RAB3A
RAB3A, member RAS oncogene family, the group of RAB, member RAS oncogene GTPases
Basic information
Region (hg38): 19:18196783-18204042
Links
Phenotypes
GenCC
Source:
No genCC data.
ClinVar
This is a list of variants' phenotypes submitted to
Variants pathogenicity by type
Statistics on ClinVar variants can assist in determining whether a specific variant type in the RAB3A gene is commonly pathogenic or not.
In the table, we include only reliable ClinVar variants with their consequences to MANE Select, Mane Plus Clinical transcripts, or transcripts with TSL equals 1. Click the count to view the source variants.
Warning: slight differences between displayed counts and the number of variants in ClinVar may occur, primarily due to (1) the application of a different transcript and/or consequence by our variant effect predictor or (2) differences in clinical significance: we classify Benign/Likely benign variants as Likely benign and Pathogenic/Likely pathogenic variants as Likely pathogenic.
| Variant type | Pathogenic | Likely pathogenic | VUS | Likely benign | Benign | Sum |
|---|---|---|---|---|---|---|
| synonymous | 2 | |||||
| missense | 9 | |||||
| nonsense | 0 | |||||
| start loss | 0 | |||||
| frameshift | 0 | |||||
| inframe indel | 0 | |||||
| splice donor/acceptor (+/-2bp) | 0 | |||||
| splice region | 0 | |||||
| non coding | 1 | |||||
| Total | 0 | 0 | 9 | 2 | 1 |
Variants in RAB3A
This is a list of pathogenic ClinVar variants found in the RAB3A region.
You can filter this list by clicking the number of variants in the Variants pathogenicity by type table.
| Position | Type | Phenotype | Significance | ClinVar |
|---|---|---|---|---|
| 19-18197483-T-G | not specified | Uncertain significance (Dec 08, 2023) | ||
| 19-18197548-G-T | not specified | Uncertain significance (Nov 30, 2022) | ||
| 19-18197619-C-T | not specified | Uncertain significance (Nov 07, 2022) | ||
| 19-18197643-C-T | not specified | Uncertain significance (Feb 22, 2023) | ||
| 19-18198715-G-C | Likely benign (Apr 04, 2018) | |||
| 19-18198733-T-C | not specified | Uncertain significance (Mar 29, 2022) | ||
| 19-18198745-C-T | not specified | Uncertain significance (Oct 06, 2021) | ||
| 19-18198770-G-A | not specified | Uncertain significance (Aug 02, 2021) | ||
| 19-18200389-A-G | Benign (Jan 19, 2022) | |||
| 19-18200404-T-C | Likely benign (Apr 16, 2018) | |||
| 19-18202619-C-T | not specified | Uncertain significance (Sep 29, 2023) | ||
| 19-18202721-G-C | not specified | Uncertain significance (Jun 03, 2022) |
GnomAD
Source:
| Gene | Type | Bio Type | Transcript | Coding Exons | Length |
|---|---|---|---|---|---|
| RAB3A | protein_coding | protein_coding | ENST00000222256 | 4 | 7291 |
| pLI Probability LOF Intolerant | pRec Probability LOF Recessive | Individuals with no LOFs | Individuals with Homozygous LOFs | Individuals with Heterozygous LOFs | Defined | p |
|---|---|---|---|---|---|---|
| 0.946 | 0.0535 | 0 | 0 | 0 | 0 | 0.00 |
| Z-Score | Observed | Expected | Observed/Expected | Mutation Rate | Total Possible in Transcript | |
|---|---|---|---|---|---|---|
| Missense | 2.32 | 71 | 152 | 0.469 | 0.0000104 | 1461 |
| Missense in 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 |
LoF frequencies by population
| Ethnicity | Sum of pLOFs | p |
|---|---|---|
| African & African-American | 0.00 | 0.00 |
| Ashkenazi Jewish | 0.00 | 0.00 |
| East Asian | 0.00 | 0.00 |
| Finnish | 0.00 | 0.00 |
| European (Non-Finnish) | 0.00 | 0.00 |
| Middle Eastern | 0.00 | 0.00 |
| South Asian | 0.00 | 0.00 |
| Other | 0.00 | 0.00 |
dbNSFP
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.;
- Pathway
- Synaptic vesicle cycle - Homo sapiens (human);Insulin secretion - Homo sapiens (human);Synaptic Vesicle Pathway;Brain-Derived Neurotrophic Factor (BDNF) signaling pathway;Neutrophil degranulation;Vesicle-mediated transport;Membrane Trafficking;Post-translational protein modification;Metabolism of proteins;Innate Immune System;Immune System;Neuronal System;Glutamate Neurotransmitter Release Cycle;Rab regulation of trafficking;Dopamine Neurotransmitter Release Cycle;Acetylcholine Neurotransmitter Release Cycle;GABA synthesis, release, reuptake and degradation;Neurotransmitter release cycle;Transmission across Chemical Synapses;RAB GEFs exchange GTP for GDP on RABs;RAB geranylgeranylation;Serotonin Neurotransmitter Release Cycle;Norepinephrine Neurotransmitter Release Cycle
(Consensus)
Recessive Scores
- pRec
- 0.350
Intolerance Scores
- loftool
- rvis_EVS
- -0.23
- rvis_percentile_EVS
- 36.86
Haploinsufficiency Scores
- pHI
- 0.441
- hipred
- Y
- hipred_score
- 0.685
- ghis
- 0.650
Essentials
- essential_gene_CRISPR
- N
- essential_gene_CRISPR2
- N
- essential_gene_gene_trap
- N
- gene_indispensability_pred
- E
- gene_indispensability_score
- 0.911
Gene Damage Prediction
| All | Recessive | Dominant | |
|---|---|---|---|
| Mendelian | Medium | Medium | Medium |
| Primary Immunodeficiency | Medium | Medium | Medium |
| Cancer | Medium | Medium | Medium |
Mouse Genome Informatics
- Gene name
- Rab3a
- Phenotype
- nervous system phenotype (the observable morphological and physiological characteristics of the extensive, intricate network of electochemical structures in the body that is comprised of the brain, spinal cord, nerves, ganglia and parts of the receptor organs that are manifested through development and lifespan); mortality/aging (the observable characteristics related to the ability of a mammalian organism to live and age that are manifested throughout development and life span); normal phenotype; behavior/neurological phenotype (the observable actions or reactions of mammalian organisms that are manifested through development and lifespan); respiratory system phenotype; homeostasis/metabolism phenotype; growth/size/body region phenotype;
Gene ontology
- Biological process
- respiratory system process;intracellular protein transport;vesicle docking involved in exocytosis;mitochondrion organization;neuromuscular synaptic transmission;axonogenesis;protein secretion;post-embryonic development;glutamate secretion;synaptic vesicle exocytosis;synaptic vesicle maturation;regulation of exocytosis;lung development;regulation of synaptic vesicle fusion to presynaptic active zone membrane;Rab protein signal transduction;positive regulation of ATPase activity;synaptic vesicle recycling;neutrophil degranulation;post-translational protein modification;constitutive secretory pathway;positive regulation of exocytosis;regulation of short-term neuronal synaptic plasticity;maintenance of presynaptic active zone structure;sensory perception of touch;response to electrical stimulus;evoked neurotransmitter secretion;protein localization to plasma membrane;positive regulation of regulated secretory pathway
- Cellular component
- acrosomal vesicle;endosome;cytosol;plasma membrane;synaptic vesicle;axon;secretory granule membrane;vesicle;protein-containing complex;terminal bouton;presynaptic active zone;clathrin-sculpted acetylcholine transport vesicle membrane;clathrin-sculpted glutamate transport vesicle membrane;clathrin-sculpted gamma-aminobutyric acid transport vesicle membrane;clathrin-sculpted monoamine transport vesicle membrane;anchored component of synaptic vesicle membrane;extracellular vesicle
- Molecular function
- ATPase activator activity;GTPase activity;protein binding;GTP binding;protein C-terminus binding;GTP-dependent protein binding;myosin V binding;GDP-dissociation inhibitor binding;ATPase binding