RAB13

Summary

RAB13 (RAB13, member RAS oncogene family, HGNC:9762) is a protein-coding gene on chromosome 1q21.3, encoding Ras-related protein Rab-13 (P51153). The small GTPases Rab are key regulators of intracellular membrane trafficking, from the formation of transport vesicles to their fusion with membranes.

This gene is a member of the Rab family of small G proteins and plays a role in regulating membrane trafficking between trans-Golgi network (TGN) and recycling endosomes (RE). The encoded protein is involved in the assembly of tight junctions, which are components of the apical junctional complex (AJC) of epithelial cells. The AJC plays a role in forming a barrier between luminal contents and the underlying tissue. Additional functions associated with the protein include endocytic recycling of occludin, regulation of epithelial cell scattering, neuronal regeneration and regulation of neurite outgrowth. Alternately spliced transcript variants have been observed for this gene. A pseudogene associated with this gene is located on chromosome 12.

Source: NCBI Gene 5872 — RefSeq curated summary.

At a glance

• GWAS associations: 12
• Clinical variants (ClinVar): 40 total
• MANE Select transcript: NM_002870

Identifiers

Gene identifiers

Field	Value
HGNC ID	HGNC:9762
Approved symbol	RAB13
Name	RAB13, member RAS oncogene family
Location	1q21.3
Locus type	gene with protein product
Status	Approved
Ensembl gene	ENSG00000143545
Ensembl biotype	protein_coding
OMIM	602672
Entrez	5872

Gene structure

Transcript identifiers

Ensembl transcripts: 14 — 11 protein_coding, 3 protein_coding_CDS_not_defined

ENST00000368575, ENST00000462680, ENST00000484297, ENST00000495720, ENST00000614713, ENST00000881244, ENST00000881245, ENST00000881246, ENST00000881247, ENST00000915980, ENST00000915981, ENST00000915982, ENST00000915983, ENST00000915984

RefSeq mRNA: 2 — MANE Select: NM_002870 NM_001272038, NM_002870

CCDS: CCDS1058, CCDS72921

Canonical transcript exons

ENST00000368575 — 8 exons

Exon	Start	End
ENSE00001447454	153981650	153982176
ENSE00001447460	153986113	153986339
ENSE00003461040	153983219	153983296
ENSE00003479653	153984721	153984781
ENSE00003580362	153982535	153982600
ENSE00003625893	153982719	153982808
ENSE00003677387	153982391	153982444
ENSE00003686967	153983521	153983581

Expression profiles

Bgee: expression breadth ubiquitous, 134 present calls, max score 98.86.

FANTOM5 (CAGE): breadth ubiquitous, TPM avg 73.9475 / max 835.1041, expressed in 1726 samples.

FANTOM5 promoters (6 alternative TSS)

Promoter ID	TPM avg	Samples expressed
14767	42.3331	1703
14766	23.0540	1667
14768	4.7606	1581
14764	2.0988	1178
14765	1.2798	903
14763	0.4211	256

Top tissues by expression

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

Tissue	Anatomy ID	Expression score	Quality
stromal cell of endometrium	CL:0002255	98.86	gold quality
mucosa of stomach	UBERON:0001199	98.47	gold quality
metanephros cortex	UBERON:0010533	98.44	gold quality
descending thoracic aorta	UBERON:0002345	98.22	gold quality
left coronary artery	UBERON:0001626	98.13	gold quality
omental fat pad	UBERON:0010414	98.13	gold quality
right adrenal gland cortex	UBERON:0035827	98.13	gold quality
right adrenal gland	UBERON:0001233	98.11	gold quality
left adrenal gland cortex	UBERON:0035825	98.08	gold quality
left adrenal gland	UBERON:0001234	98.04	gold quality
fundus of stomach	UBERON:0001160	98.01	gold quality
adipose tissue	UBERON:0001013	97.99	gold quality
prostate gland	UBERON:0002367	97.96	gold quality
lower esophagus	UBERON:0013473	97.96	gold quality
lower esophagus muscularis layer	UBERON:0035833	97.96	gold quality
esophagogastric junction muscularis propria	UBERON:0035841	97.94	gold quality
adult mammalian kidney	UBERON:0000082	97.89	gold quality
subcutaneous adipose tissue	UBERON:0002190	97.89	gold quality
thoracic aorta	UBERON:0001515	97.88	gold quality
body of stomach	UBERON:0001161	97.85	gold quality
ascending aorta	UBERON:0001496	97.84	gold quality
islet of Langerhans	UBERON:0000006	97.82	gold quality
muscle layer of sigmoid colon	UBERON:0035805	97.76	gold quality
endocervix	UBERON:0000458	97.73	gold quality
left lobe of thyroid gland	UBERON:0001120	97.71	gold quality
cortex of kidney	UBERON:0001225	97.71	gold quality
right coronary artery	UBERON:0001625	97.71	gold quality
right lobe of thyroid gland	UBERON:0001119	97.70	gold quality
pancreas	UBERON:0001264	97.67	gold quality
body of pancreas	UBERON:0001150	97.66	gold quality

Single-cell (SCXA)

Detected in 11 experiment(s), a significant marker in 10.

Experiment	Marker?	Max mean expression
E-HCAD-8	yes	427.21
E-CURD-95	yes	166.98
E-MTAB-8142	yes	130.79
E-HCAD-1	yes	34.91
E-HCAD-5	yes	32.96
E-CURD-112	yes	31.97
E-CURD-46	yes	28.30
E-ANND-3	yes	12.65
E-MTAB-10553	yes	6.93
E-MTAB-9801	yes	4.81
E-MTAB-8205	no	674.32

Regulation

Is transcription factor: no

Upstream regulators (CollecTRI, top): ANKRD11, TP53

miRNA regulators (miRDB)

31 targeting RAB13, 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-19A-3P	99.98	75.33	2762
HSA-MIR-19B-3P	99.98	75.44	2754
HSA-MIR-6825-5P	99.96	69.81	3431
HSA-MIR-1236-3P	99.94	68.04	1695
HSA-MIR-4753-3P	99.90	71.03	3786
HSA-MIR-629-3P	99.85	67.99	1875
HSA-MIR-4446-5P	99.72	69.19	2544
HSA-MIR-4755-5P	99.71	70.34	2716
HSA-MIR-5006-3P	99.71	70.26	2728
HSA-MIR-2113	99.58	71.22	1521
HSA-MIR-542-3P	99.34	67.58	1270
HSA-MIR-223-5P	99.24	68.82	1206
HSA-MIR-4279	99.19	66.70	2437
HSA-MIR-548AS-3P	99.12	69.12	2294
HSA-MIR-628-3P	99.04	68.37	814
HSA-MIR-670-3P	99.03	68.88	2404
HSA-MIR-194-5P	99.01	69.65	1465
HSA-MIR-873-5P	98.84	66.90	1348
HSA-MIR-3938	98.72	66.07	834
HSA-MIR-4726-3P	98.49	63.89	1385
HSA-MIR-6867-3P	98.12	66.07	1305
HSA-MIR-4469	97.93	65.81	1319
HSA-MIR-7111-3P	97.80	66.75	1467
HSA-MIR-4723-3P	97.67	65.91	1017
HSA-MIR-4287	97.55	67.24	1247
HSA-MIR-4685-3P	97.55	67.35	1255
HSA-MIR-6769B-3P	97.41	65.53	1036
HSA-MIR-3183	97.40	65.68	978
HSA-MIR-591	96.29	68.16	611
HSA-MIR-7976	95.75	65.67	1186

Literature-anchored findings (GeneRIF, showing 17)

• Rab13 specifically mediates the continuous endocytic recycling of occludin to the cell surface in both fibroblastic and epithelial cells (PMID:15528189)
• Involved in epithelial cell scattering. (PMID:17891173)
• Rab13 regulates membrane trafficking between the trans-Golgi network (TGN) and recycling endosomes (RE). (PMID:18779367)
• Rab13,VASP,and ZO-1 were found in apical tight junctions in normal epithelium but were dislocated to the basolateral position in patients with inactive Crohn’s disease. In patients with ulcerative colitis,these tight junction proteins were not dislocated. (PMID:19885626)
• It is suggested that Rab13 is associated with a putative secretory function in osteoclasts. (PMID:22562557)
• Disruption of Rab13-mediated trafficking dramatically limits the invasive behavior of epithelial cells in vitro and the growth and migration of highly invasive cancer cells in vivo. (PMID:25713415)
• Rab8A GTPase Ser(111) phosphorylation is not directly regulated by PINK1 in vitro and demonstrate in cells the time course of Ser(111) phosphorylation of Rab8A, 8B and 13 is markedly delayed compared to phosphorylation of Parkin at Ser(65). (PMID:26471730)
• Inactive Rab13 appears to associate with vesicles via protein-protein interactions. Only following activation does Rab13 associate with the plasma membrane, presumably with insertion of the C-terminal prenyl group into the membrane. (PMID:26969162)
• the role of Rab13 as a potent driver of cancer progression. (PMID:27044746)
• Rab13 activated the downstream AMPK and blocked mTOR signaling by its functional interaction with Grb2 to regulate autophagy in human vascular endothelial cells. (PMID:28087344)
• GGA2 and RAB13 are important specificity determinants for integrin activity-dependent traffic. (PMID:31076515)
• The deletion of RAB13 inhibited the proliferation and promoted the apoptosis in AGS and NCI-N87cells, the impairments of viability which was due to reduced amount of RAB13 anchoring the plasma membrane and attenuated cellular response to EGF treatment and the activation of downstream Akt/ERK/mTOR signaling pathways accordingly. (PMID:31474334)
• RNA localization and co-translational interactions control RAB13 GTPase function and cell migration. (PMID:32946136)
• Identification of autophagic target RAB13 with small-molecule inhibitor in low-grade glioma via integrated multi-omics approaches coupled with virtual screening of traditional Chinese medicine databases. (PMID:34632655)
• Construction of Two Independent RAB Family-Based Scoring Systems Based on Machine Learning Algorithms and Definition of RAB13 as a Novel Therapeutic Target for Hepatocellular Carcinoma. (PMID:36901767)
• Single-cell transcriptomics in ovarian cancer identify a metastasis-associated cell cluster overexpressed RAB13. (PMID:37046345)
• RAB13 regulates macrophage polarization in sepsis. (PMID:39223234)

Cross-species orthologs

4 orthologs

Organism	Symbol	Gene ID
danio_rerio	rab13	ENSDARG00000034771
mus_musculus	Rab13	ENSMUSG00000027935
rattus_norvegicus	Rab13	ENSRNOG00000016733
caenorhabditis_elegans		WBGENE00019317

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), 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), RABL2A (ENSG00000144134), RAB5A (ENSG00000144566), RAB19 (ENSG00000146955), RAB41 (ENSG00000147127)

Protein

Protein identifiers

Ras-related protein Rab-13 — P51153 (reviewed: P51153)

Alternative names: Cell growth-inhibiting gene 4 protein

All UniProt accessions (2): P51153, A0A087WWB9

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. RAB13 is involved in endocytic recycling and regulates the transport to the plasma membrane of transmembrane proteins like the tight junction protein OCLN/occludin. Thereby, it regulates the assembly and the activity of tight junctions. Moreover, it may also regulate tight junction assembly by activating the PKA signaling pathway and by reorganizing the actin cytoskeleton through the activation of the downstream effectors PRKACA and MICALL2 respectively. Through its role in tight junction assembly, may play a role in the establishment of Sertoli cell barrier. Plays also a role in angiogenesis through regulation of endothelial cells chemotaxis. Also involved in neurite outgrowth. Has also been proposed to play a role in post-Golgi membrane trafficking from the TGN to the recycling endosome. Finally, it has been involved in insulin-induced transport to the plasma membrane of the glucose transporter GLUT4 and therefore may play a role in glucose homeostasis.

Subunit / interactions. Interacts (GTP-bound form) with MICALL2; competes with RAB8A and is involved in tight junctions assembly. Interacts (GTP-bound form) with MICALL1. Interacts (GTP-bound form) with MICAL1, MICAL3, MICALCL, EHBP1 and EHBP1L1; ternary complexes of RAB8A, RAB13 and either MICAL1 or EHBP1L1 are possible. Interacts with PRKACA; downstream effector of RAB13 involved in tight junction assembly. Interacts with GRB2; may recruit RAB13 to the leading edge of migrating endothelial cells where it can activate RHOA. Interacts (isoprenylated form) with PDE6D; dissociates RAB13 from membranes. Interacts with BICDL2/BICDR2. Interacts with LEPROT and LEPROTL1.

Subcellular location. Cell membrane. Cytoplasmic vesicle membrane. Cell junction. Tight junction. Golgi apparatus. trans-Golgi network membrane. Recycling endosome membrane. Cell projection. Lamellipodium.

Tissue specificity. Detected in several types of epithelia, including intestine, kidney, liver and in endothelial cells.

Post-translational modifications. (Microbial infection) Stearoylated By S.flexneri N-epsilon-fatty acyltransferase IcsB, thereby disrupting the host actin cytoskeleton. Ubiquitinated via ‘Lys-11’-linked ubiquitination on Lys-46 and Lys-58; impairing the recruitment of guanosine diphosphate (GDP) dissociation inhibitor 1/GDI1.

Activity regulation. Regulated by guanine nucleotide exchange factors (GEFs) including DENND1C, 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). Activated in response to insulin.

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 drive interaction with specific sets of effector proteins, with most effectors only binding to GTP-bound Rab.

Induction. Up-regulated during osteoclast differentiation.

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

RefSeq proteins (2): NP_001258967, NP_002861* (*=MANE)

Domains & families (InterPro)

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

Pfam: PF00071

Enzyme classification (BRENDA):

• EC 3.6.5.2 — small monomeric GTPase (BRENDA: 49 organisms, 138 substrates, 55 inhibitors, 5 Km, 1 kcat entries)

Substrate kinetics (BRENDA)

1 substrates with measured Km, best-characterized 1. Km ranges are aggregated across organisms/conditions.

Substrate	Km (mM)	Measurements
GTP	—	0

Catalyzed reactions (Rhea), 1 shown:

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

UniProt features (33 total): binding site 16, lipid moiety-binding region 4, mutagenesis site 3, modified residue 2, cross-link 2, short sequence motif 2, chain 1, propeptide 1, region of interest 1, compositionally biased region 1

Structure

Experimental structures (PDB)

0 structures.

Predicted structure (AlphaFold)

Model	pLDDT	Fraction very-high
AF-P51153-F1	84.62	0.68

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 (16): 22; 22; 23; 40; 40; 63; 66; 121; 122; 124; 152; 153 …

Post-translational modifications (8): 178, 200, 194, 195, 199, 200, 46, 58

Mutagenesis-validated functional residues (3):

Position	Phenotype
22	dominant negative.
67	constitutively active mutant locked in the active gtp-bound form. impairs transports of cargo from the trans-golgi netwo
194–199	in 3kr mutant; abolished stearoylation in response to s.flexneri infection.

Function

Pathways and Gene Ontology

Reactome pathways

3 pathways

ID	Pathway
R-HSA-1445148	Translocation of SLC2A4 (GLUT4) to the plasma membrane
R-HSA-8873719	RAB geranylgeranylation
R-HSA-8876198	RAB GEFs exchange GTP for GDP on RABs

MSigDB gene sets: 295 (showing top): TONKS_TARGETS_OF_RUNX1_RUNX1T1_FUSION_MONOCYTE_UP, GOBP_RESPONSE_TO_NITROGEN_COMPOUND, GOBP_EPITHELIUM_DEVELOPMENT, GOBP_CELL_CHEMOTAXIS, GOBP_EPITHELIAL_CELL_DEVELOPMENT, GOCC_SECRETORY_GRANULE, GOBP_APICAL_JUNCTION_ASSEMBLY, GOBP_SERTOLI_CELL_DEVELOPMENT, DITTMER_PTHLH_TARGETS_UP, GOBP_NEUROGENESIS, KEGG_TIGHT_JUNCTION, GOBP_VESICLE_MEDIATED_TRANSPORT, REACTOME_MEMBRANE_TRAFFICKING, GOBP_CELLULAR_RESPONSE_TO_OXYGEN_CONTAINING_COMPOUND, GOBP_PROTEIN_LOCALIZATION_TO_CELL_PERIPHERY

GO Biological Process (18): exocytosis (GO:0006887), Golgi to plasma membrane transport (GO:0006893), obsolete protein kinase A signaling (GO:0010737), protein transport (GO:0015031), endosomal transport (GO:0016197), cortical actin cytoskeleton organization (GO:0030866), neuron projection development (GO:0031175), endocytic recycling (GO:0032456), cellular response to insulin stimulus (GO:0032869), endothelial cell chemotaxis (GO:0035767), trans-Golgi network to recycling endosome transport (GO:0044795), bicellular tight junction assembly (GO:0070830), protein localization to plasma membrane (GO:0072659), establishment of Sertoli cell barrier (GO:0097368), protein localization to cell leading edge (GO:1902463), intracellular protein localization (GO:0008104), toll-like receptor 4 signaling pathway (GO:0034142), localization within membrane (GO:0051668)

GO Molecular Function (7): GTPase activity (GO:0003924), G protein activity (GO:0003925), GTP binding (GO:0005525), metal ion binding (GO:0046872), nucleotide binding (GO:0000166), protein binding (GO:0005515), hydrolase activity (GO:0016787)

GO Cellular Component (23): endosome (GO:0005768), Golgi apparatus (GO:0005794), trans-Golgi network (GO:0005802), cytosol (GO:0005829), plasma membrane (GO:0005886), bicellular tight junction (GO:0005923), synaptic vesicle (GO:0008021), lateral plasma membrane (GO:0016328), lamellipodium (GO:0030027), cell junction (GO:0030054), endocytic vesicle (GO:0030139), trans-Golgi network transport vesicle (GO:0030140), cytoplasmic vesicle (GO:0031410), insulin-responsive compartment (GO:0032593), neuron projection (GO:0043005), recycling endosome (GO:0055037), recycling endosome membrane (GO:0055038), extracellular exosome (GO:0070062), cell-cell junction (GO:0005911), membrane (GO:0016020), cytoplasmic vesicle membrane (GO:0030659), cell projection (GO:0042995), anchoring junction (GO:0070161)

Reactome top-level categories

Rollup of top-3 pathways:

Category	Pathways
Membrane Trafficking	1
Post-translational protein modification	1
Rab regulation of trafficking	1

GO top-level categories

Rollup of top GO terms by namespace:

Category	Terms
cellular anatomical structure	4
cytoplasm	3
vesicle-mediated transport	2
vesicle-mediated transport to the plasma membrane	2
intracellular protein localization	2
endosomal transport	2
endomembrane system	2
cytoplasmic vesicle	2
plasma membrane bounded cell projection	2
secretion by cell	1
vesicle fusion to plasma membrane	1
post-Golgi vesicle-mediated transport	1
transport	1
establishment of protein localization	1
intracellular transport	1
actin cytoskeleton organization	1
cortical cytoskeleton organization	1
neuron development	1
plasma membrane bounded cell projection organization	1
response to insulin	1
cellular response to peptide hormone stimulus	1
endothelial cell migration	1
cell chemotaxis	1
intercellular transport	1
apical junction assembly	1
tight junction assembly	1
protein localization to membrane	1
protein localization to cell periphery	1
Sertoli cell development	1
macromolecule localization	1
cell surface toll-like receptor signaling pathway	1
cellular localization	1
ribonucleoside triphosphate phosphatase activity	1
GTPase activity	1
molecular function regulator activity	1
guanyl ribonucleotide binding	1
purine ribonucleoside triphosphate binding	1
cation binding	1
nucleoside phosphate binding	1
heterocyclic compound binding	1

Protein interactions and networks

STRING

1464 interactions, top by confidence (×1000):

Protein A	Protein B	Partner UniProt	Score
RAB13	MICALL2	Q8IY33	935
RAB13	TJP1	Q07157	832
RAB13	RSPH14	Q9UHP6	813
RAB13	MICALL1	Q8N3F8	797
RAB13	ARAP2	Q8WZ64	711
RAB13	ARAP1	Q96P48	687
RAB13	PDE6D	O43924	636
RAB13	CORO1B	Q9BR76	589
RAB13	DENND1C	Q8IV53	589
RAB13	DENND2B	P78523	576
RAB13	CGN	Q9P2M7	564
RAB13	BICDL2	A1A5D9	560
RAB13	MICAL1	Q8TDZ2	543
RAB13	MICAL3	Q7RTP6	531
RAB13	RPGR	Q92834	511

IntAct

106 interactions, top by confidence:

A	B	Type	Score
GDI1	RAB4A	psi-mi:“MI:0914”(association)	0.820
RABIF	RAB3A	psi-mi:“MI:0914”(association)	0.780
Micall2	RAB13	psi-mi:“MI:0914”(association)	0.660
RAB13	Micall2	psi-mi:“MI:0915”(physical association)	0.660
Micall2	RAB13	psi-mi:“MI:0915”(physical association)	0.660
RAB13	Micall2	psi-mi:“MI:0403”(colocalization)	0.660
Micall2	RAB13	psi-mi:“MI:0403”(colocalization)	0.660
BTN3A3	BTN3A1	psi-mi:“MI:0914”(association)	0.560
Leprotl1	RAB13	psi-mi:“MI:0915”(physical association)	0.560
RAB13	Leprotl1	psi-mi:“MI:0915”(physical association)	0.560
Leprotl1	RAB13	psi-mi:“MI:0403”(colocalization)	0.560
RAB8B	BLTP3B	psi-mi:“MI:0914”(association)	0.530
RABIF	RAB13	psi-mi:“MI:0914”(association)	0.530
FAM174A	BLTP3B	psi-mi:“MI:0914”(association)	0.530
SLC31A1	C2orf72	psi-mi:“MI:0914”(association)	0.530
APLNR	SLC33A1	psi-mi:“MI:0914”(association)	0.530
SPATA46	MDM4	psi-mi:“MI:0914”(association)	0.530
PVR	ORC4	psi-mi:“MI:0914”(association)	0.530
TACR3	C6orf47	psi-mi:“MI:0914”(association)	0.530
ANKH	FAM234B	psi-mi:“MI:0914”(association)	0.530
PDE6D	RAB13	psi-mi:“MI:0915”(physical association)	0.510
NRAS	ESYT2	psi-mi:“MI:2364”(proximity)	0.480
GYP1	RAB13	psi-mi:“MI:0407”(direct interaction)	0.440

BioGRID (163): RAB13 (Affinity Capture-MS), RAB13 (Affinity Capture-MS), RAB13 (Affinity Capture-MS), RAB13 (Affinity Capture-MS), RAB13 (Affinity Capture-MS), RAB13 (Affinity Capture-MS), RAB13 (Affinity Capture-MS), RAB13 (Affinity Capture-MS), RAB13 (Affinity Capture-MS), RAB13 (Affinity Capture-MS), RAB13 (Affinity Capture-MS), RAB13 (Affinity Capture-MS), RAB13 (Affinity Capture-MS), RAB13 (Affinity Capture-MS), RAB13 (Two-hybrid)

ESM2 similar proteins: A4FV54, F1PTE3, O24466, O42819, P01123, P11620, P17609, P20790, P20791, P22127, P22128, P24409, P31584, P33723, P34139, P34140, P35280, P35281, P35286, P36410, P51153, P55258, P61006, P61007, P61026, P61027, P61028, P62820, P62821, P62822, P70550, Q05974, Q2HJI8, Q39571, Q4R5P1, Q52NJ2, Q54NU2, Q58DS5, Q5F470, Q5KTJ6

Diamond homologs: A4D1S5, A4FV54, F1PTE3, O04486, O24466, O76173, P01123, P10536, P11620, P16976, P17609, P20790, P20791, P22125, P22128, P28186, P28188, P31584, P33723, P34139, P34140, P35280, P35286, P35294, P36410, P36863, P40392, P51153, P51156, P53994, P55258, P59279, P61006, P61007, P61019, P61028, P61105, P62820, P62821, P62822

SIGNOR signaling

1 interactions.

A	Effect	B	Mechanism
ANKRD11	“up-regulates quantity by expression”	RAB13	“transcriptional regulation”

Enriched among interaction partners

Reactome pathways and GO biological processes over-represented among this gene’s 123 IntAct physical interaction partners (hypergeometric vs the genome-wide background, BH-FDR, gene-set size 15–500, ranked by fold). A functional readout of the neighbourhood — distinct from this gene’s own memberships above, and biased toward well-studied / hub proteins, so read it as themes rather than proof.

Reactome pathways:

Pathway	Partners	Fold	FDR
NCAM signaling for neurite out-growth	5	17.4×	7e-04

Disease & clinical

Clinical variants and AI predictions

ClinVar

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

Classification	Count (floor)
Pathogenic	0
Likely pathogenic	0
Uncertain significance	19
Likely benign	1
Benign	0

Top pathogenic / likely-pathogenic (0)

SpliceAI

894 predictions. Top by Δscore:

Variant	Effect	Δscore
1:153982174:TCCC:T	acceptor_loss	1.0000
1:153982175:CC:C	acceptor_gain	1.0000
1:153982176:CC:C	acceptor_gain	1.0000
1:153982178:T:A	acceptor_loss	1.0000
1:153982389:A:AC	donor_gain	1.0000
1:153982390:C:CC	donor_gain	1.0000
1:153982390:CTGAT:C	donor_gain	1.0000
1:153982499:T:TA	donor_gain	1.0000
1:153982597:CCAA:C	acceptor_gain	1.0000
1:153982598:CAAC:C	acceptor_gain	1.0000
1:153982601:C:CC	acceptor_gain	1.0000
1:153982714:CTCAC:C	donor_loss	1.0000
1:153982716:CACCT:C	donor_loss	1.0000
1:153982717:A:AC	donor_gain	1.0000
1:153982717:A:AG	donor_loss	1.0000
1:153982718:C:CC	donor_gain	1.0000
1:153982722:ATCGG:A	donor_gain	1.0000
1:153982804:GCATT:G	acceptor_gain	1.0000
1:153982805:CATT:C	acceptor_gain	1.0000
1:153982805:CATTC:C	acceptor_gain	1.0000
1:153982806:ATT:A	acceptor_gain	1.0000
1:153982807:TT:T	acceptor_gain	1.0000
1:153982808:TC:T	acceptor_loss	1.0000
1:153982809:C:CA	acceptor_loss	1.0000
1:153982809:C:CC	acceptor_gain	1.0000
1:153982810:T:A	acceptor_loss	1.0000
1:153982816:C:CT	acceptor_gain	1.0000
1:153982817:A:T	acceptor_gain	1.0000
1:153983217:ACCT:A	donor_gain	1.0000
1:153983218:CCTC:C	donor_gain	1.0000

AlphaMissense

1345 scored. Top likely-pathogenic:

Variant	Protein change	am_pathogenicity
1:153982767:T:A	K122N	1.000
1:153982767:T:G	K122N	1.000
1:153982768:T:A	K122I	1.000
1:153982769:T:C	K122E	1.000
1:153983296:C:G	G83R	1.000
1:153983549:A:T	I73K	1.000
1:153983557:G:C	F70L	1.000
1:153983557:G:T	F70L	1.000
1:153983558:A:G	F70S	1.000
1:153983559:A:G	F70L	1.000
1:153983559:A:T	F70I	1.000
1:153983570:C:T	G66D	1.000
1:153983571:C:A	G66C	1.000
1:153983571:C:G	G66R	1.000
1:153983573:G:T	A65D	1.000
1:153983578:G:C	D63E	1.000
1:153983578:G:T	D63E	1.000
1:153983579:T:A	D63V	1.000
1:153983579:T:C	D63G	1.000
1:153983579:T:G	D63A	1.000
1:153983580:C:G	D63H	1.000
1:153984722:A:G	W62R	1.000
1:153984722:A:T	W62R	1.000
1:153984771:G:C	F45L	1.000
1:153984771:G:T	F45L	1.000
1:153984773:A:G	F45L	1.000
1:153984781:C:T	G42E	1.000
1:153986113:C:G	G42R	1.000
1:153986113:C:T	G42R	1.000
1:153986118:G:A	T40I	1.000

dbSNP variants (sampled 300 via entrez): RS1000118647 (1:153989524 C>T), RS1000509046 (1:153988937 T>C), RS1001037081 (1:153987700 G>A,T), RS1001321914 (1:153987334 A>G), RS1002193440 (1:153988067 C>A,T), RS1002259443 (1:153991943 C>G), RS1002567304 (1:153987846 C>A,G), RS1002934205 (1:153989537 C>A,G), RS1004220318 (1:153989566 G>A), RS1004277400 (1:153983025 T>C), RS1004517678 (1:153981768 T>C), RS1004610299 (1:153987946 A>C), RS1004996538 (1:153989901 A>G), RS1005026391 (1:153990217 C>T), RS1005547556 (1:153984869 T>A)

Disease associations

OMIM: gene MIM:602672 | disease phenotypes:

GenCC curated gene-disease

Mondo (0):

Orphanet (0):

HPO phenotypes

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

GWAS associations

12 associations (top):

Study	Trait	p-value
GCST010136_18	Fruit consumption	3.000000e-08
GCST010137_3	Cooked vegetable consumption	3.000000e-09
GCST010142_60	Fish- and plant-related diet	4.000000e-09
GCST010142_92	Fish- and plant-related diet	6.000000e-14
GCST010696_22	Cortical thickness (min-P)	4.000000e-10
GCST010697_50	Cortical surface area (min-P)	1.000000e-12
GCST010698_81	Subcortical volume (min-P)	1.000000e-23
GCST010699_7	Brain morphology (min-P)	1.000000e-10
GCST010700_11	Cortical thickness (MOSTest)	4.000000e-13
GCST010701_73	Cortical surface area (MOSTest)	4.000000e-09
GCST010702_45	Subcortical volume (MOSTest)	4.000000e-10
GCST010703_276	Brain morphology (MOSTest)	2.000000e-15

EFO canonical traits (3, from GWAS)

EFO ID	Trait name
EFO:0008111	diet measurement
EFO:0004346	neuroimaging measurement
EFO:0004840	cortical thickness

Drugs & pharmacology

Drug and pharmacology data

Is drug target: no

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

CTD chemical–gene interactions

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

Chemical	Actions (top 5)	PubMed papers
bisphenol A	decreases expression, increases expression, increases methylation	3
trichostatin A	affects cotreatment, increases expression	3
4-(5-benzo(1,3)dioxol-5-yl-4-pyridin-2-yl-1H-imidazol-2-yl)benzamide	increases expression, affects cotreatment	2
bisphenol AF	decreases expression, increases expression	2
Phenylmercuric Acetate	affects cotreatment, increases expression	2
Particulate Matter	decreases expression, increases abundance	2
GSK-J4	increases expression	1
FR900359	decreases phosphorylation	1
dicrotophos	decreases expression	1
methylmercuric chloride	increases expression	1
perfluorooctanoic acid	decreases expression	1
ochratoxin A	affects binding	1
dibenzo(a,l)pyrene	increases expression	1
bisphenol B	increases expression	1
abrine	increases expression	1
dorsomorphin	affects cotreatment, increases expression	1
bisphenol S	increases expression	1
4-(4-((5-(4,5-dimethyl-2-nitrophenyl)-2-furanyl)methylene)-4,5-dihydro-3-methyl-5-oxo-1H-pyrazol-1-yl)benzoic acid	increases expression	1
Decitabine	decreases methylation, increases expression	1
Sunitinib	decreases expression	1
Arsenic Trioxide	increases expression	1
Air Pollutants	decreases expression, increases abundance	1
Azacitidine	decreases methylation	1
Hydralazine	affects cotreatment, increases expression	1
Ivermectin	decreases expression	1
Phenobarbital	affects expression	1
Smoke	decreases expression	1
Tobacco Smoke Pollution	affects expression	1
Tretinoin	increases expression	1
Valproic Acid	affects cotreatment, increases expression	1

Cellosaurus cell lines

3 cell lines: 2 cancer cell line, 1 transformed cell line

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

Cellosaurus	Name	Category	Sex
CVCL_B3FI	Abcam HEK293T RAB13 KO	Transformed cell line	Female
CVCL_TH96	HAP1 RAB13 (-) 1	Cancer cell line	Male
CVCL_TH97	HAP1 RAB13 (-) 2	Cancer cell line	Male

Clinical trials (associated diseases)

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