CTSE
protein-codingcathepsin E, the group of Peptidase family A1|Cathepsins
Gene summary
This gene encodes a member of the A1 family of peptidases. Alternative splicing of this gene results in multiple transcript variants. At least one of these variants encodes a preproprotein that is proteolytically processed to generate the mature enzyme. This enzyme, an aspartic endopeptidase, may be involved in antigen processing and the maturation of secretory proteins. Elevated expression of this gene has been observed in neurodegeneration. [provided by RefSeq, Nov 2015]
MANE transcript
Inheritance
ClinVar variants
Top phenotype
gnomAD constraint
Max pathogenic AF
Genomic locus
External References & Databases
Transcript & Mutation Effects
hg38 • Region Span ~15.4 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 CTSE variants in ClinVar
ClinVar Variants & Pathogenicity by Type
Statistics based on transcript NM_001910.4. 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 | 2 | 8 | 10 | |||
| missense | 77 | 1 | 78 | |||
| nonsense | 0 | |||||
| start loss | 0 | |||||
| frameshift | 0 | |||||
| splice donor/acceptor (+/-2bp) | 1 | 1 | ||||
| Total | 0 | 0 | 80 | 9 | 0 | 89 |
Transcript Catalog
Annotated transcript isoforms across RefSeq and Ensembl databases
| Transcript ID | Source | Protein ID | Coding Exons | MANE Status |
|---|---|---|---|---|
| RefSeq | NP_001901.1 | 9 | MANE Select | |
| Ensembl | ENSP00000350911.2 | 9 | MANE Select | |
| RefSeq | NP_001304260.1 | 6 | Standard | |
| RefSeq | NP_683865.1 | 8 | Standard |
Gene Ontology (GO) Annotations & Pathways
Biological processes, molecular functions, cellular components and pathways
Pathways ConsensusPathDB
- Lysosome - Homo sapiens (human)
- MHC class II antigen presentation
- Immune System
- Adaptive Immune System
Biological Process
- proteolysis
- protein autoprocessing
- antigen processing and presentation of exogenous peptide antigen via MHC class II
- protein catabolic process
Molecular Function
- aspartic-type endopeptidase activity
- protein homodimerization activity
Cellular Component
- endosome
gnomAD Constraint
Source:
- Gene type
- protein_coding
- Transcript type
- protein_coding
- Transcript
- ENST00000358184
- Coding exons
- 9
- Length
- 14646
- Individuals with no LoFs
- 125328
- Homozygous LoFs
- 6
- Heterozygous LoFs
- 406
- Defined
- 125740
- p
- 0.00164
| Z-Score | Observed | Expected | Observed/Expected | Mutation Rate | Total Possible | |
|---|---|---|---|---|---|---|
| Missense | -0.296 | 241 | 228 | 1.06 | 0.0000123 | 2594 |
| Missense (PolyPhen) | 96 | 93.712 | 1.0244 | 1101 | ||
| Synonymous | -0.981 | 107 | 94.8 | 1.13 | 0.00000590 | 801 |
| Loss of Function | -0.469 | 20 | 17.9 | 1.12 | 7.60e-7 | 208 |
Population LoF Frequency
| Population | CAF | p-value | Status |
|---|---|---|---|
| African | 0.0054 | 0.0054 | notable |
| Latino/Admixed American | 0.00082 | 0.00081 | rare |
| Ashkenazi Jewish | 0 | 0.0 | absent |
| East Asian | 0.00011 | 0.00011 | rare |
| Finnish | 0.000092 | 0.000092 | rare |
| European (Non-Finnish) | 0.00049 | 0.00048 | rare |
| South Asian | 0.0079 | 0.0077 | notable |
| Other | 0.00049 | 0.00049 | rare |
dbNSFP Gene Annotations
Source:
- Function
- FUNCTION: May have a role in immune function. Probably involved in the processing of antigenic peptides during MHC class II-mediated antigen presentation. May play a role in activation-induced lymphocyte depletion in the thymus, and in neuronal degeneration and glial cell activation in the brain. {ECO:0000269|PubMed:8765029}.;
Recessive Scores
- pRec
- 0.242
Intolerance Scores
- LoFtool
- 0.859
- RVIS EVS
- 0.85
- RVIS percentile EVS
- 88.42
Essentials
- Essential (CRISPR)
- N
- Essential (CRISPR2)
- N
- Essential (gene trap)
- N
- Indispensability pred.
- E
- Indispensability score
- 0.866
Gene Damage Prediction
| All | Recessive | Dominant | |
|---|---|---|---|
| Mendelian | Medium | Medium | Medium |
| Primary Immunodeficiency | Medium | Medium | Medium |
| Cancer | Medium | Medium | Medium |