RAB9B
Basic information
Region (hg38): X:103822327-103832257
Links
Phenotypes
GenCC
Source:
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 RAB9B 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 | 2 | |||||
| nonsense | 0 | |||||
| start loss | 0 | |||||
| frameshift | 0 | |||||
| inframe indel | 0 | |||||
| splice donor/acceptor (+/-2bp) | 0 | |||||
| splice region | 0 | |||||
| non coding | 0 | |||||
| Total | 0 | 0 | 2 | 0 | 0 |
Variants in RAB9B
This is a list of pathogenic ClinVar variants found in the RAB9B region.
You can filter this list by clicking the number of variants in the Variants pathogenicity by type table.
| Position | Type | Phenotype | Significance | ClinVar |
|---|---|---|---|---|
| X-103825384-G-C | not specified | Uncertain significance (May 20, 2024) | ||
| X-103825520-C-T | not specified | Uncertain significance (Jan 09, 2023) | ||
| X-103825774-T-C | not specified | Uncertain significance (Oct 13, 2023) |
GnomAD
Source:
| Gene | Type | Bio Type | Transcript | Coding Exons | Length |
|---|---|---|---|---|---|
| RAB9B | protein_coding | protein_coding | ENST00000243298 | 1 | 9907 |
| pLI Probability LOF Intolerant | pRec Probability LOF Recessive | Individuals with no LOFs | Individuals with Homozygous LOFs | Individuals with Heterozygous LOFs | Defined | p |
|---|---|---|---|---|---|---|
| 0.734 | 0.255 | 0 | 0 | 0 | 0 | 0.00 |
| Z-Score | Observed | Expected | Observed/Expected | Mutation Rate | Total Possible in Transcript | |
|---|---|---|---|---|---|---|
| Missense | 1.80 | 33 | 77.8 | 0.424 | 0.00000592 | 1338 |
| Missense in Polyphen | 7 | 39.147 | 0.17881 | 696 | ||
| Synonymous | -0.668 | 35 | 30.3 | 1.15 | 0.00000238 | 379 |
| Loss of Function | 1.94 | 0 | 4.38 | 0.00 | 3.34e-7 | 70 |
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: Involved in the transport of proteins between the endosomes and the trans Golgi network. {ECO:0000250|UniProtKB:P24408}.;
- Pathway
- Measles - Homo sapiens (human);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;Retrograde transport at the Trans-Golgi-Network;Intra-Golgi and retrograde Golgi-to-ER traffic
(Consensus)
Recessive Scores
- pRec
- 0.105
Intolerance Scores
- loftool
- rvis_EVS
- -0.08
- rvis_percentile_EVS
- 47.79
Haploinsufficiency Scores
- pHI
- 0.399
- hipred
- Y
- hipred_score
- 0.573
- ghis
- 0.621
Essentials
- essential_gene_CRISPR
- N
- essential_gene_CRISPR2
- N
- essential_gene_gene_trap
- N
- gene_indispensability_pred
- N
- gene_indispensability_score
- 0.307
Gene Damage Prediction
| All | Recessive | Dominant | |
|---|---|---|---|
| Mendelian | Medium | Medium | Medium |
| Primary Immunodeficiency | Medium | Medium | Medium |
| Cancer | Medium | Medium | Medium |
Mouse Genome Informatics
- Gene name
- Rab9b
- Phenotype
Gene ontology
- Biological process
- intracellular protein transport;Rab protein signal transduction;retrograde transport, endosome to Golgi;neutrophil degranulation
- Cellular component
- cytosol;plasma membrane;secretory granule membrane;phagocytic vesicle membrane;phagocytic vesicle
- Molecular function
- GTPase activity;protein binding;GTP binding;GDP binding;identical protein binding