ARFGAP3

Summary

ARFGAP3 (ARF GTPase activating protein 3, HGNC:661) is a protein-coding gene on chromosome 22q13.2, encoding ADP-ribosylation factor GTPase-activating protein 3 (Q9NP61). GTPase-activating protein (GAP) for ADP ribosylation factor 1 (ARF1).

The protein encoded by this gene is a GTPase-activating protein (GAP) that associates with the Golgi apparatus and regulates the early secretory pathway of proteins. The encoded protein promotes hydrolysis of ADP-ribosylation factor 1 (ARF1)-bound GTP, which is required for the dissociation of coat proteins from Golgi-derived membranes and vesicles. Dissociation of the coat proteins is a prerequisite for the fusion of these vesicles with target compartments. The activity of this protein is sensitive to phospholipids. Multiple transcript variants encoding different isoforms have been found for this gene. This gene was originally known as ARFGAP1, but that is now the name of a related but different gene.

Source: NCBI Gene 26286 — RefSeq curated summary.

At a glance

• GWAS associations: 1
• Clinical variants (ClinVar): 235 total — 10 pathogenic, 1 likely-pathogenic
• MANE Select transcript: NM_014570

Identifiers

Gene identifiers

Field	Value
HGNC ID	HGNC:661
Approved symbol	ARFGAP3
Name	ARF GTPase activating protein 3
Location	22q13.2
Locus type	gene with protein product
Status	Approved
Ensembl gene	ENSG00000242247
Ensembl biotype	protein_coding
OMIM	612439
Entrez	26286

Gene structure

Transcript identifiers

Ensembl transcripts: 10 — 9 protein_coding, 1 retained_intron

ENST00000263245, ENST00000435208, ENST00000437119, ENST00000453516, ENST00000454099, ENST00000493606, ENST00000888444, ENST00000888445, ENST00000938504, ENST00000960209

RefSeq mRNA: 2 — MANE Select: NM_014570 NM_001142293, NM_014570

CCDS: CCDS14042, CCDS46722

Canonical transcript exons

ENST00000263245 — 16 exons

Exon	Start	End
ENSE00001670279	42857114	42857273
ENSE00001916931	42796502	42797605
ENSE00002991901	42831549	42831636
ENSE00002993355	42817729	42817857
ENSE00003007510	42822270	42822409
ENSE00003033703	42834242	42834325
ENSE00003036499	42835362	42835493
ENSE00003048848	42808767	42808890
ENSE00003049172	42817142	42817264
ENSE00003059885	42810813	42810944
ENSE00003060445	42799039	42799160
ENSE00003068309	42807073	42807163
ENSE00003122560	42847514	42847632
ENSE00003199562	42826940	42826999
ENSE00003566700	42840944	42841016
ENSE00003786982	42823656	42823702

Expression profiles

Bgee: expression breadth ubiquitous, 297 present calls, max score 98.49.

FANTOM5 (CAGE): breadth ubiquitous, TPM avg 32.4527 / max 144.3813, expressed in 1816 samples.

FANTOM5 promoters (2 alternative TSS)

Promoter ID	TPM avg	Samples expressed
194474	42.4054	1819
185800	32.4527	1816

Top tissues by expression

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

Tissue	Anatomy ID	Expression score	Quality
jejunal mucosa	UBERON:0000399	98.49	gold quality
parotid gland	UBERON:0001831	98.33	gold quality
body of pancreas	UBERON:0001150	97.58	gold quality
calcaneal tendon	UBERON:0003701	97.39	gold quality
tibia	UBERON:0000979	97.37	gold quality
right adrenal gland	UBERON:0001233	97.27	gold quality
right adrenal gland cortex	UBERON:0035827	97.27	gold quality
left adrenal gland	UBERON:0001234	97.05	gold quality
adrenal cortex	UBERON:0001235	96.90	gold quality
pancreas	UBERON:0001264	96.90	gold quality
adrenal gland	UBERON:0002369	96.85	gold quality
left adrenal gland cortex	UBERON:0035825	96.79	gold quality
cartilage tissue	UBERON:0002418	96.75	gold quality
corpus epididymis	UBERON:0004359	96.69	gold quality
islet of Langerhans	UBERON:0000006	96.52	gold quality
adrenal tissue	UBERON:0018303	96.52	gold quality
palpebral conjunctiva	UBERON:0001812	96.30	gold quality
seminal vesicle	UBERON:0000998	96.20	gold quality
nasal cavity mucosa	UBERON:0001826	95.58	gold quality
eye	UBERON:0000970	95.14	gold quality
cauda epididymis	UBERON:0004360	95.12	gold quality
caput epididymis	UBERON:0004358	94.89	gold quality
mucosa of paranasal sinus	UBERON:0005030	94.85	gold quality
olfactory segment of nasal mucosa	UBERON:0005386	94.76	gold quality
jejunum	UBERON:0002115	94.74	gold quality
epithelium of nasopharynx	UBERON:0001951	94.73	gold quality
nasopharynx	UBERON:0001728	94.72	gold quality
endometrium	UBERON:0001295	94.69	gold quality
duodenum	UBERON:0002114	94.64	gold quality
popliteal artery	UBERON:0002250	94.63	gold quality

Single-cell (SCXA)

Detected in 2 experiment(s), a significant marker in 1.

Experiment	Marker?	Max mean expression
E-MTAB-7249	no	199.52
E-ANND-3	no	0.00

Regulation

Is transcription factor: no

miRNA regulators (miRDB)

63 targeting ARFGAP3, 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-1277-5P	100.00	73.95	5056
HSA-MIR-3163	100.00	77.23	8605
HSA-MIR-4455	100.00	65.48	1587
HSA-MIR-6867-5P	100.00	82.21	3464
HSA-MIR-1252-5P	100.00	69.80	2774
HSA-MIR-4533	100.00	69.48	2758
HSA-MIR-513B-5P	99.99	69.96	2150
HSA-MIR-548C-3P	99.99	74.01	7587
HSA-MIR-371B-5P	99.99	75.34	4759
HSA-MIR-4789-5P	99.98	70.76	2721
HSA-MIR-5696	99.98	72.36	4487
HSA-MIR-373-5P	99.98	75.36	4753
HSA-MIR-616-5P	99.98	75.58	4775
HSA-MIR-520D-5P	99.98	73.34	4883
HSA-MIR-524-5P	99.98	73.43	4882
HSA-MIR-607	99.97	73.62	5593
HSA-MIR-3658	99.96	73.87	4379
HSA-MIR-146A-5P	99.96	68.93	988
HSA-MIR-146B-5P	99.96	69.13	977
HSA-MIR-7153-5P	99.94	68.89	1006
HSA-MIR-6835-3P	99.93	70.49	2904
HSA-MIR-3671	99.90	73.04	3897
HSA-MIR-153-5P	99.89	73.86	6317
HSA-MIR-548E-5P	99.89	72.73	4486
HSA-MIR-1323	99.83	69.89	2471
HSA-MIR-548O-3P	99.74	69.30	2228
HSA-MIR-2116-3P	99.74	64.32	889
HSA-MIR-4422	99.72	72.07	2908
HSA-MIR-494-3P	99.70	71.45	2795
HSA-MIR-1283	99.69	72.42	3009

Literature-anchored findings (GeneRIF, showing 6)

• human ARFGAP2 and ARFGAP3 are associated with COP-I-coated vesicles and function in COP I traffic (PMID:17760859)
• Differential roles of ArfGAP1, ArfGAP2, and ArfGAP3 in COPI trafficking (PMID:19015319)
• ArfGAP1, ArfGAP2, and ArfGAP3 have overlapping roles in regulating COPI function in Golgi-to-ER retrograde transport. (PMID:19299515)
• our results suggest that ARFGAP3 is a novel androgen-regulated gene that can promote prostate cancer cell proliferation and migration in collaboration with paxillin. (PMID:21647875)
• We suggest a model in which ArfGAP3 regulates Golgi association of GGA clathrin adaptors. (PMID:24076238)
• Expression of ArfGAP3 in Vaginal Anterior Wall of Patients With Pelvic Floor Organ Prolapse in Pelvic Organ Prolapse and Non-Pelvic Organ Prolapse Patients. (PMID:31868832)

Cross-species orthologs

3 orthologs

Organism	Symbol	Gene ID
danio_rerio	arfgap3	ENSDARG00000097583
mus_musculus	Arfgap3	ENSMUSG00000054277
rattus_norvegicus	Arfgap3	ENSRNOG00000046472

Paralogs (28): ARAP2 (ENSG00000047365), ACAP1 (ENSG00000072818), SMAP2 (ENSG00000084070), ASAP3 (ENSG00000088280), ARFGAP1 (ENSG00000101199), ADAP1 (ENSG00000105963), AGFG2 (ENSG00000106351), GIT1 (ENSG00000108262), SMAP1 (ENSG00000112305), ACAP2 (ENSG00000114331), ARAP3 (ENSG00000120318), ACAP3 (ENSG00000131584), AGAP3 (ENSG00000133612), AGAP2 (ENSG00000135439), APPL2 (ENSG00000136044), GIT2 (ENSG00000139436), ARFGAP2 (ENSG00000149182), ASAP2 (ENSG00000151693), ASAP1 (ENSG00000153317), APPL1 (ENSG00000157500), AGAP1 (ENSG00000157985), AGAP5 (ENSG00000172650), AGFG1 (ENSG00000173744), ADAP2 (ENSG00000184060), ARAP1 (ENSG00000186635), AGAP4 (ENSG00000188234), AGAP6 (ENSG00000204149), AGAP9 (ENSG00000204172)

Protein

Protein identifiers

ADP-ribosylation factor GTPase-activating protein 3 — Q9NP61 (reviewed: Q9NP61)

All UniProt accessions (4): B0QYV8, B0QYV9, Q9NP61, H0Y6A0

UniProt curated annotations — full annotation on UniProt →

Function. GTPase-activating protein (GAP) for ADP ribosylation factor 1 (ARF1). Hydrolysis of ARF1-bound GTP may lead to dissociation of coatomer from Golgi-derived membranes to allow fusion with target membranes.

Subcellular location. Cytoplasm. Golgi apparatus membrane.

Tissue specificity. Widely expressed. Highest expression in endocrine glands (pancreas, pituitary gland, salivary gland, and prostate) and testis with a much higher expression in the testis than in the ovary.

Activity regulation. GAP activity stimulated by phosphatidylinositol 4,5-bisphosphate (PIP2).

Isoforms (2)

UniProt ID	Names	Canonical?
Q9NP61-1	1	yes
Q9NP61-2	2

RefSeq proteins (2): NP_001135765, NP_055385* (*=MANE)

Domains & families (InterPro)

ID	Name	Type
IPR001164	ArfGAP_dom	Domain
IPR037278	ARFGAP/RecO	Homologous_superfamily
IPR038508	ArfGAP_dom_sf	Homologous_superfamily

Pfam: PF01412

UniProt features (42 total): modified residue 11, sequence variant 7, helix 6, sequence conflict 3, region of interest 3, turn 3, strand 3, chain 1, domain 1, splice variant 1, zinc finger region 1, coiled-coil region 1, compositionally biased region 1

Structure

Experimental structures (PDB)

1 structures.

PDB	Method	Resolution (Å)
2CRW	SOLUTION NMR

Predicted structure (AlphaFold)

Model	pLDDT	Fraction very-high
AF-Q9NP61-F1	66.12	0.24

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 (11): 274, 331, 370, 428, 451, 453, 455, 457, 458, 231, 270

Function

Pathways and Gene Ontology

Reactome pathways

17 pathways

ID	Pathway
R-HSA-6807878	COPI-mediated anterograde transport
R-HSA-6811434	COPI-dependent Golgi-to-ER retrograde traffic
R-HSA-9013148	CDC42 GTPase cycle
R-HSA-9013408	RHOG GTPase cycle
R-HSA-162582	Signal Transduction
R-HSA-194315	Signaling by Rho GTPases
R-HSA-199977	ER to Golgi Anterograde Transport
R-HSA-199991	Membrane Trafficking
R-HSA-392499	Metabolism of proteins
R-HSA-446203	Asparagine N-linked glycosylation
R-HSA-5653656	Vesicle-mediated transport
R-HSA-597592	Post-translational protein modification
R-HSA-6811442	Intra-Golgi and retrograde Golgi-to-ER traffic
R-HSA-8856688	Golgi-to-ER retrograde transport
R-HSA-9012999	RHO GTPase cycle
R-HSA-948021	Transport to the Golgi and subsequent modification
R-HSA-9716542	Signaling by Rho GTPases, Miro GTPases and RHOBTB3

MSigDB gene sets: 296 (showing top): REACTOME_UNFOLDED_PROTEIN_RESPONSE_UPR, GCM_GSPT1, GOBP_VESICLE_LOCALIZATION, GOBP_INTRACELLULAR_PROTEIN_TRANSPORT, GOBP_VESICLE_ORGANIZATION, GOBP_REGULATION_OF_SMALL_GTPASE_MEDIATED_SIGNAL_TRANSDUCTION, GOBP_VESICLE_TARGETING, GOBP_VESICLE_MEDIATED_TRANSPORT, REACTOME_MEMBRANE_TRAFFICKING, GOBP_REGULATION_OF_VESICLE_MEDIATED_TRANSPORT, MODULE_379, BOYLAN_MULTIPLE_MYELOMA_D_CLUSTER_DN, BLALOCK_ALZHEIMERS_DISEASE_UP, GOBP_SECRETION, CREIGHTON_ENDOCRINE_THERAPY_RESISTANCE_5

GO Biological Process (5): intracellular protein transport (GO:0006886), protein secretion (GO:0009306), vesicle-mediated transport (GO:0016192), COPI coating of Golgi vesicle (GO:0048205), protein transport (GO:0015031)

GO Molecular Function (4): GTPase activator activity (GO:0005096), zinc ion binding (GO:0008270), protein binding (GO:0005515), metal ion binding (GO:0046872)

GO Cellular Component (5): Golgi membrane (GO:0000139), Golgi apparatus (GO:0005794), cytosol (GO:0005829), membrane (GO:0016020), cytoplasm (GO:0005737)

Reactome top-level categories

Rollup of top-13 pathways:

Category	Pathways
RHO GTPase cycle	2
Membrane Trafficking	2
ER to Golgi Anterograde Transport	1
Golgi-to-ER retrograde transport	1
Signaling by Rho GTPases, Miro GTPases and RHOBTB3	1
Transport to the Golgi and subsequent modification	1
Vesicle-mediated transport	1
Post-translational protein modification	1
Metabolism of proteins	1
Intra-Golgi and retrograde Golgi-to-ER traffic	1
Signaling by Rho GTPases	1
Asparagine N-linked glycosylation	1
Signal Transduction	1

GO top-level categories

Rollup of top GO terms by namespace:

Category	Terms
cellular anatomical structure	3
intracellular protein localization	2
protein transport	2
transport	2
cytoplasm	2
intracellular transport	1
secretion by cell	1
establishment of protein localization to extracellular region	1
protein localization to extracellular region	1
cellular process	1
COPI-coated vesicle budding	1
Golgi transport vesicle coating	1
establishment of protein localization	1
GTPase activity	1
enzyme activator activity	1
GTPase regulator activity	1
transition metal ion binding	1
binding	1
cation binding	1
Golgi apparatus	1
bounding membrane of organelle	1
endomembrane system	1
intracellular membrane-bounded organelle	1
intracellular anatomical structure	1

Protein interactions and networks

STRING

1260 interactions, top by confidence (×1000):

Protein A	Protein B	Partner UniProt	Score
ARFGAP3	ARF1	P10947	817
ARFGAP3	COPB1	P53618	590
ARFGAP3	ID1	P41134	527
ARFGAP3	BET1	O15155	518
ARFGAP3	GATA1	P15976	513
ARFGAP3	NAF1	Q96HR8	497
ARFGAP3	GBF1	Q92538	488
ARFGAP3	ARL1	P40616	473
ARFGAP3	MLF2	Q15773	469
ARFGAP3	XKR7	Q5GH72	454
ARFGAP3	ARCN1	P48444	446
ARFGAP3	GTF2A2	P52657	446
ARFGAP3	COPB2	P35606	430
ARFGAP3	ARL5A	Q9Y689	412
ARFGAP3	ADORA2B	P29275	408

IntAct

180 interactions, top by confidence:

A	B	Type	Score
CFTR	ESYT2	psi-mi:“MI:2364”(proximity)	0.710
HTT	ARFGAP3	psi-mi:“MI:0915”(physical association)	0.680
ARFGAP3	HTT	psi-mi:“MI:0915”(physical association)	0.680
IGF1R	PIK3R2	psi-mi:“MI:2364”(proximity)	0.590
RTN4IP1	ARFGAP3	psi-mi:“MI:0915”(physical association)	0.560
SYPL1	ARFGAP3	psi-mi:“MI:0915”(physical association)	0.560
LIME1	ARFGAP3	psi-mi:“MI:0915”(physical association)	0.560
ARFGAP3	SERPINH1	psi-mi:“MI:0915”(physical association)	0.560
ARFGAP3	CDH1	psi-mi:“MI:0915”(physical association)	0.560

BioGRID (144): ARFGAP3 (Two-hybrid), ARFGAP3 (Affinity Capture-Western), SHPK (Affinity Capture-MS), ADI1 (Co-fractionation), ARFGAP1 (Co-fractionation), ARFGAP3 (Co-fractionation), ARFGAP3 (Co-fractionation), ARFGAP3 (Co-fractionation), ARFGAP3 (Proximity Label-MS), ARFGAP3 (Proximity Label-MS), ARFGAP3 (Proximity Label-MS), ARFGAP3 (Proximity Label-MS), ARFGAP3 (Proximity Label-MS), ARFGAP3 (Affinity Capture-MS), ARFGAP3 (Affinity Capture-MS)

ESM2 similar proteins: A1L520, A5DDB7, A8WSQ9, O80925, O82171, O94601, P03197, P0C717, P35197, P38682, P53604, P93755, Q09237, Q09446, Q09531, Q0CGL5, Q0WQ57, Q10367, Q17R07, Q20374, Q24546, Q28CM8, Q3KST5, Q3MID3, Q4KLN7, Q4KMC9, Q4R4C9, Q5R787, Q5RAT7, Q62848, Q80Y56, Q8GWI5, Q8H100, Q8N6H7, Q8N6T3, Q95XU6, Q95Y36, Q99K28, Q9C950, Q9D8S3

Diamond homologs: A1L520, A1Z7A6, A5PK26, A6NIR3, O43150, O74345, O75689, O80925, O82171, O94601, O97902, P35197, P38682, P40529, P52594, Q04412, Q09531, Q0WQQ1, Q10165, Q10367, Q14161, Q15027, Q15057, Q17R07, Q1AAU6, Q1ZXH8, Q28CM8, Q2TA45, Q3MID3, Q3UHD9, Q4KLH5, Q4KLN7, Q4LDD4, Q4R4C9, Q5F413, Q5FVC7, Q5R787, Q5RAT7, Q5U464, Q5VTM2

SIGNOR signaling

1 interactions.

A	Effect	B	Mechanism
(2S)-2-[[2-(2,3-dihydro-1H-inden-5-yloxy)-9-[(4-phenylphenyl)methyl]-6-purinyl]amino]-3-phenyl-1-propanol	“down-regulates activity”	ARFGAP3	“chemical inhibition”

Enriched among interaction partners

Reactome pathways and GO biological processes over-represented among this gene’s 98 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.

GO biological processes:

GO term	Partners	Fold	FDR
cell surface receptor protein tyrosine kinase signaling pathway	6	12.0×	5e-03
protein autophosphorylation	6	10.0×	9e-03

Disease & clinical

Clinical variants and AI predictions

ClinVar

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

Classification	Count (floor)
Pathogenic	10
Likely pathogenic	1
Uncertain significance	165
Likely benign	13
Benign	1

Top pathogenic / likely-pathogenic (11)

Variant ID	HGVS	Classification
1047899	GRCh37/hg19 20q13.33(chr20:61510452-62315381)	Pathogenic
1526700	GRCh37/hg19 20q13.33(chr20:61797521-62318983)	Pathogenic
2427488	NC_000020.10:g.(?61471874)(62078210_?)del	Pathogenic
253468	GRCh37/hg19 20q13.33(chr20:61429900-62293991)x1	Pathogenic
2579288	GRCh38/hg38 20q13.33(chr20:62632017-63794804)x1	Pathogenic
3062402	GRCh37/hg19 20q13.33(chr20:61421505-62070966)x1	Pathogenic
3062407	GRCh37/hg19 20q13.33(chr20:61716119-62416074)x1	Pathogenic
3391940	GRCh37/hg19 20q13.33(chr20:61602951-62070966)x1	Pathogenic
395261	GRCh37/hg19 20q13.33(chr20:61827144-62907467)x1	Pathogenic
58977	GRCh38/hg38 20q13.33(chr20:63095686-63524980)x1	Pathogenic
1341868	NC_000020.11:g.63255263_63498365del	Likely pathogenic

SpliceAI

2727 predictions. Top by Δscore:

Variant	Effect	Δscore
22:42807159:TCATA:T	acceptor_gain	1.0000
22:42807160:CATA:C	acceptor_gain	1.0000
22:42807160:CATAC:C	acceptor_gain	1.0000
22:42807161:ATA:A	acceptor_gain	1.0000
22:42807162:TA:T	acceptor_gain	1.0000
22:42807164:C:CC	acceptor_gain	1.0000
22:42808886:TAGGT:T	acceptor_gain	1.0000
22:42808887:AGGTC:A	acceptor_loss	1.0000
22:42808888:GGT:G	acceptor_gain	1.0000
22:42808889:GT:G	acceptor_gain	1.0000
22:42808890:TCTGC:T	acceptor_loss	1.0000
22:42808891:C:CA	acceptor_loss	1.0000
22:42808891:C:CC	acceptor_gain	1.0000
22:42808892:T:A	acceptor_loss	1.0000
22:42817260:TAACA:T	acceptor_gain	1.0000
22:42817263:CA:C	acceptor_gain	1.0000
22:42817263:CACT:C	acceptor_gain	1.0000
22:42817265:C:CC	acceptor_gain	1.0000
22:42817266:T:C	acceptor_gain	1.0000
22:42817266:T:TC	acceptor_gain	1.0000
22:42817728:CCTT:C	donor_gain	1.0000
22:42817856:CA:C	acceptor_gain	1.0000
22:42817858:C:CC	acceptor_gain	1.0000
22:42817862:C:CT	acceptor_gain	1.0000
22:42826998:ACC:A	acceptor_loss	1.0000
22:42826999:CCT:C	acceptor_loss	1.0000
22:42827000:C:CC	acceptor_gain	1.0000
22:42827000:C:CG	acceptor_loss	1.0000
22:42827001:T:G	acceptor_loss	1.0000
22:42829478:A:C	donor_gain	1.0000

AlphaMissense

3389 scored. Top likely-pathogenic:

Variant	Protein change	am_pathogenicity
22:42847544:C:G	R53P	1.000
22:42847558:G:C	C48W	1.000
22:42847567:G:C	C45W	1.000
22:42847569:A:G	C45R	1.000
22:42847591:G:C	S37R	1.000
22:42847591:G:T	S37R	1.000
22:42847593:T:G	S37R	1.000
22:42847597:C:A	W35C	1.000
22:42847597:C:G	W35C	1.000
22:42847599:A:G	W35R	1.000
22:42847599:A:T	W35R	1.000
22:42847629:A:G	C25R	1.000
22:42799064:G:T	A503D	0.999
22:42840994:A:G	W71R	0.999
22:42840994:A:T	W71R	0.999
22:42841005:A:G	L67S	0.999
22:42847514:C:G	R63P	0.999
22:42847519:A:C	F61L	0.999
22:42847519:A:T	F61L	0.999
22:42847521:A:G	F61L	0.999
22:42847522:A:C	S60R	0.999
22:42847522:A:T	S60R	0.999
22:42847524:T:G	S60R	0.999
22:42847535:C:T	G56D	0.999
22:42847545:G:C	R53G	0.999
22:42847553:C:T	G50E	0.999
22:42847559:C:A	C48F	0.999
22:42847559:C:G	C48S	0.999
22:42847559:C:T	C48Y	0.999
22:42847560:A:G	C48R	0.999

dbSNP variants (sampled 300 via entrez): RS1000009961 (22:42840600 T>TA), RS1000099782 (22:42855015 T>C), RS1000100336 (22:42801661 C>T), RS1000137448 (22:42809004 T>C), RS1000318388 (22:42849676 C>A,G), RS1000355863 (22:42803361 A>G), RS1000373161 (22:42856239 AT>A), RS1000416119 (22:42797693 G>A), RS1000427872 (22:42819993 A>G), RS1000431762 (22:42815680 T>C), RS1000439995 (22:42796496 G>A,C,T), RS1000488801 (22:42855967 G>A), RS1000562851 (22:42838627 G>A), RS1000566857 (22:42832909 C>T), RS1000570827 (22:42849465 T>C,G)

Disease associations

OMIM: gene MIM:612439 | disease phenotypes:

GenCC curated gene-disease

Mondo (4): breast ductal adenocarcinoma (MONDO:0005590), primary ovarian failure (MONDO:0005387), developmental and epileptic encephalopathy (MONDO:0100620), neurodevelopmental disorder (MONDO:0700092)

Orphanet (1): NON RARE IN EUROPE: Primary ovarian failure (Orphanet:619)

HPO phenotypes

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

GWAS associations

1 associations (top):

Study	Trait	p-value
GCST004523_3	Resting metabolic rate	2.000000e-06

EFO canonical traits (1, from GWAS)

EFO ID	Trait name
EFO:0008004	resting metabolic rate measurement

MeSH disease descriptors (3)

Descriptor	Name	Tree numbers
D018270	Carcinoma, Ductal, Breast	C04.557.470.200.025.232.500; C04.557.470.615.132.500; C04.588.180.390; C17.800.090.500.390
D065886	Neurodevelopmental Disorders	F03.625
D016649	Primary Ovarian Insufficiency	C12.050.351.500.056.630.750; C12.100.250.056.630.750; C19.391.630.750

Drugs & pharmacology

Drug and pharmacology data

Is drug target: no

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

CTD chemical–gene interactions

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

Chemical	Actions (top 5)	PubMed papers
Cyclosporine	increases expression	4
bisphenol A	decreases expression, decreases methylation, increases expression, decreases reaction, increases abundance	3
trichostatin A	affects cotreatment, decreases expression	2
sodium arsenite	increases expression, decreases expression	2
Benzo(a)pyrene	decreases expression, increases methylation	2
Valproic Acid	affects expression, decreases expression	2
aristolochic acid I	decreases expression	1
FR900359	decreases phosphorylation	1
ginger extract	decreases reaction, increases abundance, increases expression	1
triphenyl phosphate	affects expression	1
alpha-pinene	affects cotreatment, increases oxidation, increases abundance	1
beta-lapachone	increases expression	1
tris(1,3-dichloro-2-propyl)phosphate	increases expression	1
cobaltous chloride	increases expression	1
aflatoxin B2	increases methylation	1
4-aminophenylarsenoxide	affects binding, decreases reaction	1
N-benzyloxycarbonylprolylprolinal	increases expression	1
methacrylaldehyde	affects cotreatment, increases oxidation, increases abundance	1
di-n-butylphosphoric acid	affects expression	1
K 7174	increases expression	1
4-(5-benzo(1,3)dioxol-5-yl-4-pyridin-2-yl-1H-imidazol-2-yl)benzamide	affects cotreatment, decreases expression	1
erucylphospho-N,N,N-trimethylpropylammonium	increases expression	1
dorsomorphin	affects cotreatment, decreases expression	1
bisphenol AF	increases expression	1
Arsenic Trioxide	affects binding, decreases reaction	1
Acrolein	affects cotreatment, increases oxidation, increases abundance	1
Air Pollutants	affects cotreatment, increases abundance, increases oxidation	1
Caffeine	affects phosphorylation	1
Diuron	decreases expression	1
Enzyme Inhibitors	decreases activity, increases O-linked glycosylation	1

Cellosaurus cell lines

2 cell lines: 2 cancer cell line

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

Cellosaurus	Name	Category	Sex
CVCL_E1QQ	HAP1 ARFGAP3 (-) 2	Cancer cell line	Male
CVCL_XL44	HAP1 ARFGAP3 (-) 1	Cancer cell line	Male

Clinical trials (associated diseases)

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

Trial	Phase	Status	Title
NCT00417066	PHASE4	COMPLETED	Flexible GnRH Antagonist vs Flare up GnRH Agonist Protocol in Poor Responders
NCT00732693	PHASE4	COMPLETED	Evaluation of Physiologic and Standard Sex Steroid Replacement Regimens in Women With Premature Ovarian Failure
NCT00837616	PHASE4	COMPLETED	Estrogen Dosing in Turner Syndrome: Pharmacology and Metabolism
NCT01853501	PHASE4	UNKNOWN	Effects of ADSC Therapy in Women With POF
NCT02783937	PHASE4	COMPLETED	Filgrastim for Premature Ovarian Insufficiency
NCT03535480	PHASE4	UNKNOWN	Autologous Bone Marrow Stem Cell Ovarian Transplantation to Restore Ovarian Function in Premature Ovarian Failure
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,
NCT03414970	PHASE3	ACTIVE_NOT_RECRUITING	Hypofractionated Radiation Therapy After Mastectomy in Preventing Recurrence in Patients With Stage IIa-IIIa Breast Cancer
NCT00140998	PHASE3	COMPLETED	Estrogen Treatment (Oral vs. Patches) in Turner Syndrome
NCT03347526	PHASE3	SUSPENDED	A Novel Approach to Infantile Spasms
NCT03421496	PHASE3	TERMINATED	A Study to Assess Cannabidiol Oral Solution With Vigabatrin as Initial Therapy in Participants With Infantile Spasms
NCT06719141	PHASE3	RECRUITING	A Study to Investigate LP352 in Children and Adults With Developmental and Epileptic Encephalopathies (DEE)
NCT06908226	PHASE3	ENROLLING_BY_INVITATION	A Study to Investigate LP352 in Children and Adults With Developmental and Epileptic Encephalopathy (DEE)
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
NCT00461344	PHASE2	TERMINATED	Docetaxel + Doxorubicin as Neoadjuvant Chemotherapy in Patients With Breast Cancer
NCT07499999	PHASE2	NOT_YET_RECRUITING	Randomized Double-Blind Phase II Trial of Baby Exemestane Versus Baby Tamoxifen in Post-Menopausal Women at High Risk for Breast Cancer
NCT00001951	PHASE2	COMPLETED	Hormone Replacement in Young Women With Premature Ovarian Failure
NCT00370019	PHASE2	WITHDRAWN	Effects of an Estrogen Replacement Therapy Skin Patch on Ovulation in Women With Premature Ovarian Failure
NCT00429494	PHASE2	COMPLETED	GnRH Analogue for Ovarian Function Preservation in Hematopoietic Stem Cell Transplantation Patients
NCT03816852	PHASE2	SUSPENDED	The Safety and Efficiency Study of Mesenchymal Stem Cell (19#iSCLife®-POI) in Premature Ovarian Insufficiency
NCT04536467	PHASE2	UNKNOWN	Prevention of Chemotherapy-Induced Ovarian Failure With Goserelin in Premenopausal Lymphoma Patients
NCT06117982	PHASE2	COMPLETED	The Impact of Granulocyte Colony Stimulating Factor on Premature Ovarian Insufficiency
NCT04289467	PHASE2	RECRUITING	Treatment of Refractory Infantile Spasms With Fenfluramine
NCT05626634	PHASE2	COMPLETED	Open-label, Long-term Safety Study of LP352 in Subjects With Developmental and Epileptic Encephalopathy
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
NCT02912104	PHASE1	COMPLETED	A Therapeutic Trial of Human Amniotic Epithelial Cells Transplantation for Primary Ovarian Failure
NCT03178695	PHASE1	COMPLETED	Inovium Ovarian Rejuvenation Trials
NCT04815213	PHASE1	ACTIVE_NOT_RECRUITING	The Use of Expandeded Mesenchymal Stromal Cells (MSC) in Premature Ovarian Failure (POF) in Adult Humans
NCT05138367	PHASE1	COMPLETED	Effects of UCA-PSCs in Women With POF
NCT06132542	PHASE1	UNKNOWN	Autologous ADMSC Transplantation in Patients With POI
NCT04727970	PHASE1	COMPLETED	Tricaprilin Infantile Spasms Pilot Study
NCT06700811	PHASE1	RECRUITING	Ketogenic Diet for Prevention of Epileptic Spasms in Infantile Onset Genetic Epilepsies
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