RAB29

Summary

RAB29 (RAB29, member RAS oncogene family, HGNC:9789) is a protein-coding gene on chromosome 1q32.1, encoding Ras-related protein Rab-29 (O14966). The small GTPases Rab are key regulators of intracellular membrane trafficking, from the formation of transport vesicles to their fusion with membranes.

Enables several functions, including dynein complex binding activity; guanyl ribonucleotide binding activity; and kinesin binding activity. Involved in several processes, including positive regulation of T cell receptor signaling pathway; positive regulation of receptor recycling; and retrograde transport, endosome to Golgi. Located in several cellular components, including Golgi apparatus; endosome; and nucleus.

Source: NCBI Gene 8934 — RefSeq curated summary.

At a glance

• GWAS associations: 18
• Clinical variants (ClinVar): 35 total
• Druggable target: yes
• MANE Select transcript: NM_003929

Identifiers

Gene identifiers

Field	Value
HGNC ID	HGNC:9789
Approved symbol	RAB29
Name	RAB29, member RAS oncogene family
Location	1q32.1
Locus type	gene with protein product
Status	Approved
Ensembl gene	ENSG00000117280
Ensembl biotype	protein_coding
OMIM	603949
Entrez	8934

Gene structure

Transcript identifiers

Ensembl transcripts: 21 — 17 protein_coding, 2 protein_coding_CDS_not_defined, 1 retained_intron, 1 nonsense_mediated_decay

ENST00000235932, ENST00000367139, ENST00000414729, ENST00000437324, ENST00000446390, ENST00000468887, ENST00000492534, ENST00000528078, ENST00000533111, ENST00000895155, ENST00000895156, ENST00000895157, ENST00000895158, ENST00000895159, ENST00000895160, ENST00000895161, ENST00000895162, ENST00000895163, ENST00000895164, ENST00000933467, ENST00000971292

RefSeq mRNA: 4 — MANE Select: NM_003929 NM_001135662, NM_001135663, NM_001135664, NM_003929

CCDS: CCDS1459, CCDS44301, CCDS44302

Canonical transcript exons

ENST00000367139 — 6 exons

Exon	Start	End
ENSE00001443619	205774833	205775086
ENSE00001443620	205775273	205775482
ENSE00001833646	205767986	205770453
ENSE00003529892	205772496	205772567
ENSE00003577456	205770733	205770854
ENSE00003603114	205771472	205771653

Expression profiles

Bgee: expression breadth ubiquitous, 283 present calls, max score 97.07.

FANTOM5 (CAGE): breadth ubiquitous, TPM avg 9.9518 / max 138.0500, expressed in 1700 samples.

FANTOM5 promoters (6 alternative TSS)

Promoter ID	TPM avg	Samples expressed
17035	5.6007	1661
17033	3.9961	452
17034	0.1482	65
17032	0.0991	41
17031	0.0575	32
201901	0.0502	26

Top tissues by expression

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

Tissue	Anatomy ID	Expression score	Quality
nephron tubule	UBERON:0001231	97.07	gold quality
kidney epithelium	UBERON:0004819	93.94	gold quality
granulocyte	CL:0000094	93.80	gold quality
secondary oocyte	CL:0000655	93.17	gold quality
renal glomerulus	UBERON:0000074	92.04	gold quality
renal medulla	UBERON:0000362	91.89	gold quality
adult mammalian kidney	UBERON:0000082	91.52	gold quality
parotid gland	UBERON:0001831	91.37	gold quality
metanephric glomerulus	UBERON:0004736	91.32	gold quality
lymph node	UBERON:0000029	90.89	gold quality
germinal epithelium of ovary	UBERON:0001304	90.73	gold quality
islet of Langerhans	UBERON:0000006	90.59	gold quality
oocyte	CL:0000023	90.43	gold quality
kidney	UBERON:0002113	90.31	gold quality
corpus epididymis	UBERON:0004359	90.18	gold quality
CA1 field of hippocampus	UBERON:0003881	90.01	gold quality
blood	UBERON:0000178	89.86	gold quality
leukocyte	CL:0000738	89.64	gold quality
mononuclear cell	CL:0000842	89.25	gold quality
monocyte	CL:0000576	89.12	gold quality
primordial germ cell in gonad	CL:0000670 ∩ UBERON:0000991	88.62	gold quality
cortex of kidney	UBERON:0001225	88.38	gold quality
blood vessel layer	UBERON:0004797	88.36	gold quality
adult organism	UBERON:0007023	88.04	gold quality
epithelium of nasopharynx	UBERON:0001951	87.68	gold quality
vermiform appendix	UBERON:0001154	87.67	gold quality
nasopharynx	UBERON:0001728	87.67	gold quality
palpebral conjunctiva	UBERON:0001812	87.53	gold quality
superficial temporal artery	UBERON:0001614	87.49	gold quality
gall bladder	UBERON:0002110	87.44	gold quality

Single-cell (SCXA)

Detected in 8 experiment(s), a significant marker in 3.

Experiment	Marker?	Max mean expression
E-HCAD-13	yes	191.09
E-ANND-3	yes	9.55
E-MTAB-6678	yes	7.13
E-MTAB-7606	no	1733.25
E-MTAB-6379	no	1012.87
E-MTAB-10137	no	302.07
E-GEOD-99795	no	83.11
E-HCAD-31	no	1.99

Regulation

Is transcription factor: no

miRNA regulators (miRDB)

86 targeting RAB29, 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-196A-5P	100.00	68.16	684
HSA-MIR-196B-5P	100.00	68.16	681
HSA-MIR-450A-1-3P	100.00	69.33	1837
HSA-MIR-6873-3P	100.00	71.42	2626
HSA-MIR-6833-3P	100.00	70.63	3197
HSA-MIR-7110-3P	100.00	73.18	2486
HSA-MIR-4768-5P	100.00	69.49	2861
HSA-MIR-150-5P	99.99	66.69	1976
HSA-MIR-4282	99.99	75.36	6408
HSA-MIR-23B-5P	99.98	66.07	587
HSA-MIR-3688-3P	99.97	72.02	2834
HSA-MIR-3148	99.97	75.06	6478
HSA-MIR-6778-3P	99.96	67.29	2693
HSA-MIR-302E	99.96	70.74	2669
HSA-MIR-146A-5P	99.96	68.93	988
HSA-MIR-146B-5P	99.96	69.13	977
HSA-MIR-5688	99.96	73.23	4504
HSA-MIR-495-3P	99.96	72.81	4197
HSA-MIR-7153-5P	99.94	68.89	1006
HSA-MIR-23A-5P	99.94	65.39	468
HSA-MIR-9983-3P	99.94	71.48	3631
HSA-MIR-7-1-3P	99.91	71.53	4384
HSA-MIR-7-2-3P	99.91	71.40	4394
HSA-MIR-627-3P	99.90	71.42	3316
HSA-MIR-153-5P	99.89	73.86	6317
HSA-MIR-6715A-3P	99.83	68.05	1473
HSA-MIR-130B-5P	99.83	68.50	1888
HSA-MIR-6515-3P	99.82	68.19	1933
HSA-MIR-3180-5P	99.82	69.12	2422
HSA-MIR-374C-5P	99.80	72.06	2910

Literature-anchored findings (GeneRIF, showing 21)

• Direct DNA sequencing of the RAB7L1 and SLC41A1 genes within the PARK16 locus in 205 Chinese Parkinson’s disease patients shows no significant difference with controls. (PMID:21812739)
• This study demonstrated that specific SNP variations and haplotypes in the PARK16 locus are associated with reduced risk for parkinson disease in Ashkenazim. (PMID:22232350)
• This study demonistrated that RAB7L1 interacts with LRRK2 to modify intraneuronal protein sorting and Parkinson’s disease risk. (PMID:23395371)
• This study confirmed the associations of RAB7L1 with parkinson disease susceptibility and fail to show significant associations of alzheimer disease genome-wide association study (GWAS) top hits with PD susceptibility in a Korean population. (PMID:23820587)
• RAB7L1 is a binding partners of LRRK2, a candidate genes for risk for sporadic Parkinson disease, and part of a complex that promotes clearance of Golgi-derived vesicles through the autophagy-lysosome system. (PMID:24510904)
• Results suggest that Rab protein Rab29 is essential for the integrity of the trans-Golgi network (TGN) and participates in the retrograde trafficking of mannose-6-phosphate receptor (M6PR). (PMID:24788816)
• rs1572931 decreases the risk for Parkinson’s disease but not for amyotrophic lateral sclerosis (ALS) and multiple system atrophy(MSA) in the Chinese population. However, the polymorphism is unlikely to be a common cause of sporadic ALS and MSA in the Chinese population (PMID:25040112)
• Rab29 is a regulator of receptor recycling and this GTPase is a shared participant in immune synapse and primary cilium assembly. (PMID:26021297)
• Results confirmed the protective effect of the rs1572931 single nucleotide polymorphism on Parkinson’s disease and replicated the results of previous studies, in Iranian subjects. (PMID:26344175)
• Our study provides strong support for the susceptibility role of RAB7L1/NUCKS1 rs823118 and MCCC1 rs12637471 in sporadic Parkinson’s disease in a Han Chinese population (PMID:26914237)
• This study showed that the significant differences in genotypic and allelic frequencies of RAB7L1 promoter polymorphism between patients and controls. (PMID:28245721)
• Genetic ablation of RAB7L1 in SH-SY5Y cells recapitulated the findings in amyotrophic lateral sclerosis and frontotemporal dementia fibroblasts and induced pluripotent stem cell neurons (PMID:28334866)
• RAB7L1gene rs1572913 polymorphism (T allele, TC and TT genotype) was associated with decreased risk of PD. (PMID:28807727)
• Results suggest reciprocal regulation between LRRK2 and Rab protein substrates, where Rab7L1-mediated upregulation of LRRK2 kinase activity results in the stabilization of membrane and GTP-bound Rab proteins that may be unable to interact with Rab effector proteins. (PMID:29177506)
• Mutations in leucine-rich repeat kinase 2 (LRRK2) are the major genetic cause of autosomal-dominantly inherited Parkinson’s disease. LRRK2 is implicated in the regulation of intracellular trafficking, neurite outgrowth and PD risk in connection with Rab7L1, a putative interactor of LRRK2. The modulation of Ser72 phosphorylation in Rab7L1 resulted in an alteration of the trans-Golgi network. (PMID:29223392)
• This study highlights a novel role of Rab7l1 in the phagosomal maturation process and hints at unique strategies of mycobacteria used to interfere with Rab7l1 function to favor its survival inside human macrophages. (PMID:30037848)
• LRRK2 associates with and dissociates from distinct membrane compartments to phosphorylate Rab substrates including Rab29 (PMID:31624137)
• Association of RIT2 and RAB7L1 with Parkinson’s disease: a case-control study in a Taiwanese cohort and a meta-analysis in Asian populations. (PMID:31818509)
• Distinct Roles for RAB10 and RAB29 in Pathogenic LRRK2-Mediated Endolysosomal Trafficking Alterations. (PMID:32709066)
• Expression of RAB7L1 in Patients with Pituitary Adenomas. (PMID:33941558)
• The atypical Rab GTPase associated with Parkinson’s disease, Rab29, is localized to membranes. (PMID:36116551)

Cross-species orthologs

2 orthologs

Organism	Symbol	Gene ID
mus_musculus	Rab29	ENSMUSG00000026433
rattus_norvegicus	Rab29	ENSRNOG00000049641

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), RAB3D (ENSG00000105514), RAB3A (ENSG00000105649), RAB5C (ENSG00000108774), RAB34 (ENSG00000109113), RAB5B (ENSG00000111540), RAB35 (ENSG00000111737), RAB23 (ENSG00000112210), DNAJC27 (ENSG00000115137), 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-29 — O14966 (reviewed: O14966)

Alternative names: Rab-7-like protein 1, Ras-related protein Rab-7L1

All UniProt accessions (3): E9PL56, O14966, Q6FGU7

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. RAB29 is essential for maintaining the integrity of the endosome-trans-Golgi network structure. Together with LRRK2, plays a role in the retrograde trafficking pathway for recycling proteins, such as mannose 6 phosphate receptor (M6PR), between lysosomes and the Golgi apparatus in a retromer-dependent manner. Recruits LRRK2 to the Golgi complex and stimulates LRRK2 kinase activity. Stimulates phosphorylation of RAB10 ‘Thr-73’ by LRRK2. Regulates neuronal process morphology in the intact central nervous system (CNS). May play a role in the formation of typhoid toxin transport intermediates during Salmonella enterica serovar Typhi (S.typhi) epithelial cell infection.

Subunit / interactions. Interacts with LRRK2 (via the N-terminus); this interaction is direct and stimulates kinase activity.

Subcellular location. Cell membrane. Cytoplasm. Perinuclear region. Golgi apparatus. Golgi apparatus membrane. trans-Golgi network. Vacuole. Cytoskeleton.

Tissue specificity. Ubiquitous.

Post-translational modifications. In case of Salmonella enterica serovar Typhimurium (S.typhimurium) infection, is proteolytically cleaved between Gly-41 and Val-42 by the GtgE viral protease encoded on the Gifsy-2 lysogen bacteriophage, which therefore prevents the recruitment of RAB29 to S.typhimurium-containing vacuoles. In contrast, no proteolytically cleavage is detected in S.typhi-infected cells.

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).

Domain organisation. Switch I, switch II 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 drive interaction with specific sets of effector proteins, with most effectors only binding to GTP-bound Rab.

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

Isoforms (3)

UniProt ID	Names	Canonical?
O14966-1	1	yes
O14966-2	2
O14966-3	3

RefSeq proteins (4): NP_001129134, NP_001129135, NP_001129136, NP_003920* (*=MANE)

Domains & families (InterPro)

ID	Name	Type
IPR001806	Small_GTPase	Family
IPR005225	Small_GTP-bd	Domain
IPR027417	P-loop_NTPase	Homologous_superfamily
IPR030697	Rab29/Rab38/Rab32	Family

Pfam: PF00071

Catalyzed reactions (Rhea), 1 shown:

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

UniProt features (47 total): binding site 12, mutagenesis site 9, strand 7, helix 7, region of interest 2, modified residue 2, lipid moiety-binding region 2, splice variant 2, turn 2, chain 1, site 1

Structure

Experimental structures (PDB)

4 structures.

PDB	Method	Resolution (Å)
6HH2	X-RAY DIFFRACTION	1.45
8FO9	ELECTRON MICROSCOPY	3.48
8FO8	ELECTRON MICROSCOPY	3.88
8FO2	ELECTRON MICROSCOPY	4.13

Predicted structure (AlphaFold)

Model	pLDDT	Fraction very-high
AF-O14966-F1	88.85	0.72

Functional residue map

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

Catalytic / active sites (1): 41–42 (cleavage; by s.typhimurium viral protease gtge)

Ligand- & substrate-binding residues (12): 39; 63; 126; 156; 157; 21; 33; 34; 35; 36; 37; 39

Post-translational modifications (4): 71, 72, 202, 203

Mutagenesis-validated functional residues (9):

Position	Phenotype
43	abolishes interaction with lrrk2 and reduces membrane localization of lrrk2. impairs rab29-stimulated lrrk2 kinase activ
62	abolishes interaction with lrrk2 and reduces membrane localization of lrrk2. impairs rab29-stimulated lrrk2 kinase activ
67	reduces membrane localization of lrrk2 and impairs rab29-stimulated lrrk2 kinase activity on rab10 and lrrk2. reduces me
71	loss of phosphorylation by lrrk2. impairs rab29-stimulated lrrk2 kinase activity on rab10 and lrrk2; when associated wit
71	loss of phosphorylation by lrrk2. does not stimulate lrrk2 kinase activity; when associated with e-72.
72	loss of phosphorylation by lrrk2. impairs rab29-stimulated lrrk2 kinase activity on rab10 and lrrk2; when associated wit
72	loss of phosphorylation by lrrk2. does not stimulate lrrk2 kinase activity; when associated with e-71.
73	loss of lrrk2 binding. does not stimulate lrrk2 kinase activity. localized to the cytosol.
75	loss of lrrk2 binding. does not stimulate lrrk2 kinase activity. localized to the cytosol.

Function

Pathways and Gene Ontology

Reactome pathways

1 pathways

ID	Pathway
R-HSA-8873719	RAB geranylgeranylation

MSigDB gene sets: 281 (showing top): GOBP_REGULATION_OF_T_CELL_RECEPTOR_SIGNALING_PATHWAY, GOBP_REGULATION_OF_ANTIGEN_RECEPTOR_MEDIATED_SIGNALING_PATHWAY, MCLACHLAN_DENTAL_CARIES_UP, GOBP_INTRACELLULAR_PROTEIN_TRANSPORT, GOBP_SYNAPSE_ASSEMBLY, GOBP_VESICLE_ORGANIZATION, GOBP_PROTEIN_LOCALIZATION_TO_CILIUM, GOBP_POSITIVE_REGULATION_OF_INTRACELLULAR_PROTEIN_TRANSPORT, GOZGIT_ESR1_TARGETS_DN, GOBP_ANTIGEN_RECEPTOR_MEDIATED_SIGNALING_PATHWAY, GOBP_POSITIVE_REGULATION_OF_PROTEIN_LOCALIZATION, GOBP_CELLULAR_PIGMENTATION, GOBP_MODULATION_OF_PROCESS_OF_ANOTHER_ORGANISM, GOBP_NEUROGENESIS, GOBP_VESICLE_MEDIATED_TRANSPORT

GO Biological Process (21): positive regulation of receptor recycling (GO:0001921), intracellular protein transport (GO:0006886), mitochondrion organization (GO:0007005), Golgi organization (GO:0007030), synapse assembly (GO:0007416), response to bacterium (GO:0009617), negative regulation of neuron projection development (GO:0010977), cell differentiation (GO:0030154), melanosome organization (GO:0032438), T cell activation (GO:0042110), retrograde transport, endosome to Golgi (GO:0042147), host-mediated perturbation of viral process (GO:0044788), positive regulation of T cell receptor signaling pathway (GO:0050862), protein localization to membrane (GO:0072657), positive regulation of intracellular protein transport (GO:0090316), protein localization to ciliary membrane (GO:1903441), regulation of retrograde transport, endosome to Golgi (GO:1905279), regulation of motile cilium assembly (GO:1905503), cellular detoxification (GO:1990748), protein transport (GO:0015031), vesicle-mediated transport (GO:0016192)

GO Molecular Function (10): GTPase activity (GO:0003924), G protein activity (GO:0003925), GTP binding (GO:0005525), GDP binding (GO:0019003), kinase activator activity (GO:0019209), kinesin binding (GO:0019894), small GTPase binding (GO:0031267), dynein complex binding (GO:0070840), nucleotide binding (GO:0000166), protein binding (GO:0005515)

GO Cellular Component (22): Golgi membrane (GO:0000139), nucleoplasm (GO:0005654), cytoplasm (GO:0005737), mitochondrion (GO:0005739), early endosome (GO:0005769), vacuole (GO:0005773), Golgi apparatus (GO:0005794), cis-Golgi network (GO:0005801), trans-Golgi network (GO:0005802), cytosol (GO:0005829), cytoskeleton (GO:0005856), plasma membrane (GO:0005886), endomembrane system (GO:0012505), nuclear membrane (GO:0031965), melanosome (GO:0042470), perinuclear region of cytoplasm (GO:0048471), recycling endosome (GO:0055037), extracellular exosome (GO:0070062), intracellular vesicle (GO:0097708), membrane (GO:0016020), organelle membrane (GO:0031090), vesicle (GO:0031982)

Reactome top-level categories

Rollup of top-1 pathways:

Category	Pathways
Post-translational protein modification	1

GO top-level categories

Rollup of top GO terms by namespace:

Category	Terms
cellular anatomical structure	6
cytoplasm	5
intracellular membrane-bounded organelle	5
intracellular protein localization	3
organelle organization	2
guanyl ribonucleotide binding	2
Golgi apparatus	2
intracellular anatomical structure	2
endosome	2
receptor recycling	1
regulation of receptor recycling	1
positive regulation of macromolecule metabolic process	1
positive regulation of signaling	1
protein transport	1
intracellular transport	1
endomembrane system organization	1
nervous system development	1
cell junction assembly	1
synapse organization	1
response to other organism	1
regulation of neuron projection development	1
neuron projection development	1
negative regulation of cell projection organization	1
cellular developmental process	1
pigment granule organization	1
lymphocyte activation	1
intercellular transport	1
endosomal transport	1
cytosolic transport	1
host-mediated perturbation of symbiont process	1
T cell receptor signaling pathway	1
regulation of T cell receptor signaling pathway	1
positive regulation of antigen receptor-mediated signaling pathway	1
localization within membrane	1
intracellular protein transport	1
positive regulation of intracellular transport	1
regulation of intracellular protein transport	1
positive regulation of protein transport	1
protein localization to cilium	1
protein localization to membrane	1

Protein interactions and networks

STRING

1140 interactions, top by confidence (×1000):

Protein A	Protein B	Partner UniProt	Score
RAB29	LRRK2	Q5S007	989
RAB29	GAK	O14976	971
RAB29	NUCKS1	Q9H1E3	928
RAB29	SLC41A1	Q8IVJ1	924
RAB29	PM20D1	Q6GTS8	922
RAB29	BAG5	Q9UL15	851
RAB29	C9orf72	Q96LT7	786
RAB29	SLC45A3	Q96JT2	753
RAB29	VPS35	Q96QK1	749
RAB29	SNCA	P37840	748
RAB29	SMCR8	Q8TEV9	727
RAB29	RILPL1	Q5EBL4	717
RAB29	RILPL2	Q969X0	714
RAB29	MAPT	P10636	639
RAB29	WDR41	Q9HAD4	637

IntAct

96 interactions, top by confidence:

A	B	Type	Score
RAB29	LRRK2	psi-mi:“MI:0407”(direct interaction)	0.760
RAB29	LRRK2	psi-mi:“MI:0915”(physical association)	0.760
LRRK2	RAB29	psi-mi:“MI:0915”(physical association)	0.760
LRRK2	RAB29	psi-mi:“MI:0403”(colocalization)	0.760
RAB29	LRRK2	psi-mi:“MI:0403”(colocalization)	0.760
CFTR	ESYT2	psi-mi:“MI:2364”(proximity)	0.710
RAB29	LDOC1	psi-mi:“MI:0915”(physical association)	0.670
RAB29	REL	psi-mi:“MI:0915”(physical association)	0.560
RAB29	TRIM32	psi-mi:“MI:0915”(physical association)	0.560
RAB29	TRIM27	psi-mi:“MI:0915”(physical association)	0.560
RAB29	CHM	psi-mi:“MI:0914”(association)	0.530
SLC15A1	METTL15	psi-mi:“MI:0914”(association)	0.530
TMEM9	ESYT2	psi-mi:“MI:0914”(association)	0.530
APLNR	SLC33A1	psi-mi:“MI:0914”(association)	0.530
RAB29	RAB38	psi-mi:“MI:0915”(physical association)	0.400
RAB29	SMCR8	psi-mi:“MI:0915”(physical association)	0.400
RAB29	CNP	psi-mi:“MI:0915”(physical association)	0.400
RAB29	CSTPP1	psi-mi:“MI:0915”(physical association)	0.370
PPM1H	ACACB	psi-mi:“MI:0914”(association)	0.350

BioGRID (132): RAB29 (Two-hybrid), LDOC1 (Two-hybrid), C11orf49 (Two-hybrid), BEND7 (Two-hybrid), ITPR3 (Affinity Capture-MS), ITPR2 (Affinity Capture-MS), ITPR1 (Affinity Capture-MS), ATP7A (Affinity Capture-MS), RABGGTA (Affinity Capture-MS), CHM (Affinity Capture-MS), CHML (Affinity Capture-MS), ARL8B (Affinity Capture-MS), CNOT6L (Affinity Capture-MS), STRIP1 (Affinity Capture-MS), RAB29 (Affinity Capture-MS)

ESM2 similar proteins: A8ISN6, B5FYQ0, F4IZ82, O00909, O14966, O45379, P11076, P25160, P36405, P37996, P38116, P40616, P40617, P40940, P49702, P51646, P56559, P61208, P61211, P61212, P61213, P61214, Q13795, Q19705, Q1MTE5, Q2KJ96, Q2TBW6, Q2YDM1, Q32LJ2, Q3T0M9, Q52NJ4, Q54R04, Q54UF1, Q5R579, Q5R7A4, Q5RCQ6, Q627K4, Q63055, Q80ZU0, Q8BXL7

Diamond homologs: A5D7F5, A8HN58, E2RQ15, M0RC99, O01803, O04486, O14966, O35509, O35963, O49513, O80501, P01123, P17608, P18066, P19892, P20339, P22129, P25766, P28185, P29687, P31583, P34143, P35278, P36862, P40393, P46629, P46638, P51146, P51147, P51148, P57735, P61017, P61018, P61020, P61021, P61271, P62490, P62491, P62492, P62493

SIGNOR signaling

2 interactions.

A	Effect	B	Mechanism
LRRK2	“up-regulates activity”	RAB29	phosphorylation

Disease & clinical

Clinical variants and AI predictions

ClinVar

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

Classification	Count (floor)
Pathogenic	0
Likely pathogenic	0
Uncertain significance	29
Likely benign	1
Benign	1

Top pathogenic / likely-pathogenic (0)

SpliceAI

1002 predictions. Top by Δscore:

Variant	Effect	Δscore
1:205770728:CTTA:C	donor_loss	1.0000
1:205770729:TTACC:T	donor_loss	1.0000
1:205770730:TACC:T	donor_loss	1.0000
1:205770731:A:AC	donor_gain	1.0000
1:205770731:A:AT	donor_loss	1.0000
1:205770732:C:CC	donor_gain	1.0000
1:205770732:CCT:C	donor_gain	1.0000
1:205770850:TCACA:T	acceptor_gain	1.0000
1:205770851:CACA:C	acceptor_gain	1.0000
1:205770851:CACAC:C	acceptor_gain	1.0000
1:205770852:ACA:A	acceptor_gain	1.0000
1:205770853:CA:C	acceptor_gain	1.0000
1:205770853:CAC:C	acceptor_gain	1.0000
1:205770855:C:CC	acceptor_gain	1.0000
1:205771467:CATA:C	donor_loss	1.0000
1:205771468:ATAC:A	donor_loss	1.0000
1:205771469:TA:T	donor_loss	1.0000
1:205771470:A:AC	donor_gain	1.0000
1:205771470:ACCT:A	donor_loss	1.0000
1:205771471:C:CC	donor_gain	1.0000
1:205771471:C:CG	donor_loss	1.0000
1:205771649:CTGCC:C	acceptor_gain	1.0000
1:205771650:TGCCC:T	acceptor_loss	1.0000
1:205771652:CCCTG:C	acceptor_loss	1.0000
1:205771653:CCTGG:C	acceptor_loss	1.0000
1:205771654:C:CA	acceptor_loss	1.0000
1:205771654:C:CC	acceptor_gain	1.0000
1:205771655:T:A	acceptor_loss	1.0000
1:205772568:C:CC	acceptor_gain	1.0000
1:205770339:C:CT	donor_gain	0.9900

AlphaMissense

0 scored. Top likely-pathogenic:

dbSNP variants (sampled 300 via entrez): RS1000335662 (1:205774301 C>A), RS1000399272 (1:205774495 C>G,T), RS1000608558 (1:205769070 T>G), RS1000673670 (1:205767776 T>C), RS1000970962 (1:205776157 T>C), RS1001081833 (1:205769057 T>C), RS1001277380 (1:205774950 T>A), RS1001571954 (1:205774862 A>G), RS1001663095 (1:205775246 G>A,C,T), RS1001835340 (1:205768458 C>T), RS1002022517 (1:205774617 G>T), RS1002033831 (1:205767836 A>G), RS1002467608 (1:205769154 T>A), RS1002949313 (1:205776470 C>T), RS1003528849 (1:205771809 A>G)

Disease associations

OMIM: gene MIM:603949 | disease phenotypes:

GenCC curated gene-disease

Mondo (0):

Orphanet (0):

HPO phenotypes

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

GWAS associations

18 associations (top):

Study	Trait	p-value
GCST000530_4	Parkinson’s disease	2.000000e-12
GCST001796_1	Prostate-specific antigen levels	2.000000e-19
GCST001875_2	Pubertal anthropometrics	2.000000e-07
GCST002541_35	Menarche (age at onset)	2.000000e-08
GCST002544_11	Parkinson’s disease	2.000000e-16
GCST002703_5	Prostate-specific antigen levels	5.000000e-13
GCST003984_8	Parkinson’s disease	6.000000e-12
GCST004609_129	Monocyte percentage of white cells	4.000000e-10
GCST009325_83	Parkinson’s disease or first degree relation to individual with Parkinson’s disease	3.000000e-22
GCST010697_7	Cortical surface area (min-P)	8.000000e-11
GCST010698_41	Subcortical volume (min-P)	8.000000e-12
GCST010699_29	Brain morphology (min-P)	3.000000e-09
GCST010700_18	Cortical thickness (MOSTest)	5.000000e-12
GCST010701_13	Cortical surface area (MOSTest)	3.000000e-08
GCST010702_124	Subcortical volume (MOSTest)	3.000000e-09
GCST010703_107	Brain morphology (MOSTest)	2.000000e-20
GCST010796_1104	Electrocardiogram morphology (amplitude at temporal datapoints)	3.000000e-08
GCST90013406_227	Liver enzyme levels (alkaline phosphatase)	2.000000e-14

EFO canonical traits (6, from GWAS)

EFO ID	Trait name
EFO:0004703	age at menarche
EFO:0007989	monocyte percentage of leukocytes
EFO:0004346	neuroimaging measurement
EFO:0004840	cortical thickness
EFO:0004327	electrocardiography
EFO:0004533	alkaline phosphatase measurement

Drugs & pharmacology

Drug and pharmacology data

Is drug target: yes

ChEMBL targets (1): CHEMBL3879836 (SINGLE PROTEIN)

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

ChEMBL bioactivities

1 potent at pChembl≥5 of 1 total, top 1 by pChembl (potency: 10 = 0.1 nM, 6 = 1 µM).

pChembl	Type	Value	Unit	Molecule
8.40	Ki	4	nM	CHEMBL3893914

PubChem BioAssay actives

1 with measured affinity, of 5 total; 1 most potent distinct compounds. Largely complementary to BindingDB; screening values are coarse (µM, 4 dp), so sub-nM hits tie at the floor.

Compound	Assay	Type	Value	Unit
4-methyl-6-[(5-methyl-1H-pyrazol-3-yl)amino]-2-[2-[(6-methyl-3-pyridinyl)oxy]ethylamino]pyridine-3-carbonitrile	1332075: Inhibition of Aurora 2 kinase (unknown origin)	ki	0.0040	uM

CTD chemical–gene interactions

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

Chemical	Actions (top 5)	PubMed papers
Valproic Acid	affects cotreatment, increases expression, affects expression, decreases methylation	10
(+)-JQ1 compound	decreases expression	4
trichostatin A	increases expression	2
sodium arsenite	increases abundance, decreases expression	2
entinostat	increases expression, affects cotreatment	2
Nickel	increases expression	2
aristolochic acid I	increases expression	1
FR900359	increases phosphorylation	1
bisphenol F	affects cotreatment, decreases expression	1
TL8-506	affects cotreatment, increases expression	1
triphenyl phosphate	affects expression	1
bisphenol A	increases expression	1
beta-lapachone	decreases expression	1
ochratoxin A	affects binding	1
ochratoxin B	affects binding	1
di-n-butylphosphoric acid	affects expression	1
2-palmitoylglycerol	increases expression	1
monomethylarsonous acid	increases expression	1
4-(5-benzo(1,3)dioxol-5-yl-4-pyridin-2-yl-1H-imidazol-2-yl)benzamide	affects cotreatment, increases expression	1
2,2’,4,4’,5-brominated diphenyl ether	increases expression	1
belinostat	increases expression	1
2-methyl-2H-pyrazole-3-carboxylic acid (2-methyl-4-o-tolylazophenyl)amide	decreases expression, decreases reaction	1
dorsomorphin	increases expression, affects cotreatment	1
3-(2-hydroxy-4-(2-methylnonan-2-yl)phenyl)cyclohexan-1-ol	increases expression	1
Temozolomide	decreases expression	1
Sunitinib	increases expression	1
Vorinostat	increases expression	1
Acetaminophen	decreases expression	1
Air Pollutants	affects expression, increases abundance	1
Arsenic	decreases expression, increases abundance	1

ChEMBL screening assays

3 unique, capped per target: 3 binding

Representative assays (with source publication via chembl_document):

Assay ID	Type	Description	Source paper
CHEMBL3871914	Binding	Inhibition of Aurora 2 kinase (unknown origin)	3-Cyano-6-(5-methyl-3-pyrazoloamino) pyridines (Part 2): A dual inhibitor of Aurora kinase and tubulin polymerization. — Bioorg Med Chem Lett

Cellosaurus cell lines

1 cell lines: 1 cancer cell line

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

Cellosaurus	Name	Category	Sex
CVCL_B1H7	Abcam A-549 RAB29 KO	Cancer cell line	Male

Clinical trials (associated diseases)

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