RAB13
RAB13, member RAS oncogene family, the group of RAB, member RAS oncogene GTPases
Basic information
Region (hg38): 1:153981617-153986358
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 RAB13 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 | 5 | |||||
| nonsense | 0 | |||||
| start loss | 0 | |||||
| frameshift | 0 | |||||
| inframe indel | 0 | |||||
| splice donor/acceptor (+/-2bp) | 0 | |||||
| splice region | 0 | |||||
| non coding | 0 | |||||
| Total | 0 | 0 | 5 | 1 | 0 |
Variants in RAB13
This is a list of pathogenic ClinVar variants found in the RAB13 region.
You can filter this list by clicking the number of variants in the Variants pathogenicity by type table.
| Position | Type | Phenotype | Significance | ClinVar |
|---|---|---|---|---|
| 1-153982139-G-A | not specified | Uncertain significance (Apr 25, 2022) | ||
| 1-153982404-C-T | not specified | Uncertain significance (Aug 22, 2023) | ||
| 1-153982773-C-G | Likely benign (Apr 01, 2022) | |||
| 1-153984768-C-A | not specified | Uncertain significance (Mar 07, 2024) | ||
| 1-153986121-G-A | not specified | Uncertain significance (Jan 04, 2022) | ||
| 1-153986221-C-A | not specified | Uncertain significance (Jul 13, 2022) | ||
| 1-153986221-C-G | not specified | Uncertain significance (Apr 09, 2024) |
GnomAD
Source:
| Gene | Type | Bio Type | Transcript | Coding Exons | Length |
|---|---|---|---|---|---|
| RAB13 | protein_coding | protein_coding | ENST00000368575 | 8 | 4708 |
| pLI Probability LOF Intolerant | pRec Probability LOF Recessive | Individuals with no LOFs | Individuals with Homozygous LOFs | Individuals with Heterozygous LOFs | Defined | p |
|---|---|---|---|---|---|---|
| 0.0247 | 0.963 | 125739 | 0 | 9 | 125748 | 0.0000358 |
| Z-Score | Observed | Expected | Observed/Expected | Mutation Rate | Total Possible in Transcript | |
|---|---|---|---|---|---|---|
| Missense | 1.07 | 86 | 119 | 0.723 | 0.00000677 | 1342 |
| Missense in Polyphen | 38 | 63.778 | 0.59582 | 704 | ||
| Synonymous | 0.575 | 41 | 46.0 | 0.892 | 0.00000269 | 370 |
| Loss of Function | 2.20 | 5 | 13.8 | 0.362 | 7.40e-7 | 152 |
LoF frequencies by population
| Ethnicity | Sum of pLOFs | p |
|---|---|---|
| African & African-American | 0.000123 | 0.000123 |
| Ashkenazi Jewish | 0.00 | 0.00 |
| East Asian | 0.0000544 | 0.0000544 |
| Finnish | 0.00 | 0.00 |
| European (Non-Finnish) | 0.0000353 | 0.0000352 |
| Middle Eastern | 0.0000544 | 0.0000544 |
| South Asian | 0.0000656 | 0.0000653 |
| Other | 0.00 | 0.00 |
dbNSFP
Source:
- Function
- FUNCTION: The small GTPases Rab are key regulators of intracellular membrane trafficking, from the formation of transport vesicles to their fusion with membranes. Rabs cycle between an inactive GDP-bound form and an active GTP-bound form that is able to recruit to membranes different sets of downstream effectors directly responsible for vesicle formation, movement, tethering and fusion. That Rab is involved in endocytic recycling and regulates the transport to the plasma membrane of transmembrane proteins like the tight junction protein OCLN/occludin. Thereby, it regulates the assembly and the activity of tight junctions. Moreover, it may also regulate tight junction assembly by activating the PKA signaling pathway and by reorganizing the actin cytoskeleton through the activation of the downstream effectors PRKACA and MICALL2 respectively. Through its role in tight junction assembly, may play a role in the establishment of Sertoli cell barrier. Plays also a role in angiogenesis through regulation of endothelial cells chemotaxis. Also involved in neurite outgrowth. Has also been proposed to play a role in post-Golgi membrane trafficking from the TGN to the recycling endosome. Finally, it has been involved in insulin- induced transport to the plasma membrane of the glucose transporter GLUT4 and therefore may play a role in glucose homeostasis. {ECO:0000269|PubMed:12058051, ECO:0000269|PubMed:15096524, ECO:0000269|PubMed:15528189, ECO:0000269|PubMed:16525024, ECO:0000269|PubMed:18779367, ECO:0000269|PubMed:20008558}.;
- Pathway
- Tight junction - Homo sapiens (human);Vesicle-mediated transport;Membrane Trafficking;Post-translational protein modification;Metabolism of proteins;Rab regulation of trafficking;RAB GEFs exchange GTP for GDP on RABs;RAB geranylgeranylation;Translocation of GLUT4 to the plasma membrane
(Consensus)
Recessive Scores
- pRec
- 0.149
Intolerance Scores
- loftool
- 0.353
- rvis_EVS
- 0.22
- rvis_percentile_EVS
- 67.92
Haploinsufficiency Scores
- pHI
- 0.0752
- hipred
- Y
- hipred_score
- 0.818
- ghis
- 0.539
Essentials
- essential_gene_CRISPR
- N
- essential_gene_CRISPR2
- N
- essential_gene_gene_trap
- N
- gene_indispensability_pred
- E
- gene_indispensability_score
- 0.942
Gene Damage Prediction
| All | Recessive | Dominant | |
|---|---|---|---|
| Mendelian | Medium | Medium | Medium |
| Primary Immunodeficiency | Medium | Medium | Medium |
| Cancer | Medium | Medium | Medium |
Mouse Genome Informatics
- Gene name
- Rab13
- Phenotype
Zebrafish Information Network
- Gene name
- rab13
- Affected structure
- dorsal longitudinal anastomotic vessel
- Phenotype tag
- abnormal
- Phenotype quality
- aplastic
Gene ontology
- Biological process
- intracellular protein transport;protein kinase A signaling;endosomal transport;cortical actin cytoskeleton organization;neuron projection development;endocytic recycling;Rab protein signal transduction;cellular response to insulin stimulus;endothelial cell chemotaxis;post-translational protein modification;trans-Golgi network to recycling endosome transport;bicellular tight junction assembly;protein localization to plasma membrane;establishment of Sertoli cell barrier
- Cellular component
- Golgi apparatus;trans-Golgi network;cytosol;plasma membrane;bicellular tight junction;lateral plasma membrane;lamellipodium;cell junction;endocytic vesicle;cytoplasmic vesicle membrane;cytoplasmic vesicle;insulin-responsive compartment;neuron projection;recycling endosome;recycling endosome membrane;extracellular exosome
- Molecular function
- GTPase activity;protein binding;GTP binding