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CST3 cystatin C [ Homo sapiens (human) ]

Gene ID: 1471, updated on 21-Jun-2020

Summary

Official Symbol
CST3provided by HGNC
Official Full Name
cystatin Cprovided by HGNC
Primary source
HGNC:HGNC:2475
See related
Ensembl:ENSG00000101439 MIM:604312
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

Genomic context

See CST3 in Genome Data Viewer
Location:
20p11.21
Exon count:
4
Annotation release Status Assembly Chr Location
109.20200522 current GRCh38.p13 (GCF_000001405.39) 20 NC_000020.11 (23626706..23637955, complement)
105 previous assembly GRCh37.p13 (GCF_000001405.25) 20 NC_000020.10 (23608534..23618685, complement)

Chromosome 20 - NC_000020.11Genomic Context describing neighboring genes Neighboring gene cystatin 9-like pseudogene 2 Neighboring gene cystatin 9 Neighboring gene uncharacterized LOC107985383 Neighboring gene uncharacterized LOC105372573

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

NHGRI GWAS Catalog

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

Homology

Clone Names

  • MGC117328

Gene Ontology Provided by GOA

Function Evidence Code Pubs
amyloid-beta binding IPI
Inferred from Physical Interaction
more info
PubMed 
cysteine-type endopeptidase inhibitor activity IDA
Inferred from Direct Assay
more info
PubMed 
endopeptidase inhibitor activity IDA
Inferred from Direct Assay
more info
PubMed 
identical protein binding IPI
Inferred from Physical Interaction
more info
PubMed 
peptidase inhibitor activity IDA
Inferred from Direct Assay
more info
PubMed 
protease binding IPI
Inferred from Physical Interaction
more info
PubMed 
protein binding IPI
Inferred from Physical Interaction
more info
PubMed 
Process Evidence Code Pubs
Sertoli cell development IEA
Inferred from Electronic Annotation
more info
 
apoptotic process IEA
Inferred from Electronic Annotation
more info
 
brain development IEA
Inferred from Electronic Annotation
more info
 
cellular protein metabolic process TAS
Traceable Author Statement
more info
 
cellular response to hydrogen peroxide IEA
Inferred from Electronic Annotation
more info
 
circadian sleep/wake cycle, REM sleep IEA
Inferred from Electronic Annotation
more info
 
defense response IDA
Inferred from Direct Assay
more info
PubMed 
embryo implantation IEA
Inferred from Electronic Annotation
more info
 
eye development IEA
Inferred from Electronic Annotation
more info
 
negative regulation of blood vessel remodeling IEP
Inferred from Expression Pattern
more info
PubMed 
negative regulation of cell death IEA
Inferred from Electronic Annotation
more info
 
negative regulation of collagen catabolic process IEP
Inferred from Expression Pattern
more info
PubMed 
negative regulation of elastin catabolic process IMP
Inferred from Mutant Phenotype
more info
PubMed 
negative regulation of endopeptidase activity IEA
Inferred from Electronic Annotation
more info
 
negative regulation of extracellular matrix disassembly IC
Inferred by Curator
more info
PubMed 
negative regulation of extracellular matrix disassembly IEP
Inferred from Expression Pattern
more info
PubMed 
negative regulation of peptidase activity IDA
Inferred from Direct Assay
more info
PubMed 
negative regulation of proteolysis IDA
Inferred from Direct Assay
more info
PubMed 
neutrophil degranulation TAS
Traceable Author Statement
more info
 
positive regulation of DNA replication IEA
Inferred from Electronic Annotation
more info
 
positive regulation of cell proliferation IEA
Inferred from Electronic Annotation
more info
 
post-translational protein modification TAS
Traceable Author Statement
more info
 
regulation of programmed cell death IEA
Inferred from Electronic Annotation
more info
 
regulation of tissue remodeling IEP
Inferred from Expression Pattern
more info
PubMed 
response to axon injury IEA
Inferred from Electronic Annotation
more info
 
response to carbohydrate IEA
Inferred from Electronic Annotation
more info
 
response to estradiol IEA
Inferred from Electronic Annotation
more info
 
response to hypoxia IEA
Inferred from Electronic Annotation
more info
 
response to nutrient levels IEA
Inferred from Electronic Annotation
more info
 
salivary gland development IEA
Inferred from Electronic Annotation
more info
 
supramolecular fiber organization IGI
Inferred from Genetic Interaction
more info
PubMed 
Component Evidence Code Pubs
Golgi apparatus IDA
Inferred from Direct Assay
more info
PubMed 
axon IEA
Inferred from Electronic Annotation
more info
 
basement membrane IEA
Inferred from Electronic Annotation
more info
 
contractile fiber IEA
Inferred from Electronic Annotation
more info
 
endoplasmic reticulum TAS
Traceable Author Statement
more info
PubMed 
endoplasmic reticulum lumen TAS
Traceable Author Statement
more info
 
extracellular exosome HDA PubMed 
extracellular region IMP
Inferred from Mutant Phenotype
more info
PubMed 
extracellular region TAS
Traceable Author Statement
more info
 
extracellular space HDA PubMed 
extracellular space IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
extracellular space IDA
Inferred from Direct Assay
more info
PubMed 
ficolin-1-rich granule lumen TAS
Traceable Author Statement
more info
 
lysosome IEA
Inferred from Electronic Annotation
more info
 
multivesicular body IEA
Inferred from Electronic Annotation
more info
 
neuronal cell body IEA
Inferred from Electronic Annotation
more info
 
nuclear membrane IEA
Inferred from Electronic Annotation
more info
 
perinuclear region of cytoplasm IEA
Inferred from Electronic Annotation
more info
 
plasma membrane IDA
Inferred from Direct Assay
more info
PubMed 
tertiary granule lumen TAS
Traceable Author Statement
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)

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
    P01034
    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
    P01034
    UniProtKB/TrEMBL
    A0A0K0K1J1
    Related
    ENSP00000381448.1, ENST00000398411.5
    Conserved Domains (1) summary
    smart00043
    Location:34144
    CY; Cystatin-like domain

RefSeqs of Annotated Genomes: Homo sapiens Updated Annotation Release 109.

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

Reference GRCh38.p13 Primary Assembly

Genomic

  1. NC_000020.11 Reference GRCh38.p13 Primary Assembly

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