RAB5B

protein-coding

RAB5B, member RAS oncogene family, the group of RAB, member RAS oncogene GTPases

Gene summary

Enables G protein activity; GDP binding activity; and GTP-dependent protein binding activity. Involved in several processes, including endocytosis; endosomal transport; and plasma membrane to endosome transport. Located in endosome and extracellular exosome. [provided by Alliance of Genome Resources, Jun 2026]

MANE transcript

NM_002868.4

Inheritance

—

ClinVar variants

U:22B:1

Top phenotype

RAB5B-associated surfactant dysfunction disorder

gnomAD constraint

pLI —, LoF o/e 0.36

Max pathogenic AF

—

Genomic locus

chr12:55,973,913-55,996,683

External References & Databases

Ensembl (ENSG00000111540)

Transcript & Mutation Effects

hg38 • Region Span ~22.8 kb

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GenCC Phenotypes & Disease Associations

Curated gene-disease validity assertions and inheritance patterns

No GenCC data available for this gene.

ClinVar Associated Diseases & Phenotypes

Reported disease conditions connected to RAB5B variants in ClinVar

3 Conditions Cataloged

not specifiedTotal: 19

not providedTotal: 2

RAB5B-associated surfactant dysfunction disorderTotal: 1

ClinVar Variants & Pathogenicity by Type

Statistics based on transcript NM_002868.4. Only rare variants are included.

We include only reliable ClinVar variants with their consequences to MANE Select, MANE Plus Clinical transcripts, or transcripts with TSL equal to 1. Click a count to filter the variants table below.

Slight differences between displayed counts and ClinVar may occur due to a different transcript/consequence chosen by our variant effect predictor, or because we classify Benign/Likely benign as Likely benign and Pathogenic/Likely pathogenic as Likely pathogenic.

Effect	PathogenicP	Likely pathogenicLP	VUS	Likely benignLB	BenignB	Sum
synonymous				1 clinvar		1
missense			21 clinvar			21
nonsense						0
start loss						0
frameshift						0
splice donor/acceptor (+/-2bp)			1 clinvar			1
Total	0	0	22	1	0	23

Loading ClinVar variants...

Transcript Catalog

Annotated transcript isoforms across RefSeq and Ensembl databases

Showing 4 of 60 transcripts

Transcript ID	Source	Protein ID	Coding Exons	MANE Status
NM_002868.4	RefSeq	NP_002859.1	5	MANE Select
ENST00000360299.10	Ensembl	ENSP00000353444.5	5	MANE Select
NM_001252036.2	RefSeq	NP_001238965.1	5	Standard
NM_001252037.2	RefSeq	NP_001238966.1	4	Standard

Model Organisms & Knockout Phenotypes

Observed phenotypic effects in mouse and zebrafish models

Gene / Model	Organism	Observed Phenotype
rab5b	Danio rerio	Structure: skeletal muscle Quality: morphology abnormal

Gene / Model

Organism

Observed Phenotype

rab5b

Danio rerio

Structure: skeletal muscle

Quality: morphology

abnormal

Gene Ontology (GO) Annotations & Pathways

Biological processes, molecular functions, cellular components and pathways

Pathways ConsensusPathDB

Endocytosis - Homo sapiens (human)
Phagosome - Homo sapiens (human)
Vasopressin-regulated water reabsorption - Homo sapiens (human)
Amoebiasis - Homo sapiens (human)
Tuberculosis - Homo sapiens (human)

Biological Process

intracellular protein transport
endocytosis
endosome organization
antigen processing and presentation
regulation of endocytosis

Molecular Function

GTPase activity
protein binding
GTP binding
GDP binding
GTP-dependent protein binding

Cellular Component

endosome
early endosome
plasma membrane
membrane
endocytic vesicle

gnomAD Constraint

Source: gnomAD

Gene type: protein_coding
Transcript type: protein_coding
Transcript: ENST00000360299
Coding exons: 5
Length: 20794
Individuals with no LoFs: 125743
Homozygous LoFs: 0
Heterozygous LoFs: 5
Defined: 125748
p: 0.0000199

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible
Missense	1.32	82	123	0.666	0.00000663	1412
Missense (PolyPhen)		21	48.21	0.4356		556
Synonymous	-0.413	50	46.4	1.08	0.00000242	410
Loss of Function	2.23	5	14.0	0.358	9.34e-7	130

Population LoF Frequency

Population	CAF	p-value	Status
African	0	0.0	absent
Latino/Admixed American	0	0.0	absent
Ashkenazi Jewish	0	0.0	absent
East Asian	0.00011	0.00011	rare
Finnish	0	0.0	absent
European (Non-Finnish)	0.000027	0.000026	rare
South Asian	0	0.0	absent
Other	0	0.0	absent

dbNSFP Gene Annotations

Source: dbNSFP

Function: FUNCTION: Protein transport. Probably involved in vesicular traffic (By similarity). {ECO:0000250}.;

Recessive Scores

pRec: 0.125

Intolerance Scores

LoFtool: 0.336
RVIS EVS: -0.12
RVIS percentile EVS: 44.54

Essentials

Essential (CRISPR): N
Essential (CRISPR2): N
Essential (gene trap): N
Indispensability pred.: E
Indispensability score: 0.999

Gene Damage Prediction

	All	Recessive	Dominant
Mendelian	Medium	Medium	Medium
Primary Immunodeficiency	Medium	Medium	Medium
Cancer	Medium	Medium	Medium