RAB5B

Summary

RAB5B (RAB5B, member RAS oncogene family, HGNC:9784) is a protein-coding gene on chromosome 12q13.2, encoding Ras-related protein Rab-5B (P61020). The small GTPases Rab are key regulators of intracellular membrane trafficking, from the formation of transport vesicles to their fusion with membranes.

Enables GDP binding activity; GTP-dependent protein binding activity; and GTPase activity. Involved in antigen processing and presentation and plasma membrane to endosome transport. Located in endosome and extracellular exosome.

Source: NCBI Gene 5869 — RefSeq curated summary.

At a glance

• GWAS associations: 27
• Clinical variants (ClinVar): 28 total
• Druggable target: yes
• MANE Select transcript: NM_002868

Identifiers

Gene identifiers

Field	Value
HGNC ID	HGNC:9784
Approved symbol	RAB5B
Name	RAB5B, member RAS oncogene family
Location	12q13.2
Locus type	gene with protein product
Status	Approved
Ensembl gene	ENSG00000111540
Ensembl biotype	protein_coding
OMIM	179514
Entrez	5869

Gene structure

Transcript identifiers

Ensembl transcripts: 36 — 32 protein_coding, 3 retained_intron, 1 nonsense_mediated_decay

ENST00000360299, ENST00000448789, ENST00000546810, ENST00000548068, ENST00000549034, ENST00000549505, ENST00000549915, ENST00000550283, ENST00000551459, ENST00000553116, ENST00000628569, ENST00000910180, ENST00000910181, ENST00000910182, ENST00000910183, ENST00000910184, ENST00000910185, ENST00000910186, ENST00000910187, ENST00000910188, ENST00000910189, ENST00000910190, ENST00000910191, ENST00000910192, ENST00000910193, ENST00000910194, ENST00000910195, ENST00000928153, ENST00000928154, ENST00000928155, ENST00000928156, ENST00000928157, ENST00000928158, ENST00000969507, ENST00000969508, ENST00000969509

RefSeq mRNA: 5 — MANE Select: NM_002868 NM_001252036, NM_001252037, NM_001414457, NM_001414458, NM_002868

CCDS: CCDS58244, CCDS8900

Canonical transcript exons

ENST00000360299 — 6 exons

Exon	Start	End
ENSE00000938754	55989947	55990098
ENSE00001517581	55974078	55974139
ENSE00002399883	55992097	55996683
ENSE00003515375	55991360	55991453
ENSE00003588839	55986869	55987123
ENSE00003649786	55990682	55990804

Expression profiles

Bgee: expression breadth ubiquitous, 276 present calls, max score 98.30.

FANTOM5 (CAGE): breadth ubiquitous, TPM avg 75.3286 / max 839.5816, expressed in 1820 samples.

FANTOM5 promoters (6 alternative TSS)

Promoter ID	TPM avg	Samples expressed
126024	72.5308	1820
126027	0.9380	485
126025	0.7580	473
126026	0.6616	405
206741	0.3940	139
126023	0.0463	18

Top tissues by expression

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

Tissue	Anatomy ID	Expression score	Quality
lower esophagus mucosa	UBERON:0035834	98.30	gold quality
C1 segment of cervical spinal cord	UBERON:0006469	98.11	gold quality
colonic epithelium	UBERON:0000397	97.80	gold quality
skin of leg	UBERON:0001511	97.72	gold quality
lower esophagus	UBERON:0013473	97.69	gold quality
lower esophagus muscularis layer	UBERON:0035833	97.68	gold quality
spinal cord	UBERON:0002240	97.63	gold quality
esophagogastric junction muscularis propria	UBERON:0035841	97.48	gold quality
ectocervix	UBERON:0012249	97.46	gold quality
popliteal artery	UBERON:0002250	97.45	gold quality
tibial artery	UBERON:0007610	97.45	gold quality
skin of abdomen	UBERON:0001416	97.44	gold quality
muscle layer of sigmoid colon	UBERON:0035805	97.39	gold quality
esophagus	UBERON:0001043	97.38	gold quality
mucosa of stomach	UBERON:0001199	97.36	gold quality
right coronary artery	UBERON:0001625	97.33	gold quality
body of uterus	UBERON:0009853	97.30	gold quality
endocervix	UBERON:0000458	97.27	gold quality
rectum	UBERON:0001052	97.25	gold quality
aorta	UBERON:0000947	97.14	gold quality
right lung	UBERON:0002167	97.05	gold quality
descending thoracic aorta	UBERON:0002345	97.04	gold quality
esophagus mucosa	UBERON:0002469	97.04	gold quality
nucleus accumbens	UBERON:0001882	97.02	gold quality
amygdala	UBERON:0001876	96.99	gold quality
transverse colon	UBERON:0001157	96.86	gold quality
prefrontal cortex	UBERON:0000451	96.85	gold quality
left ovary	UBERON:0002119	96.84	gold quality
right frontal lobe	UBERON:0002810	96.84	gold quality
thoracic aorta	UBERON:0001515	96.78	gold quality

Single-cell (SCXA)

Detected in 2 experiment(s), a significant marker in 1.

Experiment	Marker?	Max mean expression
E-ANND-3	yes	14.72
E-MTAB-9543	no	2.38

Regulation

Is transcription factor: no

miRNA regulators (miRDB)

261 targeting RAB5B, 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-5011-5P	100.00	83.46	5820
HSA-MIR-190A-3P	100.00	80.35	5520
HSA-MIR-6127	100.00	66.76	2188
HSA-MIR-3924	100.00	72.09	2394
HSA-MIR-4510	100.00	66.60	2050
HSA-MIR-6129	100.00	66.46	2080
HSA-MIR-6130	100.00	66.69	2012
HSA-MIR-6133	100.00	66.48	2064
HSA-MIR-4476	100.00	68.18	2030
HSA-MIR-9-5P	100.00	72.28	2361
HSA-MIR-6876-5P	100.00	67.68	2126
HSA-MIR-3689D	100.00	66.14	1181
HSA-MIR-6851-5P	100.00	65.63	1294
HSA-MIR-4455	100.00	65.48	1587
HSA-MIR-5193	100.00	67.26	1744
HSA-MIR-1277-5P	100.00	73.95	5056
HSA-MIR-3163	100.00	77.23	8605
HSA-MIR-5692B	100.00	71.32	2622
HSA-MIR-5692C	100.00	71.32	2622
HSA-MIR-3667-3P	99.99	67.17	1636
HSA-MIR-520G-5P	99.99	66.76	658
HSA-MIR-12136	99.98	72.81	5713
HSA-MIR-548P	99.98	72.25	3784
HSA-MIR-8068	99.98	73.85	2376
HSA-MIR-19A-3P	99.98	75.33	2762
HSA-MIR-19B-3P	99.98	75.44	2754
HSA-MIR-4775	99.98	75.00	6394
HSA-MIR-548AN	99.97	70.91	2817
HSA-MIR-607	99.97	73.62	5593
HSA-MIR-6825-5P	99.96	69.81	3431

Literature-anchored findings (GeneRIF, showing 11)

• study shows expression of GTPase-deficient Rab5b in NRK cells results in sequential formation of 3 distinct types of endosomes; study suggests regulatory role for Rab5 in early & late endocytic pathway of membrane trafficking in coordination with PI(3)K (PMID:17927960)
• Results suggest that LRRK2, in conjunction with its interaction with Rab5b, plays an important role in synaptic function by modulating the endocytosis of synaptic vesicles. (PMID:18445495)
• suppression of Rab5A or 5B hampered the degradation of EGFR (PMID:19723633)
• combined genetic association studies in women from China/Netherlands/United States: Data suggest that an SNP in RAB5B locus (rs705702) and SNPs in other proteins are associated with polycystic ovary syndrome across ethnic differences. [META-ANALYSIS] (PMID:24106282)
• results suggest that LRRK2 kinase activity functions as a Rab5b GTPase activating protein and thus, negatively regulates Rab5b signalling (PMID:25605758)
• Knockdown of RAB5B inhibited cell proliferation, migration and invasion in breast cancer stem cell-like cells. MiR-130a-3p inhibits migration and invasion by regulating RAB5B in human breast cancer stem cell-like cells. (PMID:29746865)
• The single nucleotide polymorphisms of the rs1045435, rs11550558, rs705700, and rs11171718 loci of the RAB5B gene are associated with polycystic ovary syndrome risk. The rs1045435 locus is likely an miR-24 binding site, while rs11550558, rs705700, and rs11171718 loci may be miR-320 binding sites. (PMID:31036605)
• Therefore, it was considered that Rab5B is required for the transport of large hepatitis B virus surface proteins from the endoplasmic reticulum to multivesicular body. (PMID:31118260)
• A dominant negative variant of RAB5B disrupts maturation of surfactant protein B and surfactant protein C. (PMID:35121658)
• Loci on chromosome 12q13.2 encompassing ERBB3, PA2G4 and RAB5B are associated with polycystic ovary syndrome. (PMID:36423778)
• hsa_circRNA_BECN1 acts as a ceRNA to promote polycystic ovary syndrome progression by sponging the miR-619-5p/Rab5b axis. (PMID:37882757)

Cross-species orthologs

2 orthologs

Organism	Symbol	Gene ID
mus_musculus	Rab5b	ENSMUSG00000000711
rattus_norvegicus	Rab5b	ENSRNOG00000006130

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), 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-5B — P61020 (reviewed: P61020)

All UniProt accessions (5): P61020, F8VPW9, F8VUA5, F8VVZ0, F8VWZ7

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. Involved in early endocytic trafficking. Required for EEA1 recruitment to early endosomes. Required for EGF and transferrin endocytosis and trafficking through early endosomes.

Subunit / interactions. Interacts with EEA1. Interacts with RIN2 and RIN3, which probably regulate its pathway, possibly by acting as GEFs. Interacts with GDI1, GDI2, CHML and CHM; phosphorylation at Ser-84 disrupts this interaction. Interacts (GTP-bound) with SGSM3; SGSM3 acts as a GAP.

Subcellular location. Cell membrane. Early endosome membrane. Melanosome.

Post-translational modifications. Phosphorylation of Ser-84 in the switch II region by LRRK2 prevents the association of RAB regulatory proteins, including CHM, CHML and RAB GDP dissociation inhibitors GDI1 and GDI2. (Microbial infection) Glycosylated on arginine residues by S.typhimurium protein Ssek3.

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) including SGSM3, 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 (2)

UniProt ID	Names	Canonical?
P61020-1	1	yes
P61020-2	2

RefSeq proteins (5): NP_001238965, NP_001238966, NP_001401386, NP_001401387, NP_002859* (*=MANE)

Domains & families (InterPro)

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

Pfam: PF00071

Catalyzed reactions (Rhea), 1 shown:

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

UniProt features (48 total): binding site 18, strand 7, helix 7, mutagenesis site 4, region of interest 3, modified residue 2, lipid moiety-binding region 2, initiator methionine 1, chain 1, splice variant 1, turn 1, compositionally biased region 1

Structure

Experimental structures (PDB)

1 structures.

PDB	Method	Resolution (Å)
2HEI	X-RAY DIFFRACTION	1.55

Predicted structure (AlphaFold)

Model	pLDDT	Fraction very-high
AF-P61020-F1	86.30	0.73

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 (18): 34; 34; 35; 46; 47; 52; 52; 75; 78; 133; 134; 136 …

Post-translational modifications (4): 2, 84, 212, 213

Mutagenesis-validated functional residues (4):

Position	Phenotype
34	constitutively inactive (gdp-bound) mutant. strongly reduces interaction with rin2.
79	constitutively active (gtp-bound) mutant.
84	loss of phosphorylation. no effect on gdi1, gdi2, chml and chm binding.
84	phosphomimetic mutant. loss of gdi1, gdi2, chml and chm binding.

Function

Pathways and Gene Ontology

Reactome pathways

6 pathways

ID	Pathway
R-HSA-6798695	Neutrophil degranulation
R-HSA-8854214	TBC/RABGAPs
R-HSA-8856828	Clathrin-mediated endocytosis
R-HSA-8873719	RAB geranylgeranylation
R-HSA-8876198	RAB GEFs exchange GTP for GDP on RABs
R-HSA-9820960	Respiratory syncytial virus (RSV) attachment and entry

MSigDB gene sets: 280 (showing top): REACTOME_INNATE_IMMUNE_SYSTEM, GOBP_ENDOSOME_ORGANIZATION, GOBP_INTRACELLULAR_PROTEIN_TRANSPORT, NKX25_02, TGCACTT_MIR519C_MIR519B_MIR519A, GOCC_SECRETORY_GRANULE, GOBP_VESICLE_ORGANIZATION, GCANCTGNY_MYOD_Q6, ACEVEDO_NORMAL_TISSUE_ADJACENT_TO_LIVER_TUMOR_DN, GOBP_VESICLE_MEDIATED_TRANSPORT, REACTOME_MEMBRANE_TRAFFICKING, AAAYRNCTG_UNKNOWN, CAGCTG_AP4_Q5, GOBP_REGULATION_OF_VESICLE_MEDIATED_TRANSPORT, NKX61_01

GO Biological Process (8): intracellular protein transport (GO:0006886), endocytosis (GO:0006897), endosome organization (GO:0007032), endosomal transport (GO:0016197), antigen processing and presentation (GO:0019882), regulation of endocytosis (GO:0030100), plasma membrane to endosome transport (GO:0048227), protein transport (GO:0015031)

GO Molecular Function (9): GTPase activity (GO:0003924), G protein activity (GO:0003925), GTP binding (GO:0005525), GDP binding (GO:0019003), GTP-dependent protein binding (GO:0030742), metal ion binding (GO:0046872), nucleotide binding (GO:0000166), protein binding (GO:0005515), hydrolase activity (GO:0016787)

GO Cellular Component (11): endosome (GO:0005768), early endosome (GO:0005769), plasma membrane (GO:0005886), endomembrane system (GO:0012505), membrane (GO:0016020), endocytic vesicle (GO:0030139), secretory granule membrane (GO:0030667), synaptic vesicle membrane (GO:0030672), early endosome membrane (GO:0031901), melanosome (GO:0042470), extracellular exosome (GO:0070062)

Reactome top-level categories

Rollup of top-5 pathways:

Category	Pathways
Rab regulation of trafficking	2
Innate Immune System	1
Membrane Trafficking	1
Post-translational protein modification	1
Respiratory Syncytial Virus Infection Pathway	1

GO top-level categories

Rollup of top GO terms by namespace:

Category	Terms
vesicle-mediated transport	3
intracellular protein localization	2
intracellular transport	2
guanyl ribonucleotide binding	2
cytoplasmic vesicle	2
cellular anatomical structure	2
protein transport	1
vesicle budding from membrane	1
membrane invagination	1
import into cell	1
endomembrane system organization	1
vesicle organization	1
immune system process	1
endocytosis	1
regulation of cellular component organization	1
regulation of vesicle-mediated transport	1
transport	1
establishment of protein localization	1
ribonucleoside triphosphate phosphatase activity	1
GTPase activity	1
molecular function regulator activity	1
purine ribonucleoside triphosphate binding	1
anion binding	1
protein binding	1
cation binding	1
nucleoside phosphate binding	1
heterocyclic compound binding	1
binding	1
catalytic activity	1
endomembrane system	1
endosome	1
membrane	1
cell periphery	1
vacuole	1
plasma membrane	1
secretory granule	1
cytoplasmic vesicle membrane	1
bounding membrane of organelle	1
synaptic vesicle	1
exocytic vesicle membrane	1

Protein interactions and networks

STRING

0 interactions, top by confidence (×1000):

IntAct

130 interactions, top by confidence:

A	B	Type	Score
CEP97	CCP110	psi-mi:“MI:2364”(proximity)	0.950
GDI1	RAB4A	psi-mi:“MI:0914”(association)	0.820
LRRK2	RAB5B	psi-mi:“MI:0217”(phosphorylation reaction)	0.760
LRRK2	RAB5B	psi-mi:“MI:0915”(physical association)	0.760
RAB5B	LRRK2	psi-mi:“MI:0915”(physical association)	0.760
LRRK2	RAB5B	psi-mi:“MI:0403”(colocalization)	0.760
CFTR	ESYT2	psi-mi:“MI:2364”(proximity)	0.710
CFTR	ESYT2	psi-mi:“MI:0914”(association)	0.710
CHM	RAB5C	psi-mi:“MI:0914”(association)	0.640
FHIP1B	RAB5B	psi-mi:“MI:0407”(direct interaction)	0.600
FHIP1B	RAB5B	psi-mi:“MI:0915”(physical association)	0.600
FHIP1B	RAB5B	psi-mi:“MI:0403”(colocalization)	0.600
	RAB5B	psi-mi:“MI:0407”(direct interaction)	0.560
	RAB5B	psi-mi:“MI:0883”(gtpase reaction)	0.560
HTT	RAB5B	psi-mi:“MI:0915”(physical association)	0.560
RAB5B	SUN2	psi-mi:“MI:0915”(physical association)	0.550

BioGRID (181): RAB5B (Affinity Capture-RNA), RAB5B (Affinity Capture-RNA), RAB5B (Affinity Capture-RNA), RAB5B (Affinity Capture-MS), RAB5B (Affinity Capture-MS), RAB5B (Affinity Capture-MS), ARF1 (Co-fractionation), CLTC (Co-fractionation), CTSD (Co-fractionation), ETFA (Co-fractionation), RAB1A (Co-fractionation), RAB1B (Co-fractionation), RAB2A (Co-fractionation), RAB5B (Co-fractionation), RAB5B (Co-fractionation)

ESM2 similar proteins: E2RQ15, O01803, O23561, P05714, P10948, P19892, P20337, P20338, P25766, P28185, P28187, P31583, P36412, P46629, P51146, P56371, P57735, P61017, P61018, P61020, Q0WQN4, Q2TBH7, Q32NQ0, Q3ZC27, Q40191, Q40520, Q40522, Q40523, Q40723, Q53B90, Q58DW6, Q5KTJ7, Q5RBG1, Q63941, Q63942, Q68EK7, Q6PHI9, Q86YS6, Q8CG50, Q91ZR1

Diamond homologs: A2WSI7, A2Y7R5, A2YEQ6, H9BW96, O17915, O76742, O97572, P09527, P18067, P22127, P24408, P24409, P28748, P32835, P32836, P33519, P34139, P35288, P36411, P36864, P38542, P38543, P38544, P38545, P38546, P38547, P38548, P41914, P41915, P41916, P41917, P41918, P41919, P42558, P51149, P51150, P51151, P52301, P54765, P54766

SIGNOR signaling

4 interactions.

A	Effect	B	Mechanism
LRRK2	“up-regulates activity”	RAB5B	phosphorylation
RAB5B	“form complex”	“Early Endosome”	binding
CDK1	unknown	RAB5B	phosphorylation
LYST	“down-regulates activity”	RAB5B	binding

Enriched among interaction partners

Reactome pathways and GO biological processes over-represented among this gene’s 131 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.

GO biological processes:

GO term	Partners	Fold	FDR
post-Golgi vesicle-mediated transport	5	46.6×	4e-05
exocytosis	7	9.4×	3e-03
endocytosis	8	6.7×	5e-03
protein transport	11	4.3×	9e-03

Disease & clinical

Clinical variants and AI predictions

ClinVar

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

Classification	Count (floor)
Pathogenic	0
Likely pathogenic	0
Uncertain significance	20
Likely benign	1
Benign	0

Top pathogenic / likely-pathogenic (0)

SpliceAI

1130 predictions. Top by Δscore:

Variant	Effect	Δscore
12:55989939:A:AG	acceptor_gain	1.0000
12:55989940:T:G	acceptor_gain	1.0000
12:55989943:A:AG	acceptor_gain	1.0000
12:55989943:ATAGC:A	acceptor_gain	1.0000
12:55989944:T:G	acceptor_gain	1.0000
12:55989944:TA:T	acceptor_loss	1.0000
12:55989945:A:AC	acceptor_loss	1.0000
12:55989945:A:AG	acceptor_gain	1.0000
12:55989945:AGC:A	acceptor_gain	1.0000
12:55989945:AGCG:A	acceptor_gain	1.0000
12:55989946:G:GC	acceptor_gain	1.0000
12:55989946:GC:G	acceptor_gain	1.0000
12:55989946:GCG:G	acceptor_gain	1.0000
12:55989946:GCGG:G	acceptor_gain	1.0000
12:55989946:GCGGC:G	acceptor_gain	1.0000
12:55990094:ATCAG:A	donor_gain	1.0000
12:55990095:TCAG:T	donor_gain	1.0000
12:55990096:CAG:C	donor_gain	1.0000
12:55990096:CAGG:C	donor_loss	1.0000
12:55990099:G:GC	donor_loss	1.0000
12:55990099:G:GG	donor_gain	1.0000
12:55990100:T:A	donor_loss	1.0000
12:55990676:TCCTA:T	acceptor_loss	1.0000
12:55990680:A:AT	acceptor_loss	1.0000
12:55990681:G:GT	acceptor_loss	1.0000
12:55990798:G:GG	donor_gain	1.0000
12:55990802:G:GT	donor_gain	1.0000
12:55990802:GAA:G	donor_gain	1.0000
12:55990805:G:GG	donor_gain	1.0000
12:55991357:CAG:C	acceptor_loss	1.0000

AlphaMissense

1413 scored. Top likely-pathogenic:

Variant	Protein change	am_pathogenicity
12:55987026:A:C	K22N	1.000
12:55987026:A:T	K22N	1.000
12:55987039:G:A	G27R	1.000
12:55987039:G:C	G27R	1.000
12:55987040:G:A	G27E	1.000
12:55987040:G:T	G27V	1.000
12:55987054:G:A	G32R	1.000
12:55987054:G:C	G32R	1.000
12:55987055:G:A	G32E	1.000
12:55987055:G:T	G32V	1.000
12:55987057:A:C	K33Q	1.000
12:55987057:A:G	K33E	1.000
12:55987058:A:T	K33M	1.000
12:55987059:G:C	K33N	1.000
12:55987059:G:T	K33N	1.000
12:55987093:T:C	F45L	1.000
12:55987095:C:A	F45L	1.000
12:55987095:C:G	F45L	1.000
12:55987115:C:T	T52I	1.000
12:55987120:G:A	G54R	1.000
12:55987120:G:C	G54R	1.000
12:55987121:G:A	G54E	1.000
12:55989952:T:C	F57L	1.000
12:55989953:T:C	F57S	1.000
12:55989954:C:A	F57L	1.000
12:55989954:C:G	F57L	1.000
12:55989956:T:C	L58P	1.000
12:55990001:T:A	I73N	1.000
12:55990001:T:C	I73T	1.000
12:55990001:T:G	I73S	1.000

dbSNP variants (sampled 300 via entrez): RS1000002373 (12:55973570 C>T), RS1000461817 (12:55992792 G>A), RS1000568856 (12:55972446 T>C,G), RS1000630792 (12:55978738 G>A), RS1000638422 (12:55991646 C>T), RS1000681666 (12:55978959 G>C), RS1000844983 (12:55980922 T>C), RS1000979439 (12:55985353 G>C), RS1001191972 (12:55973993 C>T), RS1001326860 (12:55988059 G>C,T), RS1001408510 (12:55974029 A>G), RS1001425334 (12:55974919 A>C,G), RS1001529845 (12:55994330 A>C), RS1001566467 (12:55978550 A>G), RS1001692685 (12:55980431 G>A)

Disease associations

OMIM: gene MIM:179514 | disease phenotypes:

GenCC curated gene-disease

Mondo (0):

Orphanet (0):

HPO phenotypes

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

GWAS associations

27 associations (top):

Study	Trait	p-value
GCST000141_1	Type 1 diabetes	9.000000e-10
GCST001634_7	Polycystic ovary syndrome	9.000000e-26
GCST001670_1	Vitiligo	8.000000e-12
GCST002774_24	Cognitive function	3.000000e-07
GCST004367_1	Anorexia nervosa	4.000000e-09
GCST004624_144	Sum eosinophil basophil counts	5.000000e-12
GCST006481_27	Lung function (FEV1)	2.000000e-08
GCST007089_11	Polycystic ovary syndrome	5.000000e-09
GCST007431_114	Lung function (FEV1/FVC)	8.000000e-09
GCST007432_147	FEV1	6.000000e-10
GCST007563_23	Allergic disease (asthma, hay fever or eczema)	4.000000e-10
GCST007564_9	Asthma or allergic disease (pleiotropy)	1.000000e-13
GCST007798_147	Asthma	4.000000e-23
GCST007800_2	Asthma (childhood onset)	3.000000e-24
GCST007922_4	Medication use (drugs for peptic ulcer and gastro-oesophageal reflux disease)	3.000000e-09
GCST007993_28	Asthma (adult onset)	6.000000e-07
GCST007995_39	Asthma (childhood onset)	1.000000e-11
GCST008832_15	Gastroesophageal reflux disease	1.000000e-08
GCST008916_124	Asthma	1.000000e-16
GCST009798_45	Asthma	1.000000e-15
GCST010002_217	Refractive error	6.000000e-174
GCST010242_61	HDL cholesterol levels	4.000000e-09
GCST010658_16	High density lipoprotein cholesterol levels	5.000000e-07
GCST010703_297	Brain morphology (MOSTest)	4.000000e-10
GCST010984_30	Allergic disease (asthma, hay fever and/or eczema) (multivariate analysis)	6.000000e-09
GCST010985_6	Allergic disease (asthma, hay fever and/or eczema) (age of onset)	4.000000e-09
GCST90011899_144	Aspartate aminotransferase levels	8.000000e-11

EFO canonical traits (11, from GWAS)

EFO ID	Trait name
EFO:0004337	intelligence
EFO:0004842	eosinophil count
EFO:0005090	basophil count
EFO:0004314	forced expiratory volume
EFO:0004713	FEV/FVC ratio
EFO:0009923	Peptic ulcer and gastro-oesophageal reflux disease (GORD) drug use measurement
EFO:1002011	adult onset asthma
EFO:0004612	high density lipoprotein cholesterol measurement
EFO:0004346	neuroimaging measurement
EFO:0004847	age at onset
EFO:0004736	aspartate aminotransferase measurement

Drugs & pharmacology

Drug and pharmacology data

Is drug target: yes

ChEMBL targets (1): CHEMBL6067250 (SINGLE PROTEIN)

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

ChEMBL bioactivities

2 potent at pChembl≥5 of 4 total, top 2 by pChembl (potency: 10 = 0.1 nM, 6 = 1 µM).

pChembl	Type	Value	Unit	Molecule
7.49	Kd	32.73	nM	CHEMBL5653589
7.49	ED50	32.73	nM	CHEMBL5653589

PubChem BioAssay actives

1 with measured affinity, of 4 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-3-[(2-methyl-6-pyridin-3-ylpyrazolo[3,4-d]pyrimidin-4-yl)amino]-N-[3-(trifluoromethyl)phenyl]benzamide	2149176: Binding affinity to human RAB5B incubated for 45 mins by Kinobead based pull down assay	kd	0.0327	uM

CTD chemical–gene interactions

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

Chemical	Actions (top 5)	PubMed papers
bisphenol A	increases expression	2
Cisplatin	decreases expression, increases expression	2
Tobacco Smoke Pollution	affects expression, increases expression	2
Valproic Acid	affects expression, decreases expression	2
bisphenol F	affects cotreatment, increases expression	1
triphenyl phosphate	affects expression	1
sodium arsenate	decreases expression	1
beta-lapachone	decreases expression	1
sodium arsenite	increases expression	1
nickel chloride	decreases expression	1
benzo(e)pyrene	decreases methylation	1
4-(5-benzo(1,3)dioxol-5-yl-4-pyridin-2-yl-1H-imidazol-2-yl)benzamide	affects cotreatment, increases expression	1
pentabrominated diphenyl ether 100	decreases expression	1
hexabrominated diphenyl ether 153	decreases expression	1
asparanin A	decreases expression	1
bisphenol S	increases expression, affects cotreatment	1
LDN 193189	affects cotreatment, increases expression	1
Resveratrol	affects cotreatment, decreases expression	1
Zoledronic Acid	affects cotreatment, increases expression	1
Leflunomide	decreases expression	1
Fluvastatin	affects cotreatment, increases expression	1
Glyphosate	increases expression	1
Cytarabine	increases expression	1
Dichlorodiphenyl Dichloroethylene	decreases expression	1
Dexamethasone	affects cotreatment, increases expression	1
Indomethacin	increases expression, affects cotreatment	1
Ivermectin	decreases expression	1
Methapyrilene	decreases methylation	1
Plant Extracts	affects cotreatment, decreases expression	1
Potassium Dichromate	increases expression	1

ChEMBL screening assays

1 unique, capped per target: 1 binding

Representative assays (with source publication via chembl_document):

Assay ID	Type	Description	Source paper
CHEMBL5652218	Binding	Binding affinity to human RAB5B incubated for 45 mins by Kinobead based pull down assay	NVP-BHG712: Effects of Regioisomers on the Affinity and Selectivity toward the EPHrin Family. — ChemMedChem

Cellosaurus cell lines

2 cell lines: 2 cancer cell line

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

Cellosaurus	Name	Category	Sex
CVCL_E1NE	HAP1 RAB5B (-) 1	Cancer cell line	Male
CVCL_E1NF	HAP1 RAB5B (-) 2	Cancer cell line	Male

Clinical trials (associated diseases)

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