RAB5B
Basic information
Region (hg38): 12:55973913-55996683
Links
Phenotypes
GenCC
Source:
ClinVar
This is a list of variants' phenotypes submitted to
- not_specified (15 variants)
- not_provided (2 variants)
- RAB5B-associated_surfactant_dysfunction_disorder (1 variants)
Variants pathogenicity by type
Statistics on ClinVar variants can assist in determining whether a specific variant type in the RAB5B gene is commonly pathogenic or not. These statistics are base on transcript: NM_000002868.4. 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 | 1 | |||||
| missense | 16 | 16 | ||||
| nonsense | 0 | |||||
| start loss | 0 | |||||
| frameshift | 0 | |||||
| splice donor/acceptor (+/-2bp) | 0 | |||||
| Total | 0 | 0 | 16 | 1 | 0 |
GnomAD
Source:
| Gene | Type | Bio Type | Transcript | Coding Exons | Length |
|---|---|---|---|---|---|
| RAB5B | protein_coding | protein_coding | ENST00000360299 | 5 | 20794 |
| pLI Probability LOF Intolerant | pRec Probability LOF Recessive | Individuals with no LOFs | Individuals with Homozygous LOFs | Individuals with Heterozygous LOFs | Defined | p |
|---|---|---|---|---|---|---|
| 0.0264 | 0.963 | 125743 | 0 | 5 | 125748 | 0.0000199 |
| Z-Score | Observed | Expected | Observed/Expected | Mutation Rate | Total Possible in Transcript | |
|---|---|---|---|---|---|---|
| Missense | 1.32 | 82 | 123 | 0.666 | 0.00000663 | 1412 |
| Missense in Polyphen | 21 | 48.21 | 0.4356 | 556 | ||
| Synonymous | -0.413 | 50 | 46.4 | 1.08 | 0.00000242 | 410 |
| Loss of Function | 2.23 | 5 | 14.0 | 0.358 | 9.34e-7 | 130 |
LoF frequencies by population
| Ethnicity | Sum of pLOFs | p |
|---|---|---|
| African & African-American | 0.00 | 0.00 |
| Ashkenazi Jewish | 0.00 | 0.00 |
| East Asian | 0.000109 | 0.000109 |
| Finnish | 0.00 | 0.00 |
| European (Non-Finnish) | 0.0000265 | 0.0000264 |
| Middle Eastern | 0.000109 | 0.000109 |
| South Asian | 0.00 | 0.00 |
| 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);Phagosome - Homo sapiens (human);Vasopressin-regulated water reabsorption - Homo sapiens (human);Amoebiasis - Homo sapiens (human);Tuberculosis - Homo sapiens (human);Ras signaling pathway - Homo sapiens (human);Ras Signaling;Neutrophil degranulation;Vesicle-mediated transport;TBC/RABGAPs;Membrane Trafficking;Post-translational protein modification;Metabolism of proteins;Innate Immune System;Immune System;Clathrin-mediated endocytosis;Rab regulation of trafficking;RAB GEFs exchange GTP for GDP on RABs;RAB geranylgeranylation
(Consensus)
Recessive Scores
- pRec
- 0.125
Intolerance Scores
- loftool
- 0.336
- rvis_EVS
- -0.12
- rvis_percentile_EVS
- 44.54
Haploinsufficiency Scores
- pHI
- 0.720
- hipred
- Y
- hipred_score
- 0.685
- ghis
- 0.570
Essentials
- essential_gene_CRISPR
- N
- essential_gene_CRISPR2
- N
- essential_gene_gene_trap
- N
- gene_indispensability_pred
- E
- gene_indispensability_score
- 0.999
Gene Damage Prediction
| All | Recessive | Dominant | |
|---|---|---|---|
| Mendelian | Medium | Medium | Medium |
| Primary Immunodeficiency | Medium | Medium | Medium |
| Cancer | Medium | Medium | Medium |
Mouse Genome Informatics
- Gene name
- Rab5b
- Phenotype
Zebrafish Information Network
- Gene name
- rab5b
- Affected structure
- skeletal muscle
- Phenotype tag
- abnormal
- Phenotype quality
- morphology
Gene ontology
- Biological process
- intracellular protein transport;endocytosis;endosome organization;antigen processing and presentation;regulation of endocytosis;Rab protein signal transduction;neutrophil degranulation;plasma membrane to endosome transport
- Cellular component
- endosome;early endosome;plasma membrane;membrane;endocytic vesicle;secretory granule membrane;early endosome membrane;melanosome;intracellular membrane-bounded organelle;extracellular exosome;anchored component of synaptic vesicle membrane
- Molecular function
- GTPase activity;protein binding;GTP binding;GDP binding;GTP-dependent protein binding