CTSS

cathepsin S, the group of Cathepsins

Basic information

Region (hg38): 1:150730078-150765957

Links

ENSG00000163131 ∙ NCBI:1520 ∙ OMIM:116845 ∙ HGNC:2545 ∙ Uniprot:P25774 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

Phenotypes

GenCC

Source: genCC

No genCC data.

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the CTSS gene.

• Inborn genetic diseases (6 variants)
• not provided (2 variants)

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	1
missense			5	1		6
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding					1	1
Total	0	0	5	1	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: gnomAD

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: dbNSFP

• 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