CTSS
cathepsin S, the group of Cathepsins
Basic information
Region (hg38): 1:150730079-150765957
Links
Phenotypes
GenCC
Source:
No genCC data.
ClinVar
This is a list of variants' phenotypes submitted to
Variants pathogenicity by type
Statistics on ClinVar variants can assist in determining whether a specific variant type in the CTSS gene is commonly pathogenic or not.
In the table, we include only reliable ClinVar variants with their consequences to MANE Select, Mane Plus Clinical transcripts, or transcripts with TSL equals 1. Click the count to view the source variants.
Warning: slight differences between displayed counts and the number of variants in ClinVar may occur, primarily due to (1) the application of a different transcript and/or consequence by our variant effect predictor or (2) differences in clinical significance: we classify Benign/Likely benign variants as Likely benign and Pathogenic/Likely pathogenic variants as Likely pathogenic.
| Variant type | Pathogenic | Likely pathogenic | VUS | Likely benign | Benign | Sum |
|---|---|---|---|---|---|---|
| synonymous | 1 | |||||
| missense | 7 | |||||
| nonsense | 0 | |||||
| start loss | 0 | |||||
| frameshift | 0 | |||||
| inframe indel | 0 | |||||
| splice donor/acceptor (+/-2bp) | 0 | |||||
| splice region | 0 | |||||
| non coding | 1 | |||||
| Total | 0 | 0 | 5 | 2 | 2 |
Variants in CTSS
This is a list of pathogenic ClinVar variants found in the CTSS region.
You can filter this list by clicking the number of variants in the Variants pathogenicity by type table.
| Position | Type | Phenotype | Significance | ClinVar |
|---|---|---|---|---|
| 1-150747785-C-A | Benign (Jul 07, 2018) | |||
| 1-150750072-C-T | not specified | Uncertain significance (Nov 08, 2022) | ||
| 1-150750132-T-C | not specified | Uncertain significance (Sep 29, 2022) | ||
| 1-150751772-A-T | Benign (Aug 06, 2018) | |||
| 1-150751830-A-G | not specified | Uncertain significance (Dec 21, 2022) | ||
| 1-150751874-T-G | not specified | Uncertain significance (Aug 21, 2023) | ||
| 1-150755041-T-G | not specified | Uncertain significance (Jul 25, 2023) | ||
| 1-150755062-C-T | not specified | Likely benign (Jul 25, 2023) | ||
| 1-150764757-G-A | not specified | Likely benign (Jan 19, 2024) |
GnomAD
Source:
| Gene | Type | Bio Type | Transcript | Coding Exons | Length |
|---|---|---|---|---|---|
| CTSS | protein_coding | protein_coding | ENST00000368985 | 7 | 35762 |
| pLI Probability LOF Intolerant | pRec Probability LOF Recessive | Individuals with no LOFs | Individuals with Homozygous LOFs | Individuals with Heterozygous LOFs | Defined | p |
|---|---|---|---|---|---|---|
| 0.342 | 0.658 | 125738 | 0 | 10 | 125748 | 0.0000398 |
| Z-Score | Observed | Expected | Observed/Expected | Mutation Rate | Total Possible in Transcript | |
|---|---|---|---|---|---|---|
| Missense | 2.24 | 96 | 181 | 0.531 | 0.00000906 | 2174 |
| Missense in Polyphen | 30 | 81.025 | 0.37025 | 953 | ||
| Synonymous | 0.986 | 54 | 64.0 | 0.843 | 0.00000319 | 615 |
| Loss of Function | 2.98 | 4 | 17.4 | 0.229 | 8.32e-7 | 219 |
LoF frequencies by population
| Ethnicity | Sum of pLOFs | p |
|---|---|---|
| African & African-American | 0.0000289 | 0.0000289 |
| Ashkenazi Jewish | 0.00 | 0.00 |
| East Asian | 0.00 | 0.00 |
| Finnish | 0.00 | 0.00 |
| European (Non-Finnish) | 0.0000704 | 0.0000703 |
| Middle Eastern | 0.00 | 0.00 |
| South Asian | 0.0000327 | 0.0000327 |
| Other | 0.00 | 0.00 |
dbNSFP
Source:
- Function
- FUNCTION: Thiol protease. Key protease responsible for the removal of the invariant chain from MHC class II molecules. The bond- specificity of this proteinase is in part similar to the specificities of cathepsin L.;
- Pathway
- Antigen processing and presentation - Homo sapiens (human);Phagosome - Homo sapiens (human);Lysosome - Homo sapiens (human);Tuberculosis - Homo sapiens (human);Apoptosis - Homo sapiens (human);Neutrophil degranulation;Assembly of collagen fibrils and other multimeric structures;Trafficking and processing of endosomal TLR;Toll-Like Receptors Cascades;Collagen formation;Extracellular matrix organization;MHC class II antigen presentation;Innate Immune System;Immune System;Adaptive Immune System;Endosomal/Vacuolar pathway;Antigen processing-Cross presentation;Class I MHC mediated antigen processing & presentation;Degradation of the extracellular matrix
(Consensus)
Recessive Scores
- pRec
- 0.312
Intolerance Scores
- loftool
- 0.251
- rvis_EVS
- 0.22
- rvis_percentile_EVS
- 67.92
Haploinsufficiency Scores
- pHI
- 0.581
- hipred
- Y
- hipred_score
- 0.573
- ghis
- 0.536
Essentials
- essential_gene_CRISPR
- N
- essential_gene_CRISPR2
- N
- essential_gene_gene_trap
- N
- gene_indispensability_pred
- E
- gene_indispensability_score
- 0.688
Gene Damage Prediction
| All | Recessive | Dominant | |
|---|---|---|---|
| Mendelian | Medium | Medium | Medium |
| Primary Immunodeficiency | Medium | Medium | High |
| Cancer | High | Medium | High |
Mouse Genome Informatics
- Gene name
- Ctss
- Phenotype
- muscle phenotype; homeostasis/metabolism phenotype; cellular phenotype; endocrine/exocrine gland phenotype; digestive/alimentary phenotype; immune system phenotype; skeleton phenotype; respiratory system phenotype; behavior/neurological phenotype (the observable actions or reactions of mammalian organisms that are manifested through development and lifespan); cardiovascular system phenotype (the observable morphological and physiological characteristics of the mammalian heart, blood vessels, or circulatory system that are manifested through development and lifespan); hematopoietic system phenotype;
Gene ontology
- Biological process
- toll-like receptor signaling pathway;adaptive immune response;proteolysis;immune response;response to acidic pH;protein processing;antigen processing and presentation;antigen processing and presentation of exogenous peptide antigen via MHC class II;extracellular matrix disassembly;collagen catabolic process;basement membrane disassembly;neutrophil degranulation;antigen processing and presentation of peptide antigen;proteolysis involved in cellular protein catabolic process;cellular response to thyroid hormone stimulus;positive regulation of cation channel activity
- Cellular component
- extracellular region;extracellular space;lysosome;endolysosome lumen;lysosomal lumen;intracellular membrane-bounded organelle;collagen-containing extracellular matrix;tertiary granule lumen;ficolin-1-rich granule lumen
- Molecular function
- fibronectin binding;cysteine-type endopeptidase activity;serine-type endopeptidase activity;collagen binding;laminin binding;proteoglycan binding