RAB9A
protein-codingRAB9A, member RAS oncogene family, the group of RAB, member RAS oncogene GTPases
Gene summary
Enables G protein activity; GDP binding activity; and GTP binding activity. Involved in positive regulation of exocytosis; receptor-mediated endocytosis; and regulation of protein localization. Located in late endosome; lysosome; and phagocytic vesicle. [provided by Alliance of Genome Resources, Jul 2025]
- RAB9
MANE transcript
Inheritance
ClinVar variants
Top phenotype
gnomAD constraint
Max pathogenic AF
Genomic locus
External References & Databases
Transcript & Mutation Effects
hg38 • Region Span ~21.4 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 RAB9A variants in ClinVar
ClinVar Variants & Pathogenicity by Type
Statistics based on transcript NM_004251.5. 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 | 2 | 1 | 1 | 4 | ||
| missense | 18 | 18 | ||||
| nonsense | 0 | |||||
| start loss | 0 | |||||
| frameshift | 0 | |||||
| splice donor/acceptor (+/-2bp) | 4 | 4 | ||||
| Total | 0 | 0 | 24 | 1 | 1 | 26 |
Transcript Catalog
Annotated transcript isoforms across RefSeq and Ensembl databases
| Transcript ID | Source | Protein ID | Coding Exons | MANE Status |
|---|---|---|---|---|
| RefSeq | NP_004242.1 | 1 | MANE Select | |
| Ensembl | ENSP00000420127.1 | 1 | MANE Select | |
| RefSeq | NP_001182257.1 | 1 | Standard | |
| Ensembl | ENSP00000490117.1 | 1 | Standard |
Gene Ontology (GO) Annotations & Pathways
Biological processes, molecular functions, cellular components and pathways
Pathways ConsensusPathDB
- Measles - Homo sapiens (human)
- Ebola Virus Pathway on Host
- Ebola Virus Pathway on Host
- Vesicle-mediated transport
- Membrane Trafficking
Biological Process
- intracellular protein transport
- Rab protein signal transduction
- regulation of protein localization
- retrograde transport, endosome to Golgi
- positive regulation of exocytosis
Molecular Function
- GTPase activity
- protein binding
- GTP binding
- GDP binding
- identical protein binding
Cellular Component
- lysosome
- late endosome
- endoplasmic reticulum membrane
- cytosol
- plasma membrane
gnomAD Constraint
Source:
- Gene type
- protein_coding
- Transcript type
- protein_coding
- Transcript
- ENST00000464506
- Coding exons
- 1
- Length
- 21382
- 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 | 1.28 | 45 | 76.4 | 0.589 | 0.00000569 | 1331 |
| Missense (PolyPhen) | 6 | 32.714 | 0.18341 | 625 | ||
| Synonymous | 0.957 | 23 | 29.6 | 0.776 | 0.00000239 | 380 |
| Loss of Function | 2.25 | 0 | 5.87 | 0.00 | 5.74e-7 | 78 |
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. Involved in the recruitment of SGSM2 to melanosomes and is required for the proper trafficking of melanogenic enzymes TYR, TYRP1 and DCT/TYRP2 to melanosomes in melanocytes. {ECO:0000250|UniProtKB:P24408, ECO:0000250|UniProtKB:Q9R0M6}.;
Recessive Scores
- pRec
- 0.110
Intolerance Scores
- RVIS EVS
- 0.04
- RVIS percentile EVS
- 56.25
Essentials
- Essential (CRISPR)
- N
- Essential (CRISPR2)
- N
- Essential (gene trap)
- N
- Indispensability pred.
- E
- Indispensability score
- 0.539
Gene Damage Prediction
| All | Recessive | Dominant | |
|---|---|---|---|
| Mendelian | Low | Low | Low |
| Primary Immunodeficiency | Low | Low | Low |
| Cancer | Low | Low | Low |