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SDHD (succinate dehydrogenase complex II, subunit D, integral membrane protein)

Identity

Other namesSDH4 (succinate dehydrogenase 4)
HGNC (Hugo) SDHD
LocusID (NCBI) 6392
Location 11q23.1
Location_base_pair Starts at 111957548 and ends at 111966525 bp from pter ( according to hg19-Feb_2009)  [Mapping]

DNA/RNA

Description 8895 bp, 4 exons
Transcription A non transcribed sequence highly homologous to SDHD cDNA is present on chromosome 1p36-p34

Protein

Description 159 amino acids and 17 kDa
Expression widely expressed
Localisation mitochondrial inner membrane
Function Complex II (succinate-ubiquinone oxidoreductase) of the respiratory chain is involved in the oxidation of succinate, carries electrons from FADH to CoQ. It is composed of four nuclear-encoded subunits. The subunit D protein or small subunit (cybS) is one of two integral membrane proteins anchoring the complex to membrane.
Homology The complex II includes SDHC (cybL) and SDHB (iron-sulfur protein) which are also implicated in paragangliomas and pheochromocytomas.

Mutations

Germinal Germline mutations cause hereditary paraganglioma. Different types of mutations are described. False-sense mutations, insertions and deletions leading to protein truncation and missense mutations.
Somatic Loss of wild type allele in tumor DNA is usually observed.

Implicated in

Entity Hereditary paraganglioma type 1 (also called familial non chromaffin paragangliomas 1, or familial glomus tumor)
Disease Hereditary paraganglioma type 1 (PGL1) is a rare autosomal dominant disorder. The disease is transmitted through fathers and no disease phenotype is transmetted maternally in accordance with a maternal genomic imprinting. Paragangliomas are slow growing highly vascular tumor, usually benign, derived from crest-neural cells. They are preferentially located in the neck (carotid body and glomus vagal) and head (glomus jugulare and tympanicum). They may be associated with pheochromocytomas.
Prognosis It depends on extent of the disease at the time of diagnosis.
  

External links

Nomenclature
HGNC (Hugo)SDHD   10683
Cards
AtlasSDHDID390
Entrez_Gene (NCBI)SDHD  6392  succinate dehydrogenase complex, subunit D, integral membrane protein
GeneCards (Weizmann)SDHD
Ensembl (Hinxton)ENSG00000204370 [Gene_View]  chr11:111957548-111966525 [Contig_View]  SDHD [Vega]
ICGC DataPortalENSG00000204370
cBioPortalSDHD
AceView (NCBI)SDHD
Genatlas (Paris)SDHD
WikiGenes6392
SOURCE (Princeton)NM_001276503 NM_001276504 NM_001276506 NM_003002
Genomic and cartography
GoldenPath (UCSC)SDHD  -  11q23.1   chr11:111957548-111966525 +  11q23   [Description]    (hg19-Feb_2009)
EnsemblSDHD - 11q23 [CytoView]
Mapping of homologs : NCBISDHD [Mapview]
OMIM114900   168000   171300   602690   606864   615106   
Gene and transcription
Genbank (Entrez)AA374642 AB006202 AI753083 AK075360 BC005263
RefSeq transcript (Entrez)NM_001276503 NM_001276504 NM_001276506 NM_003002
RefSeq genomic (Entrez)AC_000143 NC_000011 NC_018922 NG_012337 NT_033899 NW_001838042 NW_004929381
Consensus coding sequences : CCDS (NCBI)SDHD
Cluster EST : UnigeneHs.744039 [ NCBI ]
CGAP (NCI)Hs.744039
Alternative Splicing : Fast-db (Paris)GSHG0005249
Alternative Splicing GalleryENSG00000204370
Gene ExpressionSDHD [ NCBI-GEO ]     SDHD [ SEEK ]   SDHD [ MEM ]
Protein : pattern, domain, 3D structure
UniProt/SwissProtO14521 (Uniprot)
NextProtO14521  [Medical]
With graphics : InterProO14521
Splice isoforms : SwissVarO14521 (Swissvar)
Domains : Interpro (EBI)CybS [organisation]  
Related proteins : CluSTrO14521
Domain families : Pfam (Sanger)CybS (PF05328)   
Domain families : Pfam (NCBI)pfam05328   
DMDM Disease mutations6392
Blocks (Seattle)O14521
Human Protein AtlasENSG00000204370 [gene] [tissue] [antibody] [cell] [cancer]
Peptide AtlasO14521
HPRD04069
IPIIPI00297325   IPI00980617   IPI00976555   IPI00976063   IPI00978980   IPI00985489   IPI00977732   IPI00977213   
Protein Interaction databases
DIP (DOE-UCLA)O14521
IntAct (EBI)O14521
FunCoupENSG00000204370
BioGRIDSDHD
InParanoidO14521
Interologous Interaction database O14521
IntegromeDBSDHD
STRING (EMBL)SDHD
Ontologies - Pathways
Ontology : AmiGOsuccinate dehydrogenase activity  mitochondrion  mitochondrial envelope  mitochondrial inner membrane  mitochondrial inner membrane  mitochondrial inner membrane  mitochondrial respiratory chain complex II  tricarboxylic acid cycle  tricarboxylic acid cycle  tricarboxylic acid cycle  electron carrier activity  integral component of membrane  heme binding  respiratory electron transport chain  cellular metabolic process  small molecule metabolic process  metal ion binding  ubiquinone binding  
Ontology : EGO-EBIsuccinate dehydrogenase activity  mitochondrion  mitochondrial envelope  mitochondrial inner membrane  mitochondrial inner membrane  mitochondrial inner membrane  mitochondrial respiratory chain complex II  tricarboxylic acid cycle  tricarboxylic acid cycle  tricarboxylic acid cycle  electron carrier activity  integral component of membrane  heme binding  respiratory electron transport chain  cellular metabolic process  small molecule metabolic process  metal ion binding  ubiquinone binding  
Pathways : BIOCARTAElectron Transport Reaction in Mitochondria [Genes]   
Pathways : KEGGCitrate cycle (TCA cycle)    Oxidative phosphorylation    Non-alcoholic fatty liver disease (NAFLD)    Alzheimer's disease    Parkinson's disease    Huntington's disease   
Protein Interaction DatabaseSDHD
Wikipedia pathwaysSDHD
Gene fusion - rearrangments
Polymorphisms : SNP, mutations, diseases
SNP Single Nucleotide Polymorphism (NCBI)SDHD
snp3D : Map Gene to Disease6392
SNP (GeneSNP Utah)SDHD
SNP : HGBaseSDHD
Genetic variants : HAPMAPSDHD
Exome VariantSDHD
1000_GenomesSDHD 
ICGC programENSG00000204370 
Cancer Gene: CensusSDHD 
Somatic Mutations in Cancer : COSMICSDHD 
CONAN: Copy Number AnalysisSDHD 
Mutations and Diseases : HGMDSDHD
Mutations and Diseases : intOGenSDHD
Genomic VariantsSDHD  SDHD [DGVbeta]
dbVarSDHD
ClinVarSDHD
Pred. of missensesPolyPhen-2  SIFT(SG)  SIFT(JCVI)  Align-GVGD  MutAssessor  Mutanalyser  
Pred. splicesGeneSplicer  Human Splicing Finder  MaxEntScan  
Diseases
OMIM114900    168000    171300    602690    606864    615106   
MedgenSDHD
GENETestsSDHD
Disease Genetic AssociationSDHD
Huge Navigator SDHD [HugePedia]  SDHD [HugeCancerGEM]
General knowledge
Homologs : HomoloGeneSDHD
Homology/Alignments : Family Browser (UCSC)SDHD
Phylogenetic Trees/Animal Genes : TreeFamSDHD
Chemical/Protein Interactions : CTD6392
Chemical/Pharm GKB GenePA35608
Clinical trialSDHD
Cancer Resource (Charite)ENSG00000204370
Other databases
Probes
Litterature
PubMed110 Pubmed reference(s) in Entrez
CoreMineSDHD
iHOPSDHD
OncoSearchSDHD

Bibliography

Cytochrome b in human complex II (succinate-ubiquinone oxidoreductase): cDNA cloning of the components in liver mitochondria and chromosome assignment of the genes for the large (SDHC) and small (SDHD) subunits to 1q21 and 11q23.
Hirawake H, Taniwaki M, Tamura A, Kojima S, Kita K
Cytogenetics and cell genetics. 1997 ; 79 (1-2) : 132-138.
PMID 9533030
 
Characterization of the human SDHD gene encoding the small subunit of cytochrome b (cybS) in mitochondrial succinate-ubiquinone oxidoreductase.
Hirawake H, Taniwaki M, Tamura A, Amino H, Tomitsuka E, Kita K
Biochimica et biophysica acta. 1999 ; 1412 (3) : 295-300.
PMID 10482792
 
Mutations in SDHD, a mitochondrial complex II gene, in hereditary paraganglioma.
Baysal BE, Ferrell RE, Willett-Brozick JE, Lawrence EC, Myssiorek D, Bosch A, van der Mey A, Taschner PE, Rubinstein WS, Myers EN, Richard CW 3rd, Cornelisse CJ, Devilee P, Devlin B
Science (New York, N.Y.). 2000 ; 287 (5454) : 848-851.
PMID 10657297
 
Somatic and occult germ-line mutations in SDHD, a mitochondrial complex II gene, in nonfamilial pheochromocytoma.
Gimm O, Armanios M, Dziema H, Neumann HP, Eng C
Cancer research. 2000 ; 60 (24) : 6822-6825.
PMID 11156372
 
Germline SDHD mutation in familial phaeochromocytoma.
Astuti D, Douglas F, Lennard TW, Aligianis IA, Woodward ER, Evans DG, Eng C, Latif F, Maher ER
Lancet. 2001 ; 357 (9263) : 1181-1182.
PMID 11323050
 
A high-resolution integrated map spanning the SDHD gene at 11q23: a 1.1-Mb BAC contig, a partial transcript map and 15 new repeat polymorphisms in a tumour-suppressor region.
Baysal BE, Willett-Brozick JE, Taschner PE, Dauwerse JG, Devilee P, Devlin B
European journal of human genetics : EJHG. 2001 ; 9 (2) : 121-129.
PMID 11313745
 
Novel mutations and the emergence of a common mutation in the SDHD gene causing familial paraganglioma.
Milunsky JM, Maher TA, Michels VV, Milunsky A
American journal of medical genetics. 2001 ; 100 (4) : 311-314.
PMID 11343322
 
Nearly all hereditary paragangliomas in the Netherlands are caused by two founder mutations in the SDHD gene.
Taschner PE, Jansen JC, Baysal BE, Bosch A, Rosenberg EH, Brcker-Vriends AH, van Der Mey AG, van Ommen GJ, Cornelisse CJ, Devilee P
Genes, chromosomes & cancer. 2001 ; 31 (3) : 274-281.
PMID 11391798
 
The R22X mutation of the SDHD gene in hereditary paraganglioma abolishes the enzymatic activity of complex II in the mitochondrial respiratory chain and activates the hypoxia pathway.
Gimenez-Roqueplo AP, Favier J, Rustin P, Mourad JJ, Plouin PF, Corvol P, Rtig A, Jeunemaitre X
American journal of human genetics. 2001 ; 69 (6) : 1186-1197.
PMID 11605159
 
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Contributor(s)

Written02-2002Anne-Paule Gimenez-Roqueplo

Citation

This paper should be referenced as such :
Gimenez-Roqueplo, AP
SDHD (succinate dehydrogenase complex II, subunit D, integral membrane protein)
Atlas Genet Cytogenet Oncol Haematol. 2002;6(2):115-116.
Free online version   Free pdf version   [Bibliographic record ]
URL : http://AtlasGeneticsOncology.org/Genes/SDHDID390.html

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indexed on : Sat Oct 4 12:54:13 CEST 2014

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