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GSDMB gasdermin B [ Homo sapiens (human) ]

Gene ID: 55876, updated on 12-May-2019

Summary

Official Symbol
GSDMBprovided by HGNC
Official Full Name
gasdermin Bprovided by HGNC
Primary source
HGNC:HGNC:23690
See related
Ensembl:ENSG00000073605 MIM:611221
Gene type
protein coding
RefSeq status
REVIEWED
Organism
Homo sapiens
Lineage
Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Primates; Haplorrhini; Catarrhini; Hominidae; Homo
Also known as
GSDML; PP4052; PRO2521
Summary
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]
Expression
Broad expression in small intestine (RPKM 18.8), duodenum (RPKM 16.9) and 17 other tissues See more
Orthologs

Genomic context

See GSDMB in Genome Data Viewer
Location:
17q21.1
Exon count:
11
Annotation release Status Assembly Chr Location
109 current GRCh38.p12 (GCF_000001405.38) 17 NC_000017.11 (39904595..39918650, complement)
105 previous assembly GRCh37.p13 (GCF_000001405.25) 17 NC_000017.10 (38060848..38074903, complement)

Chromosome 17 - NC_000017.11Genomic Context describing neighboring genes Neighboring gene IKAROS family zinc finger 3 Neighboring gene ribosomal protein L39 pseudogene 4 Neighboring gene zona pellucida binding protein 2 Neighboring gene GSDMB 5' regulatory region Neighboring gene uncharacterized LOC112268187 Neighboring gene ORMDL sphingolipid biosynthesis regulator 3 Neighboring gene leucine rich repeat containing 3C

Genomic regions, transcripts, and products

Expression

  • Project title: HPA RNA-seq normal tissues
  • Description: RNA-seq was performed of tissue samples from 95 human individuals representing 27 different tissues in order to determine tissue-specificity of all protein-coding genes
  • BioProject: PRJEB4337
  • Publication: PMID 24309898
  • Analysis date: Wed Apr 4 07:08:55 2018

Bibliography

GeneRIFs: Gene References Into FunctionsWhat's a GeneRIF?

Phenotypes

NHGRI GWAS Catalog

Description
A genome-wide association meta-analysis of self-reported allergy identifies shared and allergy-specific susceptibility loci.
NHGRI GWA Catalog
A genome-wide association study identifies CDHR3 as a susceptibility locus for early childhood asthma with severe exacerbations.
NHGRI GWA Catalog
A genome-wide association study identifies two new cervical cancer susceptibility loci at 4q12 and 17q12.
NHGRI GWA Catalog
A large-scale, consortium-based genomewide association study of asthma.
NHGRI GWA Catalog
Fraction of exhaled nitric oxide values in childhood are associated with 17q11.2-q12 and 17q12-q21 variants.
NHGRI GWA Catalog
Genetic variants regulating ORMDL3 expression contribute to the risk of childhood asthma.
NHGRI GWA Catalog
Genome-wide association identifies multiple ulcerative colitis susceptibility loci.
NHGRI GWA Catalog
Genome-wide association study and meta-analysis find that over 40 loci affect risk of type 1 diabetes.
NHGRI GWA Catalog
Genome-wide association study identifies TNFSF15 and POU2AF1 as susceptibility loci for primary biliary cirrhosis in the Japanese population.
NHGRI GWA Catalog
Genome-wide meta-analyses identify three loci associated with primary biliary cirrhosis.
NHGRI GWA Catalog
Host-microbe interactions have shaped the genetic architecture of inflammatory bowel disease.
NHGRI GWA Catalog
Meta-analysis identifies 29 additional ulcerative colitis risk loci, increasing the number of confirmed associations to 47.
NHGRI GWA Catalog
Meta-analysis of genome-wide association studies of asthma in ethnically diverse North American populations.
NHGRI GWA Catalog
Multiple loci are associated with white blood cell phenotypes.
NHGRI GWA Catalog

Interactions

Products Interactant Other Gene Complex Source Pubs Description

General gene information

Markers

Homology

Gene Ontology Provided by GOA

Function Evidence Code Pubs
molecular_function ND
No biological Data available
more info
 
phosphatidylinositol-4,5-bisphosphate binding IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
phosphatidylinositol-4-phosphate binding IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
phosphatidylserine binding IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
Process Evidence Code Pubs
biological_process ND
No biological Data available
more info
 
pyroptosis IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
Component Evidence Code Pubs
cellular_component ND
No biological Data available
more info
 
cytosol IEA
Inferred from Electronic Annotation
more info
 
plasma membrane IEA
Inferred from Electronic Annotation
more info
 

General protein information

Preferred Names
gasdermin-B
Names
gasdermin-like protein

NCBI Reference Sequences (RefSeq)

RefSeqs maintained independently of Annotated Genomes

These reference sequences exist independently of genome builds. Explain

These reference sequences are curated independently of the genome annotation cycle, so their versions may not match the RefSeq versions in the current genome build. Identify version mismatches by comparing the version of the RefSeq in this section to the one reported in Genomic regions, transcripts, and products above.

Genomic

  1. NG_015804.1 RefSeqGene

    Range
    5001..19056
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. NM_001042471.1NP_001035936.1  gasdermin-B isoform 1

    See identical proteins and their annotated locations for NP_001035936.1

    Status: REVIEWED

    Description
    Transcript Variant: This variant (1) lacks an alternate in-frame exon in the central coding region, compared to variant 3. The resulting isoform (1) lacks an internal segment, compared to isoform 3.
    Source sequence(s)
    AK000409, CA488357, CB136981
    Consensus CDS
    CCDS42313.1
    UniProtKB/Swiss-Prot
    Q8TAX9
    Related
    ENSP00000312584.7, ENST00000309481.11
    Conserved Domains (1) summary
    pfam04598
    Location:5361
    Gasdermin; Gasdermin family
  2. NM_001165958.1NP_001159430.1  gasdermin-B isoform 3

    See identical proteins and their annotated locations for NP_001159430.1

    Status: REVIEWED

    Description
    Transcript Variant: This variant (3) encodes the longest isoform (3).
    Source sequence(s)
    AK000409, BX538068, CB136981
    Consensus CDS
    CCDS54120.1
    UniProtKB/Swiss-Prot
    Q8TAX9
    Related
    ENSP00000415049.1, ENST00000418519.5
    Conserved Domains (1) summary
    pfam04598
    Location:5374
    Gasdermin; Gasdermin family
  3. NM_001165959.1NP_001159431.1  gasdermin-B isoform 4

    See identical proteins and their annotated locations for NP_001159431.1

    Status: REVIEWED

    Description
    Transcript Variant: This variant (4) lacks an alternate in-frame exon in the central coding region, compared to variant 3. The resulting isoform (4) lacks an internal segment, compared to isoform 3.
    Source sequence(s)
    AF119884, AK296607, CB136981
    Consensus CDS
    CCDS54119.1
    UniProtKB/Swiss-Prot
    Q8TAX9
    Related
    ENSP00000430157.1, ENST00000520542.5
    Conserved Domains (1) summary
    pfam04598
    Location:5365
    Gasdermin; Gasdermin family
  4. NM_001369402.1NP_001356331.1  gasdermin-B isoform 1

    Status: REVIEWED

    Source sequence(s)
    AC090844
  5. NM_018530.2NP_061000.2  gasdermin-B isoform 2

    See identical proteins and their annotated locations for NP_061000.2

    Status: REVIEWED

    Description
    Transcript Variant: This variant (2) lacks two alternate in-frame exons in the central coding region and uses an alternate 5' UTR, compared to variant 3. The resulting isoform (2) lacks an internal segment, compared to isoform 3. The 5' end of this transcript contains long terminal repeat (LTR) sequence and initiates from an LTR promoter.
    Source sequence(s)
    AF119884, BP366854
    Consensus CDS
    CCDS11354.1
    UniProtKB/Swiss-Prot
    Q8TAX9
    Related
    ENSP00000377729.2, ENST00000394175.6
    Conserved Domains (1) summary
    pfam04598
    Location:5352
    Gasdermin; Gasdermin family

RefSeqs of Annotated Genomes: Homo sapiens Annotation Release 109

The following sections contain reference sequences that belong to a specific genome build. Explain

Reference GRCh38.p12 Primary Assembly

Genomic

  1. NC_000017.11 Reference GRCh38.p12 Primary Assembly

    Range
    39904595..39918650 complement
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
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