RAB3B
Basic information
Region (hg38): 1:51907956-51990700
Links
Phenotypes
GenCC
Source:
ClinVar
This is a list of variants' phenotypes submitted to
- not_specified (22 variants)
- not_provided (1 variants)
Variants pathogenicity by type
Statistics on ClinVar variants can assist in determining whether a specific variant type in the RAB3B gene is commonly pathogenic or not. These statistics are base on transcript: NM_000002867.4. Only rare variants are included in the table.
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.
| Effect | PathogenicP | Likely pathogenicLP | VUSVUS | Likely benignLB | BenignB | Sum |
|---|---|---|---|---|---|---|
| synonymous | 0 | |||||
| missense | 22 | 22 | ||||
| nonsense | 0 | |||||
| start loss | 0 | |||||
| frameshift | 0 | |||||
| splice donor/acceptor (+/-2bp) | 0 | |||||
| Total | 0 | 0 | 22 | 0 | 0 |
GnomAD
Source:
| Gene | Type | Bio Type | Transcript | Coding Exons | Length |
|---|---|---|---|---|---|
| RAB3B | protein_coding | protein_coding | ENST00000371655 | 4 | 82809 |
| pLI Probability LOF Intolerant | pRec Probability LOF Recessive | Individuals with no LOFs | Individuals with Homozygous LOFs | Individuals with Heterozygous LOFs | Defined | p |
|---|---|---|---|---|---|---|
| 0.315 | 0.670 | 125740 | 0 | 6 | 125746 | 0.0000239 |
| Z-Score | Observed | Expected | Observed/Expected | Mutation Rate | Total Possible in Transcript | |
|---|---|---|---|---|---|---|
| Missense | 0.945 | 104 | 135 | 0.771 | 0.00000803 | 1455 |
| Missense in 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 |
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) | 0.0000529 | 0.0000527 |
| Middle Eastern | 0.00 | 0.00 |
| South Asian | 0.00 | 0.00 |
| Other | 0.00 | 0.00 |
dbNSFP
Source:
- Function
- FUNCTION: Protein transport. Probably involved in vesicular traffic (By similarity). {ECO:0000250}.;
- Pathway
- Post-translational protein modification;Metabolism of proteins;RAB geranylgeranylation
(Consensus)
Recessive Scores
- pRec
- 0.175
Intolerance Scores
- loftool
- 0.458
- rvis_EVS
- -0.01
- rvis_percentile_EVS
- 53.19
Haploinsufficiency Scores
- pHI
- 0.610
- hipred
- Y
- hipred_score
- 0.624
- ghis
- 0.534
Essentials
- essential_gene_CRISPR
- N
- essential_gene_CRISPR2
- N
- essential_gene_gene_trap
- N
- gene_indispensability_pred
- E
- gene_indispensability_score
- 0.668
Gene Damage Prediction
| All | Recessive | Dominant | |
|---|---|---|---|
| Mendelian | Medium | Medium | Medium |
| Primary Immunodeficiency | Medium | Medium | Medium |
| Cancer | Medium | Medium | Medium |
Mouse Genome Informatics
- Gene name
- Rab3b
- Phenotype
- homeostasis/metabolism phenotype; growth/size/body region 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); behavior/neurological phenotype (the observable actions or reactions of mammalian organisms that are manifested through development and lifespan); respiratory system phenotype; normal phenotype; 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);
Zebrafish Information Network
- Gene name
- rab3b
- Affected structure
- yolk
- Phenotype tag
- abnormal
- Phenotype quality
- edematous
Gene ontology
- Biological process
- intracellular protein transport;vesicle docking involved in exocytosis;protein secretion;regulation of exocytosis;peptidyl-cysteine methylation;antigen processing and presentation;Rab protein signal transduction;positive regulation of dopamine uptake involved in synaptic transmission;protein localization to plasma membrane;regulation of vesicle size;regulation of synaptic vesicle cycle
- Cellular component
- cytoplasm;endosome;Golgi apparatus;cytosol;plasma membrane;synaptic vesicle;secretory granule;vesicle;perinuclear region of cytoplasm;extracellular exosome;dopaminergic synapse;anchored component of synaptic vesicle membrane
- Molecular function
- GTPase activity;protein binding;GTP binding;GDP binding;GTP-dependent protein binding;myosin V binding