RILP
protein-codingRab interacting lysosomal protein
Gene summary
This gene encodes a lysosomal protein that interacts with RAB7, a small GTPase that controls transport to endocytic degradative compartments. Studies using mutant forms of the two proteins suggest that this protein represents a downstream effector for RAB7, and both proteins act together in the regulation of late endocytic traffic. A unique region of this protein has also been shown to be involved in the regulation of lysosomal morphology. [provided by RefSeq, Sep 2011]
MANE transcript
Inheritance
ClinVar variants
Top phenotype
gnomAD constraint
Max pathogenic AF
Genomic locus
External References & Databases
Transcript & Mutation Effects
hg38 • Region Span ~3.7 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 RILP variants in ClinVar
ClinVar Variants & Pathogenicity by Type
Statistics based on transcript NM_031430.3. 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 | 0 | |||||
| missense | 64 | 4 | 68 | |||
| nonsense | 1 | 1 | ||||
| start loss | 0 | |||||
| frameshift | 0 | |||||
| splice donor/acceptor (+/-2bp) | 2 | 2 | ||||
| Total | 0 | 0 | 67 | 4 | 0 | 71 |
Transcript Catalog
Annotated transcript isoforms across RefSeq and Ensembl databases
| Transcript ID | Source | Protein ID | Coding Exons | MANE Status |
|---|---|---|---|---|
| RefSeq | NP_113618.2 | 8 | MANE Select | |
| Ensembl | ENSP00000301336.6 | 8 | MANE Select | |
| Ensembl | ENSP00000459101.1 | 4 | Standard | |
| Ensembl | ENSP00000568527.1 | 8 | Standard |
Gene Ontology (GO) Annotations & Pathways
Biological processes, molecular functions, cellular components and pathways
Pathways ConsensusPathDB
- Salmonella infection - Homo sapiens (human)
- Phagosome - Homo sapiens (human)
Biological Process
- endosome to lysosome transport
- regulation of multivesicular body size
- protein transport
- antigen processing and presentation of exogenous peptide antigen via MHC class II
- endosome transport via multivesicular body sorting pathway
Molecular Function
- protein binding
- Rab GTPase binding
- small GTPase binding
- protein dimerization activity
- dynein light intermediate chain binding
Cellular Component
- cytoplasm
- lysosome
- lysosomal membrane
- late endosome
- cytosol
gnomAD Constraint
Source:
- Gene type
- protein_coding
- Transcript type
- protein_coding
- Transcript
- ENST00000301336
- Coding exons
- 8
- Length
- 3928
- Individuals with no LoFs
- 125714
- Homozygous LoFs
- 0
- Heterozygous LoFs
- 24
- Defined
- 125738
- p
- 0.0000954
| Z-Score | Observed | Expected | Observed/Expected | Mutation Rate | Total Possible | |
|---|---|---|---|---|---|---|
| Missense | -0.0185 | 197 | 196 | 1.00 | 0.0000102 | 2467 |
| Missense (PolyPhen) | 63 | 76.595 | 0.82251 | 1047 | ||
| Synonymous | -0.0958 | 90 | 88.9 | 1.01 | 0.00000463 | 849 |
| Loss of Function | -0.404 | 15 | 13.4 | 1.12 | 5.76e-7 | 176 |
Population LoF Frequency
| Population | CAF | p-value | Status |
|---|---|---|---|
| African | 0.00021 | 0.00018 | rare |
| Latino/Admixed American | 0 | 0.0 | absent |
| Ashkenazi Jewish | 0 | 0.0 | absent |
| East Asian | 0.00011 | 0.00011 | rare |
| Finnish | 0.00028 | 0.00028 | rare |
| European (Non-Finnish) | 0.00012 | 0.00011 | rare |
| South Asian | 0 | 0.0 | absent |
| Other | 0 | 0.0 | absent |
dbNSFP Gene Annotations
Source:
- Function
- FUNCTION: Rab effector playing a role in late endocytic transport to degradative compartments. Involved in the regulation of lysosomal morphology and distribution. Induces recruitment of dynein-dynactin motor complexes to Rab7A-containing late endosome and lysosome compartments. Promotes centripetal migration of phagosomes and the fusion of phagosomes with the late endosomes and lysosomes. {ECO:0000269|PubMed:11179213, ECO:0000269|PubMed:11696325, ECO:0000269|PubMed:12944476, ECO:0000269|PubMed:14668488}.;
Recessive Scores
- pRec
- 0.0897
Essentials
- Essential (CRISPR)
- N
- Essential (CRISPR2)
- N
- Essential (gene trap)
- N
- Indispensability pred.
- E
- Indispensability score
- 0.523
Gene Damage Prediction
| All | Recessive | Dominant | |
|---|---|---|---|
| Mendelian | Medium | Medium | Medium |
| Primary Immunodeficiency | Medium | Medium | Medium |
| Cancer | Medium | Medium | Medium |