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 kininogens. This gene encodes a... See more...

Aliases for CSTA Gene

Aliases for CSTA Gene

  • Cystatin A 2 3 5
  • Cystatin A (Stefin A) 2 3
  • Cystatin-A 3 4
  • STF1 3 4
  • STFA 3 4
  • Cystatin AS 3
  • Cystatin-AS 4
  • Stefin A 2
  • Stefin-A 4
  • AREI 3
  • PSS4 3
  • CSTA 5

External Ids for CSTA Gene

Previous HGNC Symbols for CSTA Gene

  • STF1
  • STFA

Previous GeneCards Identifiers for CSTA Gene

  • GC03P118765
  • GC03P121992
  • GC03P123325
  • GC03P123364
  • GC03P123526
  • GC03P122044
  • GC03P119417

Summaries for CSTA Gene

Entrez Gene Summary for CSTA Gene

  • 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 kininogens. This gene encodes a stefin that functions as a cysteine protease inhibitor, forming tight complexes with papain and the cathepsins B, H, and L. The protein is one of the precursor proteins of cornified cell envelope in keratinocytes and plays a role in epidermal development and maintenance. Stefins have been proposed as prognostic and diagnostic tools for cancer. [provided by RefSeq, Jul 2008]

GeneCards Summary for CSTA Gene

CSTA (Cystatin A) is a Protein Coding gene. Diseases associated with CSTA include Peeling Skin Syndrome 4 and Exfoliative Ichthyosis. Among its related pathways are Keratinization and Developmental Biology. Gene Ontology (GO) annotations related to this gene include structural molecule activity and protein binding, bridging. An important paralog of this gene is CSTB.

UniProtKB/Swiss-Prot Summary for CSTA Gene

  • This is an intracellular thiol proteinase inhibitor. Has an important role in desmosome-mediated cell-cell adhesion in the lower levels of the epidermis.

Gene Wiki entry for CSTA Gene

No data available for CIViC Summary , Tocris Summary , PharmGKB "VIP" Summary , Rfam classification and piRNA Summary for CSTA Gene

Genomics for CSTA Gene

GeneHancer (GH) Regulatory Elements Pubs

Promoters and enhancers for CSTA Gene
GeneHancer (GH) Identifier GH Type GH
Score
GH Sources Gene Association Score Total Score TSS distance (kb) Number of Genes Away Size (kb) Transcription Factor
Binding Sites
Gene Targets
GH03J122324 Promoter/Enhancer 1.5 EPDnew Ensembl ENCODE dbSUPER 250.7 +0.8 795 3.1 CEBPA ATF3 CEBPB EP300 JUND PRDM10 IRF9 SPI1 POLR2A HDGF CSTA HSALNG0028487 WDR5B-DT WDR5B RF00017-3684 MIX23
GH03J122099 Enhancer 1.4 FANTOM5 Ensembl ENCODE dbSUPER 12.7 -223.5 -223465 5.2 BCLAF1 SP1 ZNF654 BCL11A CTCF REST ZNF592 TRIM22 ZNF217 RXRA CSTA CD86 ILDR1 ENSG00000202388 CASR POLQ PARP9 DTX3L HCLS1 EAF2
GH03J122362 Promoter/Enhancer 1.5 Ensembl ENCODE 11.9 +39.8 39790 4.6 BCLAF1 NCOR1 CEBPA ATF3 CHD4 YY1 BCL11A FOXA1 TRIM22 HOMEZ lnc-WDR5B-1 WDR5B-DT GOLGB1 IQCB1 SEC22A WDR5B CSTA RPL7AP11 CASR HSALNG0028489
GH03J122271 Enhancer 0.7 Ensembl 22.6 -52.4 -52447 4.4 BCL11A TRIM22 CBFB BATF ZNF24 IKZF1 NR2F1 TCF7 MTA3 ATF2 CSTA WDR5B FAM162A MIX23 WDR5B-DT HSALNG0028483 HSALNG0028482-001 piR-53063-148 CASR
GH03J122356 Enhancer 1 FANTOM5 Ensembl 12 +30.2 30153 4.4 BCLAF1 ZNF654 NCOR1 IKZF1 NFIC YY1 REST TRIM22 CTCF ZNF217 WDR5B WDR5B-DT CSTA FAM162A MIX23 HSALNG0028489 hsa-miR-5095-349
- Elite GeneHancer and/or Elite GeneHancer-gene association Download GeneHancer data from 2017 publication | Request up-to-date GeneHancer data (full dataset)

GeneHancers around CSTA on the GeneHancer Hub at the UCSC Golden Path

Cistromic (ChIP-Seq) regulation report from SPP (The Signaling Pathways Project) for CSTA

Top Transcription factor binding sites by QIAGEN in the CSTA gene promoter:
  • AML1a
  • E47
  • Evi-1
  • GATA-1
  • GR
  • GR-alpha
  • HOXA9
  • IRF-2
  • ITF-2
  • Tal-1beta

Genomic Locations for CSTA Gene

Latest Assembly
chr3:122,325,248-122,341,969
(GRCh38/hg38)
Size:
16,722 bases
Orientation:
Plus strand

Previous Assembly
chr3:122,044,095-122,060,816
(GRCh37/hg19 by Entrez Gene)
Size:
16,722 bases
Orientation:
Plus strand

chr3:122,044,091-122,060,819
(GRCh37/hg19 by Ensembl)
Size:
16,729 bases
Orientation:
Plus strand

Genomic View for CSTA Gene

Genes around CSTA on UCSC Golden Path with GeneCards custom track

Cytogenetic band:
CSTA Gene in genomic location: bands according to Ensembl, locations according to GeneLoc (and/or Entrez Gene and/or Ensembl if different)
Genomic Location for CSTA Gene
GeneLoc Logo Genomic Neighborhood Exon StructureGene Density

RefSeq DNA sequence for CSTA Gene

Proteins for CSTA Gene

  • Protein details for CSTA Gene (UniProtKB/Swiss-Prot)

    Protein Symbol:
    P01040-CYTA_HUMAN
    Recommended name:
    Cystatin-A
    Protein Accession:
    P01040
    Secondary Accessions:
    • Q6IB90

    Protein attributes for CSTA Gene

    Size:
    98 amino acids
    Molecular mass:
    11006 Da
    Quaternary structure:
    No Data Available

    Three dimensional structures from OCA and Proteopedia for CSTA Gene

neXtProt entry for CSTA Gene

Post-translational modifications for CSTA Gene

  • Ubiquitination at Lys37
  • Modification sites at PhosphoSitePlus

Other Protein References for CSTA Gene

ENSEMBL proteins:
REFSEQ proteins:

No data available for DME Specific Peptides for CSTA Gene

Domains & Families for CSTA Gene

Gene Families for CSTA Gene

HGNC:
Human Protein Atlas (HPA):
  • Cancer-related genes
  • Disease related genes
  • Plasma proteins
  • Predicted intracellular proteins

Protein Domains for CSTA Gene

InterPro:
Blocks:
  • Cysteine protease inhibitor
  • Stefin A signature

Suggested Antigen Peptide Sequences for CSTA Gene

GenScript: Design optimal peptide antigens:
  • Stefin-A (CYTA_HUMAN)
  • cDNA FLJ76406, highly similar to Homo sapiens cystatin A (stefin A) (CSTA), mRNA (Q6IB90_HUMAN)

Graphical View of Domain Structure for InterPro Entry

P01040

UniProtKB/Swiss-Prot:

CYTA_HUMAN :
  • Belongs to the cystatin family.
Family:
  • Belongs to the cystatin family.
genes like me logo Genes that share domains with CSTA: view

Function for CSTA Gene

Molecular function for CSTA Gene

UniProtKB/Swiss-Prot Function:
This is an intracellular thiol proteinase inhibitor. Has an important role in desmosome-mediated cell-cell adhesion in the lower levels of the epidermis.
GENATLAS Biochemistry:
cystatin A,cysteine proteinase inhibitor,type 2 family

Phenotypes From GWAS Catalog for CSTA Gene

Gene Ontology (GO) - Molecular Function for CSTA Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0002020 protease binding IPI 6203523
GO:0004866 endopeptidase inhibitor activity IEA --
GO:0004869 cysteine-type endopeptidase inhibitor activity IEA,IDA 3488317
GO:0005515 protein binding IPI 11152132
GO:0030414 peptidase inhibitor activity IEA --
genes like me logo Genes that share ontologies with CSTA: view
genes like me logo Genes that share phenotypes with CSTA: view

Human Phenotype Ontology for CSTA Gene

HPO Id HPO Name Alternative Ids Definition Synonyms

Inhibitory RNAs for research

  • Search GeneCopoeia for shRNA, lentivirus and/or AAV clone products for CSTA

No data available for Enzyme Numbers (IUBMB) , Animal Models , miRNA , Transcription Factor Targets and HOMER Transcription for CSTA Gene

Localization for CSTA Gene

Subcellular locations from UniProtKB/Swiss-Prot for CSTA Gene

Cytoplasm.

Subcellular locations from

COMPARTMENTS
Extracellular space Cytosol Plasma membrane Cytoskeleton Lysosome Endosome Peroxisome ER Golgi Apparatus Nucleus Mitochondrion 0 1 2 3 4 5 Confidence
COMPARTMENTS Subcellular localization image for CSTA gene
Compartment Confidence
plasma membrane 5
extracellular 5
nucleus 5
cytosol 5
cytoskeleton 2
lysosome 2
mitochondrion 1
endoplasmic reticulum 1
endosome 1
golgi apparatus 1

Subcellular locations from the

Human Protein Atlas (HPA)
  • Cytosol (2)
  • Nucleoplasm (2)
See all subcellular structures

Gene Ontology (GO) - Cellular Components for CSTA Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0001533 cornified envelope IDA,TAS --
GO:0005615 extracellular space IDA 3488317
GO:0005654 nucleoplasm IDA --
GO:0005737 cytoplasm IEA,IDA 21944047
GO:0005829 cytosol TAS --
genes like me logo Genes that share ontologies with CSTA: view

Pathways & Interactions for CSTA Gene

PathCards logo

SuperPathways for CSTA Gene

genes like me logo Genes that share pathways with CSTA: view

Pathways by source for CSTA Gene

Gene Ontology (GO) - Biological Process for CSTA Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0007155 cell adhesion IEA --
GO:0010466 negative regulation of peptidase activity IDA 6203523
GO:0010951 negative regulation of endopeptidase activity IEA --
GO:0018149 peptide cross-linking IDA 10908733
GO:0030216 keratinocyte differentiation IDA 10908733
genes like me logo Genes that share ontologies with CSTA: view

No data available for SIGNOR curated interactions for CSTA Gene

Drugs & Compounds for CSTA Gene

(6) Drugs for CSTA Gene - From: ApexBio and Novoseek

Name Status Disease Links Group Role Mechanism of Action Clinical Trials
Papain Inhibitor Pharma Inhibitor of peptidase activity of Papain 0

(10) Additional Compounds for CSTA Gene - From: Novoseek

Name Synonyms Role CAS Number PubChem IDs PubMed IDs

(1) ApexBio Compounds for CSTA Gene

Compound Action Cas Number
Papain Inhibitor Inhibitor of peptidase activity of Papain 70195-20-9
genes like me logo Genes that share compounds with CSTA: view

Drug products for research

Transcripts for CSTA Gene

mRNA/cDNA for CSTA Gene

1 REFSEQ mRNAs :
7 NCBI additional mRNA sequence :
2 Ensembl transcripts including schematic representations, and UCSC links to gene/alias where relevant :

Inhibitory RNAs for research

  • Search GeneCopoeia for shRNA, lentivirus and/or AAV clone products for CSTA

Alternative Splicing Database (ASD) splice patterns (SP) for CSTA Gene

No ASD Table

Relevant External Links for CSTA Gene

GeneLoc Exon Structure for
CSTA

Expression for CSTA Gene

mRNA expression in normal human tissues from GTEx, Illumina, BioGPS, and SAGE for CSTA Gene

mRNA expression in embryonic tissues and stem cells from LifeMap Discovery

mRNA differential expression in normal tissues according to GTEx for CSTA Gene

This gene is overexpressed in Esophagus - Mucosa (x30.6), Vagina (x8.5), and Cervix - Ectocervix (x5.6).

Protein differential expression in normal tissues from HIPED for CSTA Gene

This gene is overexpressed in Oral epithelium (12.5), Saliva (12.3), Esophagus (9.4), and Tonsil (6.6).

Integrated Proteomics: protein expression in normal tissues and cell lines from ProteomicsDB, MaxQB, and MOPED for CSTA Gene



Transcriptomic regulation report from SPP (The Signaling Pathways Project) for CSTA

SOURCE GeneReport for Unigene cluster for CSTA Gene:

Hs.518198

mRNA Expression by UniProt/SwissProt for CSTA Gene:

P01040-CYTA_HUMAN
Tissue specificity: Expressed in the skin throughout the epidermis.

Evidence on tissue expression from TISSUES for CSTA Gene

  • Skin(4.6)
  • Bone marrow(4.5)
  • Liver(4.4)
  • Blood(3)
  • Lymph node(2.2)
  • Spleen(2.2)
  • Lung(2.2)
  • Intestine(2.1)
  • Stomach(2)

Phenotype-based relationships between genes and organs from Gene ORGANizer for CSTA Gene

Germ Layers:
  • ectoderm
Systems:
  • integumentary
Regions:
Limb:
  • foot
  • hand
  • lower limb
  • upper limb
General:
  • skin
genes like me logo Genes that share expression patterns with CSTA: view

Primer products for research

No data available for Protein tissue co-expression partners for CSTA Gene

Orthologs for CSTA Gene

This gene was present in the common ancestor of chordates.

Orthologs for CSTA Gene

Organism Taxonomy Gene Similarity Type Details
Chimpanzee
(Pan troglodytes)
Mammalia CSTA 29 30
  • 98.98 (n)
OneToOne
Dog
(Canis familiaris)
Mammalia CSTA 29 30
  • 84.35 (n)
OneToOne
Cow
(Bos Taurus)
Mammalia CSTA 29 30
  • 83.33 (n)
OneToOne
Mouse
(Mus musculus)
Mammalia Csta 29 30
  • 74.23 (n)
OneToMany
Gm5689 30
  • 64 (a)
OneToMany
Gm5483 30
  • 60 (a)
OneToMany
BC100530 30
  • 59 (a)
OneToMany
BC117090 30
  • 59 (a)
OneToMany
2010005H15Rik 30
  • 58 (a)
OneToMany
Stfa1 30
  • 57 (a)
OneToMany
Gm5416 30
  • 57 (a)
OneToMany
Stfa3 30
  • 56 (a)
OneToMany
Gm4758 30
  • 56 (a)
OneToMany
Stfa2 30
  • 55 (a)
OneToMany
Stfa2l1 30
  • 54 (a)
OneToMany
Gm10092 30
  • 49 (a)
OneToMany
Csta1 16
Csta2 16
Cstdc4 16
Rat
(Rattus norvegicus)
Mammalia Csta 29
  • 72.51 (n)
Platypus
(Ornithorhynchus anatinus)
Mammalia CSTA 30
  • 64 (a)
OneToOne
Oppossum
(Monodelphis domestica)
Mammalia -- 30
  • 53 (a)
OneToMany
-- 30
  • 50 (a)
OneToMany
Chicken
(Gallus gallus)
Aves CSTA 29 30
  • 60.48 (n)
OneToOne
Lizard
(Anolis carolinensis)
Reptilia -- 30
  • 52 (a)
OneToMany
-- 30
  • 49 (a)
OneToMany
Zebrafish
(Danio rerio)
Actinopterygii si:ch211-161h7.6 30
  • 46 (a)
ManyToMany
zgc:153129 30
  • 45 (a)
ManyToMany
zgc:56530 30
  • 44 (a)
ManyToMany
Species where no ortholog for CSTA was found in the sources mined by GeneCards:
  • A. gosspyii yeast (Eremothecium gossypii)
  • Actinobacteria (Mycobacterium tuberculosis)
  • African clawed frog (Xenopus laevis)
  • African malaria mosquito (Anopheles gambiae)
  • Alicante grape (Vitis vinifera)
  • Alpha proteobacteria (Wolbachia pipientis)
  • Amoeba (Dictyostelium discoideum)
  • Archea (Pyrococcus horikoshii)
  • Baker's yeast (Saccharomyces cerevisiae)
  • Barley (Hordeum vulgare)
  • Beta proteobacteria (Neisseria meningitidis)
  • Bread mold (Neurospora crassa)
  • Chromalveolata (Phytophthora infestans)
  • Common water flea (Daphnia pulex)
  • Corn (Zea mays)
  • E. coli (Escherichia coli)
  • Filamentous fungi (Aspergillus nidulans)
  • Firmicute Bacteria (Streptococcus pneumoniae)
  • Fission Yeast (Schizosaccharomyces pombe)
  • Fruit Fly (Drosophila melanogaster)
  • Green Algae (Chlamydomonas reinhardtii)
  • Honey Bee (Apis mellifera)
  • K. Lactis Yeast (Kluyveromyces lactis)
  • Loblloly Pine (Pinus taeda)
  • Malaria Parasite (Plasmodium falciparum)
  • Medicago Trunc (Medicago Truncatula)
  • Moss (Physcomitrella patens)
  • Orangutan (Pongo pygmaeus)
  • Pig (Sus scrofa)
  • Rainbow Trout (Oncorhynchus mykiss)
  • Rice (Oryza sativa)
  • Rice Blast Fungus (Magnaporthe grisea)
  • Schistosome Parasite (Schistosoma mansoni)
  • Sea Anemone (Nematostella vectensis)
  • Sea Vase (Ciona intestinalis)
  • Sea Squirt (Ciona savignyi)
  • Sea Urchin (Strongylocentrotus purpuratus)
  • Sorghum (Sorghum bicolor)
  • Soybean (Glycine max)
  • Stem Rust Fungus (Puccinia graminis)
  • Sugarcane (Saccharum officinarum)
  • Thale Cress (Arabidopsis thaliana)
  • Tomato (Lycopersicon esculentum)
  • Toxoplasmosis (Toxoplasma gondii)
  • Trichoplax (Trichoplax adhaerens)
  • Tropical Clawed Frog (Silurana tropicalis)
  • Wheat (Triticum aestivum)
  • Worm (Caenorhabditis elegans)

Evolution for CSTA Gene

ENSEMBL:
Gene Tree for CSTA (if available)
TreeFam:
Gene Tree for CSTA (if available)
Aminode:
Evolutionary constrained regions (ECRs) for CSTA: view image
Alliance of Genome Resources:
Additional Orthologs for CSTA

Paralogs for CSTA Gene

Paralogs for CSTA Gene

(1) SIMAP similar genes for CSTA Gene using alignment to 2 proteins:

  • CYTA_HUMAN
  • C9J0E4_HUMAN
genes like me logo Genes that share paralogs with CSTA: view

Variants for CSTA Gene

Sequence variations, with clinical significance, from ClinVar and Humsavar, with links to dbSNP for CSTA Gene

SNP ID Clinical significance and condition Chr 03 pos Variation AA Info Type
rs1321015847 Likely Pathogenic: not provided 122,337,581(+) CTT/C
NM_005213.4(CSTA):c.102_103del (p.Tyr35fs)
FRAMESHIFT
rs149474339 Pathogenic: Peeling skin syndrome 4 122,341,442(+) C/T
NM_005213.4(CSTA):c.172C>T (p.Arg58Ter)
NONSENSE
rs34021626 Benign: not provided 122,341,543(+) G/T
NM_005213.4(CSTA):c.273G>T (p.Lys91Asn)
MISSENSE
rs387906689 Pathogenic: Peeling skin syndrome 4 122,341,526(+) C/T
NM_005213.4(CSTA):c.256C>T (p.Gln86Ter)
NONSENSE
rs398122804 Pathogenic: Peeling skin syndrome 4 122,337,545(+) A/T
NM_005213.4(CSTA):c.67-2A>T
SPLICE_ACCEPTOR

dbSNP identifiers (rs#s) for variants without ClinVar clinical significance for CSTA Gene

All consequence types are included: molecular consequences (e.g. missense, synonymous), and location-based (e.g. intron, upstream).

Structural Variations from Database of Genomic Variants (DGV) for CSTA Gene

Variant ID Type Subtype PubMed ID
esv33139 CNV loss 17666407

Variation tolerance for CSTA Gene

Residual Variation Intolerance Score: 71.6% of all genes are more intolerant (likely to be disease-causing)
Gene Damage Index Score: 5.45; 71.52% of all genes are more intolerant (likely to be disease-causing)

Additional Variant Information for CSTA Gene

Human Gene Mutation Database (HGMD)
CSTA
SNPedia medical, phenotypic, and genealogical associations of SNPs for
CSTA
Leiden Open Variation Database (LOVD)
CSTA

SNP Genotyping and Copy Number Assays for research

No data available for Polymorphic Variants from UniProtKB/Swiss-Prot for CSTA Gene

Disorders for CSTA Gene

MalaCards: The human disease database

(14) MalaCards diseases for CSTA Gene - From: OMI, CVR, GTR, ORP, COP, and GCD

Disorder Aliases PubMed IDs
peeling skin syndrome 4
  • pss4
exfoliative ichthyosis
  • autosomal recessive exfoliative ichthyosis
peeling skin syndrome 2
  • pss2
peeling skin syndrome
  • skin peeling syndrome
ichthyosis bullosa of siemens
  • ibs
- elite association - COSMIC cancer census association via MalaCards
Search CSTA in MalaCards View complete list of genes associated with diseases

UniProtKB/Swiss-Prot

CYTA_HUMAN
  • Peeling skin syndrome 4 (PSS4) [MIM:607936]: A genodermatosis characterized by congenital exfoliative ichthyosis, sharing some features with ichthyosis bullosa of Siemens and annular epidermolytic ichthyosis. PSS4 presents shortly after birth as dry, scaly skin over most of the body with coarse peeling of non-erythematous skin on the palms and soles, which is exacerbated by excessive moisture and minor trauma. Electron microscopy analysis of skin biopsies, reveals mostly normal-appearing upper layers of the epidermis, but prominent intercellular edema of the basal and suprabasal cell layers with aggregates of tonofilaments in the basal keratinocytes. {ECO:0000269 PubMed:21944047}. Note=The disease is caused by variants affecting the gene represented in this entry.

Additional Disease Information for CSTA

Human Genome Epidemiology Navigator
(HuGE)
Atlas
ATLAS of Genetics and Cytogenetics in Oncology and Haematology
Open Targets Platform
Open Targets Platform
genes like me logo Genes that share disorders with CSTA: view

No data available for Genatlas for CSTA Gene

Publications for CSTA Gene

  1. Mutations in CSTA, encoding Cystatin A, underlie exfoliative ichthyosis and reveal a role for this protease inhibitor in cell-cell adhesion. (PMID: 21944047) Blaydon DC … Kelsell DP (American journal of human genetics 2011) 3 4 72
  2. Association analysis of the skin barrier gene cystatin A at the PSORS5 locus in psoriatic patients: evidence for interaction between PSORS1 and PSORS5. (PMID: 18364739) Vasilopoulos Y … Tazi-Ahnini R (European journal of human genetics : EJHG 2008) 3 22 40
  3. Association analysis of cystatin A and zinc finger protein 148, two genes located at the psoriasis susceptibility locus PSORS5. (PMID: 15175029) Samuelsson L … Wahlström J (The Journal of investigative dermatology 2004) 3 22 40
  4. Structure and transcriptional regulation of the human cystatin A gene. The 12-O-tetradecanoylphorbol-13-acetate (TPA) responsive element-2 site (-272 to -278) on cystatin A gene is critical for TPA-dependent regulation. (PMID: 9651321) Takahashi H … Iizuka H (The Journal of biological chemistry 1998) 3 4 22
  5. Genomic structure of human cystatin A. (PMID: 9522124) Yamazaki M … Ogawa H (DNA sequence : the journal of DNA sequencing and mapping 1997) 3 4 22

Products for CSTA Gene

Sources for CSTA Gene