RAB10
RAB10, member RAS oncogene family, the group of RAB, member RAS oncogene GTPases
Basic information
Region (hg38): 2:26034084-26137454
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 RAB10 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 | 0 | |||||
| missense | 4 | |||||
| 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 | 4 | 0 | 0 |
Variants in RAB10
This is a list of pathogenic ClinVar variants found in the RAB10 region.
You can filter this list by clicking the number of variants in the Variants pathogenicity by type table.
| Position | Type | Phenotype | Significance | ClinVar |
|---|---|---|---|---|
| 2-26109767-G-T | CIC-rearranged sarcoma | not provided (-) | ||
| 2-26109881-G-C | not specified | Uncertain significance (Nov 10, 2023) | ||
| 2-26127201-A-G | Uncertain significance (Dec 03, 2020) | |||
| 2-26134940-C-A | Benign (May 03, 2018) | |||
| 2-26134969-T-C | not specified | Uncertain significance (Apr 12, 2022) | ||
| 2-26135008-G-T | Uncertain significance (Jul 01, 2022) |
GnomAD
Source:
| Gene | Type | Bio Type | Transcript | Coding Exons | Length |
|---|---|---|---|---|---|
| RAB10 | protein_coding | protein_coding | ENST00000264710 | 6 | 103348 |
| pLI Probability LOF Intolerant | pRec Probability LOF Recessive | Individuals with no LOFs | Individuals with Homozygous LOFs | Individuals with Heterozygous LOFs | Defined | p |
|---|---|---|---|---|---|---|
| 0.972 | 0.0278 | 0 | 0 | 0 | 0 | 0.00 |
| Z-Score | Observed | Expected | Observed/Expected | Mutation Rate | Total Possible in Transcript | |
|---|---|---|---|---|---|---|
| Missense | 2.63 | 32 | 109 | 0.292 | 0.00000531 | 1338 |
| Missense in Polyphen | 2 | 45.88 | 0.043592 | 560 | ||
| Synonymous | 0.765 | 35 | 41.3 | 0.848 | 0.00000234 | 355 |
| Loss of Function | 3.08 | 0 | 11.1 | 0.00 | 6.14e-7 | 128 |
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: 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 set of downstream effectors directly responsible for vesicle formation, movement, tethering and fusion (By similarity). That Rab is mainly involved in the biosynthetic transport of proteins from the Golgi to the plasma membrane. Regulates, for instance, SLC2A4/GLUT4 glucose transporter-enriched vesicles delivery to the plasma membrane. In parallel, it regulates the transport of TLR4, a toll-like receptor to the plasma membrane and therefore may be important for innate immune response. Plays also a specific role in asymmetric protein transport to the plasma membrane within the polarized neuron and epithelial cells. In neurons, it is involved in axonogenesis through regulation of vesicular membrane trafficking toward the axonal plasma membrane while in epithelial cells, it regulates transport from the Golgi to the basolateral membrane. Moreover, may play a role in the basolateral recycling pathway and in phagosome maturation. According to PubMed:23263280, may play a role in endoplasmic reticulum dynamics and morphology controlling tubulation along microtubules and tubules fusion. {ECO:0000250, ECO:0000269|PubMed:16641372, ECO:0000269|PubMed:21248164, ECO:0000269|PubMed:23263280}.;
- Pathway
- Endocytosis - Homo sapiens (human);AMPK signaling pathway - Homo sapiens (human);Focal Adhesion-PI3K-Akt-mTOR-signaling pathway;Neutrophil degranulation;Vesicle-mediated transport;Membrane Trafficking;Post-translational protein modification;Metabolism of proteins;Innate Immune System;Immune System;Rab regulation of trafficking;RAB GEFs exchange GTP for GDP on RABs;RAB geranylgeranylation;Translocation of GLUT4 to the plasma membrane
(Consensus)
Intolerance Scores
- loftool
- rvis_EVS
- 0.01
- rvis_percentile_EVS
- 54.63
Haploinsufficiency Scores
- pHI
- 0.494
- hipred
- Y
- hipred_score
- 0.775
- ghis
- 0.567
Essentials
- essential_gene_CRISPR
- N
- essential_gene_CRISPR2
- N
- essential_gene_gene_trap
- N
- gene_indispensability_pred
- E
- gene_indispensability_score
- 0.881
Gene Damage Prediction
| All | Recessive | Dominant | |
|---|---|---|---|
| Mendelian | Low | Low | Low |
| Primary Immunodeficiency | Low | Low | Low |
| Cancer | Low | Low | Low |
Mouse Genome Informatics
- Gene name
- Rab10
- Phenotype
- embryo phenotype; growth/size/body region 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); cellular phenotype;
Zebrafish Information Network
- Gene name
- rab10
- Affected structure
- cranial nerve II
- Phenotype tag
- abnormal
- Phenotype quality
- decreased width
Gene ontology
- Biological process
- intracellular protein transport;Golgi to plasma membrane transport;vesicle docking involved in exocytosis;axonogenesis;protein secretion;vesicle-mediated transport;endosomal transport;regulation of exocytosis;antigen processing and presentation;polarized epithelial cell differentiation;Rab protein signal transduction;cellular response to insulin stimulus;Golgi to plasma membrane protein transport;neutrophil degranulation;establishment of neuroblast polarity;endoplasmic reticulum tubular network organization;protein localization to plasma membrane;establishment of protein localization to membrane;establishment of protein localization to endoplasmic reticulum membrane;cell-cell adhesion;protein localization to basolateral plasma membrane
- Cellular component
- Golgi membrane;exocyst;endosome;endoplasmic reticulum membrane;Golgi apparatus;trans-Golgi network;cytosol;plasma membrane;cell-cell adherens junction;focal adhesion;cilium;synaptic vesicle;cytoplasmic vesicle membrane;secretory granule membrane;phagocytic vesicle membrane;insulin-responsive compartment;perinuclear region of cytoplasm;recycling endosome;recycling endosome membrane;extracellular exosome;exocytic vesicle;endoplasmic reticulum tubular network
- Molecular function
- GTPase activity;protein binding;GTP binding;GDP binding;myosin V binding;cadherin binding involved in cell-cell adhesion