RABEPK
protein-codingRab9 effector protein with kelch motifs
Gene summary
Predicted to be involved in receptor-mediated endocytosis and vesicle docking involved in exocytosis. Predicted to be located in cytoplasmic vesicle; cytosol; and trans-Golgi network membrane. [provided by Alliance of Genome Resources, Jun 2026]
MANE transcript
Inheritance
ClinVar variants
Top phenotype
gnomAD constraint
Max pathogenic AF
Genomic locus
External References & Databases
Transcript & Mutation Effects
hg38 • Region Span ~33.6 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 RABEPK variants in ClinVar
ClinVar Variants & Pathogenicity by Type
Statistics based on transcript NM_005833.4. 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 | 3 | 3 | ||||
| missense | 69 | 3 | 72 | |||
| nonsense | 0 | |||||
| start loss | 0 | |||||
| frameshift | 0 | |||||
| splice donor/acceptor (+/-2bp) | 5 | 5 | ||||
| Total | 0 | 0 | 77 | 3 | 0 | 80 |
Transcript Catalog
Annotated transcript isoforms across RefSeq and Ensembl databases
| Transcript ID | Source | Protein ID | Coding Exons | MANE Status |
|---|---|---|---|---|
| RefSeq | NP_005824.2 | 7 | MANE Select | |
| Ensembl | ENSP00000362639.3 | 7 | MANE Select | |
| RefSeq | NP_001167623.1 | 7 | Standard | |
| RefSeq | NP_001167624.1 | 6 | Standard |
Gene Ontology (GO) Annotations & Pathways
Biological processes, molecular functions, cellular components and pathways
Pathways ConsensusPathDB
- Vesicle-mediated transport
- Membrane Trafficking
- Retrograde transport at the Trans-Golgi-Network
- Intra-Golgi and retrograde Golgi-to-ER traffic
Biological Process
- receptor-mediated endocytosis
- vesicle docking involved in exocytosis
Cellular Component
- endosome
- cytosol
- endosome membrane
- transport vesicle
- trans-Golgi network membrane
gnomAD Constraint
Source:
- Gene type
- protein_coding
- Transcript type
- protein_coding
- Transcript
- ENST00000373538
- Coding exons
- 7
- Length
- 33617
- Individuals with no LoFs
- 124519
- Homozygous LoFs
- 7
- Heterozygous LoFs
- 1220
- Defined
- 125746
- p
- 0.00489
| Z-Score | Observed | Expected | Observed/Expected | Mutation Rate | Total Possible | |
|---|---|---|---|---|---|---|
| Missense | 0.0477 | 207 | 209 | 0.991 | 0.0000107 | 2423 |
| Missense (PolyPhen) | 77 | 76.219 | 1.0102 | 866 | ||
| Synonymous | 0.157 | 78 | 79.8 | 0.978 | 0.00000441 | 741 |
| Loss of Function | 0.284 | 17 | 18.3 | 0.928 | 0.00000101 | 207 |
Population LoF Frequency
| Population | CAF | p-value | Status |
|---|---|---|---|
| African | 0.0012 | 0.0012 | notable |
| Latino/Admixed American | 0.0051 | 0.0051 | notable |
| Ashkenazi Jewish | 0.0034 | 0.0034 | notable |
| East Asian | 0.00038 | 0.00038 | rare |
| Finnish | 0.00097 | 0.00097 | rare |
| European (Non-Finnish) | 0.0067 | 0.0066 | notable |
| South Asian | 0.0058 | 0.0057 | notable |
| Other | 0.0072 | 0.0072 | notable |
dbNSFP Gene Annotations
Source:
- Function
- FUNCTION: Rab9 effector required for endosome to trans-Golgi network (TGN) transport. {ECO:0000269|PubMed:9230071}.;
Recessive Scores
- pRec
- 0.0851
Intolerance Scores
- LoFtool
- 0.995
- RVIS EVS
- -0.02
- RVIS percentile EVS
- 52.09
Essentials
- Essential (CRISPR)
- N
- Essential (CRISPR2)
- N
- Essential (gene trap)
- N
- Indispensability pred.
- E
- Indispensability score
- 0.887
Gene Damage Prediction
| All | Recessive | Dominant | |
|---|---|---|---|
| Mendelian | Medium | Medium | Medium |
| Primary Immunodeficiency | Medium | Medium | Medium |
| Cancer | Medium | Medium | Medium |