RAB2A
Basic information
Region (hg38): 8:60516936-60623644
Previous symbols: [ "RAB2" ]
Links
Phenotypes
GenCC
Source:
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 RAB2A 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 | 1 | |||||
| missense | 3 | |||||
| nonsense | 0 | |||||
| start loss | 0 | |||||
| frameshift | 0 | |||||
| inframe indel | 0 | |||||
| splice donor/acceptor (+/-2bp) | 0 | |||||
| splice region | 1 | 1 | ||||
| non coding | 0 | |||||
| Total | 0 | 0 | 3 | 1 | 0 |
Variants in RAB2A
This is a list of pathogenic ClinVar variants found in the RAB2A region.
You can filter this list by clicking the number of variants in the Variants pathogenicity by type table.
| Position | Type | Phenotype | Significance | ClinVar |
|---|---|---|---|---|
| 8-60539487-A-G | Vascular endothelial growth factor (VEGF) inhibitor response | association (-) | ||
| 8-60572038-CTATT-C | Likely benign (Aug 22, 2018) | |||
| 8-60572056-C-T | not specified | Likely benign (Jul 26, 2024) | ||
| 8-60584772-C-T | Uncertain significance (Oct 11, 2022) | |||
| 8-60620702-A-G | not specified | Uncertain significance (Jul 26, 2022) | ||
| 8-60620726-C-G | not specified | Uncertain significance (Feb 13, 2024) |
GnomAD
Source:
| Gene | Type | Bio Type | Transcript | Coding Exons | Length |
|---|---|---|---|---|---|
| RAB2A | protein_coding | protein_coding | ENST00000262646 | 8 | 106771 |
| pLI Probability LOF Intolerant | pRec Probability LOF Recessive | Individuals with no LOFs | Individuals with Homozygous LOFs | Individuals with Heterozygous LOFs | Defined | p |
|---|---|---|---|---|---|---|
| 0.989 | 0.0109 | 0 | 0 | 0 | 0 | 0.00 |
| Z-Score | Observed | Expected | Observed/Expected | Mutation Rate | Total Possible in Transcript | |
|---|---|---|---|---|---|---|
| Missense | 2.99 | 24 | 114 | 0.211 | 0.00000599 | 1385 |
| Missense in Polyphen | 2 | 39.665 | 0.050422 | 477 | ||
| Synonymous | 0.856 | 31 | 37.7 | 0.823 | 0.00000207 | 372 |
| Loss of Function | 3.42 | 0 | 13.6 | 0.00 | 7.39e-7 | 160 |
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: Required for protein transport from the endoplasmic reticulum to the Golgi complex.;
- Pathway
- AMPK signaling pathway - Homo sapiens (human);Focal Adhesion-PI3K-Akt-mTOR-signaling pathway;Post-translational protein modification;Metabolism of proteins;Golgi Cisternae Pericentriolar Stack Reorganization;Mitotic Prophase;M Phase;Cell Cycle;RAB geranylgeranylation;Cell Cycle, Mitotic
(Consensus)
Recessive Scores
- pRec
- 0.240
Intolerance Scores
- loftool
- rvis_EVS
- 0.01
- rvis_percentile_EVS
- 54.63
Haploinsufficiency Scores
- pHI
- 0.660
- hipred
- Y
- hipred_score
- 0.825
- ghis
- 0.680
Essentials
- essential_gene_CRISPR
- N
- essential_gene_CRISPR2
- N
- essential_gene_gene_trap
- N
- gene_indispensability_pred
- E
- gene_indispensability_score
- 0.914
Gene Damage Prediction
| All | Recessive | Dominant | |
|---|---|---|---|
| Mendelian | Medium | Low | Low |
| Primary Immunodeficiency | Medium | Low | Medium |
| Cancer | Low | Low | Low |
Mouse Genome Informatics
- Gene name
- Rab2a
- Phenotype
Gene ontology
- Biological process
- intracellular protein transport;endoplasmic reticulum to Golgi vesicle-mediated transport;Golgi organization;Rab protein signal transduction;post-translational protein modification
- Cellular component
- Golgi membrane;nucleus;lysosomal membrane;endoplasmic reticulum membrane;Golgi apparatus;cytosol;endoplasmic reticulum-Golgi intermediate compartment membrane;melanosome;extracellular exosome
- Molecular function
- GTPase activity;protein binding;GTP binding;GDP binding