CTSV
protein-codingcathepsin V, the group of Cathepsins
Gene summary
The protein encoded by this gene, a member of the peptidase C1 family, is a lysosomal cysteine proteinase that may play an important role in corneal physiology. This gene is expressed in colorectal and breast carcinomas but not in normal colon, mammary gland, or peritumoral tissues, suggesting a possible role for this gene in tumor processes. Alternatively spliced variants, encoding the same protein, have been identified. [provided by RefSeq, Jan 2011]
- CTSL2
MANE transcript
Inheritance
ClinVar variants
Top phenotype
gnomAD constraint
Max pathogenic AF
Genomic locus
External References & Databases
Transcript & Mutation Effects
hg38 • Region Span ~126.9 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 CTSV variants in ClinVar
ClinVar Variants & Pathogenicity by Type
Statistics based on transcript NM_001333.4. 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 | 1 | 1 | 2 | |||
| missense | 43 | 3 | 46 | |||
| nonsense | 0 | |||||
| start loss | 1 | 1 | ||||
| frameshift | 0 | |||||
| splice donor/acceptor (+/-2bp) | 1 | 1 | ||||
| Total | 0 | 0 | 46 | 3 | 1 | 50 |
Transcript Catalog
Annotated transcript isoforms across RefSeq and Ensembl databases
| Transcript ID | Source | Protein ID | Coding Exons | MANE Status |
|---|---|---|---|---|
| RefSeq | NP_001324.2 | 7 | MANE Select | |
| Ensembl | ENSP00000259470.5 | 7 | MANE Select | |
| RefSeq | NP_001188504.1 | 7 | Standard | |
| Ensembl | ENSP00000445052.2 | 6 | Standard |
Gene Ontology (GO) Annotations & Pathways
Biological processes, molecular functions, cellular components and pathways
Pathways ConsensusPathDB
- Lysosome - Homo sapiens (human)
- Apoptosis - Homo sapiens (human)
- Endochondral Ossification
- Assembly of collagen fibrils and other multimeric structures
- Gene expression (Transcription)
Biological Process
- spermatogenesis
- cellular response to starvation
- response to glucose
- multicellular organism aging
- antigen processing and presentation of exogenous peptide antigen via MHC class II
Molecular Function
- aminopeptidase activity
- cysteine-type endopeptidase activity
- serine-type endopeptidase activity
- protein binding
- cysteine-type peptidase activity
Cellular Component
- extracellular region
- extracellular space
- lysosome
- microvillus
- external side of plasma membrane
gnomAD Constraint
Source:
- Gene type
- protein_coding
- Transcript type
- protein_coding
- Transcript
- ENST00000259470
- Coding exons
- 7
- Length
- 6986
- Individuals with no LoFs
- 125689
- Homozygous LoFs
- 0
- Heterozygous LoFs
- 59
- Defined
- 125748
- p
- 0.000235
| Z-Score | Observed | Expected | Observed/Expected | Mutation Rate | Total Possible | |
|---|---|---|---|---|---|---|
| Missense | 0.289 | 177 | 188 | 0.941 | 0.0000103 | 2218 |
| Missense (PolyPhen) | 48 | 69.073 | 0.69492 | 867 | ||
| Synonymous | 0.0908 | 71 | 72.0 | 0.986 | 0.00000450 | 602 |
| Loss of Function | 0.833 | 12 | 15.5 | 0.772 | 7.24e-7 | 187 |
Population LoF Frequency
| Population | CAF | p-value | Status |
|---|---|---|---|
| African | 0.00063 | 0.00062 | rare |
| Latino/Admixed American | 0.00015 | 0.00014 | rare |
| Ashkenazi Jewish | 0.00060 | 0.00060 | rare |
| East Asian | 0.00016 | 0.00016 | rare |
| Finnish | 0.000097 | 0.000092 | rare |
| European (Non-Finnish) | 0.00028 | 0.00027 | rare |
| South Asian | 0 | 0.0 | absent |
| Other | 0.00034 | 0.00033 | rare |
dbNSFP Gene Annotations
Source:
- Function
- FUNCTION: Cysteine protease. May have an important role in corneal physiology. {ECO:0000269|PubMed:10029531, ECO:0000269|PubMed:9727401}.;
Recessive Scores
- pRec
- 0.133
Intolerance Scores
- RVIS EVS
- -0.36
- RVIS percentile EVS
- 29.16
Essentials
- Essential (CRISPR)
- N
- Essential (gene trap)
- N
Gene Damage Prediction
| All | Recessive | Dominant | |
|---|---|---|---|
| Mendelian | Medium | Medium | Medium |
| Primary Immunodeficiency | Medium | Medium | Medium |
| Cancer | Medium | Medium | Medium |