTPases and RHOBTB3	5	8.4×	7e-03

Disease & clinical

Cancer significance

From intOGen — cancer-driver classification: activating (oncogene-like) across 1 cancer types — PLMESO.

Clinical variants and AI predictions

ClinVar

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

Classification	Count (floor)
Pathogenic	2
Likely pathogenic	1
Uncertain significance	132
Likely benign	31
Benign	16

Top pathogenic / likely-pathogenic (3)

Variant ID	HGVS	Classification
1706499	GRCh37/hg19 3p26.1-25.3(chr3:7694117-9546173)x1	Pathogenic
562752	GRCh37/hg19 3p25.3(chr3:9043040-9454382)x1	Pathogenic
982231	NM_014850.4(SRGAP3):c.2281C>T (p.Arg761Cys)	Likely pathogenic

SpliceAI

4248 predictions. Top by Δscore:

Variant	Effect	Δscore
3:8992919:C:A	donor_gain	1.0000
3:8992931:AAT:A	donor_gain	1.0000
3:8993051:CATCC:C	acceptor_gain	1.0000
3:8993053:TCCC:T	acceptor_loss	1.0000
3:8993054:CC:C	acceptor_gain	1.0000
3:8993055:CC:C	acceptor_gain	1.0000
3:8993055:CCTGG:C	acceptor_loss	1.0000
3:8993056:C:CC	acceptor_gain	1.0000
3:8993056:CT:C	acceptor_loss	1.0000
3:8993057:T:A	acceptor_loss	1.0000
3:8994341:A:AC	donor_gain	1.0000
3:8994342:C:CC	donor_gain	1.0000
3:8994362:A:AC	donor_gain	1.0000
3:8994363:C:CC	donor_gain	1.0000
3:8994521:CTT:C	acceptor_gain	1.0000
3:8994524:C:CC	acceptor_gain	1.0000
3:9010304:TCA:T	donor_loss	1.0000
3:9010305:CACCT:C	donor_loss	1.0000
3:9010306:A:AC	donor_gain	1.0000
3:9010306:A:T	donor_loss	1.0000
3:9010307:C:CC	donor_gain	1.0000
3:9010307:C:CG	donor_loss	1.0000
3:9010383:TGTCA:T	acceptor_gain	1.0000
3:9010386:CA:C	acceptor_gain	1.0000
3:9010387:ACTG:A	acceptor_loss	1.0000
3:9010388:C:CC	acceptor_gain	1.0000
3:9010388:CTG:C	acceptor_loss	1.0000
3:9013304:TTA:T	donor_loss	1.0000
3:9013305:TAC:T	donor_loss	1.0000
3:9013306:A:AC	donor_gain	1.0000

AlphaMissense

7328 scored. Top likely-pathogenic:

Variant	Protein change	am_pathogenicity
3:8994358:A:T	I798K	1.000
3:8994379:C:T	G791E	1.000
3:8994397:C:G	R785P	1.000
3:8994400:C:T	G784D	1.000
3:8994401:C:G	G784R	1.000
3:8994405:C:A	W782C	1.000
3:8994405:C:G	W782C	1.000
3:8994407:A:G	W782R	1.000
3:8994407:A:T	W782R	1.000
3:8994408:C:A	W781C	1.000
3:8994408:C:G	W781C	1.000
3:8994410:A:G	W781R	1.000
3:8994410:A:T	W781R	1.000
3:8994433:A:G	L773P	1.000
3:8994439:A:G	L771P	1.000
3:8994439:A:T	L771Q	1.000
3:8994457:A:G	F765S	1.000
3:8994463:A:G	L763P	1.000
3:8994492:A:C	F753L	1.000
3:8994492:A:T	F753L	1.000
3:8994494:A:G	F753L	1.000
3:8994499:G:T	A751D	1.000
3:8994505:G:T	A749D	1.000
3:8994506:C:G	A749P	1.000
3:9047432:A:G	L456P	1.000
3:9056273:A:G	L362P	1.000
3:9058420:A:G	L285P	1.000
3:9060292:A:G	L247P	1.000
3:9060313:C:G	R240P	1.000
3:9060317:C:G	A239P	1.000

dbSNP variants (sampled 300 via entrez): RS1000007243 (3:9203769 G>C), RS1000010347 (3:9029096 C>T), RS1000019080 (3:9108349 T>A), RS1000022374 (3:9315698 T>C), RS1000024181 (3:9363348 T>A), RS1000025979 (3:9280500 G>A), RS1000031493 (3:9204248 G>A,T), RS1000035256 (3:8982858 T>A,C,G), RS1000041262 (3:9048939 T>G), RS1000049842 (3:9362763 A>C,T), RS1000065279 (3:9032004 A>G), RS1000068518 (3:9154595 T>C), RS1000081461 (3:9059265 GCTC>G), RS1000090915 (3:9328062 T>C), RS1000102561 (3:9245440 G>A,C)

Disease associations

OMIM: gene MIM:606525 | disease phenotypes:

GenCC curated gene-disease

Mondo (0):

Orphanet (1): Moyamoya angiopathy (Orphanet:477768)

HPO phenotypes

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

GWAS associations

4 associations (top):

Study	Trait	p-value
GCST002831_4	Lead levels in blood	4.000000e-06
GCST007470_3	Rapid automatized naming of letters	5.000000e-06
GCST007672_10	3-month functional outcome in ischaemic stroke (modified Rankin score)	9.000000e-06
GCST009531_10	Body fat percentage	2.000000e-08

EFO canonical traits (3, from GWAS)

EFO ID	Trait name
EFO:0005301	reading and spelling ability
EFO:0009603	stroke outcome severity measurement
EFO:0007800	body fat percentage

Drugs & pharmacology

Drug and pharmacology data

Is drug target: no

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

CTD chemical–gene interactions

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

Chemical	Actions (top 5)	PubMed papers
Valproic Acid	affects expression, decreases expression, increases expression, increases methylation	4
bisphenol A	increases methylation, affects cotreatment, affects methylation, decreases expression, increases expression	3
sodium arsenite	decreases expression, increases expression	2
Air Pollutants	decreases expression, increases abundance	2
Benzo(a)pyrene	affects methylation	2
Cytarabine	increases expression	2
Diethylhexyl Phthalate	decreases expression, increases abundance, increases methylation	2
Estradiol	affects expression, affects cotreatment, decreases expression	2
Phenylmercuric Acetate	affects cotreatment, decreases expression	2
Smoke	increases abundance, decreases expression	2
Aflatoxin B1	increases methylation	2
FR900359	increases phosphorylation	1
methylmercuric chloride	decreases expression	1
sodium arsenate	increases abundance, increases expression	1
trichostatin A	affects expression	1
arsenite	affects binding, decreases reaction	1
mono-(2-ethylhexyl)phthalate	increases abundance, increases methylation	1
sulforaphane	decreases expression	1
perfluorooctanoic acid	increases expression	1
benzo(e)pyrene	decreases methylation	1
rutecarpine	increases expression	1
aflatoxin B2	decreases methylation	1
cupric chloride	decreases expression	1
HC toxin	increases expression	1
S-(1,2-dichlorovinyl)cysteine	decreases reaction, decreases expression	1
di-n-butylphosphoric acid	affects expression	1
CGP 52608	affects binding, increases reaction	1
apicidin	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
dorsomorphin	affects cotreatment, decreases expression	1

Clinical trials (associated diseases)

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