RAB3B

protein-coding

RAB3B, member RAS oncogene family, the group of RAB, member RAS oncogene GTPases

Gene summary

Enables G protein activity; GDP binding activity; and myosin V binding activity. Involved in several processes, including positive regulation of dopamine uptake involved in synaptic transmission; regulation of synaptic vesicle cycle; and regulation of vesicle size. Located in perinuclear region of cytoplasm and vesicle. Is active in dopaminergic synapse and synaptic vesicle membrane. [provided by Alliance of Genome Resources, Jun 2026]

MANE transcript

NM_002867.4

Inheritance

—

ClinVar variants

U:25

Top phenotype

—

gnomAD constraint

pLI —, LoF o/e 0.24

Max pathogenic AF

—

Genomic locus

chr1:51,907,956-51,990,700

External References & Databases

Ensembl (ENSG00000169213)

Transcript & Mutation Effects

hg38 • Region Span ~82.7 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 RAB3B variants in ClinVar

2 Conditions Cataloged

not specifiedTotal: 24

not providedTotal: 1

ClinVar Variants & Pathogenicity by Type

Statistics based on transcript NM_002867.4. 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			24 clinvar			24
nonsense						0
start loss						0
frameshift						0
splice donor/acceptor (+/-2bp)						0
Total	0	0	25	0	0	25

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Transcript Catalog

Annotated transcript isoforms across RefSeq and Ensembl databases

Showing 4 of 12 transcripts

Transcript ID	Source	Protein ID	Coding Exons	MANE Status
NM_002867.4	RefSeq	NP_002858.2	4	MANE Select
ENST00000371655.4	Ensembl	ENSP00000360718.3	4	MANE Select
ENST00000900195.1	Ensembl	ENSP00000570254.1	4	Standard
ENST00000900195.2	Ensembl	ENSP00000570254.1	4	Standard

Model Organisms & Knockout Phenotypes

Observed phenotypic effects in mouse and zebrafish models

Gene / Model	Organism	Observed Phenotype
rab3b	Danio rerio	Structure: yolk Quality: edematous abnormal

Gene / Model

Organism

Observed Phenotype

rab3b

Danio rerio

Structure: yolk

Quality: edematous

abnormal

Gene Ontology (GO) Annotations & Pathways

Biological processes, molecular functions, cellular components and pathways

Pathways ConsensusPathDB

Post-translational protein modification
Metabolism of proteins
RAB geranylgeranylation

Biological Process

intracellular protein transport
vesicle docking involved in exocytosis
protein secretion
regulation of exocytosis
peptidyl-cysteine methylation

Molecular Function

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

Cellular Component

cytoplasm
endosome
Golgi apparatus
cytosol
plasma membrane

gnomAD Constraint

Source: gnomAD

Gene type: protein_coding
Transcript type: protein_coding
Transcript: ENST00000371655
Coding exons: 4
Length: 82809
Individuals with no LoFs: 125740
Homozygous LoFs: 0
Heterozygous LoFs: 6
Defined: 125746
p: 0.0000239

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible
Missense	0.945	104	135	0.771	0.00000803	1455
Missense (PolyPhen)		30	52.989	0.56615		582
Synonymous	0.807	45	52.4	0.858	0.00000318	423
Loss of Function	2.04	2	8.35	0.240	3.54e-7	98

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	0.0	absent
Finnish	0	0.0	absent
European (Non-Finnish)	0.000053	0.000053	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: 0.175

Intolerance Scores

LoFtool: 0.458
RVIS EVS: -0.01
RVIS percentile EVS: 53.19

Essentials

Essential (CRISPR): N
Essential (CRISPR2): N
Essential (gene trap): N
Indispensability pred.: E
Indispensability score: 0.668

Gene Damage Prediction

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