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    CTSS cathepsin S [ Homo sapiens (human) ]

    Gene ID: 1520, updated on 5-Mar-2024

    Summary

    Official Symbol
    CTSSprovided by HGNC
    Official Full Name
    cathepsin Sprovided by HGNC
    Primary source
    HGNC:HGNC:2545
    See related
    Ensembl:ENSG00000163131 MIM:116845; AllianceGenome:HGNC:2545
    Gene type
    protein coding
    RefSeq status
    REVIEWED
    Organism
    Homo sapiens
    Lineage
    Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Primates; Haplorrhini; Catarrhini; Hominidae; Homo
    Summary
    The preproprotein encoded by this gene, a member of the peptidase C1 family, is a lysosomal cysteine proteinase that participates in the degradation of antigenic proteins to peptides for presentation on MHC class II molecules. The mature protein cleaves the invariant chain of MHC class II molecules in endolysosomal compartments and enables the formation of antigen-MHC class II complexes and the proper display of extracellular antigenic peptides by MHC-II. The mature protein also functions as an elastase over a broad pH range. When secreted from cells, this protein can remodel components of the extracellular matrix such as elastin, collagen, and fibronectin. This gene is implicated in the pathology of many inflammatory and autoimmune diseases and, given its elastase activity, plays a significant role in some pulmonary diseases. Alternatively spliced transcript variants encoding distinct isoforms have been found for this gene. [provided by RefSeq, May 2020]
    Annotation information
    Note: This gene has been reviewed for its involvement in coronavirus biology, and is involved in immune response or antiviral activity.
    Expression
    Broad expression in spleen (RPKM 89.0), appendix (RPKM 75.4) and 18 other tissues See more
    Orthologs
    NEW
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    Try the new Transcript table

    Genomic context

    See CTSS in Genome Data Viewer
    Location:
    1q21.3
    Exon count:
    8
    Annotation release Status Assembly Chr Location
    RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 1 NC_000001.11 (150730188..150765778, complement)
    RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 1 NC_060925.1 (149853594..149889583, complement)
    105.20220307 previous assembly GRCh37.p13 (GCF_000001405.25) 1 NC_000001.10 (150702664..150738254, complement)

    Chromosome 1 - NC_000001.11Genomic Context describing neighboring genes Neighboring gene H3K27ac hESC enhancer GRCh37_chr1:150619341-150619842 Neighboring gene golgi phosphoprotein 3 like Neighboring gene RNA, U6 small nuclear 1042, pseudogene Neighboring gene HORMA domain containing 1 Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr1:150700761-150701526 Neighboring gene melanoma risk locus-associated MPRA allelic enhancer 1:150703034 Neighboring gene melanoma risk locus-associated MPRA allelic enhancer 1:150703366 Neighboring gene melanoma risk locus-associated MPRA allelic enhancer 1:150707596 Neighboring gene melanoma risk locus-associated MPRA allelic enhancer 1:150709723 Neighboring gene melanoma risk locus-associated MPRA allelic enhancer 1:150721175 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr1:150721583-150722232 Neighboring gene melanoma risk locus-associated MPRA allelic enhancer 1:150727539 Neighboring gene melanoma risk locus-associated MPRA allelic enhancer 1:150728676 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 1698 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 1699 Neighboring gene melanoma risk locus-associated MPRA allelic enhancers 1:150738197 and 1:150738200 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 1305 Neighboring gene melanoma risk locus-associated MPRA allelic enhancer 1:150748803 Neighboring gene short coiled-coil protein pseudogene Neighboring gene H3K27ac hESC enhancer GRCh37_chr1:150753350-150754207 Neighboring gene NANOG-H3K27ac hESC enhancer GRCh37_chr1:150754208-150755064 Neighboring gene melanoma risk locus-associated MPRA allelic enhancer 1:150766964 Neighboring gene ubiquitin conjugating enzyme E2 D3 pseudogene 3 Neighboring gene cathepsin K

    Genomic regions, transcripts, and products

    Expression

    • Project title: HPA RNA-seq normal tissues
    • Description: RNA-seq was performed of tissue samples from 95 human individuals representing 27 different tissues in order to determine tissue-specificity of all protein-coding genes
    • BioProject: PRJEB4337
    • Publication: PMID 24309898
    • Analysis date: Wed Apr 4 07:08:55 2018

    Bibliography

    GeneRIFs: Gene References Into Functions

    What's a GeneRIF?

    Phenotypes

    EBI GWAS Catalog

    Description
    Genome-wide association study identifies genetic risk underlying primary rhegmatogenous retinal detachment.
    EBI GWAS Catalog
    Meta-analysis of genome-wide association data identifies novel susceptibility loci for obesity.
    EBI GWAS Catalog

    HIV-1 interactions

    Protein interactions

    Protein Gene Interaction Pubs
    Envelope surface glycoprotein gp120 env Cathepsin S cleaves HIV-1 gp120 at positions Q208-A209 and S261-T262 (C2 domain), T322-T323 (V3 domain), and Y435-A436 (C4 domain), which is important for antigen processing and presentation PubMed
    Tat tat Microarray analysis indicates HIV-1 Tat-induced upregulation of cathepsin S (CTSS) in primary human brain microvascular endothelial cells PubMed

    Go to the HIV-1, Human Interaction Database

    Interactions

    Products Interactant Other Gene Complex Source Pubs Description

    General gene information

    Markers

    Clone Names

    • MGC3886, FLJ50259

    Gene Ontology Provided by GOA

    Function Evidence Code Pubs
    enables collagen binding IDA
    Inferred from Direct Assay
    more info
    PubMed 
    enables cysteine-type endopeptidase activator activity involved in apoptotic process IBA
    Inferred from Biological aspect of Ancestor
    more info
     
    enables cysteine-type endopeptidase activity IBA
    Inferred from Biological aspect of Ancestor
    more info
     
    enables cysteine-type endopeptidase activity IDA
    Inferred from Direct Assay
    more info
    PubMed 
    enables cysteine-type endopeptidase activity TAS
    Traceable Author Statement
    more info
     
    enables fibronectin binding IPI
    Inferred from Physical Interaction
    more info
    PubMed 
    enables laminin binding IDA
    Inferred from Direct Assay
    more info
    PubMed 
    enables proteoglycan binding IPI
    Inferred from Physical Interaction
    more info
    PubMed 
    enables serine-type endopeptidase activity TAS
    Traceable Author Statement
    more info
     
    Process Evidence Code Pubs
    involved_in adaptive immune response IEP
    Inferred from Expression Pattern
    more info
    PubMed 
    involved_in antigen processing and presentation TAS
    Traceable Author Statement
    more info
    PubMed 
    involved_in antigen processing and presentation of exogenous peptide antigen via MHC class II IDA
    Inferred from Direct Assay
    more info
    PubMed 
    involved_in antigen processing and presentation of exogenous peptide antigen via MHC class II TAS
    Traceable Author Statement
    more info
     
    involved_in antigen processing and presentation of peptide antigen IDA
    Inferred from Direct Assay
    more info
    PubMed 
    involved_in apoptotic process IEA
    Inferred from Electronic Annotation
    more info
     
    involved_in basement membrane disassembly IDA
    Inferred from Direct Assay
    more info
    PubMed 
    involved_in cellular response to thyroid hormone stimulus IEP
    Inferred from Expression Pattern
    more info
    PubMed 
    involved_in collagen catabolic process IDA
    Inferred from Direct Assay
    more info
    PubMed 
    involved_in extracellular matrix disassembly TAS
    Traceable Author Statement
    more info
     
    involved_in immune response IBA
    Inferred from Biological aspect of Ancestor
    more info
     
    involved_in positive regulation of apoptotic signaling pathway IBA
    Inferred from Biological aspect of Ancestor
    more info
     
    involved_in positive regulation of cation channel activity IDA
    Inferred from Direct Assay
    more info
    PubMed 
    involved_in positive regulation of peptidase activity IBA
    Inferred from Biological aspect of Ancestor
    more info
     
    involved_in protein processing IDA
    Inferred from Direct Assay
    more info
    PubMed 
    involved_in proteolysis IDA
    Inferred from Direct Assay
    more info
    PubMed 
    involved_in proteolysis involved in protein catabolic process IBA
    Inferred from Biological aspect of Ancestor
    more info
     
    involved_in proteolysis involved in protein catabolic process IDA
    Inferred from Direct Assay
    more info
    PubMed 
    involved_in response to acidic pH IDA
    Inferred from Direct Assay
    more info
    PubMed 
    involved_in toll-like receptor signaling pathway TAS
    Traceable Author Statement
    more info
     
    Component Evidence Code Pubs
    located_in collagen-containing extracellular matrix HDA PubMed 
    located_in endolysosome lumen TAS
    Traceable Author Statement
    more info
     
    located_in extracellular region NAS
    Non-traceable Author Statement
    more info
    PubMed 
    located_in extracellular region TAS
    Traceable Author Statement
    more info
     
    located_in extracellular space HDA PubMed 
    is_active_in extracellular space IBA
    Inferred from Biological aspect of Ancestor
    more info
     
    located_in extracellular space IDA
    Inferred from Direct Assay
    more info
    PubMed 
    located_in ficolin-1-rich granule lumen TAS
    Traceable Author Statement
    more info
     
    located_in intracellular membrane-bounded organelle IDA
    Inferred from Direct Assay
    more info
     
    located_in late endosome IDA
    Inferred from Direct Assay
    more info
    PubMed 
    located_in lysosomal lumen TAS
    Traceable Author Statement
    more info
     
    is_active_in lysosome IBA
    Inferred from Biological aspect of Ancestor
    more info
     
    located_in lysosome IDA
    Inferred from Direct Assay
    more info
    PubMed 
    located_in phagocytic vesicle IDA
    Inferred from Direct Assay
    more info
    PubMed 
    located_in tertiary granule lumen TAS
    Traceable Author Statement
    more info
     

    General protein information

    Preferred Names
    cathepsin S
    NP_001186668.1
    NP_004070.3

    NCBI Reference Sequences (RefSeq)

    NEW Try the new Transcript table

    RefSeqs maintained independently of Annotated Genomes

    These reference sequences exist independently of genome builds. Explain

    These reference sequences are curated independently of the genome annotation cycle, so their versions may not match the RefSeq versions in the current genome build. Identify version mismatches by comparing the version of the RefSeq in this section to the one reported in Genomic regions, transcripts, and products above.

    mRNA and Protein(s)

    1. NM_001199739.2NP_001186668.1  cathepsin S isoform 2 preproprotein

      See identical proteins and their annotated locations for NP_001186668.1

      Status: REVIEWED

      Description
      Transcript Variant: This variant (2) lacks an in-frame exon in the CDS, so encodes a shorter isoform (2), as compared to variant 1.
      Source sequence(s)
      AK301472, AL356292
      Consensus CDS
      CCDS55634.1
      UniProtKB/TrEMBL
      A0A7P0T904
      Related
      ENSP00000506001.1, ENST00000680288.1
      Conserved Domains (2) summary
      smart00848
      Location:2883
      Inhibitor_I29; Cathepsin propeptide inhibitor domain (I29)
      pfam00112
      Location:82279
      Peptidase_C1; Papain family cysteine protease
    2. NM_004079.5NP_004070.3  cathepsin S isoform 1 preproprotein

      See identical proteins and their annotated locations for NP_004070.3

      Status: REVIEWED

      Description
      Transcript Variant: This variant (1) encodes a longer isoform (1).
      Source sequence(s)
      AL356292, BC002642, M90696
      Consensus CDS
      CCDS968.1
      UniProtKB/Swiss-Prot
      B4DWC9, D3DV05, P25774, Q5T5I0, Q6FHS5, Q9BUG3
      UniProtKB/TrEMBL
      A0A7P0T844
      Related
      ENSP00000357981.3, ENST00000368985.8
      Conserved Domains (3) summary
      PTZ00203
      Location:5326
      PTZ00203; cathepsin L protease; Provisional
      smart00848
      Location:2887
      Inhibitor_I29; Cathepsin propeptide inhibitor domain (I29)
      pfam00112
      Location:115329
      Peptidase_C1; Papain family cysteine protease

    RefSeqs of Annotated Genomes: GCF_000001405.40-RS_2023_10

    The following sections contain reference sequences that belong to a specific genome build. Explain

    Reference GRCh38.p14 Primary Assembly

    Genomic

    1. NC_000001.11 Reference GRCh38.p14 Primary Assembly

      Range
      150730188..150765778 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    Alternate T2T-CHM13v2.0

    Genomic

    1. NC_060925.1 Alternate T2T-CHM13v2.0

      Range
      149853594..149889583 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)