RAB9B
protein-codingRAB9B, member RAS oncogene family, the group of RAB, member RAS oncogene GTPases
Gene summary
This gene encodes a member of a subfamily of RAS small guanosine triphosphate (GTP)-binding proteins that regulate membrane trafficking. The encoded protein may be involved in endosome-to-Golgi transport. [provided by RefSeq, Jan 2010]
MANE transcript
Inheritance
ClinVar variants
Top phenotype
gnomAD constraint
Max pathogenic AF
Genomic locus
External References & Databases
Transcript & Mutation Effects
hg38 • Region Span ~9.9 kbGenCC Phenotypes & Disease Associations
Curated gene-disease validity assertions and inheritance patterns
No GenCC data available for this gene.
ClinVar Associated Diseases & Phenotypes
Reported disease conditions connected to RAB9B variants in ClinVar
ClinVar Variants & Pathogenicity by Type
Statistics based on transcript NM_016370.4. Only rare variants are included.
We include only reliable ClinVar variants with their consequences to MANE Select, MANE Plus Clinical transcripts, or transcripts with TSL equal to 1. Click a count to filter the variants table below.
Slight differences between displayed counts and ClinVar may occur due to a different transcript/consequence chosen by our variant effect predictor, or because we classify Benign/Likely benign as Likely benign and Pathogenic/Likely pathogenic as Likely pathogenic.
| Effect | PathogenicP | Likely pathogenicLP | VUS | Likely benignLB | BenignB | Sum |
|---|---|---|---|---|---|---|
| synonymous | 4 | 4 | ||||
| missense | 17 | 17 | ||||
| nonsense | 1 | 1 | ||||
| start loss | 0 | |||||
| frameshift | 0 | |||||
| splice donor/acceptor (+/-2bp) | 3 | 3 | ||||
| Total | 0 | 0 | 25 | 0 | 0 | 25 |
Transcript Catalog
Annotated transcript isoforms across RefSeq and Ensembl databases
| Transcript ID | Source | Protein ID | Coding Exons | MANE Status |
|---|---|---|---|---|
| RefSeq | NP_057454.1 | 1 | MANE Select | |
| Ensembl | ENSP00000243298.2 | 1 | MANE Select | |
| Ensembl | ENSP00000543795.1 | 1 | Standard | |
| Ensembl | ENSP00000543795.1 | 1 | Standard |
Gene Ontology (GO) Annotations & Pathways
Biological processes, molecular functions, cellular components and pathways
Pathways ConsensusPathDB
- Measles - Homo sapiens (human)
- Neutrophil degranulation
- Vesicle-mediated transport
- Membrane Trafficking
- Post-translational protein modification
Biological Process
- intracellular protein transport
- Rab protein signal transduction
- retrograde transport, endosome to Golgi
- neutrophil degranulation
Molecular Function
- GTPase activity
- protein binding
- GTP binding
- GDP binding
- identical protein binding
Cellular Component
- cytosol
- plasma membrane
- secretory granule membrane
- phagocytic vesicle membrane
- phagocytic vesicle
gnomAD Constraint
Source:
- Gene type
- protein_coding
- Transcript type
- protein_coding
- Transcript
- ENST00000243298
- Coding exons
- 1
- Length
- 9907
- Individuals with no LoFs
- 0
- Homozygous LoFs
- 0
- Heterozygous LoFs
- 0
- Defined
- 0
- p
- 0.00
| Z-Score | Observed | Expected | Observed/Expected | Mutation Rate | Total Possible | |
|---|---|---|---|---|---|---|
| Missense | 1.80 | 33 | 77.8 | 0.424 | 0.00000592 | 1338 |
| Missense (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 |
Population LoF Frequency
| Population | CAF | p-value | Status |
|---|---|---|---|
| African | 0 | 0.0 | absent |
| Latino/Admixed American | 0 | 0.0 | absent |
| Ashkenazi Jewish | 0 | 0.0 | absent |
| East Asian | 0 | 0.0 | absent |
| Finnish | 0 | 0.0 | absent |
| European (Non-Finnish) | 0 | 0.0 | absent |
| South Asian | 0 | 0.0 | absent |
| Other | 0 | 0.0 | absent |
dbNSFP Gene Annotations
Source:
- Function
- FUNCTION: Involved in the transport of proteins between the endosomes and the trans Golgi network. {ECO:0000250|UniProtKB:P24408}.;
Recessive Scores
- pRec
- 0.105
Intolerance Scores
- RVIS EVS
- -0.08
- RVIS percentile EVS
- 47.79
Essentials
- Essential (CRISPR)
- N
- Essential (CRISPR2)
- N
- Essential (gene trap)
- N
- Indispensability pred.
- N
- Indispensability score
- 0.307
Gene Damage Prediction
| All | Recessive | Dominant | |
|---|---|---|---|
| Mendelian | Medium | Medium | Medium |
| Primary Immunodeficiency | Medium | Medium | Medium |
| Cancer | Medium | Medium | Medium |