ACAP2

Summary

ACAP2 (ArfGAP with coiled-coil, ankyrin repeat and PH domains 2, HGNC:16469) is a protein-coding gene on chromosome 3q29, encoding Arf-GAP with coiled-coil, ANK repeat and PH domain-containing protein 2 (Q15057). GTPase-activating protein (GAP) for ADP ribosylation factor 6 (ARF6).

Enables GTPase activator activity. Acts upstream of or within actin filament-based process. Located in ruffle.

Source: NCBI Gene 23527 — RefSeq curated summary.

At a glance

• GWAS associations: 5
• Clinical variants (ClinVar): 87 total — 5 pathogenic
• MANE Select transcript: NM_012287

Identifiers

Gene identifiers

Field	Value
HGNC ID	HGNC:16469
Approved symbol	ACAP2
Name	ArfGAP with coiled-coil, ankyrin repeat and PH domains 2
Location	3q29
Locus type	gene with protein product
Status	Approved
Aliases	KIAA0041, CNT-B2
Ensembl gene	ENSG00000114331
Ensembl biotype	protein_coding
OMIM	607766
Entrez	23527

Gene structure

Transcript identifiers

Ensembl transcripts: 31 — 22 protein_coding, 5 retained_intron, 3 protein_coding_CDS_not_defined, 1 nonsense_mediated_decay

ENST00000326793, ENST00000423531, ENST00000439666, ENST00000439758, ENST00000447662, ENST00000450200, ENST00000466876, ENST00000471593, ENST00000472860, ENST00000475905, ENST00000480906, ENST00000481463, ENST00000484296, ENST00000490224, ENST00000635383, ENST00000867112, ENST00000867113, ENST00000867114, ENST00000867115, ENST00000867116, ENST00000867117, ENST00000867118, ENST00000867119, ENST00000867120, ENST00000912823, ENST00000912824, ENST00000957234, ENST00000957235, ENST00000957236, ENST00000957237, ENST00000957238

RefSeq mRNA: 1 — MANE Select: NM_012287 NM_012287

CCDS: CCDS33924

Canonical transcript exons

ENST00000326793 — 23 exons

Exon	Start	End
ENSE00000781722	195308786	195308837
ENSE00000781723	195307223	195307323
ENSE00000781724	195306511	195306616
ENSE00001057142	195336932	195336976
ENSE00001057144	195295708	195295892
ENSE00001057148	195292265	195292452
ENSE00001057152	195294719	195294811
ENSE00001057153	195291706	195291815
ENSE00001188363	195285796	195285857
ENSE00001188404	195320701	195320813
ENSE00001188407	195326885	195326959
ENSE00001289119	195442795	195443020
ENSE00001402165	195274745	195279428
ENSE00003467231	195289121	195289231
ENSE00003502739	195301966	195302174
ENSE00003557007	195333028	195333123
ENSE00003579792	195301575	195301644
ENSE00003622054	195392090	195392147
ENSE00003642808	195381903	195382022
ENSE00003664915	195297190	195297281
ENSE00003669637	195342471	195342654
ENSE00003679849	195345259	195345317
ENSE00003790456	195381009	195381062

Expression profiles

Bgee: expression breadth ubiquitous, 288 present calls, max score 98.33.

FANTOM5 (CAGE): breadth ubiquitous, TPM avg 51.4223 / max 1215.5765, expressed in 1825 samples.

FANTOM5 promoters (8 alternative TSS)

Promoter ID	TPM avg	Samples expressed
46267	40.7713	1825
46268	5.5449	1474
46266	2.0926	1156
46265	1.6562	985
46270	0.6905	215
46269	0.5037	182
46263	0.0871	53
46262	0.0759	49

Top tissues by expression

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

Tissue	Anatomy ID	Expression score	Quality
epithelium of nasopharynx	UBERON:0001951	98.33	gold quality
bone marrow cell	CL:0002092	97.14	gold quality
superficial temporal artery	UBERON:0001614	97.00	gold quality
trabecular bone tissue	UBERON:0002483	96.79	gold quality
penis	UBERON:0000989	96.63	gold quality
calcaneal tendon	UBERON:0003701	96.55	gold quality
palpebral conjunctiva	UBERON:0001812	96.54	gold quality
oral cavity	UBERON:0000167	96.43	gold quality
jejunal mucosa	UBERON:0000399	96.43	gold quality
mucosa of paranasal sinus	UBERON:0005030	96.30	gold quality
parietal pleura	UBERON:0002400	96.16	gold quality
bone marrow	UBERON:0002371	95.65	gold quality
monocyte	CL:0000576	95.58	gold quality
mononuclear cell	CL:0000842	95.56	gold quality
germinal epithelium of ovary	UBERON:0001304	95.56	gold quality
visceral pleura	UBERON:0002401	95.47	gold quality
pleura	UBERON:0000977	95.42	gold quality
colonic epithelium	UBERON:0000397	95.37	gold quality
mammary duct	UBERON:0001765	95.37	gold quality
tonsil	UBERON:0002372	95.27	gold quality
leukocyte	CL:0000738	95.26	gold quality
synovial joint	UBERON:0002217	95.21	gold quality
urethra	UBERON:0000057	95.18	gold quality
seminal vesicle	UBERON:0000998	95.10	gold quality
gingival epithelium	UBERON:0001949	95.10	gold quality
gingiva	UBERON:0001828	95.04	gold quality
choroid plexus epithelium	UBERON:0003911	95.01	gold quality
mammalian vulva	UBERON:0000997	94.91	gold quality
epithelium of mammary gland	UBERON:0003244	94.84	gold quality
lower lobe of lung	UBERON:0008949	94.63	gold quality

Single-cell (SCXA)

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

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

Regulation

Is transcription factor: no

miRNA regulators (miRDB)

225 targeting ACAP2, 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-4262	100.00	73.26	3931
HSA-MIR-340-5P	100.00	72.50	4437
HSA-MIR-3163	100.00	77.23	8605
HSA-LET-7A-3P	100.00	74.03	3932
HSA-LET-7B-3P	100.00	74.08	3913
HSA-LET-7F-1-3P	100.00	74.02	3928
HSA-MIR-98-3P	100.00	74.08	3907
HSA-MIR-513A-5P	100.00	69.77	2465
HSA-MIR-190A-3P	100.00	80.35	5520
HSA-MIR-30A-5P	100.00	76.31	3233
HSA-MIR-30B-5P	100.00	76.29	3248
HSA-MIR-30C-5P	100.00	76.29	3248
HSA-MIR-30D-5P	100.00	76.32	3233
HSA-MIR-30E-5P	100.00	76.32	3242
HSA-MIR-656-3P	100.00	72.15	2788
HSA-MIR-548AW	99.99	72.57	3559
HSA-MIR-181A-5P	99.99	72.96	2995
HSA-MIR-181B-5P	99.99	72.97	2996
HSA-MIR-181C-5P	99.99	72.95	2996
HSA-MIR-181D-5P	99.99	73.04	2997
HSA-MIR-548C-3P	99.99	74.01	7587
HSA-MIR-4789-3P	99.99	70.75	2484
HSA-MIR-3185	99.99	68.12	1959
HSA-MIR-12136	99.98	72.81	5713
HSA-MIR-4775	99.98	75.00	6394
HSA-MIR-4789-5P	99.98	70.76	2721
HSA-MIR-8068	99.98	73.85	2376
HSA-MIR-548N	99.98	71.94	4170
HSA-MIR-433-3P	99.98	69.37	1203
HSA-LET-7F-2-3P	99.98	70.98	2588

Literature-anchored findings (GeneRIF, showing 8)

• Centaurin beta2/KIAA0041, is a member of the centaurin family of ADP-ribosylation factor directed GTPase-activating proteins. Binding of phosphoinositides to a pleckstrin homology domain may regulate subcellular localisation and activity. (PMID:11050434)
• ACAP2 has robust, constitutive Arf6 GAP activity in vivo, with little activity toward Arf1. (PMID:18003747)
• ACAP2 is a functional homolog of C. elegans CNT-1 and its inactivation or downregulation in human cells may contribute to cancer development (PMID:25853217)
• Data suggest that Rab35, interacting with TBC1D10A, functions in vascular endothelial cells as a negative regulator of histamine-evoked, Ca2+-dependent Weibel-Palade body exocytosis, most likely acting through the downstream effectors ACAP2 and Arf6. (Rab35 = rab GTP-binding protein 53; TBC1D10A = TBC1 domain family member 10A; ACAP2 = centaurin beta2; Arf6 = ADP-ribosylation factor 6) (PMID:28566286)
• The down-regulation of circRNA-ACAP2 promoted miR-21-5p expression, which further suppressed the transcription and translation of Tiam1. (PMID:30212824)
• analysis of structural basis for effector recognition in Rab35/ACAP2 and Rab35/RUSC2 complexes (PMID:30905672)
• Elevated expression of circACAP2 in breast cancer tissues leads to malignant phenotype upon cancerous cells. CircACAP2-miR-29a/b-3p-COL5A1 axis leads to breast cancer tumorigenesis (PMID:31863774)
• Circ-ACAP2 facilitates the progression of colorectal cancer through mediating miR-143-3p/FZD4 axis. (PMID:34085707)

Cross-species orthologs

4 orthologs

Organism	Symbol	Gene ID
danio_rerio	acap2a	ENSDARG00000056478
danio_rerio	acap2b	ENSDARG00000060783
mus_musculus	Acap2	ENSMUSG00000049076
rattus_norvegicus	Acap2	ENSRNOG00000001730

Paralogs (28): ARAP2 (ENSG00000047365), ACAP1 (ENSG00000072818), SMAP2 (ENSG00000084070), ASAP3 (ENSG00000088280), ARFGAP1 (ENSG00000101199), ADAP1 (ENSG00000105963), AGFG2 (ENSG00000106351), GIT1 (ENSG00000108262), SMAP1 (ENSG00000112305), 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), ARFGAP3 (ENSG00000242247)

Protein

Protein identifiers

Arf-GAP with coiled-coil, ANK repeat and PH domain-containing protein 2 — Q15057 (reviewed: Q15057)

Alternative names: Centaurin-beta-2

All UniProt accessions (7): A0A0U1RQT1, A0A5F9ZHJ9, C9J8L1, Q15057, F8WAU0, H7C3K3, H7C3Q8

UniProt curated annotations — full annotation on UniProt →

Function. GTPase-activating protein (GAP) for ADP ribosylation factor 6 (ARF6). Doesn’t show GAP activity for RAB35.

Subunit / interactions. Interacts (via KANK domains) with RAB35 (GTP-bound form); the interaction is direct and probably recruits ACAP2 to membranes including plasma membrane. Interacts with MICALL1; the interaction is indirect through RAB35.

Subcellular location. Cell membrane. Endosome membrane.

Tissue specificity. Widely expressed. Highest level in lung.

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

Domain organisation. The ANK domains are required for interaction with RAB35.

RefSeq proteins (1): NP_036419* (*=MANE)

Domains & families (InterPro)

ID	Name	Type
IPR001164	ArfGAP_dom	Domain
IPR001849	PH_domain	Domain
IPR002110	Ankyrin_rpt	Repeat
IPR004148	BAR_dom	Domain
IPR011993	PH-like_dom_sf	Homologous_superfamily
IPR027267	AH/BAR_dom_sf	Homologous_superfamily
IPR036770	Ankyrin_rpt-contain_sf	Homologous_superfamily
IPR037278	ARFGAP/RecO	Homologous_superfamily
IPR038508	ArfGAP_dom_sf	Homologous_superfamily
IPR045258	ACAP1/2/3-like	Family

Pfam: PF00169, PF01412, PF12796, PF16746

UniProt features (42 total): helix 9, modified residue 7, sequence conflict 7, mutagenesis site 6, domain 3, repeat 3, compositionally biased region 2, region of interest 2, chain 1, turn 1, zinc finger region 1

Structure

Experimental structures (PDB)

1 structures.

PDB	Method	Resolution (Å)
6IF3	X-RAY DIFFRACTION	1.5

Predicted structure (AlphaFold)

Model	pLDDT	Fraction very-high
AF-Q15057-F1	81.71	0.63

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 (7): 384, 387, 521, 581, 584, 742, 775

Mutagenesis-validated functional residues (6):

Position	Phenotype
442	loss of gap activity.
721	strong decrease in interaction with rab35.
727	decreased interaction with rab35.
727	loss of interaction with rab35.
731	strong decrease in interaction with rab35.
756	decreased interaction with rab35.

Function

Pathways and Gene Ontology

Reactome pathways

0 pathways

MSigDB gene sets: 162 (showing top): BORCZUK_MALIGNANT_MESOTHELIOMA_UP, RODRIGUES_THYROID_CARCINOMA_ANAPLASTIC_UP, DACOSTA_UV_RESPONSE_VIA_ERCC3_XPCS_DN, MORF_HDAC2, GOBP_VESICLE_MEDIATED_TRANSPORT, GOCC_RUFFLE, SHEPARD_BMYB_MORPHOLINO_DN, GOBP_RESPONSE_TO_NERVE_GROWTH_FACTOR, GNF2_MCL1, GNF2_ICAM3, DACOSTA_UV_RESPONSE_VIA_ERCC3_TTD_DN, GROSS_HYPOXIA_VIA_ELK3_DN, GROSS_HYPOXIA_VIA_HIF1A_DN, GROSS_HYPOXIA_VIA_ELK3_AND_HIF1A_UP, GNF2_PAK2

GO Biological Process (3): actin filament-based process (GO:0030029), endocytic recycling (GO:0032456), cellular response to nerve growth factor stimulus (GO:1990090)

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 (7): ruffle (GO:0001726), plasma membrane (GO:0005886), endosome membrane (GO:0010008), membrane (GO:0016020), cytoplasm (GO:0005737), endosome (GO:0005768), endomembrane system (GO:0012505)

GO top-level categories

Rollup of top GO terms by namespace:

Category	Terms
cellular anatomical structure	3
cellular process	1
endosomal transport	1
vesicle-mediated transport to the plasma membrane	1
cellular response to growth factor stimulus	1
response to nerve growth factor	1
GTPase activity	1
enzyme activator activity	1
GTPase regulator activity	1
transition metal ion binding	1
binding	1
cation binding	1
cell leading edge	1
plasma membrane bounded cell projection	1
membrane	1
cell periphery	1
endosome	1
cytoplasmic vesicle membrane	1
bounding membrane of organelle	1
intracellular anatomical structure	1
endomembrane system	1
cytoplasmic vesicle	1
vacuole	1
plasma membrane	1

Protein interactions and networks

STRING

1188 interactions, top by confidence (×1000):

Protein A	Protein B	Partner UniProt	Score
ACAP2	RAB35	Q15286	987
ACAP2	ARF6	P26438	897
ACAP2	ARF5	P26437	802
ACAP2	ARF1	P10947	710
ACAP2	OCRL	Q01968	606
ACAP2	RUSC2	Q8N2Y8	571
ACAP2	TBC1D10A	Q9BXI6	571
ACAP2	PLEK	P08567	565
ACAP2	PLEK2	Q9NYT0	562
ACAP2	VAMP3	Q15836	556
ACAP2	ASAP1	Q9ULH1	549
ACAP2	MICALL1	Q8N3F8	506
ACAP2	EHD1	Q9H4M9	501
ACAP2	TBC1D10B	Q4KMP7	495
ACAP2	MICAL1	Q8TDZ2	471

IntAct

33 interactions, top by confidence:

A	B	Type	Score
MED4	MED19	psi-mi:“MI:0914”(association)	0.900
ACAP2	ACAP3	psi-mi:“MI:0915”(physical association)	0.640
ACAP3	ACAP2	psi-mi:“MI:0915”(physical association)	0.640
RAB8A	WDR91	psi-mi:“MI:0914”(association)	0.600
ACAP2	HSPB1	psi-mi:“MI:0915”(physical association)	0.370
Naa10	MYO9A	psi-mi:“MI:0914”(association)	0.350
PDK3	ECD	psi-mi:“MI:0914”(association)	0.350
Tgs1	EFCAB5	psi-mi:“MI:0914”(association)	0.350
RASA1		psi-mi:“MI:0914”(association)	0.350
DOK2	MYO1C	psi-mi:“MI:0914”(association)	0.350
ELK4	MYO1C	psi-mi:“MI:0914”(association)	0.350
RAB5A	EIF3CL	psi-mi:“MI:0914”(association)	0.350
P		psi-mi:“MI:0914”(association)	0.350
M		psi-mi:“MI:0914”(association)	0.350
	PLEKHG3	psi-mi:“MI:0914”(association)	0.350
	HLA-C	psi-mi:“MI:0914”(association)	0.350
MAPT	SHTN1	psi-mi:“MI:0914”(association)	0.350
CAPZB	ENAH	psi-mi:“MI:0914”(association)	0.350
ACAP3	SEPTIN6	psi-mi:“MI:0914”(association)	0.350
OPG039	NEFH	psi-mi:“MI:0914”(association)	0.350
GPAA1	ACAP2	psi-mi:“MI:0915”(physical association)	0.000
NDUFS1	ACAP2	psi-mi:“MI:0915”(physical association)	0.000
GDI1	ACAP2	psi-mi:“MI:0915”(physical association)	0.000
SOAT1	ACAP2	psi-mi:“MI:0915”(physical association)	0.000
NDUFA9	ACAP2	psi-mi:“MI:0915”(physical association)	0.000
EHBP1	ACAP2	psi-mi:“MI:0915”(physical association)	0.000

BioGRID (67): ACAP2 (Two-hybrid), RAB11FIP3 (Affinity Capture-Western), ACAP2 (Affinity Capture-MS), ACAP2 (Affinity Capture-MS), ACAP2 (Affinity Capture-MS), ACAP2 (Affinity Capture-MS), ACAP2 (Affinity Capture-MS), ACAP2 (Affinity Capture-MS), ACAP2 (Affinity Capture-MS), ACAP2 (Affinity Capture-MS), ACAP2 (Affinity Capture-MS), ACAP2 (Affinity Capture-MS), ACAP2 (Affinity Capture-MS), ACAP2 (Affinity Capture-MS), ACAP2 (Affinity Capture-MS)

ESM2 similar proteins: A0A1D5P556, A6H7I5, B0DOB5, D3ZGS3, F1M386, F1MSG6, F1PBJ0, G5EGS5, H2KZZ6, O95466, P21575, P23678, P27619, P39052, P39053, P39054, P39055, P48608, P50570, P78344, P79398, Q01968, Q05193, Q08877, Q08DF4, Q15057, Q15172, Q24564, Q2KI89, Q5R629, Q5R7J9, Q5ZK62, Q62448, Q6IVG4, Q6NXC0, Q6ZQK5, Q7SIG6, Q7XPJ0, Q80U19, Q86T65

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

0 interactions.

Disease & clinical

Clinical variants and AI predictions

ClinVar

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

Classification	Count (floor)
Pathogenic	5
Likely pathogenic	0
Uncertain significance	54
Likely benign	1
Benign	0

Top pathogenic / likely-pathogenic (5)

Variant ID	HGVS	Classification
147306	GRCh38/hg38 3q29(chr3:194338534-197693741)x1	Pathogenic
562850	GRCh37/hg19 3q27.1-29(chr3:184003967-197851986)x3	Pathogenic
562852	GRCh37/hg19 3q27.3-29(chr3:186374365-197851986)x3	Pathogenic
58000	GRCh38/hg38 3q29(chr3:194424496-198168758)x3	Pathogenic
980655	GRCh37/hg19 3q29(chr3:195068028-197851986)x3	Pathogenic

SpliceAI

4930 predictions. Top by Δscore:

Variant	Effect	Δscore
3:195289115:ACTT:A	donor_loss	1.0000
3:195289116:CTT:C	donor_loss	1.0000
3:195289117:TTACA:T	donor_loss	1.0000
3:195289118:TA:T	donor_loss	1.0000
3:195289119:A:AC	donor_gain	1.0000
3:195289120:C:CA	donor_gain	1.0000
3:195289120:C:T	donor_loss	1.0000
3:195289120:CA:C	donor_gain	1.0000
3:195289120:CAA:C	donor_gain	1.0000
3:195289120:CAAG:C	donor_gain	1.0000
3:195289120:CAAGG:C	donor_gain	1.0000
3:195289230:GC:G	acceptor_gain	1.0000
3:195289231:CC:C	acceptor_gain	1.0000
3:195289231:CCTGT:C	acceptor_loss	1.0000
3:195291704:AC:A	donor_gain	1.0000
3:195291705:CC:C	donor_gain	1.0000
3:195292259:GCATA:G	donor_loss	1.0000
3:195292260:CATAC:C	donor_loss	1.0000
3:195292261:ATAC:A	donor_gain	1.0000
3:195292261:ATACC:A	donor_gain	1.0000
3:195292262:TA:T	donor_loss	1.0000
3:195292263:AC:A	donor_gain	1.0000
3:195292263:ACC:A	donor_gain	1.0000
3:195292264:C:CG	donor_loss	1.0000
3:195292264:CC:C	donor_gain	1.0000
3:195292264:CCC:C	donor_gain	1.0000
3:195292272:ACAG:A	donor_gain	1.0000
3:195292273:CAGC:C	donor_gain	1.0000
3:195292275:G:GA	donor_gain	1.0000
3:195292302:T:TA	donor_gain	1.0000

AlphaMissense

5157 scored. Top likely-pathogenic:

Variant	Protein change	am_pathogenicity
3:195279394:A:C	F757L	1.000
3:195279394:A:T	F757L	1.000
3:195279395:A:C	F757C	1.000
3:195279395:A:G	F757S	1.000
3:195279396:A:G	F757L	1.000
3:195279407:A:T	I753K	1.000
3:195285840:A:G	M731T	1.000
3:195285849:A:G	L728S	1.000
3:195285852:C:G	R727P	1.000
3:195285853:G:T	R727S	1.000
3:195285855:A:G	L726S	1.000
3:195289121:A:C	L725W	1.000
3:195289121:A:G	L725S	1.000
3:195289127:A:T	V723D	1.000
3:195289130:A:T	I722K	1.000
3:195289133:T:A	D721V	1.000
3:195289133:T:C	D721G	1.000
3:195289134:C:G	D721H	1.000
3:195289136:G:T	A720D	1.000
3:195289154:G:T	A714D	1.000
3:195289155:C:G	A714P	1.000
3:195289208:C:G	R696P	1.000
3:195289214:A:G	L694P	1.000
3:195289224:A:G	C691R	1.000
3:195291727:G:T	A681D	1.000
3:195291728:C:G	A681P	1.000
3:195291736:A:C	L678W	1.000
3:195291787:A:G	L661P	1.000
3:195291790:A:G	L660P	1.000
3:195295862:T:A	K506N	1.000

dbSNP variants (sampled 300 via entrez): RS1000009344 (3:195313803 T>C), RS1000029154 (3:195428561 G>T), RS1000043543 (3:195429877 C>T), RS1000080714 (3:195419301 T>C), RS1000083922 (3:195393052 C>A), RS1000092650 (3:195351507 C>A,T), RS1000136489 (3:195393287 A>G), RS1000138682 (3:195428004 C>T), RS1000148647 (3:195359679 G>A), RS1000162038 (3:195319081 C>G), RS1000218875 (3:195308174 G>A), RS1000224181 (3:195345906 C>T), RS1000239599 (3:195368306 T>C), RS1000261341 (3:195350479 A>G), RS1000269453 (3:195282486 A>T)

Disease associations

OMIM: gene MIM:607766 | disease phenotypes: MIM:609425, MIM:611936

GenCC curated gene-disease

Mondo (2): chromosome 3q29 microdeletion syndrome (MONDO:0012269), chromosome 3q29 microduplication syndrome (MONDO:0012761)

Orphanet (2): 3q29 microdeletion syndrome (Orphanet:65286), 3q29 microduplication syndrome (Orphanet:251038)

HPO phenotypes

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

GWAS associations

5 associations (top):

Study	Trait	p-value
GCST002783_171	Body mass index	1.000000e-06
GCST002783_225	Body mass index	3.000000e-07
GCST008839_325	Height	3.000000e-10
GCST009391_572	Metabolite levels	4.000000e-06
GCST90002395_557	Mean platelet volume	1.000000e-10

EFO canonical traits (2, from GWAS)

EFO ID	Trait name
EFO:0004340	body mass index
EFO:0021604	hypoxanthine measurement

MeSH disease descriptors (2)

Descriptor	Name	Tree numbers
C567184	Chromosome 3q29 Deletion Syndrome (supp.)
C567626	Chromosome 3q29 Duplication Syndrome (supp.)

Drugs & pharmacology

Drug and pharmacology data

Is drug target: no

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

CTD chemical–gene interactions

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

Chemical	Actions (top 5)	PubMed papers
sodium arsenite	increases expression, decreases expression, affects cotreatment, increases abundance	4
bisphenol A	decreases expression, increases expression	2
Benzo(a)pyrene	affects methylation, decreases expression	2
Valproic Acid	decreases methylation, increases expression	2
Cyclosporine	increases expression	2
geldanamycin	increases expression	1
beta-lapachone	increases expression	1
arsenite	affects binding, decreases reaction	1
tris(1,3-dichloro-2-propyl)phosphate	increases expression	1
tetrabromobisphenol A	decreases expression	1
potassium chromate(VI)	affects cotreatment, decreases expression	1
coumarin	decreases phosphorylation	1
epigallocatechin gallate	affects cotreatment, decreases expression	1
CC-8490	increases expression	1
2,2’,4,4’-tetrabromodiphenyl ether	decreases expression	1
pentabrominated diphenyl ether 100	decreases expression	1
hexabrominated diphenyl ether 153	decreases expression	1
jinfukang	decreases expression	1
Resveratrol	affects cotreatment, increases expression	1
Acetaminophen	increases expression	1
Arsenic	increases abundance, increases expression, affects cotreatment	1
Clorgyline	increases expression	1
Diethylstilbestrol	increases expression	1
Dimethyl Sulfoxide	decreases expression	1
Ethyl Methanesulfonate	increases expression	1
Formaldehyde	increases expression	1
Ivermectin	decreases expression	1
Methyl Methanesulfonate	increases expression	1
Plant Extracts	affects cotreatment, increases expression	1
Polychlorinated Biphenyls	affects expression	1

Clinical trials (associated diseases)

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