RAB4A
Basic information
Region (hg38): 1:229271062-229305894
Previous symbols: [ "RAB4" ]
Links
Phenotypes
GenCC
Source:
ClinVar
This is a list of variants' phenotypes submitted to
- not_specified (22 variants)
Variants pathogenicity by type
Statistics on ClinVar variants can assist in determining whether a specific variant type in the RAB4A gene is commonly pathogenic or not. These statistics are base on transcript: NM_000004578.4. 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 |
|---|---|---|---|---|---|
| RAB4A | protein_coding | protein_coding | ENST00000366690 | 7 | 34820 |
| pLI Probability LOF Intolerant | pRec Probability LOF Recessive | Individuals with no LOFs | Individuals with Homozygous LOFs | Individuals with Heterozygous LOFs | Defined | p |
|---|---|---|---|---|---|---|
| 0.203 | 0.796 | 125725 | 0 | 19 | 125744 | 0.0000756 |
| Z-Score | Observed | Expected | Observed/Expected | Mutation Rate | Total Possible in Transcript | |
|---|---|---|---|---|---|---|
| Missense | 1.28 | 84 | 124 | 0.676 | 0.00000736 | 1414 |
| Missense in Polyphen | 26 | 41.982 | 0.61931 | 476 | ||
| Synonymous | -0.369 | 51 | 47.8 | 1.07 | 0.00000329 | 406 |
| Loss of Function | 2.71 | 4 | 15.5 | 0.258 | 0.00000101 | 169 |
LoF frequencies by population
| Ethnicity | Sum of pLOFs | p |
|---|---|---|
| African & African-American | 0.000120 | 0.000120 |
| Ashkenazi Jewish | 0.00 | 0.00 |
| East Asian | 0.000414 | 0.000381 |
| Finnish | 0.00 | 0.00 |
| European (Non-Finnish) | 0.0000634 | 0.0000615 |
| Middle Eastern | 0.000414 | 0.000381 |
| South Asian | 0.0000333 | 0.0000327 |
| Other | 0.00 | 0.00 |
dbNSFP
Source:
- Function
- FUNCTION: Protein transport. Probably involved in vesicular traffic (By similarity). {ECO:0000250}.;
- Pathway
- Endocytosis - Homo sapiens (human);VEGFA-VEGFR2 Signaling Pathway;Insulin Signaling;Vesicle-mediated transport;TBC/RABGAPs;Membrane Trafficking;Metabolism of lipids;Post-translational protein modification;Metabolism of proteins;Metabolism;Rab regulation of trafficking;Synthesis of PIPs at the plasma membrane;PI Metabolism;Phospholipid metabolism;RAB geranylgeranylation;Translocation of GLUT4 to the plasma membrane;PDGFR-beta signaling pathway
(Consensus)
Recessive Scores
- pRec
- 0.107
Intolerance Scores
- loftool
- 0.435
- rvis_EVS
- -0.12
- rvis_percentile_EVS
- 44.54
Haploinsufficiency Scores
- pHI
- 0.224
- hipred
- Y
- hipred_score
- 0.792
- ghis
- 0.598
Essentials
- essential_gene_CRISPR
- N
- essential_gene_CRISPR2
- N
- essential_gene_gene_trap
- N
- gene_indispensability_pred
- E
- gene_indispensability_score
- 0.915
Gene Damage Prediction
| All | Recessive | Dominant | |
|---|---|---|---|
| Mendelian | Medium | Medium | Medium |
| Primary Immunodeficiency | Medium | Medium | Medium |
| Cancer | Medium | Medium | Medium |
Mouse Genome Informatics
- Gene name
- Rab4a
- Phenotype
Zebrafish Information Network
- Gene name
- rab4a
- Affected structure
- vasculature
- Phenotype tag
- abnormal
- Phenotype quality
- malformed
Gene ontology
- Biological process
- phosphatidylinositol biosynthetic process;intracellular protein transport;antigen processing and presentation;regulation of endocytosis;Rab protein signal transduction;positive regulation of ATPase activity
- Cellular component
- endosome;cytosol;plasma membrane;cytoplasmic vesicle membrane;early endosome membrane;vesicle;insulin-responsive compartment;intracellular membrane-bounded organelle;perinuclear region of cytoplasm;recycling endosome membrane;extracellular exosome;postsynaptic recycling endosome;anchored component of synaptic vesicle membrane
- Molecular function
- ATPase activator activity;GTPase activity;protein binding;GTP binding;protein transporter activity;GDP binding;syntaxin binding;ionotropic glutamate receptor binding;ATPase binding