RAB40C
protein-codingRAB40C, member RAS oncogene family, the group of RAB, member RAS oncogene GTPases
Gene summary
Enables G protein activity and ubiquitin-like ligase-substrate adaptor activity. Involved in several processes, including lipid droplet formation; negative regulation of focal adhesion assembly; and proteasome-mediated ubiquitin-dependent protein catabolic process. Located in Golgi membrane; cytosol; and lipid droplet. Part of Cul5-RING ubiquitin ligase complex. [provided by Alliance of Genome Resources, Jun 2026]
- RASL8C
MANE transcript
Inheritance
ClinVar variants
Top phenotype
gnomAD constraint
Max pathogenic AF
Genomic locus
External References & Databases
Transcript & Mutation Effects
hg38 • Region Span ~39.9 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 RAB40C variants in ClinVar
ClinVar Variants & Pathogenicity by Type
Statistics based on transcript NM_021168.5. 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 | 22 | 1 | 23 | |||
| nonsense | 0 | |||||
| start loss | 0 | |||||
| frameshift | 0 | |||||
| splice donor/acceptor (+/-2bp) | 3 | 3 | ||||
| Total | 0 | 0 | 27 | 2 | 1 | 30 |
Transcript Catalog
Annotated transcript isoforms across RefSeq and Ensembl databases
| Transcript ID | Source | Protein ID | Coding Exons | MANE Status |
|---|---|---|---|---|
| RefSeq | NP_066991.3 | 6 | MANE Select | |
| Ensembl | ENSP00000248139.3 | 6 | MANE Select | |
| RefSeq | NP_001166134.1 | 6 | Standard | |
| RefSeq | NP_001166135.1 | 6 | Standard |
Gene Ontology (GO) Annotations & Pathways
Biological processes, molecular functions, cellular components and pathways
Pathways ConsensusPathDB
- Post-translational protein modification
- Metabolism of proteins
- RAB geranylgeranylation
Biological Process
- intracellular protein transport
- protein ubiquitination
- Rab protein signal transduction
Molecular Function
- GTPase activity
- GTP binding
- GDP binding
Cellular Component
- Golgi membrane
- plasma membrane
- perinuclear region of cytoplasm
gnomAD Constraint
Source:
- Gene type
- protein_coding
- Transcript type
- protein_coding
- Transcript
- ENST00000535977
- Coding exons
- 6
- Length
- 39916
- Individuals with no LoFs
- 125647
- Homozygous LoFs
- 0
- Heterozygous LoFs
- 5
- Defined
- 125652
- p
- 0.0000199
| Z-Score | Observed | Expected | Observed/Expected | Mutation Rate | Total Possible | |
|---|---|---|---|---|---|---|
| Missense | 2.34 | 110 | 204 | 0.539 | 0.0000143 | 1840 |
| Missense (PolyPhen) | 57 | 107.36 | 0.5309 | 1030 | ||
| Synonymous | -1.03 | 101 | 88.6 | 1.14 | 0.00000668 | 551 |
| Loss of Function | 1.97 | 5 | 12.5 | 0.399 | 6.20e-7 | 134 |
Population LoF Frequency
| Population | CAF | p-value | Status |
|---|---|---|---|
| African | 0 | 0.0 | absent |
| Latino/Admixed American | 0.000029 | 0.000029 | rare |
| Ashkenazi Jewish | 0 | 0.0 | absent |
| East Asian | 0 | 0.0 | absent |
| Finnish | 0.000048 | 0.000046 | rare |
| European (Non-Finnish) | 0.000027 | 0.000026 | rare |
| South Asian | 0 | 0.0 | absent |
| Other | 0 | 0.0 | absent |
dbNSFP Gene Annotations
Source:
- Function
- FUNCTION: Probable substrate-recognition component of a SCF-like ECS (Elongin-Cullin-SOCS-box protein) E3 ubiquitin ligase complex which mediates the ubiquitination and subsequent proteasomal degradation of target proteins. {ECO:0000269|PubMed:15601820}.;
Recessive Scores
- pRec
- 0.118
Intolerance Scores
- LoFtool
- 0.353
- RVIS EVS
- -0.56
- RVIS percentile EVS
- 19.31
Essentials
- Essential (CRISPR)
- N
- Essential (CRISPR2)
- N
- Essential (gene trap)
- N
- Indispensability pred.
- E
- Indispensability score
- 0.754
Gene Damage Prediction
| All | Recessive | Dominant | |
|---|---|---|---|
| Mendelian | Medium | Low | Low |
| Primary Immunodeficiency | Medium | Low | Medium |
| Cancer | Medium | Medium | Medium |