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CST3 cystatin C [ Homo sapiens (human) ]

Gene ID: 1471, updated on 12-Mar-2019

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 current GRCh38.p12 (GCF_000001405.38) 20 NC_000020.11 (23627897..23638048, 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 FunctionsWhat'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 BioSystems

  • Amyloid fiber formation, organism-specific biosystem (from REACTOME)
    Amyloid fiber formation, organism-specific biosystemAmyloid is a term used to describe deposits of fibrillar proteins, typically extracellular. The abnormal accumulation of amyloid, amyloidosis, is a term associated with tissue damage caused by amyloi...
  • Amyotrophic lateral sclerosis (ALS), organism-specific biosystem (from WikiPathways)
    Amyotrophic lateral sclerosis (ALS), organism-specific biosystemAmyotrophic lateral sclerosis (ALS) is a progressive, lethal, degenerative disorder of motor neurons. The hallmark of this disease is the selective death of motor neurons in the brain and spinal cord...
  • Circadian rythm related genes, organism-specific biosystem (from WikiPathways)
    Circadian rythm related genes, organism-specific biosystemThis is currently not a pathway but a list of circadian rhythm related genes and proteins. The source for this information is the gene ontology. The genes and proteins were filtered for "circadian rh...
  • Immune System, organism-specific biosystem (from REACTOME)
    Immune System, organism-specific biosystemHumans are exposed to millions of potential pathogens daily, through contact, ingestion, and inhalation. Our ability to avoid infection depends on the adaptive immune system and during the first crit...
  • Innate Immune System, organism-specific biosystem (from REACTOME)
    Innate Immune System, organism-specific biosystemInnate immunity encompases the nonspecific part of immunity tha are part of an individual's natural biologic makeup
  • Integrated Pancreatic Cancer Pathway, organism-specific biosystem (from WikiPathways)
    Integrated Pancreatic Cancer Pathway, organism-specific biosystemAn integrated pathway model which displays the protein-protein interactions (PPIs) among the relevant proteins for pancreatic cancer. This pathway is a collection of different mechanistic protein pat...
  • Metabolism of proteins, organism-specific biosystem (from REACTOME)
    Metabolism of proteins, organism-specific biosystemProtein metabolism comprises the pathways of translation, post-translational modification and protein folding.
  • Neutrophil degranulation, organism-specific biosystem (from REACTOME)
    Neutrophil degranulation, organism-specific biosystemNeutrophils are the most abundant leukocytes (white blood cells), indispensable in defending the body against invading microorganisms. In response to infection, neutrophils leave the circulation and ...
  • Salivary secretion, organism-specific biosystem (from KEGG)
    Salivary secretion, organism-specific biosystemSaliva has manifold functions in maintaining the integrity of the oral tissues, in protecting teeth from caries, in the tasting and ingestion of food, in speech and in the tolerance of tenures, for e...
  • Salivary secretion, conserved biosystem (from KEGG)
    Salivary secretion, conserved biosystemSaliva has manifold functions in maintaining the integrity of the oral tissues, in protecting teeth from caries, in the tasting and ingestion of food, in speech and in the tolerance of tenures, for e...

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 
protease binding IPI
Inferred from Physical Interaction
more info
PubMed 
protein binding IPI
Inferred from Physical Interaction
more info
PubMed 
Component Evidence Code Pubs
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
 
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_012887.2 RefSeqGene

    Range
    4890..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, ENST00000376925.7
    Conserved Domains (1) summary
    smart00043
    Location:34144
    CY; Cystatin-like domain
  2. NM_001288614.1NP_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)
    BF509512, BX647523, HY042866
    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 Annotation Release 109

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

Reference GRCh38.p12 Primary Assembly

Genomic

  1. NC_000020.11 Reference GRCh38.p12 Primary Assembly

    Range
    23627897..23638048 complement
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
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