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    CST3 cystatin C [ Homo sapiens (human) ]

    Gene ID: 1471, updated on 9-Dec-2024

    Summary

    Official Symbol
    CST3provided by HGNC
    Official Full Name
    cystatin Cprovided by HGNC
    Primary source
    HGNC:HGNC:2475
    See related
    Ensembl:ENSG00000101439 MIM:604312; AllianceGenome:HGNC:2475
    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
    Also known as
    ARMD11; HEL-S-2
    Summary
    The cystatin superfamily encompasses proteins that contain multiple cystatin-like sequences. Some of the members are active cysteine protease inhibitors, while others have lost or perhaps never acquired this inhibitory activity. There are three inhibitory families in the superfamily, including the type 1 cystatins (stefins), type 2 cystatins and the kininogens. The type 2 cystatin proteins are a class of cysteine proteinase inhibitors found in a variety of human fluids and secretions, where they appear to provide protective functions. The cystatin locus on chromosome 20 contains the majority of the type 2 cystatin genes and pseudogenes. This gene is located in the cystatin locus and encodes the most abundant extracellular inhibitor of cysteine proteases, which is found in high concentrations in biological fluids and is expressed in virtually all organs of the body. A mutation in this gene has been associated with amyloid angiopathy. Expression of this protein in vascular wall smooth muscle cells is severely reduced in both atherosclerotic and aneurysmal aortic lesions, establishing its role in vascular disease. In addition, this protein has been shown to have an antimicrobial function, inhibiting the replication of herpes simplex virus. Alternative splicing results in multiple transcript variants encoding a single protein. [provided by RefSeq, Nov 2014]
    Expression
    Ubiquitous expression in brain (RPKM 148.6), salivary gland (RPKM 118.0) and 25 other tissues See more
    Orthologs
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    Genomic context

    See CST3 in Genome Data Viewer
    Location:
    20p11.21
    Exon count:
    4
    Annotation release Status Assembly Chr Location
    RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 20 NC_000020.11 (23626706..23637955, complement)
    RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 20 NC_060944.1 (23686282..23697531, complement)
    RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 20 NC_000020.10 (23607343..23618592, complement)

    Chromosome 20 - NC_000020.11Genomic Context describing neighboring genes Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr20:23570170-23570774 Neighboring gene cystatin 9-like pseudogene 2 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr20:23583003-23583504 Neighboring gene cystatin 9 Neighboring gene ReSE screen-validated silencer GRCh37_chr20:23603438-23603648 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 12733 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 12734 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 17643 Neighboring gene uncharacterized LOC124904965 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr20:23638069-23638568 Neighboring gene uncharacterized LOC107985383

    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

    Associated conditions

    Description Tests
    Age related macular degeneration 11
    MedGen: C2677774 OMIM: 611953 GeneReviews: Not available
    Compare labs
    Hereditary cerebral amyloid angiopathy, Icelandic type
    MedGen: C1527338 OMIM: 105150 GeneReviews: Not available
    Compare labs

    EBI GWAS Catalog

    Description
    A genome-wide association for kidney function and endocrine-related traits in the NHLBI's Framingham Heart Study.
    EBI GWAS Catalog
    New loci associated with kidney function and chronic kidney disease.
    EBI GWAS Catalog
    Polymorphism of the cystatin C gene in patients with acute coronary syndromes: Results from the PLATelet inhibition and patient Outcomes study.
    EBI GWAS Catalog

    HIV-1 interactions

    Replication interactions

    Interaction Pubs
    HIV-1 infection increases cathepsin B, cystatin B, and cystatin C in the frontal white matter of patients with HIV-Associated Neurocognitive Disorders PubMed
    HIV-1 infection upregulates CST3 in CHME-5 cells PubMed

    Protein interactions

    Protein Gene Interaction Pubs
    Envelope surface glycoprotein gp160, precursor env HIV-1 gp160 interacts with CST3 PubMed
    capsid gag HIV-1 capsid interacts with CST3 PubMed
    integrase gag-pol HIV-1 integrase interacts with CST3 PubMed
    retropepsin gag-pol HIV-1 protease activity is inhibited by CST3 PubMed
    gag-pol HIV-1 protease interacts with CST3 PubMed

    Go to the HIV-1, Human Interaction Database

    Pathways from PubChem

    Interactions

    Products Interactant Other Gene Complex Source Pubs Description

    General gene information

    Markers

    Clone Names

    • MGC117328

    Gene Ontology Provided by GOA

    Function Evidence Code Pubs
    enables amyloid-beta binding IPI
    Inferred from Physical Interaction
    more info
    PubMed 
    enables cysteine-type endopeptidase inhibitor activity IBA
    Inferred from Biological aspect of Ancestor
    more info
     
    enables cysteine-type endopeptidase inhibitor activity IDA
    Inferred from Direct Assay
    more info
    PubMed 
    enables endopeptidase inhibitor activity IDA
    Inferred from Direct Assay
    more info
    PubMed 
    enables identical protein binding IPI
    Inferred from Physical Interaction
    more info
    PubMed 
    enables peptidase inhibitor activity IDA
    Inferred from Direct Assay
    more info
    PubMed 
    enables protease binding IPI
    Inferred from Physical Interaction
    more info
    PubMed 
    enables protein binding IPI
    Inferred from Physical Interaction
    more info
    PubMed 
    Component Evidence Code Pubs
    located_in Golgi apparatus IDA
    Inferred from Direct Assay
    more info
    PubMed 
    is_active_in cytoplasm IBA
    Inferred from Biological aspect of Ancestor
    more info
     
    located_in endoplasmic reticulum TAS
    Traceable Author Statement
    more info
    PubMed 
    located_in endoplasmic reticulum lumen TAS
    Traceable Author Statement
    more info
     
    located_in extracellular exosome HDA PubMed 
    located_in extracellular region IMP
    Inferred from Mutant Phenotype
    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 plasma membrane IDA
    Inferred from Direct Assay
    more info
    PubMed 
    located_in tertiary granule lumen TAS
    Traceable Author Statement
    more info
     
    is_active_in vesicle IBA
    Inferred from Biological aspect of Ancestor
    more info
     

    General protein information

    Preferred Names
    cystatin-C
    Names
    bA218C14.4 (cystatin C)
    cystatin 3
    epididymis secretory protein Li 2
    gamma-trace
    neuroendocrine basic polypeptide
    post-gamma-globulin

    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.

    Genomic

    1. NG_012887.3 RefSeqGene

      Range
      4983..9281
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. NM_000099.4NP_000090.1  cystatin-C precursor

      See identical proteins and their annotated locations for NP_000090.1

      Status: REVIEWED

      Description
      Transcript Variant: This variant (1) differs in the 3' UTR compared to variant 2. Variants 1 and 2 encode the same protein.
      Source sequence(s)
      AL121894
      Consensus CDS
      CCDS13158.1
      UniProtKB/Swiss-Prot
      B2R5J9, D3DW42, P01034, Q6FGW9
      UniProtKB/TrEMBL
      A0A0K0K1J1
      Related
      ENSP00000366124.3, ENST00000376925.8
      Conserved Domains (1) summary
      smart00043
      Location:34144
      CY; Cystatin-like domain
    2. NM_001288614.2NP_001275543.1  cystatin-C precursor

      See identical proteins and their annotated locations for NP_001275543.1

      Status: REVIEWED

      Description
      Transcript Variant: This variant (2) represents the longer variant. Variants 1 and 2 encode the same protein.
      Source sequence(s)
      AL121894
      Consensus CDS
      CCDS13158.1
      UniProtKB/Swiss-Prot
      B2R5J9, D3DW42, P01034, Q6FGW9
      UniProtKB/TrEMBL
      A0A0K0K1J1
      Related
      ENSP00000381448.1, ENST00000398411.5
      Conserved Domains (1) summary
      smart00043
      Location:34144
      CY; Cystatin-like domain

    RefSeqs of Annotated Genomes: GCF_000001405.40-RS_2024_08

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

    Reference GRCh38.p14 Primary Assembly

    Genomic

    1. NC_000020.11 Reference GRCh38.p14 Primary Assembly

      Range
      23626706..23637955 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    Alternate T2T-CHM13v2.0

    Genomic

    1. NC_060944.1 Alternate T2T-CHM13v2.0

      Range
      23686282..23697531 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)