RAB5A
RAB5A, member RAS oncogene family, the group of RAB, member RAS oncogene GTPases
Basic information
Region (hg38): 3:19947097-19985175
Previous symbols: [ "RAB5" ]
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 RAB5A 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 | 7 | |||||
| nonsense | 0 | |||||
| start loss | 0 | |||||
| frameshift | 0 | |||||
| inframe indel | 0 | |||||
| splice donor/acceptor (+/-2bp) | 0 | |||||
| splice region | 0 | |||||
| non coding | 1 | |||||
| Total | 0 | 0 | 7 | 0 | 2 |
Variants in RAB5A
This is a list of pathogenic ClinVar variants found in the RAB5A region.
You can filter this list by clicking the number of variants in the Variants pathogenicity by type table.
| Position | Type | Phenotype | Significance | ClinVar |
|---|---|---|---|---|
| 3-19950914-G-A | not specified | Uncertain significance (Oct 14, 2021) | ||
| 3-19975627-C-T | not specified | Uncertain significance (Mar 07, 2023) | ||
| 3-19975726-A-G | not specified | Uncertain significance (Mar 28, 2024) | ||
| 3-19976056-G-A | not specified | Uncertain significance (Feb 15, 2023) | ||
| 3-19976101-C-G | not specified | Uncertain significance (May 14, 2024) | ||
| 3-19976104-A-G | not specified | Uncertain significance (Oct 03, 2022) | ||
| 3-19976126-G-A | Uncertain significance (Aug 30, 2023) | |||
| 3-19976147-A-G | not specified | Uncertain significance (Sep 27, 2022) | ||
| 3-19978349-A-C | not specified | Uncertain significance (Feb 26, 2024) | ||
| 3-19978378-T-A | not specified | Uncertain significance (May 12, 2024) | ||
| 3-19983742-A-G | Benign (Oct 24, 2018) | |||
| 3-19984917-C-G | Benign (Feb 25, 2021) |
GnomAD
Source:
| Gene | Type | Bio Type | Transcript | Coding Exons | Length |
|---|---|---|---|---|---|
| RAB5A | protein_coding | protein_coding | ENST00000273047 | 5 | 38097 |
| pLI Probability LOF Intolerant | pRec Probability LOF Recessive | Individuals with no LOFs | Individuals with Homozygous LOFs | Individuals with Heterozygous LOFs | Defined | p |
|---|---|---|---|---|---|---|
| 0.625 | 0.374 | 125561 | 0 | 2 | 125563 | 0.00000796 |
| Z-Score | Observed | Expected | Observed/Expected | Mutation Rate | Total Possible in Transcript | |
|---|---|---|---|---|---|---|
| Missense | 0.851 | 92 | 118 | 0.780 | 0.00000591 | 1410 |
| Missense in Polyphen | 11 | 35.773 | 0.30749 | 451 | ||
| Synonymous | -0.599 | 48 | 43.0 | 1.12 | 0.00000251 | 407 |
| Loss of Function | 2.63 | 2 | 11.7 | 0.170 | 6.62e-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) | 0.0000178 | 0.0000176 |
| 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 sets of downstream effectors directly responsible for vesicle formation, movement, tethering and fusion. RAB5A is required for the fusion of plasma membranes and early endosomes (PubMed:10818110, PubMed:14617813, PubMed:16410077, PubMed:15378032). Contributes to the regulation of filopodia extension (PubMed:14978216). Required for the exosomal release of SDCBP, CD63, PDCD6IP and syndecan (PubMed:22660413). Regulates maturation of apoptotic cell- containing phagosomes, probably downstream of DYN2 and PIK3C3 (By similarity). {ECO:0000250|UniProtKB:Q9CQD1, ECO:0000269|PubMed:10818110, ECO:0000269|PubMed:14617813, ECO:0000269|PubMed:14978216, ECO:0000269|PubMed:15378032, ECO:0000269|PubMed:16410077, ECO:0000269|PubMed:22660413}.;
- Pathway
- Endocytosis - Homo sapiens (human);Phagosome - Homo sapiens (human);Amyotrophic lateral sclerosis (ALS) - Homo sapiens (human);Vasopressin-regulated water reabsorption - Homo sapiens (human);Amoebiasis - Homo sapiens (human);Tuberculosis - Homo sapiens (human);Ras signaling pathway - Homo sapiens (human);Amyotrophic lateral sclerosis (ALS);VEGFA-VEGFR2 Signaling Pathway;Ebola Virus Pathway on Host;Ebola Virus Pathway on Host;Ras Signaling;EGF-EGFR Signaling Pathway;Vesicle-mediated transport;phosphoinositides and their downstream targets;TBC/RABGAPs;Membrane Trafficking;Metabolism of lipids;Factors involved in megakaryocyte development and platelet production;Post-translational protein modification;Metabolism of proteins;Metabolism;Clathrin-mediated endocytosis;EGFR1;ErbB1 downstream signaling;Hemostasis;Rab regulation of trafficking;Posttranslational regulation of adherens junction stability and dissassembly;Synthesis of PIPs at the plasma membrane;PI Metabolism;Phospholipid metabolism;RAB GEFs exchange GTP for GDP on RABs;RAB geranylgeranylation;Signaling mediated by p38-alpha and p38-beta;Signaling events mediated by Hepatocyte Growth Factor Receptor (c-Met);IL8- and CXCR1-mediated signaling events;Internalization of ErbB1;PDGFR-beta signaling pathway;IL8- and CXCR2-mediated signaling events
(Consensus)
Recessive Scores
- pRec
- 0.460
Intolerance Scores
- loftool
- 0.314
- rvis_EVS
- -0.32
- rvis_percentile_EVS
- 31.46
Haploinsufficiency Scores
- pHI
- 0.754
- hipred
- Y
- hipred_score
- 0.783
- ghis
- 0.654
Essentials
- essential_gene_CRISPR
- N
- essential_gene_CRISPR2
- N
- essential_gene_gene_trap
- N
- gene_indispensability_pred
- E
- gene_indispensability_score
- 0.706
Gene Damage Prediction
| All | Recessive | Dominant | |
|---|---|---|---|
| Mendelian | Medium | Medium | Medium |
| Primary Immunodeficiency | Medium | Medium | Medium |
| Cancer | Medium | Medium | Medium |
Mouse Genome Informatics
- Gene name
- Rab5a
- Phenotype
- behavior/neurological phenotype (the observable actions or reactions of mammalian organisms that are manifested through development and lifespan); cardiovascular system phenotype (the observable morphological and physiological characteristics of the mammalian heart, blood vessels, or circulatory system that are manifested through development and lifespan); hematopoietic system phenotype; homeostasis/metabolism phenotype;
Zebrafish Information Network
- Gene name
- rab5ab
- Affected structure
- blastoderm
- Phenotype tag
- abnormal
- Phenotype quality
- morphology
Gene ontology
- Biological process
- phosphatidylinositol biosynthetic process;intracellular protein transport;endocytosis;phagocytosis;blood coagulation;regulation of endocytosis;Rab protein signal transduction;synaptic vesicle recycling;viral RNA genome replication;post-translational protein modification;early endosome to late endosome transport;transcytosis;positive regulation of exocytosis;regulation of long-term neuronal synaptic plasticity;regulation of endosome size;regulation of filopodium assembly;membrane organization;receptor internalization involved in canonical Wnt signaling pathway;regulation of synaptic vesicle exocytosis;regulation of autophagosome assembly
- Cellular component
- ruffle;cytoplasm;endosome;early endosome;cytosol;plasma membrane;synaptic vesicle;endosome membrane;actin cytoskeleton;endocytic vesicle;axon;dendrite;clathrin-coated vesicle membrane;phagocytic vesicle membrane;early endosome membrane;somatodendritic compartment;melanosome;neuronal cell body;terminal bouton;axon terminus;membrane raft;extracellular exosome;cytoplasmic side of early endosome membrane;postsynaptic early endosome;anchored component of synaptic vesicle membrane
- Molecular function
- GTPase activity;protein binding;GTP binding;GDP binding