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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. Diseases associated with GSDMB include Oral Squamous Cell Carcinoma.

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).

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

Regulatory Elements for GSDMB Gene

Enhancers for GSDMB Gene
GeneHancer Identifier Enhancer Score Enhancer Sources Gene-Enhancer Score TSS distance (kb) Number of Genes Away Size (kb) Transcription Factor Binding Sites within enhancer Gene Targets for Enhancer
GH17G039766 1.9 FANTOM5 Ensembl ENCODE dbSUPER 36 +145.0 144967 17.2 HDGF PKNOX1 FOXA2 WRNIP1 SIN3A FEZF1 ZNF2 CBX5 FOS SP3 GSDMB ENSG00000266469 MED1 ORMDL3 GSDMA CDK12 ERBB2 MIEN1 GRB7 SNORA21
GH17G039859 1.6 Ensembl ENCODE dbSUPER 40.2 +55.4 55426 9.7 HDGF PKNOX1 FOXA2 MLX CREB3L1 ZFP64 WRNIP1 ARID4B SIN3A DMAP1 GSDMB ORMDL3 GSDMA TMEM99 LRRC3C ENSG00000266469 MED1 PGAP3 IKZF3 PIR51928
GH17G039817 1.4 FANTOM5 ENCODE dbSUPER 38 +99.7 99661 4.8 CTCF TAL1 BACH1 RELA ZNF121 ARID3A EED RELB IKZF2 CREM GSDMB IKZF3 GSDMA PGAP3 FBXL20 WIPF2 ORMDL3 CASC3 GC17P039815 KRT8P34
GH17G039753 2 FANTOM5 Ensembl ENCODE dbSUPER 24.5 +163.3 163260 7.1 HDGF PKNOX1 CREB3L1 WRNIP1 ARID4B SIN3A DMAP1 YBX1 ZNF766 ZNF143 GSDMB ORMDL3 THRA IKZF3 KRT222 MED24 STARD3 FBXL20 CDK12 WIPF2
GH17G039916 1.7 FANTOM5 ENCODE dbSUPER 27.4 -3.5 -3515 14.4 MLX CREB3L1 ZFP64 DMAP1 YY1 SLC30A9 ZNF143 ZNF548 ZNF263 SP3 ORMDL3 GSDMB ENSG00000264968 MED1 ENSG00000266469 CDK12 GSDMA IKZF3 ERBB2 GC17P039921
- Elite enhancer and/or Elite enhancer-gene association Download GeneHancer data dump

Enhancers around GSDMB on UCSC Golden Path with GeneCards custom track

Genomic Location for GSDMB Gene

Chromosome:
17
Start:
39,904,595 bp from pter
End:
39,919,854 bp from pter
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:
    • 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.
    • Long terminal repeat (LTR) of endogenous retroviruse HERV-H with reverse orientation may serve as alternative promoters of GSDML gene.
    • 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.

    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

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

No data available for Gene Families for GSDMB Gene

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).
genes like me logo Genes that share phenotypes with GSDMB: view

Animal Model Products

CRISPR Products

miRNA for GSDMB Gene

miRTarBase miRNAs that target GSDMB

Inhibitory RNA Products

Flow Cytometry Products

No data available for Enzyme Numbers (IUBMB) , Gene Ontology (GO) - Molecular Function , 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:0005829 cytosol IEA --
GO:0005886 plasma membrane IEA --
GO:0016020 membrane IEA --
genes like me logo Genes that share ontologies with GSDMB: view

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://string-db.org/version_10/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:0012501 programmed cell death IEA --
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

Transcripts for GSDMB Gene

Unigene Clusters for GSDMB Gene

Gasdermin B:
Representative Sequences:

CRISPR Products

Inhibitory RNA Products

Flow Cytometry 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

Primer Products

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 35
  • 99.44 (n)
dog
(Canis familiaris)
Mammalia GSDMB 34 35
  • 74.88 (n)
cow
(Bos Taurus)
Mammalia GSDMB 34 35
  • 73.12 (n)
oppossum
(Monodelphis domestica)
Mammalia GSDMB 35
  • 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)

Paralogs for GSDMB Gene

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

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

No data available for Paralogs for GSDMB Gene

Variants for GSDMB Gene

Sequence variations from dbSNP and Humsavar for GSDMB Gene

SNP ID Clin Chr 17 pos Sequence Context AA Info Type
VAR_042634 A breast cancer sample
rs1000014002 -- 39,920,026(+) AGGCA(C/T)TATCT upstream-variant-2KB
rs1000029296 -- 39,906,610(+) TTGGA(A/G)AAAGT intron-variant, utr-variant-3-prime
rs1000056489 -- 39,907,658(+) AGGAG(A/G)TAGAG intron-variant, downstream-variant-500B
rs1000066259 -- 39,919,781(+) CTCAG(A/G)AGGCT upstream-variant-2KB

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)

Relevant External Links for GSDMB Gene

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

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

Disorders for GSDMB Gene

MalaCards: The human disease database

(1) MalaCards diseases for GSDMB Gene - From: GeneCards

Disorder Aliases PubMed IDs
oral squamous cell carcinoma
  • mouth squamous cell carcinoma
- elite association - COSMIC cancer census association via MalaCards
Search GSDMB in MalaCards View complete list of genes associated with diseases

Relevant External Links for GSDMB

Genetic Association Database (GAD)
GSDMB
Human Genome Epidemiology (HuGE) Navigator
GSDMB
Atlas of Genetics and Cytogenetics in Oncology and Haematology:
GSDMB
genes like me logo Genes that share disorders with GSDMB: view

No data available for 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 S.J. (Allergy 2009) 3 22 46 64
  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. … Roecken C. (Pathology 2008) 3 4 22 64
  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 64
  4. Transcriptional control of the HERV-H LTR element of the GSDML gene in human tissues and cancer cells. (PMID: 16625320) Sin H.-S. … Kim H.-S. (Arch. Virol. 2006) 3 4 22 64
  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. (Int. J. Oncol. 2004) 2 3 22 64

Products for GSDMB Gene

Sources for GSDMB Gene

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