ARHGAP1

Summary

ARHGAP1 (Rho GTPase activating protein 1, HGNC:673) is a protein-coding gene on chromosome 11p11.2, encoding Rho GTPase-activating protein 1 (Q07960). GTPase activator for the Rho, Rac and Cdc42 proteins, converting them to the putatively inactive GDP-bound state.

This gene encodes a member of a large family of proteins that activate Rho-type guanosine triphosphate (GTP) metabolizing enzymes. The encoded protein contains a SRC homology 3 domain and interacts with Bcl-2-associated protein family members.

Source: NCBI Gene 392 — RefSeq curated summary.

At a glance

• GWAS associations: 13
• Clinical variants (ClinVar): 76 total
• MANE Select transcript: NM_004308

Identifiers

Gene identifiers

Field	Value
HGNC ID	HGNC:673
Approved symbol	ARHGAP1
Name	Rho GTPase activating protein 1
Location	11p11.2
Locus type	gene with protein product
Status	Approved
Aliases	RhoGAP, p50rhoGAP, CDC42GAP, Cdc42GAP
Ensembl gene	ENSG00000175220
Ensembl biotype	protein_coding
OMIM	602732
Entrez	392

Gene structure

Transcript identifiers

Ensembl transcripts: 21 — 17 protein_coding, 4 retained_intron

ENST00000311956, ENST00000524594, ENST00000525488, ENST00000526423, ENST00000527588, ENST00000528837, ENST00000529960, ENST00000873834, ENST00000873835, ENST00000873836, ENST00000873837, ENST00000873838, ENST00000873839, ENST00000873840, ENST00000917227, ENST00000917228, ENST00000917229, ENST00000917230, ENST00000917231, ENST00000970419, ENST00000970420

RefSeq mRNA: 1 — MANE Select: NM_004308 NM_004308

CCDS: CCDS7922

Canonical transcript exons

ENST00000311956 — 13 exons

Exon	Start	End
ENSE00001181578	46679648	46679776
ENSE00001181598	46681293	46681379
ENSE00001181605	46682051	46682182
ENSE00001181611	46677080	46679225
ENSE00001228757	46688173	46688260
ENSE00002153911	46700551	46700619
ENSE00003466025	46695660	46695755
ENSE00003477867	46679365	46679468
ENSE00003616560	46680640	46680747
ENSE00003618382	46681011	46681109
ENSE00003624251	46680487	46680563
ENSE00003641077	46695975	46696156
ENSE00003652081	46680205	46680282

Expression profiles

Bgee: expression breadth ubiquitous, 297 present calls, max score 98.93.

FANTOM5 (CAGE): breadth ubiquitous, TPM avg 60.3324 / max 341.6828, expressed in 1824 samples.

FANTOM5 promoters (3 alternative TSS)

Promoter ID	TPM avg	Samples expressed
119535	59.4175	1824
119534	0.5490	96
119536	0.3659	181

Top tissues by expression

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

Tissue	Anatomy ID	Expression score	Quality
gingival epithelium	UBERON:0001949	98.93	gold quality
saphenous vein	UBERON:0007318	98.79	gold quality
epithelium of esophagus	UBERON:0001976	98.57	gold quality
esophagus squamous epithelium	UBERON:0006920	98.55	gold quality
squamous epithelium	UBERON:0006914	98.48	gold quality
gingiva	UBERON:0001828	98.43	gold quality
parietal pleura	UBERON:0002400	98.20	gold quality
visceral pleura	UBERON:0002401	98.15	gold quality
cervix squamous epithelium	UBERON:0006922	98.03	silver quality
amniotic fluid	UBERON:0000173	98.02	gold quality
urethra	UBERON:0000057	98.00	gold quality
pleura	UBERON:0000977	97.92	gold quality
decidua	UBERON:0002450	97.91	gold quality
vena cava	UBERON:0004087	97.86	gold quality
cauda epididymis	UBERON:0004360	97.86	gold quality
synovial joint	UBERON:0002217	97.82	gold quality
urinary bladder	UBERON:0001255	97.78	gold quality
parotid gland	UBERON:0001831	97.63	gold quality
seminal vesicle	UBERON:0000998	97.60	gold quality
skin of hip	UBERON:0001554	97.59	gold quality
epithelium of nasopharynx	UBERON:0001951	97.57	gold quality
right coronary artery	UBERON:0001625	97.53	gold quality
superficial temporal artery	UBERON:0001614	97.47	gold quality
blood vessel layer	UBERON:0004797	97.46	gold quality
mammary duct	UBERON:0001765	97.43	gold quality
penis	UBERON:0000989	97.39	gold quality
popliteal artery	UBERON:0002250	97.34	gold quality
tibial artery	UBERON:0007610	97.34	gold quality
aorta	UBERON:0000947	97.20	gold quality
mammalian vulva	UBERON:0000997	97.20	gold quality

Single-cell (SCXA)

Detected in 2 experiment(s), a significant marker in 2.

Experiment	Marker?	Max mean expression
E-ANND-3	yes	21.94
E-MTAB-6678	yes	10.47

Regulation

Is transcription factor: no

miRNA regulators (miRDB)

109 targeting ARHGAP1, 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-4283	100.00	66.42	2097
HSA-MIR-6077	99.99	68.04	2299
HSA-MIR-34A-5P	99.99	71.21	1784
HSA-MIR-449A	99.99	71.05	1776
HSA-MIR-10401-5P	99.99	65.79	948
HSA-MIR-4650-5P	99.98	64.69	999
HSA-MIR-19A-3P	99.98	75.33	2762
HSA-MIR-19B-3P	99.98	75.44	2754
HSA-MIR-34C-5P	99.97	70.45	1577
HSA-MIR-449B-5P	99.97	70.26	1580
HSA-MIR-185-3P	99.95	67.01	1743
HSA-MIR-454-3P	99.91	74.01	1925
HSA-MIR-106A-5P	99.90	73.94	2683
HSA-MIR-130B-3P	99.90	73.27	1850
HSA-MIR-130A-3P	99.90	73.31	1861
HSA-MIR-301A-3P	99.90	73.15	1839
HSA-MIR-301B-3P	99.90	73.19	1836
HSA-MIR-3666	99.90	73.24	1833
HSA-MIR-4295	99.90	73.11	1838
HSA-MIR-17-5P	99.89	73.83	2665
HSA-MIR-153-5P	99.89	73.86	6317
HSA-MIR-4731-5P	99.89	67.23	2537
HSA-MIR-106B-5P	99.88	74.72	2795
HSA-MIR-20A-5P	99.88	74.76	2769
HSA-MIR-20B-5P	99.88	74.01	2621
HSA-MIR-519D-3P	99.88	73.97	2607
HSA-MIR-526B-3P	99.88	74.06	2587
HSA-MIR-93-5P	99.88	73.98	2606
HSA-MIR-4492	99.87	68.25	3611
HSA-MIR-3919	99.87	69.45	2489

Literature-anchored findings (GeneRIF, showing 17)

• Mutation of three residues of CDC42GAP involved in specific interactions of CDC42GAP with switch domain residues of Cdc42, as well as individual mutations of each of these residues, yields GAPs that are defective in stimulating GTP hydrolysis. (PMID:12501193)
• CDC42GAP was identified as a counter-regulatory mediator for tubule formation. (PMID:18060510)
• two potential interaction partners of Prx6: the calcium-activated cysteine endopeptidase calpain and the p50RhoGAP protein of the family of Sec14-like proteins. (PMID:18619034)
• RhoGAP Stard13 temporally and spatially regulates Rho activity in the developing pancreas to ensure that morphogenesis and establishment of tissue architecture are coordinated with organ growth. (PMID:23175628)
• In PC3 cells, ARHGAP21 presented GAP activity for RhoA and RhoC and induced changes in cell morphology. Moreover, its silencing altered the expression of genes involved in cell proliferation and cytoskeleton organization (PMID:23200924)
• The interaction of RhoGap protein stabilizes the tetrameric conformation of p53 and enhances its DNA-binding activity, thereby inducing cell-cycle arrest and apoptosis. (PMID:23684608)
• study shows that HMHA1 acts as a RhoGAP to regulate GTPase activity, cytoskeletal remodeling and cell spreading, which are crucial functions in normal hematopoietic and cancer cells (PMID:24086303)
• to complete invasion of the endothelium, staphylococci reorient recycling endocytic vesicles to recruit Cdc42GAP. (PMID:27311480)
• we identified novel associations in WLS , ARHGAP1 , and 5’ of MEF2C ( P- values < 8x10 - 5 ; false discovery rate (FDR) q-values < 0.01) that were much more strongly associated with BMD compared to the GWAS SNPs. (PMID:27616567)
• identified ARHGAP1, which is a negative regulator of CDC42, as a novel, direct target of miR-130b (PMID:28748534)
• Angio-associated migratory cell protein (AAMP) interacts with cell division cycle 42 (CDC42) and enhances migration and invasion in human non-small cell lung cancer cells. (PMID:33279622)
• Exosome miR-134-5p restrains breast cancer progression via regulating PI3K/AKT pathway by targeting ARHGAP1. (PMID:34378285)
• circRNA RPPH1 Facilitates the Aggravation of Breast Cancer Development by Regulating miR-542-3p/ARHGAP1 Pathway. (PMID:34402683)
• Cdc42GAP deficiency contributes to the Alzheimer’s disease phenotype. (PMID:37254741)
• The Role of ARHGAP1 in Rho GTPase Inactivation during Metastasizing of Breast Cancer Cell Line MCF-7 after Treatment with Doxorubicin. (PMID:37511111)
• Structural basis for the distinct roles of non-conserved Pro116 and conserved Tyr124 of BCH domain of yeast p50RhoGAP. (PMID:38740643)
• Early gastric cancer with RhoGAP fusion is linked to frequent nodal metastasis and a part of microtubular-mucocellular histology. (PMID:38755445)

Cross-species orthologs

3 orthologs

Organism	Symbol	Gene ID
danio_rerio	arhgap1	ENSDARG00000024324
mus_musculus	Arhgap1	ENSMUSG00000027247
rattus_norvegicus	Arhgap1	ENSRNOG00000016610

Paralogs (1): ARHGAP8 (ENSG00000241484)

Protein

Protein identifiers

Rho GTPase-activating protein 1 — Q07960 (reviewed: Q07960)

Alternative names: CDC42 GTPase-activating protein, GTPase-activating protein rhoGAP, Rho-related small GTPase protein activator, Rho-type GTPase-activating protein 1, p50-RhoGAP

All UniProt accessions (3): E9PNR6, Q07960, H0YE29

UniProt curated annotations — full annotation on UniProt →

Function. GTPase activator for the Rho, Rac and Cdc42 proteins, converting them to the putatively inactive GDP-bound state. Cdc42 seems to be the preferred substrate.

Subunit / interactions. Found in a complex with XPO7, EIF4A1, ARHGAP1, VPS26A, VPS29, VPS35 and SFN. Interacts with BNIPL.

Subcellular location. Cytoplasm.

Tissue specificity. Ubiquitous.

RefSeq proteins (1): NP_004299* (*=MANE)

Domains & families (InterPro)

ID	Name	Type
IPR000198	RhoGAP_dom	Domain
IPR001251	CRAL-TRIO_dom	Domain
IPR008936	Rho_GTPase_activation_prot	Homologous_superfamily
IPR036865	CRAL-TRIO_dom_sf	Homologous_superfamily
IPR049592	ARHGAP1_RhoGAP	Domain

Pfam: PF00620, PF13716

UniProt features (35 total): helix 16, modified residue 7, domain 2, strand 2, turn 2, chain 1, sequence variant 1, region of interest 1, short sequence motif 1, compositionally biased region 1, site 1

Structure

Experimental structures (PDB)

11 structures.

PDB	Method	Resolution (Å)
1TX4	X-RAY DIFFRACTION	1.65
6R3V	X-RAY DIFFRACTION	1.75
1OW3	X-RAY DIFFRACTION	1.8
2NGR	X-RAY DIFFRACTION	1.9
7QSC	X-RAY DIFFRACTION	1.91
1RGP	X-RAY DIFFRACTION	2
1GRN	X-RAY DIFFRACTION	2.1
5M70	X-RAY DIFFRACTION	2.2
7QTM	X-RAY DIFFRACTION	2.25
5M6X	X-RAY DIFFRACTION	2.4
1AM4	X-RAY DIFFRACTION	2.7

Predicted structure (AlphaFold)

Model	pLDDT	Fraction very-high
AF-Q07960-F1	82.64	0.53

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

Post-translational modifications (7): 50, 51, 65, 80, 1, 44, 47

Function

Pathways and Gene Ontology

Reactome pathways

13 pathways

ID	Pathway
R-HSA-8980692	RHOA GTPase cycle
R-HSA-9013026	RHOB GTPase cycle
R-HSA-9013106	RHOC GTPase cycle
R-HSA-9013148	CDC42 GTPase cycle
R-HSA-9013149	RAC1 GTPase cycle
R-HSA-9013404	RAC2 GTPase cycle
R-HSA-9013405	RHOD GTPase cycle
R-HSA-9013406	RHOQ GTPase cycle
R-HSA-9013408	RHOG GTPase cycle
R-HSA-9013409	RHOJ GTPase cycle
R-HSA-9013423	RAC3 GTPase cycle
R-HSA-9035034	RHOF GTPase cycle
R-HSA-9696270	RND2 GTPase cycle

MSigDB gene sets: 303 (showing top): BIOCARTA_RHO_PATHWAY, GSE45365_NK_CELL_VS_CD8A_DC_MCMV_INFECTION_DN, RNGTGGGC_UNKNOWN, DAVIES_MULTIPLE_MYELOMA_VS_MGUS_DN, TGCACTT_MIR519C_MIR519B_MIR519A, GOBP_TRANSITION_METAL_ION_TRANSPORT, KAAB_HEART_ATRIUM_VS_VENTRICLE_UP, ROVERSI_GLIOMA_COPY_NUMBER_UP, GOBP_REGULATION_OF_SMALL_GTPASE_MEDIATED_SIGNAL_TRANSDUCTION, HSIAO_HOUSEKEEPING_GENES, THEILGAARD_NEUTROPHIL_AT_SKIN_WOUND_DN, LINDGREN_BLADDER_CANCER_CLUSTER_3_DN, GOBP_VESICLE_MEDIATED_TRANSPORT, GOCC_RUFFLE, GOMF_GTPASE_BINDING

GO Biological Process (7): small GTPase-mediated signal transduction (GO:0007264), Rho protein signal transduction (GO:0007266), endosomal transport (GO:0016197), transferrin transport (GO:0033572), regulation of small GTPase mediated signal transduction (GO:0051056), negative regulation of endocytic recycling (GO:2001136), signal transduction (GO:0007165)

GO Molecular Function (5): GTPase activator activity (GO:0005096), SH3 domain binding (GO:0017124), small GTPase binding (GO:0031267), cadherin binding (GO:0045296), protein binding (GO:0005515)

GO Cellular Component (12): ruffle (GO:0001726), cytoplasm (GO:0005737), cytosol (GO:0005829), plasma membrane (GO:0005886), cilium (GO:0005929), endosome membrane (GO:0010008), perinuclear region of cytoplasm (GO:0048471), extracellular exosome (GO:0070062), membrane (GO:0016020), cell leading edge (GO:0031252), sorting endosome (GO:0097443), plasma membrane bounded cell projection (GO:0120025)

Reactome top-level categories

Rollup of top-1 pathways:

Category	Pathways
RHO GTPase cycle	13

GO top-level categories

Rollup of top GO terms by namespace:

Category	Terms
cellular anatomical structure	5
small GTPase-mediated signal transduction	2
plasma membrane bounded cell projection	2
cytoplasm	2
endosome	2
intracellular signaling cassette	1
vesicle-mediated transport	1
intracellular transport	1
iron ion transport	1
protein transport	1
regulation of intracellular signal transduction	1
negative regulation of intracellular transport	1
endocytic recycling	1
regulation of endocytic recycling	1
cell communication	1
cellular process	1
signaling	1
regulation of cellular process	1
cellular response to stimulus	1
GTPase activity	1
enzyme activator activity	1
GTPase regulator activity	1
protein domain specific binding	1
GTPase binding	1
cell adhesion molecule binding	1
binding	1
cell leading edge	1
intracellular anatomical structure	1
membrane	1
cell periphery	1
intraciliary transport particle	1
membrane-bounded organelle	1
cytoplasmic vesicle membrane	1
bounding membrane of organelle	1
extracellular vesicle	1
cell projection	1
plasma membrane region	1

Protein interactions and networks

STRING

1452 interactions, top by confidence (×1000):

Protein A	Protein B	Partner UniProt	Score
ARHGAP1	CDC42	P21181	997
ARHGAP1	RHOA	P06749	917
ARHGAP1	RASA1	P20936	913
ARHGAP1	AMOT	Q4VCS5	864
ARHGAP1	NDEL1	Q9GZM8	859
ARHGAP1	TRIP10	Q15642	802
ARHGAP1	OCRL	Q01968	759
ARHGAP1	PLEK2	Q9NYT0	733
ARHGAP1	PLEK	P08567	732
ARHGAP1	BNIP2	Q12982	717
ARHGAP1	PATJ	Q8NI35	698
ARHGAP1	ARHGDIA	P52565	693
ARHGAP1	ECT2	Q9H8V3	687
ARHGAP1	PALS1	Q8N3R9	669
ARHGAP1	PARD3	Q8TEW0	660

IntAct

113 interactions, top by confidence:

A	B	Type	Score
CCM2	KRIT1	psi-mi:“MI:0914”(association)	0.960
CFTR	ESYT2	psi-mi:“MI:2364”(proximity)	0.710
RHOA	ARHGAP1	psi-mi:“MI:0407”(direct interaction)	0.690
RHOA	ARHGAP1	psi-mi:“MI:0915”(physical association)	0.690
ARHGAP1	CDC42	psi-mi:“MI:0407”(direct interaction)	0.620
CDC42	ARHGAP1	psi-mi:“MI:0407”(direct interaction)	0.620
IGF1R	PIK3R2	psi-mi:“MI:2364”(proximity)	0.590
INSR	PIK3R2	psi-mi:“MI:2364”(proximity)	0.570
ARHGAP1	RHOC	psi-mi:“MI:0915”(physical association)	0.570
RHOC	ARHGAP1	psi-mi:“MI:0915”(physical association)	0.570
ARHGAP1	SH3GL1	psi-mi:“MI:0915”(physical association)	0.560
FOXR2	NME2P1	psi-mi:“MI:0914”(association)	0.530
FSD1	UBFD1	psi-mi:“MI:0914”(association)	0.530
NRAS	ESYT2	psi-mi:“MI:2364”(proximity)	0.480
CDC42	ARHGAP1	psi-mi:“MI:0407”(direct interaction)	0.440
ARHGAP1	RAN	psi-mi:“MI:0915”(physical association)	0.400
ARHGAP1	CHEK2	psi-mi:“MI:0915”(physical association)	0.370
AGTRAP	ARHGAP1	psi-mi:“MI:0915”(physical association)	0.370
STK4	EIF3CL	psi-mi:“MI:0914”(association)	0.350
Xpo1	IFT56	psi-mi:“MI:0914”(association)	0.350
	VWA8	psi-mi:“MI:0914”(association)	0.350
	IPO5	psi-mi:“MI:0914”(association)	0.350
PPP1CA	ACO2	psi-mi:“MI:0914”(association)	0.350
Xpo7	VPS26A	psi-mi:“MI:0914”(association)	0.350
CDK15	A2ML1	psi-mi:“MI:0914”(association)	0.350

BioGRID (312): ARHGAP1 (Affinity Capture-MS), ARHGAP1 (Affinity Capture-MS), ARHGAP1 (Affinity Capture-MS), ARHGAP1 (Two-hybrid), ARHGAP1 (Two-hybrid), ARHGAP1 (Co-fractionation), ARHGAP1 (Co-fractionation), ARHGAP1 (Co-fractionation), ARHGAP1 (Co-fractionation), ARHGAP1 (Co-fractionation), ARHGAP1 (Co-fractionation), ARHGAP1 (Co-fractionation), ARHGAP1 (Co-fractionation), ARHGAP1 (Co-fractionation), ARHGAP1 (Co-fractionation)

ESM2 similar proteins: A6JFQ6, A6JUQ6, A8Y5H7, E1C1U1, G1SPE9, O15228, O35296, O43304, O76054, P10123, P12271, P24815, P27600, P27601, P41034, P49638, P98192, Q03113, Q05AK6, Q07960, Q14344, Q2KIX2, Q4R678, Q5CZL1, Q5FWK3, Q5M7E1, Q5RCA6, Q5SYC1, Q5XGM5, Q63210, Q64421, Q66H63, Q66HX8, Q7JUR6, Q7L5N7, Q80SY6, Q8BG92, Q8BWP5, Q8BYI6, Q8IUQ0

Diamond homologs: A0A0G2JTR4, A1A4S6, A2AB59, A2RUV4, A4IF90, A4II46, A6NI28, A6QNS3, A7E300, A7YY57, B2RQE8, B5DFQ4, B9VTT2, D3ZZN9, E9Q6X9, F1LQX4, O14559, O60890, O74360, O94466, P0CAX5, P11274, P15882, P30337, P34288, P40809, P46941, P52757, P97393, Q03070, Q07960, Q08DP6, Q12979, Q13017, Q13459, Q17QN0, Q17R89, Q53QZ3, Q54FG5, Q54TH9

SIGNOR signaling

2 interactions.

A	Effect	B	Mechanism
ARHGAP1	“down-regulates activity”	RHOA	“gtpase-activating protein”
ARHGAP1	“down-regulates activity”	CDC42	“gtpase-activating protein”

Enriched among interaction partners

Reactome pathways and GO biological processes over-represented among this gene’s 135 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
Signaling by SCF-KIT	5	15.3×	3e-04
Constitutive Signaling by Aberrant PI3K in Cancer	7	11.0×	1e-04
Signaling by BRAF and RAF1 fusions	5	10.5×	1e-03
PI5P, PP2A and IER3 Regulate PI3K/AKT Signaling	8	9.6×	1e-04
PIP3 activates AKT signaling	9	7.4×	1e-04
RAC3 GTPase cycle	5	7.3×	5e-03
CDC42 GTPase cycle	6	5.3×	7e-03
RAF/MAP kinase cascade	7	5.3×	3e-03

GO biological processes:

GO term	Partners	Fold	FDR
positive regulation of MAPK cascade	9	6.5×	5e-03
positive regulation of cell migration	11	6.1×	2e-03

Disease & clinical

Clinical variants and AI predictions

ClinVar

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

Classification	Count (floor)
Pathogenic	0
Likely pathogenic	0
Uncertain significance	49
Likely benign	5
Benign	3

Top pathogenic / likely-pathogenic (0)

SpliceAI

2155 predictions. Top by Δscore:

Variant	Effect	Δscore
11:46679168:C:CT	acceptor_gain	1.0000
11:46679221:GAAAT:G	acceptor_gain	1.0000
11:46679223:AATC:A	acceptor_loss	1.0000
11:46679224:AT:A	acceptor_gain	1.0000
11:46679225:TCTG:T	acceptor_loss	1.0000
11:46679226:C:CC	acceptor_gain	1.0000
11:46679226:CTGTG:C	acceptor_loss	1.0000
11:46679361:TCA:T	donor_loss	1.0000
11:46679363:A:AT	donor_loss	1.0000
11:46679464:AATGT:A	acceptor_gain	1.0000
11:46679465:ATGT:A	acceptor_gain	1.0000
11:46679466:TGT:T	acceptor_gain	1.0000
11:46679467:GT:G	acceptor_gain	1.0000
11:46679468:TC:T	acceptor_loss	1.0000
11:46679469:C:CA	acceptor_loss	1.0000
11:46679469:C:CC	acceptor_gain	1.0000
11:46679470:T:G	acceptor_loss	1.0000
11:46679471:A:AC	acceptor_gain	1.0000
11:46679471:A:C	acceptor_gain	1.0000
11:46679646:A:AC	donor_gain	1.0000
11:46679647:C:CG	donor_gain	1.0000
11:46680175:ATGGC:A	donor_gain	1.0000
11:46680199:GCTCA:G	donor_loss	1.0000
11:46680200:CTCA:C	donor_loss	1.0000
11:46680201:TCA:T	donor_loss	1.0000
11:46680202:CACCC:C	donor_loss	1.0000
11:46680203:A:AC	donor_gain	1.0000
11:46680203:A:T	donor_loss	1.0000
11:46680203:AC:A	donor_gain	1.0000
11:46680203:ACC:A	donor_gain	1.0000

AlphaMissense

2907 scored. Top likely-pathogenic:

Variant	Protein change	am_pathogenicity
11:46681345:G:C	H162D	1.000
11:46681371:T:A	K153I	1.000
11:46681373:C:A	K152N	1.000
11:46681373:C:G	K152N	1.000
11:46679158:A:G	L400P	0.999
11:46679167:C:T	G397D	0.999
11:46679168:C:G	G397R	0.999
11:46679179:G:T	A393D	0.999
11:46679182:A:G	L392P	0.999
11:46679197:A:G	M387T	0.999
11:46679701:A:G	L325P	0.999
11:46679718:C:A	K319N	0.999
11:46679718:C:G	K319N	0.999
11:46681100:G:C	F182L	0.999
11:46681100:G:T	F182L	0.999
11:46681102:A:G	F182L	0.999
11:46681347:A:T	V161E	0.999
11:46681350:A:T	I160N	0.999
11:46681361:C:A	K156N	0.999
11:46681361:C:G	K156N	0.999
11:46681370:T:A	K153N	0.999
11:46681370:T:G	K153N	0.999
11:46681375:T:C	K152E	0.999
11:46682073:C:G	A143P	0.999
11:46682081:A:G	L140P	0.999
11:46682085:A:G	W139R	0.999
11:46682085:A:T	W139R	0.999
11:46682130:A:C	Y124D	0.999
11:46682135:A:G	L122P	0.999
11:46682135:A:T	L122H	0.999

dbSNP variants (sampled 300 via entrez): RS1000133654 (11:46691698 C>T), RS1000254810 (11:46691373 C>T), RS1000381273 (11:46691572 A>C,G), RS1000622670 (11:46689835 G>A,T), RS1000927200 (11:46696520 T>C), RS1001008040 (11:46685447 C>T), RS1001034957 (11:46683313 G>A), RS1001121527 (11:46678889 G>A), RS1001191765 (11:46694783 T>C), RS1001253271 (11:46696265 T>A), RS1001696019 (11:46676815 G>A), RS1001727078 (11:46676585 C>CCGT), RS1001790700 (11:46677001 C>T), RS1001791343 (11:46681234 C>T), RS1001909812 (11:46681541 C>T)

Disease associations

OMIM: gene MIM:602732 | disease phenotypes:

GenCC curated gene-disease

Mondo (0):

Orphanet (0):

HPO phenotypes

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

GWAS associations

13 associations (top):

Study	Trait	p-value
GCST000495_8	Bone mineral density (hip)	4.000000e-09
GCST004521_122	Autism spectrum disorder or schizophrenia	3.000000e-13
GCST004521_165	Autism spectrum disorder or schizophrenia	3.000000e-08
GCST006268_466	Reaction time	7.000000e-09
GCST006585_265	Blood protein levels	8.000000e-14
GCST006803_20	Schizophrenia	3.000000e-13
GCST006940_124	Neurociticism	3.000000e-14
GCST006943_8	Feeling miserable	2.000000e-13
GCST006944_46	Experiencing mood swings	1.000000e-11
GCST006948_60	Feeling nervous	1.000000e-09
GCST006949_1	Suffering from nerves	7.000000e-12
GCST007691_35	Femoral neck bone mineral density	5.000000e-18
GCST007825_4	Alzheimer’s disease or fasting glucose levels (pleiotropy)	3.000000e-16

EFO canonical traits (6, from GWAS)

EFO ID	Trait name
EFO:0008393	reaction time measurement
EFO:0007660	neuroticism measurement
EFO:0009598	feeling miserable measurement
EFO:0008475	mood instability measurement
EFO:0009597	feeling nervous measurement
EFO:0007785	femoral neck bone mineral density

Drugs & pharmacology

Drug and pharmacology data

Is drug target: no

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

CTD chemical–gene interactions

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

Chemical	Actions (top 5)	PubMed papers
sodium arsenite	decreases expression, increases abundance, increases expression	4
Air Pollutants	decreases expression, increases abundance, increases expression	2
Smoke	increases expression, decreases expression, increases abundance	2
Cadmium Chloride	decreases expression, increases abundance	2
aristolochic acid I	increases expression	1
FR900359	affects phosphorylation	1
bisphenol F	increases expression	1
dicrotophos	increases expression	1
triphenyl phosphate	affects expression	1
bisphenol A	increases expression	1
pyrogallol 1,3-dimethyl ether	affects cotreatment, affects localization, increases expression	1
tetrahydropalmatine	decreases expression	1
cobaltous chloride	decreases expression	1
butyraldehyde	decreases expression	1
ochratoxin A	increases expression	1
butylidenephthalide	increases expression	1
aflatoxin B2	increases methylation	1
coumarin	increases phosphorylation	1
muconaldehyde	decreases expression	1
beta-methylcholine	affects expression	1
di-n-butylphosphoric acid	affects expression	1
4-(5-benzo(1,3)dioxol-5-yl-4-pyridin-2-yl-1H-imidazol-2-yl)benzamide	affects cotreatment, decreases expression	1
ICG 001	decreases expression	1
bisphenol B	increases expression	1
abrine	decreases expression	1
2-amino-14,16-dimethyloctadecan-3-ol	decreases expression	1
bisphenol S	increases expression	1
LDN 193189	affects cotreatment, decreases expression	1
bisphenol AF	increases expression	1
Bortezomib	decreases expression	1

Clinical trials (associated diseases)

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