RAB3D

protein-coding

RAB3D, member RAS oncogene family, the group of RAB, member RAS oncogene GTPases

Gene summary

Enables G protein activity and myosin V binding activity. Involved in bone resorption and positive regulation of regulated secretory pathway. Located in cytoplasmic microtubule and secretory vesicle. [provided by Alliance of Genome Resources, Jun 2026]

Previous symbols:

MANE transcript

NM_004283.4

Inheritance

—

ClinVar variants

U:44B:2

Top phenotype

—

gnomAD constraint

pLI —, LoF o/e 0.87

Max pathogenic AF

—

Genomic locus

chr19:11,322,068-11,346,270

External References & Databases

Ensembl (ENSG00000105514)

Transcript & Mutation Effects

hg38 • Region Span ~24.2 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 RAB3D variants in ClinVar

2 Conditions Cataloged

not specifiedTotal: 43

not providedTotal: 2

ClinVar Variants & Pathogenicity by Type

Statistics based on transcript NM_004283.4. 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				2 clinvar		2
missense			43 clinvar			43
nonsense						0
start loss						0
frameshift						0
splice donor/acceptor (+/-2bp)			1 clinvar			1
Total	0	0	44	2	0	46

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Transcript Catalog

Annotated transcript isoforms across RefSeq and Ensembl databases

Showing 4 of 10 transcripts

Transcript ID	Source	Protein ID	Coding Exons	MANE Status
NM_004283.4	RefSeq	NP_004274.1	4	MANE Select
ENST00000222120.8	Ensembl	ENSP00000222120.2	4	MANE Select
ENST00000589655.1	Ensembl	ENSP00000466000.1	4	Standard
ENST00000589655.2	Ensembl	ENSP00000466000.1	4	Standard

Gene Ontology (GO) Annotations & Pathways

Biological processes, molecular functions, cellular components and pathways

Pathways ConsensusPathDB

Pancreatic secretion - Homo sapiens (human)
Neutrophil degranulation
Post-translational protein modification
Metabolism of proteins
Innate Immune System

Biological Process

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

Molecular Function

GTPase activity
GTP binding
GTP-dependent protein binding
myosin V binding

Cellular Component

endosome
cytoplasmic microtubule
plasma membrane
synaptic vesicle
vesicle

gnomAD Constraint

Source: gnomAD

Gene type: protein_coding
Transcript type: protein_coding
Transcript: ENST00000222120
Coding exons: 4
Length: 24225
Individuals with no LoFs: 125721
Homozygous LoFs: 0
Heterozygous LoFs: 27
Defined: 125748
p: 0.000107

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible
Missense	0.892	113	143	0.790	0.00000961	1444
Missense (PolyPhen)		43	54.191	0.79349		595
Synonymous	0.0998	61	62.0	0.984	0.00000483	427
Loss of Function	0.373	8	9.22	0.868	4.82e-7	94

Population LoF Frequency

Population	CAF	p-value	Status
African	0.000062	0.000062	rare
Latino/Admixed American	0.00023	0.00023	rare
Ashkenazi Jewish	0	0.0	absent
East Asian	0.00016	0.00016	rare
Finnish	0	0.0	absent
European (Non-Finnish)	0.000097	0.000097	rare
South Asian	0.00013	0.00013	rare
Other	0	0.0	absent

dbNSFP Gene Annotations

Source: dbNSFP

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

Recessive Scores

pRec: 0.215

Intolerance Scores

LoFtool: 0.449
RVIS EVS: 0.11
RVIS percentile EVS: 61.73

Essentials

Essential (CRISPR): N
Essential (CRISPR2): N
Essential (gene trap): N
Indispensability pred.: E
Indispensability score: 0.932

Gene Damage Prediction

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