FGD5

Summary

FGD5 (FYVE, RhoGEF and PH domain containing 5, HGNC:19117) is a protein-coding gene on chromosome 3p25.1, encoding FYVE, RhoGEF and PH domain-containing protein 5 (Q6ZNL6). Activates CDC42, a member of the Ras-like family of Rho- and Rac proteins, by exchanging bound GDP for free GTP.

Predicted to enable guanyl-nucleotide exchange factor activity and small GTPase binding activity. Predicted to be involved in actin cytoskeleton organization; filopodium assembly; and regulation of cell shape. Located in plasma membrane.

Source: NCBI Gene 152273 — RefSeq curated summary.

At a glance

• GWAS associations: 36
• Clinical variants (ClinVar): 297 total — 2 pathogenic
• Cancer driver (intOGen): activating (oncogene-like) across 1 cancer types
• MANE Select transcript: NM_152536

Identifiers

Gene identifiers

Field	Value
HGNC ID	HGNC:19117
Approved symbol	FGD5
Name	FYVE, RhoGEF and PH domain containing 5
Location	3p25.1
Locus type	gene with protein product
Status	Approved
Aliases	ZFYVE23, FLJ39957, FLJ00274
Ensembl gene	ENSG00000154783
Ensembl biotype	protein_coding
OMIM	614788
Entrez	152273

Gene structure

Transcript identifiers

Ensembl transcripts: 15 — 12 protein_coding, 2 protein_coding_CDS_not_defined, 1 retained_intron

ENST00000285046, ENST00000457774, ENST00000468662, ENST00000476851, ENST00000487605, ENST00000543601, ENST00000640506, ENST00000859932, ENST00000859933, ENST00000918364, ENST00000918365, ENST00000969461, ENST00000969462, ENST00000969463, ENST00000969464

RefSeq mRNA: 2 — MANE Select: NM_152536 NM_001320276, NM_152536

CCDS: CCDS46767

Canonical transcript exons

ENST00000285046 — 20 exons

Exon	Start	End
ENSE00001287651	14880742	14880772
ENSE00001287657	14880572	14880630
ENSE00001287662	14864128	14864260
ENSE00001287670	14933131	14934571
ENSE00001287677	14818962	14821596
ENSE00003459624	14918754	14918833
ENSE00003482298	14923046	14923175
ENSE00003503747	14910861	14910929
ENSE00003513926	14897509	14897669
ENSE00003530040	14907640	14907711
ENSE00003564001	14932577	14932731
ENSE00003583916	14917249	14917332
ENSE00003591260	14924008	14924138
ENSE00003620760	14901003	14901061
ENSE00003643176	14926070	14926198
ENSE00003646140	14898739	14898826
ENSE00003649596	14922411	14922548
ENSE00003651744	14921918	14922017
ENSE00003653722	14897939	14898095
ENSE00003788560	14900403	14900453

Expression profiles

Bgee: expression breadth ubiquitous, 220 present calls, max score 95.49.

FANTOM5 (CAGE): breadth broad, TPM avg 3.6532 / max 151.2561, expressed in 564 samples.

FANTOM5 promoters (3 alternative TSS)

Promoter ID	TPM avg	Samples expressed
35477	2.0969	470
35476	1.1587	394
35475	0.3976	222

Top tissues by expression

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

Tissue	Anatomy ID	Expression score	Quality
synovial joint	UBERON:0002217	95.49	gold quality
layer of synovial tissue	UBERON:0007616	95.00	gold quality
tendon of biceps brachii	UBERON:0008188	94.79	gold quality
sural nerve	UBERON:0015488	93.29	gold quality
visceral pleura	UBERON:0002401	93.19	gold quality
right lung	UBERON:0002167	91.20	gold quality
subcutaneous adipose tissue	UBERON:0002190	89.75	gold quality
parietal pleura	UBERON:0002400	89.66	gold quality
tendon	UBERON:0000043	89.48	gold quality
upper lobe of left lung	UBERON:0008952	89.15	gold quality
upper lobe of lung	UBERON:0008948	89.14	gold quality
lower lobe of lung	UBERON:0008949	89.12	gold quality
lung	UBERON:0002048	88.93	gold quality
apex of heart	UBERON:0002098	88.86	gold quality
kidney epithelium	UBERON:0004819	88.75	gold quality
spleen	UBERON:0002106	88.64	gold quality
decidua	UBERON:0002450	88.37	gold quality
calcaneal tendon	UBERON:0003701	88.11	gold quality
omental fat pad	UBERON:0010414	87.74	gold quality
peritoneum	UBERON:0002358	87.69	gold quality
adipose tissue of abdominal region	UBERON:0007808	87.53	gold quality
adipose tissue	UBERON:0001013	87.50	gold quality
pericardium	UBERON:0002407	87.33	gold quality
saphenous vein	UBERON:0007318	86.21	gold quality
urethra	UBERON:0000057	86.14	gold quality
gall bladder	UBERON:0002110	85.77	gold quality
smooth muscle tissue	UBERON:0001135	85.45	gold quality
secondary oocyte	CL:0000655	85.40	gold quality
primordial germ cell in gonad	CL:0000670 ∩ UBERON:0000991	84.68	gold quality
cardiac muscle of right atrium	UBERON:0003379	84.55	silver quality

Single-cell (SCXA)

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

Experiment	Marker?	Max mean expression
E-ANND-3	yes	8.76

Regulation

Is transcription factor: no

miRNA regulators (miRDB)

92 targeting FGD5, 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-3613-3P	100.00	76.36	7965
HSA-MIR-371B-5P	99.99	75.34	4759
HSA-MIR-373-5P	99.98	75.36	4753
HSA-MIR-616-5P	99.98	75.58	4775
HSA-MIR-12136	99.98	72.81	5713
HSA-MIR-548P	99.98	72.25	3784
HSA-MIR-4650-5P	99.98	64.69	999
HSA-MIR-3148	99.97	75.06	6478
HSA-MIR-302E	99.96	70.74	2669
HSA-MIR-548AJ-3P	99.96	73.38	5345
HSA-MIR-548X-3P	99.96	73.38	5345
HSA-MIR-651-3P	99.94	73.48	5177
HSA-MIR-548J-3P	99.94	72.61	4881
HSA-MIR-548AE-3P	99.93	72.66	4867
HSA-MIR-548AH-3P	99.93	72.54	4872
HSA-MIR-548AM-3P	99.93	72.54	4872
HSA-MIR-548AQ-3P	99.93	72.66	4867
HSA-MIR-6809-3P	99.91	71.45	3814
HSA-MIR-106A-5P	99.90	73.94	2683
HSA-MIR-4753-3P	99.90	71.03	3786
HSA-MIR-17-5P	99.89	73.83	2665
HSA-MIR-124-3P	99.89	73.74	3043
HSA-MIR-506-3P	99.89	73.55	3057
HSA-MIR-345-3P	99.89	70.23	1421
HSA-MIR-548E-5P	99.89	72.73	4486
HSA-MIR-302A-3P	99.89	71.23	1777
HSA-MIR-302B-3P	99.89	71.23	1777
HSA-MIR-302C-3P	99.89	71.20	1778
HSA-MIR-302D-3P	99.89	71.25	1777
HSA-MIR-106B-5P	99.88	74.72	2795

Literature-anchored findings (GeneRIF, showing 17)

• Suggest that FGD5 regulates proangiogenic action of VEGF in vascular endothelial cells, including network formation, permeability, directional movement, and proliferation. (PMID:22328776)
• FGD5 inhibits neovascularization, indicated by in vitro tube-formation, aortic-ring, and coated-bead assays and by in vivo coated-bead plug assays and studies in the murine retina model. (PMID:22661514)
• FGD5 regulates endothelial adhesion, survival, and angiogenesis by modulating phosphatidylinositol 3-kinase signaling. (PMID:22922960)
• We provide the first report that pro-angiogenic genes PECAM1, PTGS1, FGD5, and MCAM may play a vital role in pathological dermal angiogenesis disorders of psoriasis. (PMID:26748901)
• FGD5 is a new prognostic marker in breast cancer, and increased copy number is associated with higher tumour proliferation and poorer long-term prognosis. (PMID:28124285)
• We found that depletion of FGD5 in microvascular cells inhibited their migration towards a stable VEGFA gradient. Furthermore, depletion of FGD5 resulted in accelerated VEGFR2 degradation, which was reverted by lactacystin-mediated proteasomal inhibition. Our results thus suggest a mechanism whereby FGD5 sustains VEGFA signaling and endothelial cell chemotaxis via inhibition of proteasome-dependent VEGFR2 degradation. (PMID:28927665)
• FGD5 regulates VEGFR2 retention in recycling endosomes and coupling to PI3 (phosphoinositide-3) kinase/mTORC2-dependent cytoskeletal remodeling in endothelial cells. (PMID:29051140)
• The study demonstrated cytoplasmic and nuclear FGD5 staining in a large proportion of primary breast cancers and lymph node metastases. The proportion of FGD5-positive lymph nodes was higher compared with the corresponding primary tumors. There was an association between FGD5 amplification status and nuclear FGD5 staining; however, neither proliferation nor prognosis was found to be associated with FGD5 expression. (PMID:30052477)
• Human FYVE domain containing proteins, those within the faciogenital dysplasia (Fgd) subfamily are particularly divergent and couple with GTPases to exert unique cellular functions. (PMID:30308128)
• *FGD5 tyrosine phosphorylation is essential for endothelial junction stabilization. (PMID:31267715)
• Faciogenital Dysplasia 5 supports cancer stem cell traits in basal-like breast cancer by enhancing EGFR stability. (PMID:33762435)
• Long non-coding RNA FGD5-AS1 enhances osteosarcoma cell proliferation and migration by targeting miR-506-3p/RAB3D axis. (PMID:33891267)
• A high level of lncFGD5-AS1 inhibits epithelial-to-Mesenchymal transition by regulating the miR-196a-5p/SMAD6/BMP axis in gastric Cancer. (PMID:33892661)
• FGD5 facilitates tumor growth by regulating EGFR ubiquitination in gastric cancer. (PMID:34034092)
• Faciogenital dysplasia 5 confers the cancer stem cell-like traits of gastric cancer cells through enhancing Sox2 protein stability. (PMID:34427968)
• FGD5 regulates endothelial cell PI3 kinase-beta to promote neo-angiogenesis. (PMID:34882832)
• Common Variants on FGD5 Increase Hazard of Mortality or Rehospitalization in Patients With Heart Failure From the ASCEND-HF Trial. (PMID:37725680)

Cross-species orthologs

6 orthologs

Organism	Symbol	Gene ID
danio_rerio	fgd5a	ENSDARG00000088801
danio_rerio	fgd5b	ENSDARG00000089622
mus_musculus	Fgd5	ENSMUSG00000034037
rattus_norvegicus	Fgd5	ENSRNOG00000010213
caenorhabditis_elegans		WBGENE00001366
caenorhabditis_elegans		WBGENE00001490

Paralogs (10): FARP2 (ENSG00000006607), FGD1 (ENSG00000102302), FGD3 (ENSG00000127084), ARHGEF39 (ENSG00000137135), FGD4 (ENSG00000139132), FGD2 (ENSG00000146192), FARP1 (ENSG00000152767), FRMD7 (ENSG00000165694), FGD6 (ENSG00000180263), ECT2L (ENSG00000203734)

Protein

Protein identifiers

FYVE, RhoGEF and PH domain-containing protein 5 — Q6ZNL6 (reviewed: Q6ZNL6)

Alternative names: Zinc finger FYVE domain-containing protein 23

All UniProt accessions (5): Q6ZNL6, A0A1W2PRG7, A0A2X0SFF2, B7ZM68, H7C0G2

UniProt curated annotations — full annotation on UniProt →

Function. Activates CDC42, a member of the Ras-like family of Rho- and Rac proteins, by exchanging bound GDP for free GTP. Mediates VEGF-induced CDC42 activation. May regulate proangiogenic action of VEGF in vascular endothelial cells, including network formation, directional movement and proliferation. May play a role in regulating the actin cytoskeleton and cell shape.

Subcellular location. Cytoplasm. Cytoskeleton. Cell projection. Ruffle membrane. Endoplasmic reticulum. Golgi apparatus. Early endosome.

Tissue specificity. Expressed in endothelial cells (at protein level).

Isoforms (2)

UniProt ID	Names	Canonical?
Q6ZNL6-1	1	yes
Q6ZNL6-2	2

RefSeq proteins (2): NP_001307205, NP_689749* (*=MANE)

Domains & families (InterPro)

ID	Name	Type
IPR000219	DH_dom	Domain
IPR000306	Znf_FYVE	Domain
IPR001849	PH_domain	Domain
IPR011993	PH-like_dom_sf	Homologous_superfamily
IPR013083	Znf_RING/FYVE/PHD	Homologous_superfamily
IPR017455	Znf_FYVE-rel	Domain
IPR035899	DBL_dom_sf	Homologous_superfamily
IPR051092	FYVE_RhoGEF_PH	Family

Pfam: PF00169, PF00621, PF01363

UniProt features (59 total): helix 10, compositionally biased region 9, sequence conflict 9, binding site 8, region of interest 6, strand 6, domain 3, sequence variant 3, turn 2, chain 1, splice variant 1, zinc finger region 1

Structure

Experimental structures (PDB)

1 structures.

PDB	Method	Resolution (Å)
3MPX	X-RAY DIFFRACTION	2.8

Predicted structure (AlphaFold)

Model	pLDDT	Fraction very-high
AF-Q6ZNL6-F1	54.36	0.23

Functional residue map

Curated UniProt residues grouped by drug-discovery relevance — catalytic, ligand-binding, modification, and mutation-validated positions. Source: UniProtKB sequence features.

Ligand- & substrate-binding residues (8): 1248; 1251; 1264; 1267; 1272; 1275; 1293; 1296

Function

Pathways and Gene Ontology

Reactome pathways

1 pathways

ID	Pathway
R-HSA-9013149	RAC1 GTPase cycle

MSigDB gene sets: 130 (showing top): GSE45365_NK_CELL_VS_CD8_TCELL_DN, GSE45365_CTRL_VS_MCMV_INFECTION_NK_CELL_UP, GOBP_REGULATION_OF_CELL_MORPHOGENESIS, GOBP_REGULATION_OF_GTPASE_ACTIVITY, GOBP_REGULATION_OF_SMALL_GTPASE_MEDIATED_SIGNAL_TRANSDUCTION, GOCC_RUFFLE, GOMF_GTPASE_BINDING, GOBP_REGULATION_OF_HYDROLASE_ACTIVITY, LASTOWSKA_NEUROBLASTOMA_COPY_NUMBER_DN, JAATINEN_HEMATOPOIETIC_STEM_CELL_UP, GOBP_CELL_PROJECTION_ORGANIZATION, CUI_TCF21_TARGETS_2_DN, GOBP_SMALL_GTPASE_MEDIATED_SIGNAL_TRANSDUCTION, ACEVEDO_METHYLATED_IN_LIVER_CANCER_DN, GOBP_FILOPODIUM_ASSEMBLY

GO Biological Process (6): cytoskeleton organization (GO:0007010), regulation of cell shape (GO:0008360), actin cytoskeleton organization (GO:0030036), regulation of GTPase activity (GO:0043087), filopodium assembly (GO:0046847), regulation of small GTPase mediated signal transduction (GO:0051056)

GO Molecular Function (5): guanyl-nucleotide exchange factor activity (GO:0005085), zinc ion binding (GO:0008270), small GTPase binding (GO:0031267), protein binding (GO:0005515), metal ion binding (GO:0046872)

GO Cellular Component (13): ruffle (GO:0001726), cytoplasm (GO:0005737), early endosome (GO:0005769), endoplasmic reticulum (GO:0005783), Golgi apparatus (GO:0005794), cytosol (GO:0005829), cytoskeleton (GO:0005856), plasma membrane (GO:0005886), lamellipodium (GO:0030027), ruffle membrane (GO:0032587), endosome (GO:0005768), membrane (GO:0016020), cell projection (GO:0042995)

Reactome top-level categories

Rollup of top-1 pathways:

Category	Pathways
RHO GTPase cycle	1

GO top-level categories

Rollup of top GO terms by namespace:

Category	Terms
cellular anatomical structure	4
cytoplasm	3
endomembrane system	3
cell leading edge	2
plasma membrane bounded cell projection	2
intracellular membrane-bounded organelle	2
organelle organization	1
regulation of cell morphogenesis	1
regulation of biological quality	1
cytoskeleton organization	1
actin filament-based process	1
GTPase activity	1
regulation of hydrolase activity	1
plasma membrane bounded cell projection assembly	1
small GTPase-mediated signal transduction	1
regulation of intracellular signal transduction	1
GTP binding	1
GDP binding	1
GTPase regulator activity	1
transition metal ion binding	1
GTPase binding	1
binding	1
cation binding	1
intracellular anatomical structure	1
endosome	1
intracellular membraneless organelle	1
membrane	1
cell periphery	1
ruffle	1
cell projection membrane	1
leading edge membrane	1
cytoplasmic vesicle	1

Protein interactions and networks

STRING

1151 interactions, top by confidence (×1000):

Protein A	Protein B	Partner UniProt	Score
FGD5	CTNNAL1	Q9UBT7	531
FGD5	ARHGEF15	O94989	504
FGD5	ECT2L	Q008S8	416
FGD5	PDZK1IP1	Q13113	411
FGD5	SLAMF1	Q13291	408
FGD5	HOXB5	P09067	404
FGD5	LRRC3B	Q96PB8	395
FGD5	GPRC5C	Q9NQ84	391
FGD5	ARHGEF16	Q5VV41	387
FGD5	ARHGEF38	Q9NXL2	386
FGD5	FGD3	Q5JSP0	385
FGD5	ARHGEF7	Q14155	384
FGD5	CD48	P09326	377
FGD5	CDC42	P21181	375
FGD5	ARHGEF6	Q15052	372

IntAct

30 interactions, top by confidence:

A	B	Type	Score
CASP6	FGD5	psi-mi:“MI:0915”(physical association)	0.560
LAMP2	FGD5	psi-mi:“MI:0915”(physical association)	0.560
RAN	FGD5	psi-mi:“MI:0915”(physical association)	0.560
PRPF40A	FGD5	psi-mi:“MI:0915”(physical association)	0.560
FGD5	COQ8A	psi-mi:“MI:0915”(physical association)	0.560
FGD5	SUV39H1	psi-mi:“MI:0915”(physical association)	0.510
Dlg4	FGD5	psi-mi:“MI:0407”(direct interaction)	0.440
FGD5	RPS14	psi-mi:“MI:0915”(physical association)	0.400
FGD5	PHB2	psi-mi:“MI:0915”(physical association)	0.400
FGD5	PLEC	psi-mi:“MI:0915”(physical association)	0.400
CFTR	FGD5	psi-mi:“MI:0915”(physical association)	0.370
FGD5	JMJD6	psi-mi:“MI:0915”(physical association)	0.370
BCAR1	PSMD11	psi-mi:“MI:0914”(association)	0.350
BCAR1	MYO1C	psi-mi:“MI:0914”(association)	0.350
FGD5	PRKACB	psi-mi:“MI:0914”(association)	0.350
CREB3L2	PLEKHG3	psi-mi:“MI:0914”(association)	0.350
CDH5	ESYT2	psi-mi:“MI:2364”(proximity)	0.270

BioGRID (214): FGD5 (Affinity Capture-MS), FGD5 (Proximity Label-MS), PHB2 (Proximity Label-MS), FGD5 (Proximity Label-MS), FGD5 (FRET), ARF1 (Affinity Capture-MS), DBNL (Affinity Capture-MS), DCAF7 (Affinity Capture-MS), MCM3 (Affinity Capture-MS), CBX3 (Affinity Capture-MS), SDHA (Affinity Capture-MS), AGK (Affinity Capture-MS), CKMT1B (Affinity Capture-MS), HSPA4L (Affinity Capture-MS), KPNA2 (Affinity Capture-MS)

ESM2 similar proteins: A0A8I5ZM56, A2AJI0, A2AKB4, D3ZFB6, E9PUL5, O08715, O75128, O88884, P18302, Q07266, Q0VGB7, Q149B8, Q2KI80, Q32LQ1, Q3UZ39, Q3UZA1, Q498S6, Q4V9L6, Q5FVJ4, Q5RAC1, Q5T7N3, Q60829, Q66HF9, Q6J4I0, Q6JBY9, Q6NV74, Q6P9J5, Q6PG95, Q6PJW8, Q6ZNL6, Q6ZSG2, Q7Z6L0, Q80XI1, Q8BGW2, Q8BRJ3, Q8CBC4, Q8CCJ4, Q8IY92, Q8K124, Q8NC24

Diamond homologs: A0JMD2, A1DFP5, A2QWA2, A3LX75, A4QTV1, A8QCE4, A8XJZ8, B0WAQ0, B3MT31, B3P851, B4G2G5, B4IC49, B4JHI7, B4K982, B4M140, B4NFJ7, B4PRU6, D2H5P6, D3ZVP7, D4A8G9, E1BLZ4, O13821, O14964, O95405, O96838, P0CS26, P0CS27, P34657, P40343, P53191, Q05B78, Q06651, Q0CJV3, Q0P4S0, Q0U4Z8, Q0V8S0, Q0WUR5, Q13615, Q15075, Q17AN2

SIGNOR signaling

1 interactions.

A	Effect	B	Mechanism
FGD5	“up-regulates activity”	RAC1	“guanine nucleotide exchange factor”

Disease & clinical

Cancer significance

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

Clinical variants and AI predictions

ClinVar

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

Classification	Count (floor)
Pathogenic	2
Likely pathogenic	0
Uncertain significance	241
Likely benign	25
Benign	9

Top pathogenic / likely-pathogenic (2)

Variant ID	HGVS	Classification
1526968	GRCh37/hg19 3p26.3-22.2(chr3:61891-36710181)	Pathogenic
1703229	Single allele	Pathogenic

SpliceAI

3471 predictions. Top by Δscore:

Variant	Effect	Δscore
3:14821592:GAAAG:G	donor_gain	1.0000
3:14821593:AAAGG:A	donor_loss	1.0000
3:14821594:AAGGT:A	donor_loss	1.0000
3:14821595:AGG:A	donor_loss	1.0000
3:14821596:GGTAC:G	donor_loss	1.0000
3:14821597:G:A	donor_loss	1.0000
3:14821598:T:A	donor_loss	1.0000
3:14864115:T:A	acceptor_gain	1.0000
3:14864120:T:A	acceptor_gain	1.0000
3:14864126:A:AG	acceptor_gain	1.0000
3:14864127:G:GA	acceptor_gain	1.0000
3:14864127:GC:G	acceptor_gain	1.0000
3:14880629:GC:G	donor_gain	1.0000
3:14880631:G:GG	donor_gain	1.0000
3:14897503:TTTCA:T	acceptor_loss	1.0000
3:14897505:TCA:T	acceptor_loss	1.0000
3:14897506:CA:C	acceptor_loss	1.0000
3:14897507:A:AG	acceptor_gain	1.0000
3:14897507:AG:A	acceptor_gain	1.0000
3:14897507:AGGA:A	acceptor_loss	1.0000
3:14897508:G:A	acceptor_loss	1.0000
3:14897508:G:GC	acceptor_gain	1.0000
3:14897508:GG:G	acceptor_gain	1.0000
3:14897508:GGA:G	acceptor_gain	1.0000
3:14897508:GGAT:G	acceptor_gain	1.0000
3:14897508:GGATT:G	acceptor_gain	1.0000
3:14897654:A:T	donor_gain	1.0000
3:14897666:ATTG:A	donor_gain	1.0000
3:14897667:TTG:T	donor_gain	1.0000
3:14897667:TTGG:T	donor_loss	1.0000

AlphaMissense

9583 scored. Top likely-pathogenic:

Variant	Protein change	am_pathogenicity
3:14922483:T:C	C1248R	1.000
3:14922531:T:C	C1264R	1.000
3:14922532:G:A	C1264Y	1.000
3:14922533:T:G	C1264W	1.000
3:14923052:T:C	C1272R	1.000
3:14923115:T:C	C1293R	1.000
3:14923116:G:A	C1293Y	1.000
3:14918791:T:C	L1176P	0.999
3:14921940:T:A	W1198R	0.999
3:14921940:T:C	W1198R	0.999
3:14922483:T:A	C1248S	0.999
3:14922484:G:A	C1248Y	0.999
3:14922484:G:C	C1248S	0.999
3:14922485:C:G	C1248W	0.999
3:14922504:T:C	F1255L	0.999
3:14922505:T:C	F1255S	0.999
3:14922506:C:A	F1255L	0.999
3:14922506:C:G	F1255L	0.999
3:14922522:C:A	R1261S	0.999
3:14922531:T:A	C1264S	0.999
3:14922532:G:C	C1264S	0.999
3:14922532:G:T	C1264F	0.999
3:14922540:T:C	C1267R	0.999
3:14922541:G:A	C1267Y	0.999
3:14922542:T:G	C1267W	0.999
3:14922544:G:A	G1268D	0.999
3:14922544:G:T	G1268V	0.999
3:14923052:T:A	C1272S	0.999
3:14923053:G:A	C1272Y	0.999
3:14923053:G:C	C1272S	0.999

dbSNP variants (sampled 300 via entrez): RS1000025326 (3:14866222 C>T), RS1000120644 (3:14896961 A>G), RS1000134738 (3:14821974 C>T), RS1000136442 (3:14819517 G>T), RS1000145695 (3:14833077 G>T), RS1000164696 (3:14913761 C>T), RS1000181028 (3:14846551 C>T), RS1000193153 (3:14882333 T>A,G), RS1000226563 (3:14920444 G>A), RS1000240604 (3:14840381 G>A), RS1000246678 (3:14857483 A>C,G), RS1000254688 (3:14871303 T>A,C), RS1000275319 (3:14919230 C>T), RS1000313842 (3:14933297 A>C,G), RS1000324962 (3:14881400 A>T)

Disease associations

OMIM: gene MIM:614788 | disease phenotypes: MIM:613792

GenCC curated gene-disease

Mondo (1): 3p- syndrome (MONDO:0013424)

Orphanet (1): Distal deletion 3p syndrome (Orphanet:1620)

HPO phenotypes

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

GWAS associations

36 associations (top):

Study	Trait	p-value
GCST004280_23	Diastolic blood pressure	5.000000e-06
GCST004711_40	Alcohol dependence	5.000000e-06
GCST005194_112	Coronary artery disease	3.000000e-10
GCST005194_113	Coronary artery disease	4.000000e-08
GCST005195_121	Coronary artery disease	3.000000e-11
GCST005196_102	Coronary artery disease	2.000000e-10
GCST005978_7	Diastolic blood pressure	6.000000e-10
GCST005979_9	Systolic blood pressure	1.000000e-10
GCST006010_6	Mean arterial pressure	6.000000e-12
GCST006258_27	Diastolic blood pressure	4.000000e-11
GCST006259_35	Systolic blood pressure	4.000000e-11
GCST007094_161	Diastolic blood pressure	5.000000e-10
GCST007095_61	Systolic blood pressure	1.000000e-06
GCST007099_43	Systolic blood pressure	6.000000e-12
GCST007267_299	Systolic blood pressure	4.000000e-13
GCST007269_83	Pulse pressure	2.000000e-08
GCST007703_103	Systolic blood pressure	3.000000e-06
GCST007703_104	Systolic blood pressure	3.000000e-11
GCST007704_121	Diastolic blood pressure	9.000000e-06
GCST007704_5	Diastolic blood pressure	8.000000e-11
GCST007706_106	Mean arterial pressure	1.000000e-06
GCST007706_46	Mean arterial pressure	2.000000e-12
GCST007707_32	Hypertension	2.000000e-07
GCST007707_91	Hypertension	2.000000e-11
GCST007990_7	Coronary artery disease	3.000000e-08
GCST008036_2	Hypertension	2.000000e-08
GCST008363_104	Offspring birth weight	1.000000e-08
GCST010479_64	Coronary artery disease	4.000000e-08
GCST010866_6	Coronary artery disease	3.000000e-17
GCST010867_29	Coronary artery disease	6.000000e-06

EFO canonical traits (10, from GWAS)

EFO ID	Trait name
EFO:0006336	diastolic blood pressure
EFO:0007835	alcohol dependence measurement
EFO:0006335	systolic blood pressure
EFO:0006340	mean arterial pressure
EFO:0005763	pulse pressure measurement
EFO:0004344	birth weight
EFO:0005939	parental genotype effect measurement
EFO:0004348	hematocrit
EFO:0004509	hemoglobin measurement
EFO:0004305	erythrocyte count

MeSH disease descriptors (1)

Descriptor	Name	Tree numbers
C536804	Chromosome 3, monosomy 3p (supp.)

Drugs & pharmacology

Drug and pharmacology data

Is drug target: no

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

CTD chemical–gene interactions

29 total (human), top 29 by PubMed support.

Chemical	Actions (top 5)	PubMed papers
Valproic Acid	affects expression, increases methylation, affects cotreatment, increases expression	8
Benzo(a)pyrene	affects methylation, decreases expression, increases mutagenesis	4
trichostatin A	affects cotreatment, increases expression	3
entinostat	increases expression, affects cotreatment	2
Panobinostat	affects cotreatment, increases expression	2
Aflatoxin B1	decreases expression, decreases methylation	2
methyleugenol	decreases expression	1
ethyl-p-hydroxybenzoate	increases expression	1
cobaltous chloride	decreases expression	1
benzo(e)pyrene	increases methylation	1
aflatoxin B2	increases methylation	1
S-(1,2-dichlorovinyl)cysteine	affects cotreatment, decreases expression, affects response to substance, increases expression	1
CGP 52608	affects binding, increases reaction	1
4-(5-benzo(1,3)dioxol-5-yl-4-pyridin-2-yl-1H-imidazol-2-yl)benzamide	affects cotreatment, increases expression	1
dorsomorphin	affects cotreatment, increases expression	1
bisphenol S	decreases methylation	1
Resveratrol	affects cotreatment, decreases expression	1
Decitabine	affects expression	1
Amiodarone	increases expression	1
Cisplatin	affects expression	1
Estradiol	affects binding, increases expression	1
Lipopolysaccharides	increases expression, affects cotreatment, decreases expression, affects response to substance	1
Methapyrilene	increases methylation	1
N-Nitrosopyrrolidine	decreases expression	1
Nickel	decreases expression	1
Phenylmercuric Acetate	affects cotreatment, increases expression	1
Plant Extracts	affects cotreatment, decreases expression	1
Cyclosporine	decreases expression	1
Okadaic Acid	decreases expression	1

Cellosaurus cell lines

1 cell lines: 1 hybrid cell line

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

Cellosaurus	Name	Category	Sex
CVCL_F1ML	HyCyte AC16 KO-hFGD5-AS1	Hybrid cell line

Clinical trials (associated diseases)

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