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GSDMB (gasdermin B)

Written2011-11Masaru Tamura, Toshihiko Shiroishi
Mammalian Genetics Laboratory, Genetic Strains Research Center, National Institute of Genetics, 1111 Yata, Mishima, Shizuoka, Japan

(Note : for Links provided by Atlas : click)

Identity

Alias_namesGSDML
gasdermin-like
Alias_symbol (synonym)PRO2521
Other alias
HGNC (Hugo) GSDMB
LocusID (NCBI) 55876
Atlas_Id 43972
Location 17q12  [Link to chromosome band 17q12]
Location_base_pair Starts at 39904595 and ends at 39918650 bp from pter ( according to hg19-Feb_2009)  [Mapping GSDMB.png]
Local_order ERBB2, GRB7, IKZF3, ZPBP2, GSDMB, ORMDL3, GSDMA, PSMD3, CSF3.
Fusion genes
(updated 2016)
GSDMB (17q12) / MIR3134 (9q31.3)PGAP3 (17q12) / GSDMB (17q12)SLC6A6 (3p25.1) / GSDMB (17q12)
STARD3 (17q12) / GSDMB (17q12)TATDN1 (8q24.13) / GSDMB (17q12)WHSC1 (4p16.3) / GSDMB (17q12)

DNA/RNA

Description GSDMB belongs to the novel gene family Gasdermin (GSDM) that consists of four genes in human: GSDMA, GSDMB, GSDMC and GSDMD (Tamura et al., 2007). The human GSDMB gene is located on chromosome 17q21 and consists of 12 exons, spanning 14 kb of genomic DNA.
Transcription GSDMB has at least four alternatively spliced transcripts variants that range from 1578 to 1646 bp in length. These splicing variants, which lack exon 6, 7, and both, are named GSDMB transcript variant 1 (Delta exon 6), GSDMB transcript variant 2 (Delta exon 6 and exon 7), GSDMB transcript variant 3 (full length) and GSDMB transcript variant 4 (Delta exon 7). GSDMB has two different promoters, Alu-derived promoter and long-terminal-repeat (LTR)-derived promoter (Sin et al., 2006; Huh et al., 2008; Komiyama et al., 2010). These two promoters drive all GSDMB transcriptions except for those starting from exon1a and exon1b.
Pseudogene No GSDMB pseudogene has been identified in the human genome.

Protein

Description The full length of GSDMB gene (GSDMB transcript variant 3) encodes a 416 amino acid protein with estimated molecular weight of 47345,44 Da. GSDM family proteins have 9 conserved and unknown function motifs (motif I to IX). GSDMB lacks motif VIII where mouse alopecia mutation Rex-denuded occurs (Runkel et al., 2004; Tamura et al., 2007).
Expression Expression of GSDMB was observed in esophagus and gastric epithelium (Saeki et al., 2009). In addition, GSDMB was frequently expressed in several cancer tissues and cancer-derived cell lines.
Localisation Cytoplasm (Carl-McGrath et al., 2008).
Function The function of GSDMB is largely unknown, because GSDMB is a novel protein without characteristic domains related to known function.
Expression level of GSDMB seems to be changed along progression of several cancers. However, forced expression of GSDMB could neither promote malignant transformation of CHO cells nor confer colony formation ability or carcinogenicity to CHO cells in nude mice (Sun et al., 2008). Recent large-scale genome wide association studies (GWAS) revealed that GSDMB locus is strongly correlated with asthma (Moffatt et al., 2010).
Homology GSDMB protein shares homology with other GSDM family members for N- and C- terminal sequences. Its N-terminal sequence is also shared by DFNA5 (deafness, autosomal dominant 5) and DFNB59 (deafness, autosomal recessive 59, also known as pejvakin), although the extent of similarity to these proteins is lower than to the other GSDM family members.
GSDMB ortholog is identified in the chimpanzee, dog and cow, but not in the rat and mouse (Katoh and Katoh, 2004; Tamura et al., 2007).

Mutations

Note No human GSDMB mutations have been reported to date.
Germinal Not known.
Somatic Not known.

Implicated in

Note
  
Entity Various cancers
Note GSDMB is up-regulated in several cancers, such as gastric, colorectal, hepatic, cervical carcinomas, suggesting the possibility that it is used as a marker for cancer development and progression.
  
  
Entity Asthma
Note The genome wide association study (GWAS) demonstrated that GSDMB locus is strongly associated with asthma (Moffatt et al., 2010).
  

Bibliography

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.
Carl-McGrath S, Schneider-Stock R, Ebert M, Rocken C.
Pathology. 2008 Jan;40(1):13-24.
PMID 18038310
 
Transcriptional regulation of GSDML gene by antisense-oriented HERV-H LTR element.
Huh JW, Kim DS, Kang DW, Ha HS, Ahn K, Noh YN, Min DS, Chang KT, Kim HS.
Arch Virol. 2008;153(6):1201-5. Epub 2008 May 14.
PMID 18478180
 
Evolutionary recombination hotspot around GSDML-GSDM locus is closely linked to the oncogenomic recombination hotspot around the PPP1R1B-ERBB2-GRB7 amplicon.
Katoh M, Katoh M.
Int J Oncol. 2004 Apr;24(4):757-63.
PMID 15010812
 
Alu-derived cis-element regulates tumorigenesis-dependent gastric expression of GASDERMIN B (GSDMB).
Komiyama H, Aoki A, Tanaka S, Maekawa H, Kato Y, Wada R, Maekawa T, Tamura M, Shiroishi T.
Genes Genet Syst. 2010 Feb;85(1):75-83.
PMID 20410667
 
A large-scale, consortium-based genomewide association study of asthma.
Moffatt MF, Gut IG, Demenais F, Strachan DP, Bouzigon E, Heath S, von Mutius E, Farrall M, Lathrop M, Cookson WO; GABRIEL Consortium.
N Engl J Med. 2010 Sep 23;363(13):1211-21.
PMID 20860503
 
The dominant alopecia phenotypes Bareskin, Rex-denuded, and Reduced Coat 2 are caused by mutations in gasdermin 3.
Runkel F, Marquardt A, Stoeger C, Kochmann E, Simon D, Kohnke B, Korthaus D, Wattler F, Fuchs H, Hrabe de Angelis M, Stumm G, Nehls M, Wattler S, Franz T, Augustin M.
Genomics. 2004 Nov;84(5):824-35.
PMID 15475261
 
Distinctive expression and function of four GSDM family genes (GSDMA-D) in normal and malignant upper gastrointestinal epithelium.
Saeki N, Usui T, Aoyagi K, Kim DH, Sato M, Mabuchi T, Yanagihara K, Ogawa K, Sakamoto H, Yoshida T, Sasaki H.
Genes Chromosomes Cancer. 2009 Mar;48(3):261-71.
PMID 19051310
 
Transcriptional control of the HERV-H LTR element of the GSDML gene in human tissues and cancer cells.
Sin HS, Huh JW, Kim DS, Kang DW, Min DS, Kim TH, Ha HS, Kim HH, Lee SY, Kim HS.
Arch Virol. 2006 Oct;151(10):1985-94. Epub 2006 Apr 20.
PMID 16625320
 
Expression of GSDML Associates with Tumor Progression in Uterine Cervix Cancer.
Sun Q, Yang J, Xing G, Sun Q, Zhang L, He F.
Transl Oncol. 2008 Jul;1(2):73-83.
PMID 18633457
 
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.
Tamura M, Tanaka S, Fujii T, Aoki A, Komiyama H, Ezawa K, Sumiyama K, Sagai T, Shiroishi T.
Genomics. 2007 May;89(5):618-29. Epub 2007 Mar 12.
PMID 17350798
 

Citation

This paper should be referenced as such :
Tamura, M ; Shiroishi, T
GSDMB (gasdermin B)
Atlas Genet Cytogenet Oncol Haematol. 2012;16(4):271-272.
Free journal version : [ pdf ]   [ DOI ]
On line version : http://AtlasGeneticsOncology.org/Genes/GSDMBID43972ch17q12.html


External links

Nomenclature
HGNC (Hugo)GSDMB   23690
Cards
AtlasGSDMBID43972ch17q12
Entrez_Gene (NCBI)GSDMB  55876  gasdermin B
AliasesGSDML; PP4052; PRO2521
GeneCards (Weizmann)GSDMB
Ensembl hg19 (Hinxton)ENSG00000073605 [Gene_View]
Ensembl hg38 (Hinxton)ENSG00000073605 [Gene_View]  chr17:39904595-39918650 [Contig_View]  GSDMB [Vega]
ICGC DataPortalENSG00000073605
TCGA cBioPortalGSDMB
AceView (NCBI)GSDMB
Genatlas (Paris)GSDMB
WikiGenes55876
SOURCE (Princeton)GSDMB
Genetics Home Reference (NIH)GSDMB
Genomic and cartography
GoldenPath hg38 (UCSC)GSDMB  -     chr17:39904595-39918650 -  17q21.1   [Description]    (hg38-Dec_2013)
GoldenPath hg19 (UCSC)GSDMB  -     17q21.1   [Description]    (hg19-Feb_2009)
EnsemblGSDMB - 17q21.1 [CytoView hg19]  GSDMB - 17q21.1 [CytoView hg38]
Mapping of homologs : NCBIGSDMB [Mapview hg19]  GSDMB [Mapview hg38]
OMIM611221   
Gene and transcription
Genbank (Entrez)AF119884 AF258572 AK000409 AK025174 AK057588
RefSeq transcript (Entrez)NM_001042471 NM_001165958 NM_001165959 NM_018530
RefSeq genomic (Entrez)
Consensus coding sequences : CCDS (NCBI)GSDMB
Cluster EST : UnigeneHs.306777 [ NCBI ]
CGAP (NCI)Hs.306777
Alternative Splicing GalleryENSG00000073605
Gene ExpressionGSDMB [ NCBI-GEO ]   GSDMB [ EBI - ARRAY_EXPRESS ]   GSDMB [ SEEK ]   GSDMB [ MEM ]
Gene Expression Viewer (FireBrowse)GSDMB [ Firebrowse - Broad ]
SOURCE (Princeton)Expression in : [Datasets]   [Normal Tissue Atlas]  [carcinoma Classsification]  [NCI60]
GenevisibleExpression in : [tissues]  [cell-lines]  [cancer]  [perturbations]  
BioGPS (Tissue expression)55876
GTEX Portal (Tissue expression)GSDMB
Protein : pattern, domain, 3D structure
UniProt/SwissProtQ8TAX9   [function]  [subcellular_location]  [family_and_domains]  [pathology_and_biotech]  [ptm_processing]  [expression]  [interaction]
NextProtQ8TAX9  [Sequence]  [Exons]  [Medical]  [Publications]
With graphics : InterProQ8TAX9
Splice isoforms : SwissVarQ8TAX9
PhosPhoSitePlusQ8TAX9
Domains : Interpro (EBI)Gasdermin   
Domain families : Pfam (Sanger)Gasdermin (PF04598)   
Domain families : Pfam (NCBI)pfam04598   
Conserved Domain (NCBI)GSDMB
DMDM Disease mutations55876
Blocks (Seattle)GSDMB
PDB (SRS)5TIB    5TJ2    5TJ4   
PDB (PDBSum)5TIB    5TJ2    5TJ4   
PDB (IMB)5TIB    5TJ2    5TJ4   
PDB (RSDB)5TIB    5TJ2    5TJ4   
Structural Biology KnowledgeBase5TIB    5TJ2    5TJ4   
SCOP (Structural Classification of Proteins)5TIB    5TJ2    5TJ4   
CATH (Classification of proteins structures)5TIB    5TJ2    5TJ4   
SuperfamilyQ8TAX9
Human Protein AtlasENSG00000073605
Peptide AtlasQ8TAX9
HPRD17082
IPIIPI00889494   IPI00788788   IPI00031998   IPI00889597   IPI00748097   IPI00154592   IPI00985115   IPI01013560   IPI00894508   IPI00976214   
Protein Interaction databases
DIP (DOE-UCLA)Q8TAX9
IntAct (EBI)Q8TAX9
FunCoupENSG00000073605
BioGRIDGSDMB
STRING (EMBL)GSDMB
ZODIACGSDMB
Ontologies - Pathways
QuickGOQ8TAX9
Ontology : AmiGOcytosol  plasma membrane  programmed cell death  
Ontology : EGO-EBIcytosol  plasma membrane  programmed cell death  
NDEx NetworkGSDMB
Atlas of Cancer Signalling NetworkGSDMB
Wikipedia pathwaysGSDMB
Orthology - Evolution
OrthoDB55876
GeneTree (enSembl)ENSG00000073605
Phylogenetic Trees/Animal Genes : TreeFamGSDMB
HOVERGENQ8TAX9
HOGENOMQ8TAX9
Homologs : HomoloGeneGSDMB
Homology/Alignments : Family Browser (UCSC)GSDMB
Gene fusions - Rearrangements
Fusion : MitelmanTATDN1/GSDMB [8q24.13/17q12]  [t(8;17)(q24;q12)]  
Fusion : MitelmanWHSC1/GSDMB [4p16.3/17q12]  [t(4;17)(p16;q12)]  
Fusion: TCGASTARD3 17q12 GSDMB 17q12 LUAD
Fusion: TCGAWHSC1 4p16.3 GSDMB 17q12 LUAD
Fusion Cancer (Beijing)SLC6A6 [3p25.1]  -  GSDMB [17q12]  [FUSC003749]
Polymorphisms : SNP and Copy number variants
NCBI Variation ViewerGSDMB [hg38]
dbSNP Single Nucleotide Polymorphism (NCBI)GSDMB
dbVarGSDMB
ClinVarGSDMB
1000_GenomesGSDMB 
Exome Variant ServerGSDMB
ExAC (Exome Aggregation Consortium)GSDMB (select the gene name)
Genetic variants : HAPMAP55876
Genomic Variants (DGV)GSDMB [DGVbeta]
DECIPHERGSDMB [patients]   [syndromes]   [variants]   [genes]  
CONAN: Copy Number AnalysisGSDMB 
Mutations
ICGC Data PortalGSDMB 
TCGA Data PortalGSDMB 
Broad Tumor PortalGSDMB
OASIS PortalGSDMB [ Somatic mutations - Copy number]
Somatic Mutations in Cancer : COSMICGSDMB  [overview]  [genome browser]  [tissue]  [distribution]  
Mutations and Diseases : HGMDGSDMB
LOVD (Leiden Open Variation Database)Whole genome datasets
LOVD (Leiden Open Variation Database)LOVD - Leiden Open Variation Database
LOVD (Leiden Open Variation Database)LOVD 3.0 shared installation
BioMutasearch GSDMB
DgiDB (Drug Gene Interaction Database)GSDMB
DoCM (Curated mutations)GSDMB (select the gene name)
CIViC (Clinical Interpretations of Variants in Cancer)GSDMB (select a term)
intoGenGSDMB
NCG5 (London)GSDMB
Cancer3DGSDMB(select the gene name)
Impact of mutations[PolyPhen2] [SIFT Human Coding SNP] [Buck Institute : MutDB] [Mutation Assessor] [Mutanalyser]
Diseases
OMIM611221   
Orphanet
MedgenGSDMB
Genetic Testing Registry GSDMB
NextProtQ8TAX9 [Medical]
TSGene55876
GENETestsGSDMB
Target ValidationGSDMB
Huge Navigator GSDMB [HugePedia]
snp3D : Map Gene to Disease55876
BioCentury BCIQGSDMB
ClinGenGSDMB
Clinical trials, drugs, therapy
Chemical/Protein Interactions : CTD55876
Chemical/Pharm GKB GenePA162390303
Clinical trialGSDMB
Miscellaneous
canSAR (ICR)GSDMB (select the gene name)
Probes
Litterature
PubMed54 Pubmed reference(s) in Entrez
GeneRIFsGene References Into Functions (Entrez)
CoreMineGSDMB
EVEXGSDMB
GoPubMedGSDMB
iHOPGSDMB
REVIEW articlesautomatic search in PubMed
Last year publicationsautomatic search in PubMed

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