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Aliases for CSTB Gene

Aliases for CSTB Gene

  • Cystatin B 2 3 5
  • Liver Thiol Proteinase Inhibitor 3 4
  • Cystatin B (Stefin B) 2 3
  • CPI-B 3 4
  • STFB 3 4
  • CST6 3 4
  • Cystatin-B 3
  • Stefin-B 4
  • Stefin B 2
  • EPM1A 3
  • EPM1 3
  • PME 3
  • ULD 3

External Ids for CSTB Gene

Previous HGNC Symbols for CSTB Gene

  • EPM1
  • STFB

Previous GeneCards Identifiers for CSTB Gene

  • GC21M041703
  • GC21M044050
  • GC21M044018
  • GC21M045192
  • GC21M030562

Summaries for CSTB Gene

Entrez Gene Summary for CSTB 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 an intracellular thiol protease inhibitor. The protein is able to form a dimer stabilized by noncovalent forces, inhibiting papain and cathepsins l, h and b. The protein is thought to play a role in protecting against the proteases leaking from lysosomes. Evidence indicates that mutations in this gene are responsible for the primary defects in patients with progressive myoclonic epilepsy (EPM1). One type of mutation responsible for EPM1 is the expansion in the promoter region of this gene of a CCCCGCCCCGCG repeat from 2-3 copies to 30-78 copies. [provided by RefSeq, Jul 2016]

GeneCards Summary for CSTB Gene

CSTB (Cystatin B) is a Protein Coding gene. Diseases associated with CSTB include Myoclonic Epilepsy Of Unverricht And Lundborg and Unverricht-Lundborg Syndrome. Among its related pathways are Innate Immune System. Gene Ontology (GO) annotations related to this gene include endopeptidase inhibitor activity. An important paralog of this gene is CSTA.

UniProtKB/Swiss-Prot for CSTB Gene

  • This is an intracellular thiol proteinase inhibitor. Tightly binding reversible inhibitor of cathepsins L, H and B.

Gene Wiki entry for CSTB Gene

Additional gene information for CSTB Gene

No data available for CIViC summary , Tocris Summary , PharmGKB "VIP" Summary , fRNAdb sequence ontologies and piRNA Summary for CSTB Gene

Genomics for CSTB Gene

GeneHancer (GH) Regulatory Elements for CSTB Gene

Promoters and enhancers for CSTB Gene
GeneHancer (GH) Identifier GH Type GH
GH Sources Gene Association Score Total Score TSS distance (kb) Number of Genes Away Size (kb) Transcription Factor
Binding Sites
Gene Targets
GH21J043774 Promoter/Enhancer 2.2 EPDnew Ensembl ENCODE dbSUPER 677.1 +0.6 587 2.4 ARID4B SIN3A DMAP1 ZBTB7B YY1 POLR2B ZNF207 SP3 SP5 MXD4 CSTB GC21M043771 WDR4 ENSG00000184441 U2AF1 RRP1B PKNOX1 PWP2 ENSG00000233754 C21orf2
GH21J043782 Enhancer 1.4 FANTOM5 ENCODE dbSUPER 25.9 -6.6 -6625 1.7 FOXA2 MLX ARID4B NEUROD1 DMAP1 ZNF48 YY1 SLC30A9 FOS NFKBIZ TMEM97P1 CSTB RRP1 AATBC LOC105372825
GH21J043804 Enhancer 1.1 Ensembl ENCODE 27.9 -29.3 -29344 3.2 HDGF PKNOX1 SMAD1 RB1 STAT5A BMI1 YBX1 BATF KLF5 IRF4 CSTB U2AF1 UBE2G2 WDR4 RRP1B PWP2 RRP1 AATBC GC21P043803
GH21J043767 Enhancer 1.7 FANTOM5 Ensembl ENCODE dbSUPER 17.3 +8.2 8173 2.4 HDGF SMAD1 ATF1 FOXA2 ZNF48 TCF12 POLR2B ZNF766 GLIS2 E2F8 CSTB PDXK ICOSLG GC21M043771 PIR43884
GH21J043809 Enhancer 1.2 Ensembl ENCODE 23.7 -35.1 -35145 3.4 HDGF PKNOX1 ARNT ARID4B SIN3A ZNF2 ZBTB7B ZNF213 ZNF207 ZNF143 AATBC ENSG00000184441 CSTB WDR4 PWP2 TRAPPC10 RRP1B C21orf2 RRP1 GC21P043803
- Elite GeneHancer and/or Elite GeneHancer-gene association Download GeneHancer data from 2017 publication | Request up-to-date GeneHancer data (full dataset)

GeneHancers around CSTB on UCSC Golden Path with GeneCards custom track

Top Transcription factor binding sites by QIAGEN in the CSTB gene promoter:
  • ATF
  • USF2
  • USF1
  • USF-1:USF-2
  • USF-1
  • Max
  • c-Myc
  • AP-4
  • SREBP-1a
  • SREBP-1b

Genomic Locations for CSTB Gene

Genomic Locations for CSTB Gene
3,935 bases
Minus strand
3,934 bases
Minus strand

Genomic View for CSTB Gene

Genes around CSTB on UCSC Golden Path with GeneCards custom track

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

RefSeq DNA sequence for CSTB Gene

Proteins for CSTB Gene

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

    Protein Symbol:
    Recommended name:
    Protein Accession:

    Protein attributes for CSTB Gene

    98 amino acids
    Molecular mass:
    11140 Da
    Quaternary structure:
    • Able to form dimers stabilized by noncovalent forces.

    Three dimensional structures from OCA and Proteopedia for CSTB Gene

neXtProt entry for CSTB Gene

Post-translational modifications for CSTB Gene

  • Ubiquitination at Lys78, Lys44, and posLast=3939
  • Modification sites at PhosphoSitePlus

Other Protein References for CSTB Gene

ENSEMBL proteins:
REFSEQ proteins:

Antibody Products

No data available for DME Specific Peptides for CSTB Gene

Domains & Families for CSTB Gene

Gene Families for CSTB Gene

Human Protein Atlas (HPA):
  • Cancer-related genes
  • Disease related genes
  • Plasma proteins
  • Potential drug targets
  • Predicted intracellular proteins
  • Transporters

Protein Domains for CSTB Gene

Suggested Antigen Peptide Sequences for CSTB Gene

Graphical View of Domain Structure for InterPro Entry



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

Function for CSTB Gene

Molecular function for CSTB Gene

UniProtKB/Swiss-Prot Function:
This is an intracellular thiol proteinase inhibitor. Tightly binding reversible inhibitor of cathepsins L, H and B.
GENATLAS Biochemistry:
cystatin B,cysteine proteinase inhibitor,type 2 family,widely expressed

Phenotypes From GWAS Catalog for CSTB Gene

Gene Ontology (GO) - Molecular Function for CSTB Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0002020 protease binding IPI 6203523
GO:0003723 RNA binding HDA 22658674
GO:0004866 endopeptidase inhibitor activity TAS,IEA 3053245
GO:0004869 cysteine-type endopeptidase inhibitor activity IDA,IEA 3488317
GO:0030414 peptidase inhibitor activity IEA --
genes like me logo Genes that share ontologies with CSTB: view
genes like me logo Genes that share phenotypes with CSTB: view

Human Phenotype Ontology for CSTB Gene

HPO Id HPO Name Alternative Ids Definition Synonyms

Animal Models for CSTB Gene

MGI Knock Outs for CSTB:

Animal Model Products

CRISPR Products

miRNA for CSTB Gene

Inhibitory RNA Products

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

No data available for Enzyme Numbers (IUBMB) , Transcription Factor Targets and HOMER Transcription for CSTB Gene

Localization for CSTB Gene

Subcellular locations from UniProtKB/Swiss-Prot for CSTB Gene

Cytoplasm. Nucleus.

Subcellular locations from

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 CSTB gene
Compartment Confidence
extracellular 5
nucleus 5
cytosol 5
peroxisome 2
lysosome 2
cytoskeleton 1
mitochondrion 1
endoplasmic reticulum 1

Subcellular locations from the

Human Protein Atlas (HPA)
  • Cytosol (3)
  • Nucleoli (2)
See all subcellular structures

Gene Ontology (GO) - Cellular Components for CSTB Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0005576 extracellular region TAS --
GO:0005615 extracellular space IDA 3488317
GO:0005622 intracellular IEA --
GO:0005634 nucleus IEA --
GO:0005730 nucleolus IDA --
genes like me logo Genes that share ontologies with CSTB: view

Pathways & Interactions for CSTB Gene

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

Pathways by source for CSTB Gene

3 Reactome pathways for CSTB Gene

Gene Ontology (GO) - Biological Process for CSTB Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0008344 adult locomotory behavior IEA --
GO:0010466 negative regulation of peptidase activity IDA 6203523
GO:0010951 negative regulation of endopeptidase activity IEA --
GO:0043312 neutrophil degranulation TAS --
GO:0045861 negative regulation of proteolysis IDA 3488317
genes like me logo Genes that share ontologies with CSTB: view

No data available for SIGNOR curated interactions for CSTB Gene

Drugs & Compounds for CSTB Gene

(7) Drugs for CSTB Gene - From: DrugBank and Novoseek

Name Status Disease Links Group Role Mechanism of Action Clinical Trials
Cupric Chloride Approved, Investigational Pharma Target 0
Papain Inhibitor Pharma Inhibitor of peptidase activity of Papain 0

(4) Additional Compounds for CSTB Gene - From: Novoseek

Name Synonyms Role CAS Number PubChem IDs PubMed IDs
genes like me logo Genes that share compounds with CSTB: view

Transcripts for CSTB Gene

mRNA/cDNA for CSTB Gene

(1) REFSEQ mRNAs :
(6) Additional mRNA sequences :
(454) Selected AceView cDNA sequences:
(4) Ensembl transcripts including schematic representations, and UCSC links where relevant :

Unigene Clusters for CSTB Gene

Cystatin B (stefin B):
Representative Sequences:

CRISPR Products

Inhibitory RNA Products

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

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

ExUns: 1a · 1b ^ 2 ^ 3a · 3b

Relevant External Links for CSTB Gene

GeneLoc Exon Structure for
ECgene alternative splicing isoforms for

Expression for CSTB Gene

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

mRNA expression in embryonic tissues and stem cells from LifeMap Discovery

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

This gene is overexpressed in Esophagus - Mucosa (x24.9) and Vagina (x5.1).

Protein differential expression in normal tissues from HIPED for CSTB Gene

This gene is overexpressed in Esophagus (7.9), Oral epithelium (6.5), and Saliva (6.1).

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

Protein tissue co-expression partners for CSTB Gene

NURSA nuclear receptor signaling pathways regulating expression of CSTB Gene:


SOURCE GeneReport for Unigene cluster for CSTB Gene:


Evidence on tissue expression from TISSUES for CSTB Gene

  • Liver(4.6)
  • Nervous system(3.9)
  • Lung(3.6)
  • Intestine(3.2)
  • Blood(2.6)
  • Pancreas(2.5)
  • Heart(2.3)
  • Muscle(2.3)
  • Kidney(2.2)
  • Skin(2.2)
  • Stomach(2.2)

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

Germ Layers:
  • ectoderm
  • mesoderm
  • nervous
  • skeletal muscle
Head and neck:
  • brain
  • head
  • foot
  • lower limb
  • peripheral nerve
  • peripheral nervous system
genes like me logo Genes that share expression patterns with CSTB: view

No data available for mRNA Expression by UniProt/SwissProt for CSTB Gene

Orthologs for CSTB Gene

This gene was present in the common ancestor of chordates.

Orthologs for CSTB Gene

Organism Taxonomy Gene Similarity Type Details
(Pan troglodytes)
Mammalia CSTB 34 33
  • 99.32 (n)
(Bos Taurus)
Mammalia CSTB 34 34 33
  • 81.29 (n)
-- 34
  • 60 (a)
(Canis familiaris)
Mammalia CSTB 34
  • 79 (a)
(Rattus norvegicus)
Mammalia Cstb 33
  • 78.57 (n)
(Mus musculus)
Mammalia Cstb 16 34 33
  • 77.21 (n)
(Monodelphis domestica)
Mammalia CSTB 34
  • 57 (a)
(Ornithorhynchus anatinus)
Mammalia CSTB 34
  • 22 (a)
(Gallus gallus)
Aves CSTB 34 33
  • 72.79 (n)
(Anolis carolinensis)
Reptilia CSTB 34
  • 59 (a)
(Danio rerio)
Actinopterygii zgc:56530 34 33
  • 57.82 (n)
si:ch211-161h7.6 34
  • 53 (a)
zgc:153129 34
  • 47 (a)
Species where no ortholog for CSTB was found in the sources mined by GeneCards:
  • A. gosspyii yeast (Ashbya 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 squirt (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 CSTB Gene

Gene Tree for CSTB (if available)
Gene Tree for CSTB (if available)
Evolutionary constrained regions (ECRs) for CSTB: view image

Paralogs for CSTB Gene

Paralogs for CSTB Gene

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

  • Q76LA1_HUMAN Pseudogenes for CSTB Gene

genes like me logo Genes that share paralogs with CSTB: view

Variants for CSTB Gene

Sequence variations from dbSNP and Humsavar for CSTB Gene

SNP ID Clin Chr 21 pos Variation AA Info Type
rs1026016803 uncertain-significance, Unverricht-Lundborg syndrome 43,776,312(-) G/C 5_prime_UTR_variant
rs121909346 pathogenic, Unverricht-Lundborg syndrome 43,774,287(-) T/G coding_sequence_variant, missense_variant
rs142767585 uncertain-significance, Unverricht-Lundborg syndrome 43,774,133(-) T/C 3_prime_UTR_variant
rs143062585 uncertain-significance, Unverricht-Lundborg syndrome 43,773,847(-) G/C 3_prime_UTR_variant
rs143153487 uncertain-significance, conflicting-interpretations-of-pathogenicity, not provided, not specified, Progressive myoclonic epilepsy 43,774,705(-) C/T coding_sequence_variant, missense_variant

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

Variant ID Type Subtype PubMed ID
esv33817 CNV loss 17666407
nsv470904 CNV loss 18288195
nsv509799 CNV insertion 20534489
nsv520305 CNV loss 19592680
nsv834107 CNV loss 17160897
nsv834108 CNV loss 17160897
nsv953642 CNV deletion 24416366

Variation tolerance for CSTB Gene

Residual Variation Intolerance Score: 44.6% of all genes are more intolerant (likely to be disease-causing)
Gene Damage Index Score: 0.40; 8.69% of all genes are more intolerant (likely to be disease-causing)

Additional Variant Information for CSTB Gene

Human Gene Mutation Database (HGMD)
SNPedia medical, phenotypic, and genealogical associations of SNPs for

SNP Genotyping and Copy Number Assay Products

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

Disorders for CSTB Gene

MalaCards: The human disease database

(16) MalaCards diseases for CSTB Gene - From: HGMD, OMIM, ClinVar, GTR, Orphanet, Swiss-Prot, DISEASES, Novoseek, and GeneCards

- elite association - COSMIC cancer census association via MalaCards
Search CSTB in MalaCards View complete list of genes associated with diseases


  • Epilepsy, progressive myoclonic 1 (EPM1) [MIM:254800]: An autosomal recessive disorder characterized by severe, stimulus-sensitive myoclonus and tonic-clonic seizures. The onset, occurring between 6 and 13 years of age, is characterized by convulsions. Myoclonus begins 1 to 5 years later. The twitchings occur predominantly in the proximal muscles of the extremities and are bilaterally symmetrical, although asynchronous. At first small, they become late in the clinical course so violent that the victim is thrown to the floor. Mental deterioration and eventually dementia develop. {ECO:0000269 PubMed:9012407}. Note=The disease is caused by mutations affecting the gene represented in this entry.

Additional Disease Information for CSTB

Genetic Association Database
Human Genome Epidemiology Navigator
ATLAS of Genetics and Cytogenetics in Oncology and Haematology
genes like me logo Genes that share disorders with CSTB: view

No data available for Genatlas for CSTB Gene

Publications for CSTB Gene

  1. Mutations in the gene encoding cystatin B in progressive myoclonus epilepsy (EPM1) (PMID: 8596935) Pennacchio LA … Myers RM (Science (New York, N.Y.) 1996) 2 3 4 22 58
  2. Nuclear localization of cystatin B, the cathepsin inhibitor implicated in myoclonus epilepsy (EPM1). (PMID: 11139332) Riccio M … Santi S (Experimental cell research 2001) 3 4 22 58
  3. Identification of mutations in cystatin B, the gene responsible for the Unverricht-Lundborg type of progressive myoclonus epilepsy (EPM1). (PMID: 9012407) Lalioti MD … Antonarakis SE (American journal of human genetics 1997) 3 4 22 58
  4. The refined 2.4 A X-ray crystal structure of recombinant human stefin B in complex with the cysteine proteinase papain: a novel type of proteinase inhibitor interaction. (PMID: 2347312) Stubbs MT … Turk V (The EMBO journal 1990) 3 4 22 58
  5. Variation at the NFATC2 locus increases the risk of thiazolidinedione-induced edema in the Diabetes REduction Assessment with ramipril and rosiglitazone Medication (DREAM) study. (PMID: 20628086) Bailey SD … DREAM investigators (Diabetes care 2010) 3 44 58

Products for CSTB Gene

Sources for CSTB Gene

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