RAB3D

Summary

RAB3D (RAB3D, member RAS oncogene family, HGNC:9779) is a protein-coding gene on chromosome 19p13.2, encoding Ras-related protein Rab-3D (O95716). The small GTPases Rab are key regulators of intracellular membrane trafficking, from the formation of transport vesicles to their fusion with membranes.

Enables myosin V binding activity. Involved in bone resorption and positive regulation of regulated secretory pathway. Located in cytoplasmic microtubule and secretory vesicle.

Source: NCBI Gene 9545 — RefSeq curated summary.

At a glance

• GWAS associations: 2
• Clinical variants (ClinVar): 48 total
• MANE Select transcript: NM_004283

Identifiers

Gene identifiers

Field	Value
HGNC ID	HGNC:9779
Approved symbol	RAB3D
Name	RAB3D, member RAS oncogene family
Location	19p13.2
Locus type	gene with protein product
Status	Approved
Aliases	RAB16, D2-2, RAD3D
Ensembl gene	ENSG00000105514
Ensembl biotype	protein_coding
OMIM	604350
Entrez	9545

Gene structure

Transcript identifiers

Ensembl transcripts: 3 — 3 protein_coding

ENST00000222120, ENST00000589655, ENST00000903414

RefSeq mRNA: 1 — MANE Select: NM_004283 NM_004283

CCDS: CCDS12257

Canonical transcript exons

ENST00000222120 — 5 exons

Exon	Start	End
ENSE00000680487	11335447	11335571
ENSE00000680489	11335665	11335783
ENSE00001061192	11337172	11337460
ENSE00001061194	11339469	11339657
ENSE00001255557	11322068	11325585

Expression profiles

Bgee: expression breadth ubiquitous, 239 present calls, max score 96.78.

FANTOM5 (CAGE): breadth ubiquitous, TPM avg 17.6014 / max 294.4261, expressed in 1598 samples.

FANTOM5 promoters (3 alternative TSS)

Promoter ID	TPM avg	Samples expressed
179217	17.2676	1794
179210	16.6266	1584
179208	0.9748	498

Top tissues by expression

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

Tissue	Anatomy ID	Expression score	Quality
parotid gland	UBERON:0001831	96.78	gold quality
dorsal root ganglion	UBERON:0000044	96.19	gold quality
esophagus squamous epithelium	UBERON:0006920	95.84	gold quality
penis	UBERON:0000989	95.68	gold quality
nipple	UBERON:0002030	94.93	gold quality
upper leg skin	UBERON:0004262	94.50	gold quality
pharyngeal mucosa	UBERON:0000355	93.65	gold quality
mammalian vulva	UBERON:0000997	93.39	gold quality
blood	UBERON:0000178	92.94	gold quality
cardia of stomach	UBERON:0001162	92.88	gold quality
trigeminal ganglion	UBERON:0001675	92.84	gold quality
body of pancreas	UBERON:0001150	92.54	gold quality
monocyte	CL:0000576	92.43	gold quality
leukocyte	CL:0000738	92.27	gold quality
mononuclear cell	CL:0000842	92.26	gold quality
cerebellar vermis	UBERON:0004720	91.60	gold quality
epithelium of esophagus	UBERON:0001976	91.23	gold quality
lower esophagus mucosa	UBERON:0035834	91.22	gold quality
pylorus	UBERON:0001166	91.11	gold quality
skin of hip	UBERON:0001554	91.09	gold quality
gingiva	UBERON:0001828	90.33	gold quality
body of tongue	UBERON:0011876	89.88	silver quality
superior surface of tongue	UBERON:0007371	89.78	silver quality
esophagus mucosa	UBERON:0002469	89.76	gold quality
gingival epithelium	UBERON:0001949	89.15	gold quality
tongue	UBERON:0001723	88.88	silver quality
vena cava	UBERON:0004087	88.69	gold quality
pancreas	UBERON:0001264	88.52	gold quality
skin of leg	UBERON:0001511	87.76	gold quality
trachea	UBERON:0003126	87.47	gold quality

Single-cell (SCXA)

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

Experiment	Marker?	Max mean expression
E-MTAB-6678	yes	23.77
E-ANND-3	yes	14.62

Regulation

Is transcription factor: no

Upstream regulators (CollecTRI, top): BHLHA15

miRNA regulators (miRDB)

119 targeting RAB3D, 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-6748-5P	100.00	65.81	1057
HSA-MIR-3613-3P	100.00	76.36	7965
HSA-MIR-6851-5P	100.00	65.63	1294
HSA-MIR-3689D	100.00	66.14	1181
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-3185	99.99	68.12	1959
HSA-MIR-371B-5P	99.99	75.34	4759
HSA-MIR-548C-3P	99.99	74.01	7587
HSA-MIR-373-5P	99.98	75.36	4753
HSA-MIR-616-5P	99.98	75.58	4775
HSA-MIR-548P	99.98	72.25	3784
HSA-MIR-545-3P	99.95	70.74	2783
HSA-MIR-6835-3P	99.93	70.49	2904
HSA-MIR-6721-5P	99.93	68.92	2981
HSA-MIR-205-3P	99.92	69.92	3165
HSA-MIR-15B-5P	99.90	72.78	2798
HSA-MIR-124-3P	99.89	73.74	3043
HSA-MIR-506-3P	99.89	73.55	3057
HSA-MIR-7162-3P	99.89	68.16	1682
HSA-MIR-548E-5P	99.89	72.73	4486
HSA-MIR-424-5P	99.89	71.90	2641
HSA-MIR-345-3P	99.89	70.23	1421
HSA-MIR-9902	99.89	69.15	2250
HSA-MIR-605-3P	99.88	69.22	1833
HSA-MIR-6780A-5P	99.88	66.69	2776
HSA-MIR-4447	99.85	67.81	2900

Literature-anchored findings (GeneRIF, showing 14)

• mutant Rab3D proteins interfere with the formation of bona fide Weibel-Palade bodies and consequently the acute, histamine-induced release of von-Willebrand factor (PMID:15257287)
• MIST1 binds to highly conserved CATATG E-boxes to directly activate transcription of 6 genes, including those encoding the small GTPases RAB26 and RAB3D. (PMID:20038531)
• Our findings indicate that Rab3D regulates the exocytosis of many components critical for the maintenance of oral physiology. (PMID:21702009)
• The presence of Rab3D(N135I) decreases the restriction of maturing secretory granules (SGs) to the F-actin-rich cell cortex, blocks the removal of the endoprotease furin from SGs and impedes the processing of the luminal SG protein secretogranin II. (PMID:23526941)
• High expression of small GTPase Rab3D promotes cancer progression and metastasis. (PMID:25823663)
• increased Rab3D expression is associated with invasiveness of CRC cells (PMID:27046094)
• targeting the Rab3D may be a potential therapeutic target for treatment of esophageal squamous cell carcinoma. (PMID:28472755)
• Long non-coding RNA FGD5-AS1 enhances osteosarcoma cell proliferation and migration by targeting miR-506-3p/RAB3D axis. (PMID:33891267)
• Rab3 proteins and cancer: Exit strategies. (PMID:33982832)
• GDP/GTP exchange factor MADD drives activation and recruitment of secretory Rab GTPases to Weibel-Palade bodies. (PMID:34551092)
• Hsa_circ_0103232 promotes melanoma cells proliferation and invasion via targeting miR-661/RAB3D. (PMID:35549813)
• Hsa_circ_0006732 regulates colorectal cancer cell proliferation, invasion and EMT by miR-127-5p/RAB3D axis. (PMID:35616807)
• [miR-125b-5p inhibits proliferation and migration of osteosarcoma cells by negatively regulating RAB3D expression]. (PMID:36856212)
• CircECE1 promotes osteosarcoma progression through regulating RAB3D by sponging miR-588. (PMID:37559140)

Cross-species orthologs

4 orthologs

Organism	Symbol	Gene ID
danio_rerio	rab3da	ENSDARG00000018107
danio_rerio	rab3db	ENSDARG00000101534
mus_musculus	Rab3d	ENSMUSG00000019066
rattus_norvegicus	Rab3d	ENSRNOG00000011582

Paralogs (68): RAB27B (ENSG00000041353), RAB27A (ENSG00000069974), RAB7A (ENSG00000075785), RABL2B (ENSG00000079974), RAB21 (ENSG00000080371), RAB10 (ENSG00000084733), RAB18 (ENSG00000099246), RAB36 (ENSG00000100228), IFT27 (ENSG00000100360), RAB40AL (ENSG00000102128), RAB11A (ENSG00000103769), RAB2A (ENSG00000104388), RAB3A (ENSG00000105649), RAB5C (ENSG00000108774), RAB34 (ENSG00000109113), RAB5B (ENSG00000111540), RAB35 (ENSG00000111737), RAB23 (ENSG00000112210), DNAJC27 (ENSG00000115137), RAB29 (ENSG00000117280), RAB32 (ENSG00000118508), RAB14 (ENSG00000119396), RAB9B (ENSG00000123570), RAB9A (ENSG00000123595), RAB38 (ENSG00000123892), RAB22A (ENSG00000124209), RAB17 (ENSG00000124839), RAB2B (ENSG00000129472), RAB25 (ENSG00000132698), RAB33A (ENSG00000134594), RAB30 (ENSG00000137502), RAB1A (ENSG00000138069), RAB20 (ENSG00000139832), RAB15 (ENSG00000139998), RAB40B (ENSG00000141542), RAB13 (ENSG00000143545), RABL2A (ENSG00000144134), RAB5A (ENSG00000144566), RAB19 (ENSG00000146955), RAB41 (ENSG00000147127)

Protein

Protein identifiers

Ras-related protein Rab-3D — O95716 (reviewed: O95716)

All UniProt accessions (2): O95716, A0A024R7G2

UniProt curated annotations — full annotation on UniProt →

Function. The small GTPases Rab are key regulators of intracellular membrane trafficking, from the formation of transport vesicles to their fusion with membranes. Rabs cycle between an inactive GDP-bound form and an active GTP-bound form that is able to recruit to membranes different sets of downstream effectors directly responsible for vesicle formation, movement, tethering and fusion. RAB3D may be involved in the insulin-induced exocytosis of GLUT4-containing vesicles in adipocytes.

Subunit / interactions. Interacts with RIMS1, RIMS2, RPH3A, RPH3AL and RAB3IP. The GTP-bound form interacts with REP15. Interacts with CHM and CHML; phosphorylation at Thr-86 disrupts these interactions. Interacts with MADD (via uDENN domain); the GTP-bound form is preferred for interaction.

Subcellular location. Cell membrane.

Tissue specificity. Highly expressed in granulocytes of peripheral blood. Constitutively expressed at low levels in all hematopoietic cell lines investigated.

Post-translational modifications. Phosphorylation of Thr-86 in the switch II region by LRRK2 prevents the association of RAB regulatory proteins, including CHM and CHML.

Activity regulation. Regulated by guanine nucleotide exchange factors (GEFs) which promote the exchange of bound GDP for free GTP. Regulated by GTPase activating proteins (GAPs) which increase the GTP hydrolysis activity. Inhibited by GDP dissociation inhibitors (GDIs) which prevent Rab-GDP dissociation.

Domain organisation. Switch 1, switch 2 and the interswitch regions are characteristic of Rab GTPases and mediate the interactions with Rab downstream effectors. The switch regions undergo conformational changes upon nucleotide binding which drives interaction with specific sets of effector proteins, with most effectors only binding to GTP-bound Rab.

Induction. Activated in myeloid differentiation.

Similarity. Belongs to the small GTPase superfamily. Rab family.

RefSeq proteins (1): NP_004274* (*=MANE)

Domains & families (InterPro)

ID	Name	Type
IPR001806	Small_GTPase	Family
IPR005225	Small_GTP-bd	Domain
IPR027417	P-loop_NTPase	Homologous_superfamily
IPR037872	Rab3	Family
IPR050305	Small_GTPase_Rab	Family

Pfam: PF00071

Catalyzed reactions (Rhea), 1 shown:

• GTP + H2O = GDP + phosphate + H(+) (RHEA:19669)

UniProt features (50 total): binding site 21, helix 7, strand 6, modified residue 4, short sequence motif 2, lipid moiety-binding region 2, mutagenesis site 2, initiator methionine 1, chain 1, region of interest 1, sequence variant 1, turn 1, compositionally biased region 1

Structure

Experimental structures (PDB)

1 structures.

PDB	Method	Resolution (Å)
2GF9	X-RAY DIFFRACTION	1.53

Predicted structure (AlphaFold)

Model	pLDDT	Fraction very-high
AF-O95716-F1	85.03	0.62

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 (21): 34; 35; 36; 36; 37; 49; 53; 54; 77; 80; 135–138; 135 …

Post-translational modifications (6): 2, 86, 190, 219, 217, 219

Mutagenesis-validated functional residues (2):

Position	Phenotype
86	loss of phosphorylation. reduced binding of chm and chml binding.
86	phosphomimetic mutant. loss of chm and chml binding.

Function

Pathways and Gene Ontology

Reactome pathways

2 pathways

ID	Pathway
R-HSA-6798695	Neutrophil degranulation
R-HSA-8873719	RAB geranylgeranylation

MSigDB gene sets: 218 (showing top): AP1_01, REACTOME_INNATE_IMMUNE_SYSTEM, GOCC_VACUOLAR_MEMBRANE, GOCC_SECRETORY_GRANULE, GRAESSMANN_APOPTOSIS_BY_SERUM_DEPRIVATION_DN, GRAESSMANN_APOPTOSIS_BY_DOXORUBICIN_DN, GRAESSMANN_RESPONSE_TO_MC_AND_DOXORUBICIN_DN, GOBP_REGULATION_OF_EXOCYTOSIS, GOBP_VESICLE_MEDIATED_TRANSPORT, GGGTGGRR_PAX4_03, GOBP_REGULATION_OF_VESICLE_MEDIATED_TRANSPORT, GTGCCTT_MIR506, BORLAK_LIVER_CANCER_EGF_UP, GOBP_EXOCYTOSIS, AP1_Q4_01

GO Biological Process (6): exocytosis (GO:0006887), protein transport (GO:0015031), bone resorption (GO:0045453), positive regulation of regulated secretory pathway (GO:1903307), intracellular protein transport (GO:0006886), regulation of exocytosis (GO:0017157)

GO Molecular Function (9): GTPase activity (GO:0003924), G protein activity (GO:0003925), GTP binding (GO:0005525), GTP-dependent protein binding (GO:0030742), myosin V binding (GO:0031489), metal ion binding (GO:0046872), nucleotide binding (GO:0000166), protein binding (GO:0005515), hydrolase activity (GO:0016787)

GO Cellular Component (10): endosome (GO:0005768), cytoplasmic microtubule (GO:0005881), plasma membrane (GO:0005886), synaptic vesicle (GO:0008021), azurophil granule membrane (GO:0035577), zymogen granule (GO:0042588), extracellular exosome (GO:0070062), secretory vesicle (GO:0099503), membrane (GO:0016020), secretory granule (GO:0030141)

Reactome top-level categories

Rollup of top-2 pathways:

Category	Pathways
Innate Immune System	1
Post-translational protein modification	1

GO top-level categories

Rollup of top GO terms by namespace:

Category	Terms
intracellular protein localization	2
endomembrane system	2
cytoplasmic vesicle	2
vesicle-mediated transport	1
secretion by cell	1
vesicle fusion to plasma membrane	1
transport	1
establishment of protein localization	1
tissue homeostasis	1
bone remodeling	1
regulated exocytosis	1
positive regulation of exocytosis	1
regulation of regulated secretory pathway	1
protein transport	1
intracellular transport	1
exocytosis	1
regulation of vesicle-mediated transport	1
regulation of secretion by cell	1
ribonucleoside triphosphate phosphatase activity	1
GTPase activity	1
molecular function regulator activity	1
guanyl ribonucleotide binding	1
purine ribonucleoside triphosphate binding	1
protein binding	1
myosin binding	1
cation binding	1
nucleoside phosphate binding	1
heterocyclic compound binding	1
binding	1
catalytic activity	1
cytoplasm	1
microtubule	1
membrane	1
cell periphery	1
exocytic vesicle	1
presynapse	1
lysosomal membrane	1
secretory granule membrane	1
azurophil granule	1
secretory granule	1

Protein interactions and networks

STRING

800 interactions, top by confidence (×1000):

Protein A	Protein B	Partner UniProt	Score
RAB3D	LRPAP1	P30533	709
RAB3D	RPH3A	Q9Y2J0	546
RAB3D	DYNLT1	P63172	544
RAB3D	RAB3IP	Q96QF0	542
RAB3D	STX4	Q12846	520
RAB3D	VAMP3	Q15836	513
RAB3D	VAMP8	Q9BV40	493
RAB3D	SNAP23	O00161	488
RAB3D	RPH3AL	Q9UNE2	477
RAB3D	RIMS2	Q9UQ26	451
RAB3D	MADD	Q8WXG6	443
RAB3D	UNC13D	Q70J99	435
RAB3D	STX11	O75558	432
RAB3D	VAMP4	O75379	430
RAB3D	STX2	P32856	428

IntAct

40 interactions, top by confidence:

A	B	Type	Score
RAB3D	SYTL4	psi-mi:“MI:0915”(physical association)	0.560
RAB3D	VRTN	psi-mi:“MI:0915”(physical association)	0.560
RAB3D	RAB3IP	psi-mi:“MI:0915”(physical association)	0.560
RAB3D	RABIF	psi-mi:“MI:0915”(physical association)	0.560
RAB3D	MAST1	psi-mi:“MI:0915”(physical association)	0.370
CYP2C9	RAB3D	psi-mi:“MI:0915”(physical association)	0.370
RAB3D	CEP55	psi-mi:“MI:0915”(physical association)	0.370
GOLM1	RAB19	psi-mi:“MI:0914”(association)	0.350
CD177	MYO1G	psi-mi:“MI:0914”(association)	0.350
M		psi-mi:“MI:0914”(association)	0.350
	SHTN1	psi-mi:“MI:0914”(association)	0.350
NCAPD3	NDUFS8	psi-mi:“MI:0914”(association)	0.350
MAPT	SHTN1	psi-mi:“MI:0914”(association)	0.350
RAB3D	ATXN7	psi-mi:“MI:0914”(association)	0.350
NCLN	PGRMC1	psi-mi:“MI:0914”(association)	0.350
PPP2R2B	A2ML1	psi-mi:“MI:0914”(association)	0.350
CCR1	UBA6	psi-mi:“MI:0914”(association)	0.350
PINK1	A2ML1	psi-mi:“MI:0914”(association)	0.350
MBNL1	A2ML1	psi-mi:“MI:0914”(association)	0.350
SLC13A5	POLR3A	psi-mi:“MI:0914”(association)	0.350
SLC22A2	RAB27B	psi-mi:“MI:0914”(association)	0.350
SLC51B	CTNND1	psi-mi:“MI:0914”(association)	0.350
ATF3	TMEM223	psi-mi:“MI:0914”(association)	0.350
FOS	TMEM223	psi-mi:“MI:0914”(association)	0.350

BioGRID (51): RAB3D (Affinity Capture-MS), RAB3D (Affinity Capture-MS), RAB3D (Affinity Capture-MS), RAB3D (Two-hybrid), RAB3IP (Two-hybrid), VRTN (Two-hybrid), RABIF (Two-hybrid), RAB3D (Affinity Capture-MS), RAB3D (Proximity Label-MS), RAB3D (Proximity Label-MS), RAB3D (Proximity Label-MS), RAB3D (Proximity Label-MS), RAB3D (Proximity Label-MS), RAB3D (Proximity Label-MS), RAB3D (Proximity Label-MS)

ESM2 similar proteins: A8NU18, D3Z8L7, G4N1S3, O08989, O14807, O42785, O93856, O95716, P01114, P08647, P0CQ42, P0CQ43, P10301, P10833, P22126, P28775, P35276, P46629, P51146, P51156, P56371, P59190, P61017, P61018, P62070, P62071, P70425, P70426, P97538, Q01387, Q05058, Q12526, Q1RMR4, Q29RR0, Q3SZA1, Q4X241, Q53B90, Q5BJQ5, Q63942, Q86YS6

Diamond homologs: A4FV54, C4YL11, F1PTE3, O24466, O42819, O76173, O95716, P01123, P07560, P0CY30, P0CY31, P10536, P10949, P11023, P11620, P16976, P17609, P20336, P20790, P20791, P22125, P22127, P22128, P24409, P25228, P28186, P28188, P31584, P33723, P34139, P34140, P35276, P35280, P35281, P35286, P35289, P36861, P40392, P41924, P51153

SIGNOR signaling

0 interactions.

Disease & clinical

Clinical variants and AI predictions

ClinVar

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

Classification	Count (floor)
Pathogenic	0
Likely pathogenic	0
Uncertain significance	42
Likely benign	2
Benign	1

Top pathogenic / likely-pathogenic (0)

SpliceAI

1431 predictions. Top by Δscore:

Variant	Effect	Δscore
19:11335443:TAACC:T	donor_loss	1.0000
19:11335444:AACCA:A	donor_loss	1.0000
19:11335445:A:AC	donor_gain	1.0000
19:11335445:ACCA:A	donor_loss	1.0000
19:11335446:C:CC	donor_gain	1.0000
19:11335570:CC:C	acceptor_gain	1.0000
19:11335571:CC:C	acceptor_gain	1.0000
19:11335572:C:CC	acceptor_gain	1.0000
19:11335662:CA:C	donor_loss	1.0000
19:11335663:A:AC	donor_gain	1.0000
19:11335663:A:T	donor_loss	1.0000
19:11335664:C:CA	donor_gain	1.0000
19:11335664:CCA:C	donor_gain	1.0000
19:11335664:CCAGT:C	donor_gain	1.0000
19:11335784:C:CC	acceptor_gain	1.0000
19:11335784:CT:C	acceptor_loss	1.0000
19:11335785:T:A	acceptor_loss	1.0000
19:11337166:GCCTA:G	donor_loss	1.0000
19:11337167:CCTA:C	donor_loss	1.0000
19:11337168:CTAC:C	donor_loss	1.0000
19:11337169:TACCC:T	donor_loss	1.0000
19:11337170:A:AC	donor_gain	1.0000
19:11337170:AC:A	donor_gain	1.0000
19:11337171:C:CA	donor_loss	1.0000
19:11337171:C:CC	donor_gain	1.0000
19:11337171:CC:C	donor_gain	1.0000
19:11337171:CCCAG:C	donor_gain	1.0000
19:11337189:T:TA	donor_gain	1.0000
19:11343120:GCT:G	acceptor_loss	1.0000
19:11343121:C:CC	acceptor_gain	1.0000

AlphaMissense

1456 scored. Top likely-pathogenic:

Variant	Protein change	am_pathogenicity
19:11335773:C:T	G80D	1.000
19:11335782:T:A	D77V	1.000
19:11335782:T:G	D77A	1.000
19:11335783:C:G	D77H	1.000
19:11337174:A:G	W76R	1.000
19:11337174:A:T	W76R	1.000
19:11337223:G:C	F59L	1.000
19:11337223:G:T	F59L	1.000
19:11337225:A:G	F59L	1.000
19:11337233:C:T	G56D	1.000
19:11337234:C:G	G56R	1.000
19:11337239:G:A	T54I	1.000
19:11337259:G:C	F47L	1.000
19:11337259:G:T	F47L	1.000
19:11337261:A:G	F47L	1.000
19:11337293:G:A	T36I	1.000
19:11337299:C:T	G34D	1.000
19:11337314:C:A	G29V	1.000
19:11325561:G:T	A166D	0.999
19:11325563:A:C	S165R	0.999
19:11325563:A:T	S165R	0.999
19:11325565:T:G	S165R	0.999
19:11335511:C:A	K136N	0.999
19:11335511:C:G	K136N	0.999
19:11335513:T:C	K136E	0.999
19:11335519:C:A	G134W	0.999
19:11335666:A:G	W116R	0.999
19:11335666:A:T	W116R	0.999
19:11335722:C:T	G97D	0.999
19:11335723:C:G	G97R	0.999

dbSNP variants (sampled 300 via entrez): RS1000143239 (19:11338023 C>T), RS1000192517 (19:11324606 C>T), RS1000492575 (19:11337739 T>C), RS1000655333 (19:11328552 CAGA>C), RS1000878478 (19:11324403 C>T), RS1000886506 (19:11334515 G>T), RS1000929389 (19:11339380 G>A), RS1000930258 (19:11323385 G>A), RS1000937805 (19:11328423 G>A), RS1001079041 (19:11326711 C>A), RS1001598219 (19:11323761 C>T), RS1001670154 (19:11334920 C>G), RS1001742155 (19:11329383 G>A,C), RS1001801559 (19:11322299 A>T), RS1001820152 (19:11329276 T>C)

Disease associations

OMIM: gene MIM:604350 | disease phenotypes:

GenCC curated gene-disease

Mondo (0):

Orphanet (0):

HPO phenotypes

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

GWAS associations

2 associations (top):

Study	Trait	p-value
GCST001904_5	HDL cholesterol	3.000000e-09
GCST008991_5	Early cardiac repolarization	3.000000e-06

EFO canonical traits (2, from GWAS)

EFO ID	Trait name
EFO:0004612	high density lipoprotein cholesterol measurement
EFO:0004885	early cardiac repolarization measurement

Drugs & pharmacology

Drug and pharmacology data

Is drug target: no

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

PharmGKB variants

2 variants.

Variant	Genes	Level	Score	#Clin annots	Drugs
rs172731	RAB3D, TMEM205		0.00	0
rs896412	RAB3D, TMEM205		0.00	0

CTD chemical–gene interactions

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

Chemical	Actions (top 5)	PubMed papers
Tobacco Smoke Pollution	affects expression, decreases expression	3
Valproic Acid	affects cotreatment, increases expression	3
sodium arsenite	decreases expression, increases expression	2
Benzo(a)pyrene	increases methylation, affects methylation	2
Cisplatin	affects cotreatment, increases expression	2
Estradiol	affects cotreatment, decreases expression	2
Tretinoin	increases expression	2
FR900359	increases phosphorylation	1
triphenyl phosphate	affects expression	1
trichostatin A	increases expression	1
arsenite	affects binding, increases reaction	1
tris(1,3-dichloro-2-propyl)phosphate	decreases expression	1
perfluorooctanoic acid	increases expression	1
benzo(e)pyrene	increases methylation	1
nickel sulfate	increases expression	1
S-(1,2-dichlorovinyl)cysteine	decreases expression, affects response to substance, increases expression, affects cotreatment	1
epigallocatechin gallate	increases expression	1
abrine	decreases expression	1
jinfukang	affects cotreatment, increases expression	1
Sunitinib	decreases expression	1
Air Pollutants	decreases expression, increases abundance	1
Ethanol	increases expression	1
Doxorubicin	decreases expression	1
Ethyl Methanesulfonate	decreases expression	1
Hydralazine	affects cotreatment, increases expression	1
Ivermectin	decreases expression	1
Lipopolysaccharides	affects cotreatment, decreases expression, affects response to substance, increases expression	1
Methapyrilene	increases methylation	1
Methyl Methanesulfonate	decreases expression	1
Ribonucleotides	affects binding	1

Clinical trials (associated diseases)

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