RAB3A
protein-codingRAB3A, 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 several processes, including acrosomal vesicle exocytosis; plasma membrane repair; and regulation of plasma membrane repair. Located in perinuclear region of cytoplasm. [provided by Alliance of Genome Resources, Jun 2026]
MANE transcript
Inheritance
ClinVar variants
Top phenotype
gnomAD constraint
Max pathogenic AF
Genomic locus
External References & Databases
Transcript & Mutation Effects
hg38 • Region Span ~7.3 kbGenCC 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 RAB3A variants in ClinVar
ClinVar Variants & Pathogenicity by Type
Statistics based on transcript NM_002866.5. 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 | 1 | 2 | |||
| missense | 1 | 18 | 19 | |||
| nonsense | 0 | |||||
| start loss | 0 | |||||
| frameshift | 0 | |||||
| splice donor/acceptor (+/-2bp) | 4 | 4 | ||||
| Total | 0 | 1 | 23 | 1 | 0 | 25 |
Transcript Catalog
Annotated transcript isoforms across RefSeq and Ensembl databases
| Transcript ID | Source | Protein ID | Coding Exons | MANE Status |
|---|---|---|---|---|
| RefSeq | NP_002857.1 | 4 | MANE Select | |
| Ensembl | ENSP00000222256.3 | 4 | MANE Select | |
| Ensembl | ENSP00000474603.1 | 3 | Standard | |
| Ensembl | ENSP00000474603.1 | 3 | Standard |
Gene Ontology (GO) Annotations & Pathways
Biological processes, molecular functions, cellular components and pathways
Pathways ConsensusPathDB
- Synaptic vesicle cycle - Homo sapiens (human)
- Insulin secretion - Homo sapiens (human)
- Synaptic Vesicle Pathway
- Brain-Derived Neurotrophic Factor (BDNF) signaling pathway
- Neutrophil degranulation
Biological Process
- respiratory system process
- intracellular protein transport
- vesicle docking involved in exocytosis
- mitochondrion organization
- neuromuscular synaptic transmission
Molecular Function
- ATPase activator activity
- GTPase activity
- protein binding
- GTP binding
- protein C-terminus binding
Cellular Component
- acrosomal vesicle
- endosome
- cytosol
- plasma membrane
- synaptic vesicle
gnomAD Constraint
Source:
- Gene type
- protein_coding
- Transcript type
- protein_coding
- Transcript
- ENST00000222256
- Coding exons
- 4
- Length
- 7291
- Individuals with no LoFs
- 0
- Homozygous LoFs
- 0
- Heterozygous LoFs
- 0
- Defined
- 0
- p
- 0.00
| Z-Score | Observed | Expected | Observed/Expected | Mutation Rate | Total Possible | |
|---|---|---|---|---|---|---|
| Missense | 2.32 | 71 | 152 | 0.469 | 0.0000104 | 1461 |
| Missense (PolyPhen) | 16 | 55.689 | 0.28731 | 562 | ||
| Synonymous | 0.615 | 60 | 66.4 | 0.904 | 0.00000533 | 413 |
| Loss of Function | 2.82 | 0 | 9.23 | 0.00 | 3.94e-7 | 107 |
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 | 0.0 | absent |
| South Asian | 0 | 0.0 | absent |
| Other | 0 | 0.0 | absent |
dbNSFP Gene Annotations
Source:
- Function
- FUNCTION: Involved in exocytosis by regulating a late step in synaptic vesicle fusion. Could play a role in neurotransmitter release by regulating membrane flow in the nerve terminal.;
Recessive Scores
- pRec
- 0.350
Intolerance Scores
- RVIS EVS
- -0.23
- RVIS percentile EVS
- 36.86
Essentials
- Essential (CRISPR)
- N
- Essential (CRISPR2)
- N
- Essential (gene trap)
- N
- Indispensability pred.
- E
- Indispensability score
- 0.911
Gene Damage Prediction
| All | Recessive | Dominant | |
|---|---|---|---|
| Mendelian | Medium | Medium | Medium |
| Primary Immunodeficiency | Medium | Medium | Medium |
| Cancer | Medium | Medium | Medium |