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Aliases for GSDMB Gene

Aliases for GSDMB Gene

  • Gasdermin B 2 3 5
  • Gasdermin-Like Protein 3 4
  • GSDML 3 4
  • Gasdermin-Like 2
  • Gasdermin-B 3
  • PRO2521 3
  • PP4052 3

External Ids for GSDMB Gene

Previous HGNC Symbols for GSDMB Gene

  • GSDML

Previous GeneCards Identifiers for GSDMB Gene

  • GC17M035315
  • GC17M038060
  • GC17M033854

Summaries for GSDMB Gene

Entrez Gene Summary for GSDMB Gene

  • This gene encodes a member of the gasdermin-domain containing protein family. Other gasdermin-family genes are implicated in the regulation of apoptosis in epithelial cells, and are linked to cancer. Alternative splicing and the use of alternative promoters results in multiple transcript variants. Additional variants have been described, but they are candidates for nonsense-mediated mRNA decay (NMD) and are unlikely to be protein-coding. [provided by RefSeq, Nov 2016]

GeneCards Summary for GSDMB Gene

GSDMB (Gasdermin B) is a Protein Coding gene. An important paralog of this gene is GSDMA.

UniProtKB/Swiss-Prot for GSDMB Gene

  • The N-terminal moiety promotes pyroptosis. May be acting by homooligomerizing within the membrane and forming pores (PubMed:27281216). The physiological relevance of this observation is unknown (Probable).

Additional gene information for GSDMB Gene

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

Genomics for GSDMB Gene

GeneHancer (GH) Regulatory Elements for GSDMB Gene

Promoters and enhancers for GSDMB 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
GH17J039916 Promoter/Enhancer 2.6 EPDnew FANTOM5 Ensembl ENCODE dbSUPER 677.4 -3.5 -3515 14.4 MLX ZFP64 DMAP1 YY1 SLC30A9 E2F8 ZNF143 ZNF548 ZNF263 SP3 ORMDL3 GSDMB GC17P039921 CDK12 MED1 SMARCE1 ENSG00000264968 MSL1 STARD3 RARA
GH17J039859 Promoter/Enhancer 2.5 EPDnew Ensembl ENCODE dbSUPER 40.2 +55.4 55425 9.7 HDGF PKNOX1 FOXA2 SMAD1 MLX ZFP64 ARID4B SIN3A DMAP1 ZNF2 IKZF3 ZPBP2 GSDMB ORMDL3 MED24 GSDMA TMEM99 LRRC3C MSL1 MED1
GH17J039766 Enhancer 1.7 FANTOM5 Ensembl ENCODE dbSUPER 36 +145.0 144967 17.2 HDGF PKNOX1 CLOCK FOXA2 SMAD1 FEZF1 ZNF2 IRF4 ZNF213 FOS GC17P039774 GSDMB MED1 ORMDL3 GSDMA SNORD124 MED24 CDK12 ERBB2 MIEN1
GH17J039817 Enhancer 1.2 FANTOM5 ENCODE dbSUPER 38 +99.7 99661 4.8 TAL1 BACH1 EBF1 RELA ZNF121 EED IKZF2 RUNX3 CREM ZNF687 GSDMB IKZF3 GSDMA PGAP3 FBXL20 WIPF2 ORMDL3 CASC3 GC17P039815 KRT8P34
GH17J039753 Enhancer 1.8 FANTOM5 Ensembl ENCODE dbSUPER 24.6 +163.3 163260 7.1 HDGF PKNOX1 FOXA2 SMAD1 ARID4B SIN3A DMAP1 YBX1 IRF4 YY1 GSDMB ORMDL3 THRA IKZF3 KRT222 SNORD124 MED24 STARD3 FBXL20 CDK12
- Elite GeneHancer and/or Elite GeneHancer-gene association Download GeneHancer data from 2017 publication | Request up-to-date GeneHancer data (full dataset)

GeneHancers around GSDMB on UCSC Golden Path with GeneCards custom track

Top Transcription factor binding sites by QIAGEN in the GSDMB gene promoter:
  • AP-4
  • COUP-TF
  • C/EBPbeta
  • COUP
  • COUP-TF1
  • HNF-4alpha2

Genomic Locations for GSDMB Gene

Genomic Locations for GSDMB Gene
chr17:39,904,595-39,919,854
(GRCh38/hg38)
Size:
15,260 bases
Orientation:
Minus strand
chr17:38,060,848-38,076,107
(GRCh37/hg19)
Size:
15,260 bases
Orientation:
Minus strand

Genomic View for GSDMB Gene

Genes around GSDMB on UCSC Golden Path with GeneCards custom track

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

RefSeq DNA sequence for GSDMB Gene

Proteins for GSDMB Gene

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

    Protein Symbol:
    Q8TAX9-GSDMB_HUMAN
    Recommended name:
    Gasdermin-B
    Protein Accession:
    Q8TAX9
    Secondary Accessions:
    • B4DKK7
    • Q7Z377
    • Q8WY76
    • Q9NX71
    • Q9P163

    Protein attributes for GSDMB Gene

    Size:
    411 amino acids
    Molecular mass:
    46786 Da
    Quaternary structure:
    • The N-terminal moiety forms homooligomer; disulfide-linked. May form an 16-mer complex. Oligomerization occurs in the presence of membranes.
    Miscellaneous:
    • The GSDML gene is predicted to be generated due to a duplication of GSDM gene; the rodent GSDML ortholog failed to be yet identified. The evolutionary recombination hotspot around GSDML-GSDM locus is closely related to the oncogenomic recombination hotspot or fragile sites within the human genome.
    • Long terminal repeat (LTR) of endogenous retroviruse HERV-H with reverse orientation may serve as alternative promoters of GSDML gene.
    • GSDML may be used as predictive markers of cervical lymph node metastasis and may help, with a panel of other genes, to discriminate between primary tumors of oral squamous cell carcinoma that metastasize to cervical lymph node and those that do not metastasize.

    Three dimensional structures from OCA and Proteopedia for GSDMB Gene

    Alternative splice isoforms for GSDMB Gene

neXtProt entry for GSDMB Gene

Post-translational modifications for GSDMB Gene

  • Modification sites at PhosphoSitePlus
  • Modification sites at neXtProt

No data available for DME Specific Peptides for GSDMB Gene

Domains & Families for GSDMB Gene

Gene Families for GSDMB Gene

HGNC:
Human Protein Atlas (HPA):
  • Predicted intracellular proteins
  • Transporters

Protein Domains for GSDMB Gene

InterPro:
ProtoNet:

Suggested Antigen Peptide Sequences for GSDMB Gene

Graphical View of Domain Structure for InterPro Entry

Q8TAX9

UniProtKB/Swiss-Prot:

GSDMB_HUMAN :
  • Intramolecular interactions between N- and C-terminal domains may be important for autoinhibition in the absence of activation signal. The intrinsic pyroptosis-inducing activity is carried by the N-terminal domain.
  • Belongs to the gasdermin family.
Domain:
  • Intramolecular interactions between N- and C-terminal domains may be important for autoinhibition in the absence of activation signal. The intrinsic pyroptosis-inducing activity is carried by the N-terminal domain.
Family:
  • Belongs to the gasdermin family.
genes like me logo Genes that share domains with GSDMB: view

Function for GSDMB Gene

Molecular function for GSDMB Gene

UniProtKB/Swiss-Prot Function:
The N-terminal moiety promotes pyroptosis. May be acting by homooligomerizing within the membrane and forming pores (PubMed:27281216). The physiological relevance of this observation is unknown (Probable).

Phenotypes From GWAS Catalog for GSDMB Gene

Gene Ontology (GO) - Molecular Function for GSDMB Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0001786 phosphatidylserine binding IBA --
GO:0003674 molecular_function ND --
GO:0005546 phosphatidylinositol-4,5-bisphosphate binding IBA --
GO:0070273 phosphatidylinositol-4-phosphate binding IBA --
genes like me logo Genes that share ontologies with GSDMB: view
genes like me logo Genes that share phenotypes with GSDMB: view

Animal Model Products

miRNA for GSDMB Gene

miRTarBase miRNAs that target GSDMB

Clone Products

No data available for Enzyme Numbers (IUBMB) , Human Phenotype Ontology , Animal Models , Transcription Factor Targets and HOMER Transcription for GSDMB Gene

Localization for GSDMB Gene

Subcellular locations from UniProtKB/Swiss-Prot for GSDMB Gene

Cytoplasm. Cytoplasm, cytosol. Cell membrane. Note=Vesicular localization in the apical region of gastric chief cells and colonic surface mucous cells, and the basal region of neuroendocrine cells. {ECO:0000269 PubMed:18038310}.

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 GSDMB gene
Compartment Confidence
cytosol 4
plasma membrane 3
nucleus 1

Gene Ontology (GO) - Cellular Components for GSDMB Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0005575 cellular_component ND --
GO:0005737 cytoplasm IEA,IBA --
GO:0005829 cytosol IEA --
GO:0005886 plasma membrane IEA --
GO:0016020 membrane IEA --
genes like me logo Genes that share ontologies with GSDMB: view

No data available for Subcellular locations from the Human Protein Atlas (HPA) for GSDMB Gene

Pathways & Interactions for GSDMB Gene

SuperPathways for GSDMB Gene

No Data Available

Interacting Proteins for GSDMB Gene

STRING Interaction Network Preview (showing 1 interactants - click image to see details)
http://version10.5.string-db.org/api/image/networkList?limit=0&targetmode=proteins&caller_identity=gene_cards&network_flavor=evidence&identifiers=9606.ENSP00000353465%0d%0a9606.ENSP00000259396%0d%0a
Selected Interacting proteins: Q8TAX9-GSDMB_HUMAN ENSP00000353465 for GSDMB Gene via IID STRING

Gene Ontology (GO) - Biological Process for GSDMB Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0008150 biological_process ND --
GO:0012501 programmed cell death IEA --
GO:0042742 defense response to bacterium IBA --
GO:0070269 pyroptosis IBA --
genes like me logo Genes that share ontologies with GSDMB: view

No data available for Pathways by source and SIGNOR curated interactions for GSDMB Gene

Drugs & Compounds for GSDMB Gene

No Compound Related Data Available

Transcripts for GSDMB Gene

mRNA/cDNA for GSDMB Gene

Unigene Clusters for GSDMB Gene

Gasdermin B:
Representative Sequences:

Clone Products

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

ExUns: 1a · 1b ^ 2a · 2b · 2c · 2d · 2e · 2f ^ 3a · 3b ^ 4a · 4b ^ 5a · 5b ^ 6a · 6b ^ 7 ^ 8a · 8b ^ 9 ^ 10 ^ 11
SP1: - - - - -
SP2: - -
SP3: - -
SP4: - - - -
SP5: - - - - -
SP6:
SP7: - - -
SP8: - - - -
SP9: - - - - - -

Relevant External Links for GSDMB Gene

GeneLoc Exon Structure for
GSDMB
ECgene alternative splicing isoforms for
GSDMB

Expression for GSDMB Gene

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

mRNA expression in embryonic tissues and stem cells from LifeMap Discovery

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

This gene is overexpressed in Liver (x4.8), Colon - Transverse (x4.2), and Small Intestine - Terminal Ileum (x4.1).

Protein differential expression in normal tissues from HIPED for GSDMB Gene

This gene is overexpressed in Stomach (26.8), Islet of Langerhans (15.1), and Rectum (15.0).

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



Protein tissue co-expression partners for GSDMB Gene

NURSA nuclear receptor signaling pathways regulating expression of GSDMB Gene:

GSDMB

SOURCE GeneReport for Unigene cluster for GSDMB Gene:

Hs.306777

mRNA Expression by UniProt/SwissProt for GSDMB Gene:

Q8TAX9-GSDMB_HUMAN
Tissue specificity: In the gastrointestinal tract, expressed in proliferating cells, including in the basal cell layer of esophagus and in isthmus/neck of stomach.

Evidence on tissue expression from TISSUES for GSDMB Gene

  • Intestine(4.3)
  • Lung(4.3)
genes like me logo Genes that share expression patterns with GSDMB: view

No data available for Phenotype-based relationships between genes and organs from Gene ORGANizer for GSDMB Gene

Orthologs for GSDMB Gene

This gene was present in the common ancestor of mammals.

Orthologs for GSDMB Gene

Organism Taxonomy Gene Similarity Type Details
chimpanzee
(Pan troglodytes)
Mammalia GSDMB 34 33
  • 99.44 (n)
OneToOne
dog
(Canis familiaris)
Mammalia GSDMB 34 33
  • 74.88 (n)
OneToOne
cow
(Bos Taurus)
Mammalia GSDMB 34 33
  • 73.12 (n)
OneToOne
oppossum
(Monodelphis domestica)
Mammalia GSDMB 34
  • 30 (a)
OneToOne
Species where no ortholog for GSDMB 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)
  • chicken (Gallus gallus)
  • 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)
  • lizard (Anolis carolinensis)
  • loblloly pine (Pinus taeda)
  • malaria parasite (Plasmodium falciparum)
  • medicago trunc (Medicago Truncatula)
  • moss (Physcomitrella patens)
  • mouse (Mus musculus)
  • orangutan (Pongo pygmaeus)
  • pig (Sus scrofa)
  • platypus (Ornithorhynchus anatinus)
  • rainbow trout (Oncorhynchus mykiss)
  • rat (Rattus norvegicus)
  • 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)
  • zebrafish (Danio rerio)

Evolution for GSDMB Gene

ENSEMBL:
Gene Tree for GSDMB (if available)
TreeFam:
Gene Tree for GSDMB (if available)
Aminode:
Evolutionary constrained regions (ECRs) for GSDMB: view image

Paralogs for GSDMB Gene

Paralogs for GSDMB Gene

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

  • GSDMB_HUMAN
  • J3QLF0_HUMAN
genes like me logo Genes that share paralogs with GSDMB: view

Variants for GSDMB Gene

Sequence variations from dbSNP and Humsavar for GSDMB Gene

SNP ID Clin Chr 17 pos Variation AA Info Type
VAR_042634 A breast cancer sample p.Asp245Gly
rs1000014002 -- 39,920,026(-) T/C upstream_transcript_variant
rs1000029296 -- 39,906,610(-) G/A 3_prime_UTR_variant, genic_downstream_transcript_variant, intron_variant
rs1000056489 -- 39,907,658(-) G/A downstream_transcript_variant, genic_downstream_transcript_variant, intron_variant
rs1000066259 -- 39,919,781(-) G/A upstream_transcript_variant

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

Variant ID Type Subtype PubMed ID
esv3573064 CNV gain 25503493
esv3640549 CNV loss 21293372
nsv1146669 OTHER inversion 26484159

Variation tolerance for GSDMB Gene

Residual Variation Intolerance Score: 75.7% of all genes are more intolerant (likely to be disease-causing)
Gene Damage Index Score: 11.87; 93.50% of all genes are more intolerant (likely to be disease-causing)

Additional Variant Information for GSDMB Gene

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

SNP Genotyping and Copy Number Assay Products

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

Disorders for GSDMB Gene

Additional Disease Information for GSDMB

Genetic Association Database
(GAD)
Human Genome Epidemiology Navigator
(HuGE)
ATLAS of Genetics and Cytogenetics in Oncology and Haematology

No disorders were found for GSDMB Gene.

No data available for MalaCards , UniProtKB/Swiss-Prot and Genatlas for GSDMB Gene

Publications for GSDMB Gene

  1. Genetic variation in ORM1-like 3 (ORMDL3) and gasdermin-like (GSDML) and childhood asthma. (PMID: 19133921) Wu H … London SJ (Allergy 2009) 3 22 44 58
  2. Differential expression and localisation of gasdermin-like (GSDML), a novel member of the cancer-associated GSDMDC protein family, in neoplastic and non-neoplastic gastric, hepatic, and colon tissues. (PMID: 18038310) Carl-McGrath S … Röcken C (Pathology 2008) 3 4 22 58
  3. Members of a novel gene family, Gsdm, are expressed exclusively in the epithelium of the skin and gastrointestinal tract in a highly tissue-specific manner. (PMID: 17350798) Tamura M … Shiroishi T (Genomics 2007) 2 3 4 58
  4. Transcriptional control of the HERV-H LTR element of the GSDML gene in human tissues and cancer cells. (PMID: 16625320) Sin HS … Kim HS (Archives of virology 2006) 3 4 22 58
  5. Evolutionary recombination hotspot around GSDML-GSDM locus is closely linked to the oncogenomic recombination hotspot around the PPP1R1B-ERBB2-GRB7 amplicon. (PMID: 15010812) Katoh M … Katoh M (International journal of oncology 2004) 2 3 22 58

Products for GSDMB Gene

Sources for GSDMB Gene

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