RGP1
protein-codingRGP1 homolog, RAB6A GEF complex partner 1
Gene summary
Enables guanyl-nucleotide exchange factor activity and small GTPase binding activity. Involved in negative regulation of protein catabolic process; positive regulation of GTPase activity; and retrograde transport, endosome to Golgi. Located in cytosol and membrane. Part of Ric1-Rgp1 guanyl-nucleotide exchange factor complex. [provided by Alliance of Genome Resources, Jun 2026]
- KIAA0258
MANE transcript
Inheritance
ClinVar variants
Top phenotype
gnomAD constraint
Max pathogenic AF
Genomic locus
External References & Databases
Transcript & Mutation Effects
hg38 • Region Span ~9.3 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 RGP1 variants in ClinVar
ClinVar Variants & Pathogenicity by Type
Statistics based on transcript NM_001080496.3. 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 | 1 | 1 | ||||
| missense | 57 | 1 | 58 | |||
| nonsense | 0 | |||||
| start loss | 0 | |||||
| frameshift | 0 | |||||
| splice donor/acceptor (+/-2bp) | 1 | 1 | ||||
| Total | 0 | 0 | 59 | 1 | 0 | 60 |
Transcript Catalog
Annotated transcript isoforms across RefSeq and Ensembl databases
| Transcript ID | Source | Protein ID | Coding Exons | MANE Status |
|---|---|---|---|---|
| RefSeq | NP_001073965.2 | 8 | MANE Select | |
| Ensembl | ENSP00000367318.4 | 8 | MANE Select | |
| Ensembl | ENSP00000551035.1 | 8 | Standard | |
| Ensembl | ENSP00000551036.1 | 8 | Standard |
Gene Ontology (GO) Annotations & Pathways
Biological processes, molecular functions, cellular components and pathways
Pathways ConsensusPathDB
- Vesicle-mediated transport
- Membrane Trafficking
- Rab regulation of trafficking
- Intra-Golgi traffic
- RAB GEFs exchange GTP for GDP on RABs
Biological Process
- retrograde transport, endosome to Golgi
- positive regulation of GTPase activity
- negative regulation of cellular protein catabolic process
Molecular Function
- protein binding
- Rab guanyl-nucleotide exchange factor activity
- Rab GTPase binding
Cellular Component
- Golgi membrane
- cytosol
- plasma membrane
- membrane
- trans-Golgi network membrane
gnomAD Constraint
Source:
- Gene type
- protein_coding
- Transcript type
- protein_coding
- Transcript
- ENST00000378078
- Coding exons
- 8
- Length
- 9370
- Individuals with no LoFs
- 124601
- Homozygous LoFs
- 0
- Heterozygous LoFs
- 39
- Defined
- 124640
- p
- 0.000156
| Z-Score | Observed | Expected | Observed/Expected | Mutation Rate | Total Possible | |
|---|---|---|---|---|---|---|
| Missense | 0.718 | 196 | 226 | 0.866 | 0.0000126 | 2477 |
| Missense (PolyPhen) | 39 | 59.999 | 0.65001 | 717 | ||
| Synonymous | 0.0815 | 91 | 92.0 | 0.989 | 0.00000501 | 854 |
| Loss of Function | 1.12 | 16 | 21.6 | 0.741 | 0.00000140 | 208 |
Population LoF Frequency
| Population | CAF | p-value | Status |
|---|---|---|---|
| African | 0.00013 | 0.00013 | rare |
| Latino/Admixed American | 0.00018 | 0.00017 | rare |
| Ashkenazi Jewish | 0.00011 | 0.000099 | rare |
| East Asian | 0.00050 | 0.00050 | rare |
| Finnish | 0.000093 | 0.000046 | rare |
| European (Non-Finnish) | 0.00013 | 0.00013 | rare |
| South Asian | 0.00016 | 0.00016 | rare |
| Other | 0 | 0.0 | absent |
dbNSFP Gene Annotations
Source:
- Function
- FUNCTION: The RIC1-RGP1 complex acts as a guanine nucleotide exchange factor (GEF), which activates RAB6A by exchanging bound GDP for free GTP and may thereby required for efficient fusion of endosome-derived vesicles with the Golgi compartment. The RIC1- RGP1 complex participates in the recycling of mannose-6-phosphate receptors. {ECO:0000269|PubMed:23091056}.;
Intolerance Scores
- LoFtool
- 0.459
- RVIS EVS
- -0.43
- RVIS percentile EVS
- 25.37
Essentials
- Essential (CRISPR)
- N
- Essential (CRISPR2)
- N
- Essential (gene trap)
- N
- Indispensability pred.
- N
- Indispensability score
- 0.410
Gene Damage Prediction
| All | Recessive | Dominant | |
|---|---|---|---|
| Mendelian | Medium | Medium | Medium |
| Primary Immunodeficiency | Medium | Medium | Medium |
| Cancer | Medium | Medium | Medium |