Human Gene SDHD (ENST00000375549.8) Description and Page Index
  Description: Homo sapiens succinate dehydrogenase complex subunit D (SDHD), transcript variant 5, non-coding RNA. (from RefSeq NR_077060)
RefSeq Summary (NM_003002): This gene encodes a member of complex II of the respiratory chain, which is responsible for the oxidation of succinate. The encoded protein is one of two integral membrane proteins anchoring the complex to the matrix side of the mitochondrial inner membrane. Mutations in this gene are associated with the formation of tumors, including hereditary paraganglioma. Transmission of disease occurs almost exclusively through the paternal allele, suggesting that this locus may be maternally imprinted. There are pseudogenes for this gene on chromosomes 1, 2, 3, 7, and 18. Alternative splicing results in multiple transcript variants. [provided by RefSeq, Feb 2013].
Gencode Transcript: ENST00000375549.8
Gencode Gene: ENSG00000204370.13
Transcript (Including UTRs)
   Position: hg38 chr11:112,086,873-112,095,794 Size: 8,922 Total Exon Count: 4 Strand: +
Coding Region
   Position: hg38 chr11:112,086,908-112,094,970 Size: 8,063 Coding Exon Count: 4 

Page IndexSequence and LinksUniProtKB CommentsMalaCardsCTDRNA-Seq Expression
Microarray ExpressionRNA StructureProtein StructureOther SpeciesGO AnnotationsmRNA Descriptions
PathwaysOther NamesGeneReviewsMethods
Data last updated at UCSC: 2021-01-14 15:32:12

-  Sequence and Links to Tools and Databases
 
Genomic Sequence (chr11:112,086,873-112,095,794)mRNA (may differ from genome)Protein (159 aa)
Gene SorterGenome BrowserOther Species FASTAGene interactionsTable SchemaBioGPS
CGAPEnsemblEntrez GeneExonPrimerGeneCardsHGNC
HPRDLynxMGIneXtProtOMIMPubMed
ReactomeUniProtKBWikipedia

-  Comments and Description Text from UniProtKB
  ID: DHSD_HUMAN
DESCRIPTION: RecName: Full=Succinate dehydrogenase [ubiquinone] cytochrome b small subunit, mitochondrial; Short=CybS; AltName: Full=CII-4; AltName: Full=QPs3; AltName: Full=Succinate dehydrogenase complex subunit D; AltName: Full=Succinate-ubiquinone oxidoreductase cytochrome b small subunit; AltName: Full=Succinate-ubiquinone reductase membrane anchor subunit; Flags: Precursor;
FUNCTION: Membrane-anchoring subunit of succinate dehydrogenase (SDH) that is involved in complex II of the mitochondrial electron transport chain and is responsible for transferring electrons from succinate to ubiquinone (coenzyme Q) (By similarity).
PATHWAY: Carbohydrate metabolism; tricarboxylic acid cycle.
SUBUNIT: Component of complex II composed of four subunits: the flavoprotein (FP) SDHA, iron-sulfur protein (IP) SDHB, and a cytochrome b560 composed of SDHC and SDHD.
SUBCELLULAR LOCATION: Mitochondrion inner membrane; Multi-pass membrane protein.
DISEASE: Defects in SDHD are a cause of paragangliomas type 1 (PGL1) [MIM:168000]. A neural crest tumor usually derived from the chromoreceptor tissue of a paraganglion. PGL1 is a rare autosomal dominant disorder which is characterized by the development of mostly benign, highly vascular, slowly growing tumors in the head and neck. In the head and neck region, the carotid body is the largest of all paraganglia and is also the most common site of the tumors.
DISEASE: Defects in SDHD are a cause of susceptibility to pheochromocytoma (PCC) [MIM:171300]. A catecholamine-producing tumor of chromaffin tissue of the adrenal medulla or sympathetic paraganglia. The cardinal symptom, reflecting the increased secretion of epinephrine and norepinephrine, is hypertension, which may be persistent or intermittent.
DISEASE: Defects in SDHD may be a cause of susceptibility to intestinal carcinoid tumor (ICT) [MIM:114900]. A yellow, well- differentiated, circumscribed tumor that arises from enterochromaffin cells in the small intestine or, less frequently, in other parts of the gastrointestinal tract.
DISEASE: Defects in SDHD are a cause of paraganglioma and gastric stromal sarcoma (PGGSS) [MIM:606864]; also called Carney-Stratakis syndrome. Gastrointestinal stromal tumors may be sporadic or inherited in an autosomal dominant manner, alone or as a component of a syndrome associated with other tumors, such as in the context of neurofibromatosis type 1 (NF1). Patients have both gastrointestinal stromal tumors and paragangliomas. Susceptibility to the tumors was inherited in an apparently autosomal dominant manner, with incomplete penetrance.
DISEASE: Defects in SDHD are a cause of Cowden-like syndrome (CWDLS) [MIM:612359]. Cowden-like syndrome is a cancer predisposition syndrome associated with elevated risk for tumors of the breast, thyroid, kidney and uterus.
SIMILARITY: Belongs to the CybS family.
WEB RESOURCE: Name=Atlas of Genetics and Cytogenetics in Oncology and Haematology; URL="http://atlasgeneticsoncology.org/Genes/SDHDID390.html";
WEB RESOURCE: Name=GeneReviews; URL="http://www.ncbi.nlm.nih.gov/sites/GeneTests/lab/gene/SDHD";
WEB RESOURCE: Name=Wikipedia; Note=SDHD entry; URL="http://en.wikipedia.org/wiki/SDHD";
WEB RESOURCE: Name=TCA Cycle Gene Mutation Database; URL="http://chromium.liacs.nl/LOVD2/SDH/home.php?select_db=SDHD";

-  MalaCards Disease Associations
  MalaCards Gene Search: SDHD
Diseases sorted by gene-association score: paragangliomas 1, with or without deafness* (1321), paraganglioma and gastric stromal sarcoma* (1270), mitochondrial complex ii deficiency* (1129), cowden syndrome 3* (1019), hereditary paraganglioma-pheochromocytoma syndromes* (868), carcinoid tumors, intestinal* (628), pheochromocytoma* (625), cowden disease* (145), sdhd-related paraganglioma and gastric stromal sarcoma* (100), mitochondrial respiratory chain complex ii deficiency, sdhd-related* (100), paraganglioma (62), neurofibromatosis, type 1 (30), extra-adrenal pheochromocytoma (25), chondroma (23), cerebellopontine angle tumor (22), von hippel-lindau syndrome (21), sporadic pheochromocytoma* (19), phaeochromocytoma (15), carney triad (12), adrenal medulla cancer (12), neuroendocrine tumor (10), persistent generalized lymphadenopathy (9), borderline leprosy (9), lymph node disease (9), pancreatic neuroendocrine tumor (9), neural crest tumor (8), glomus tumor (8), multiple endocrine neoplasia iia (8), spastic quadriplegia (7), gastrointestinal stromal tumor (6), quadriplegia (6), multiple endocrine neoplasia 1 (5), gastric leiomyosarcoma (5), tuberculoid leprosy (5), lymphatic system disease (5), renal cell carcinoma (3), endocrine gland cancer (2), kearns-sayre syndrome (2), leigh syndrome (2)
* = Manually curated disease association

-  Comparative Toxicogenomics Database (CTD)
  The following chemicals interact with this gene           more ... click here to view the complete list

-  RNA-Seq Expression Data from GTEx (53 Tissues, 570 Donors)
  Highest median expression: 61.00 RPKM in Kidney - Cortex
Total median expression: 1729.64 RPKM



View in GTEx track of Genome Browser    View at GTEx portal     View GTEx Body Map

+  Microarray Expression Data
  Press "+" in the title bar above to open this section.

-  mRNA Secondary Structure of 3' and 5' UTRs
 
RegionFold EnergyBasesEnergy/Base
Display As
5' UTR -9.3035-0.266 Picture PostScript Text
3' UTR -169.70824-0.206 Picture PostScript Text

The RNAfold program from the Vienna RNA Package is used to perform the secondary structure predictions and folding calculations. The estimated folding energy is in kcal/mol. The more negative the energy, the more secondary structure the RNA is likely to have.

-  Protein Domain and Structure Information
  InterPro Domains: Graphical view of domain structure
IPR007992 - Cyt_b_succ_DH_CybS

Pfam Domains:
PF05328 - CybS, succinate dehydrogenase cytochrome B small subunit

ModBase Predicted Comparative 3D Structure on O14521
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-  Orthologous Genes in Other Species
  Orthologies between human, mouse, and rat are computed by taking the best BLASTP hit, and filtering out non-syntenic hits. For more distant species reciprocal-best BLASTP hits are used. Note that the absence of an ortholog in the table below may reflect incomplete annotations in the other species rather than a true absence of the orthologous gene.
MouseRatZebrafishD. melanogasterC. elegansS. cerevisiae
Genome BrowserGenome BrowserNo orthologGenome BrowserNo orthologNo ortholog
Gene Details     
Gene Sorter     
MGIRGDEnsemblEnsembl  
Protein SequenceProtein Sequence Protein Sequence  
AlignmentAlignment Alignment  

-  Gene Ontology (GO) Annotations with Structured Vocabulary
  Molecular Function:
GO:0000104 succinate dehydrogenase activity
GO:0009055 electron carrier activity
GO:0020037 heme binding
GO:0046872 metal ion binding
GO:0048039 ubiquinone binding
GO:0008177 succinate dehydrogenase (ubiquinone) activity

Biological Process:
GO:0006099 tricarboxylic acid cycle
GO:0006121 mitochondrial electron transport, succinate to ubiquinone
GO:0055114 oxidation-reduction process

Cellular Component:
GO:0005739 mitochondrion
GO:0005740 mitochondrial envelope
GO:0005743 mitochondrial inner membrane
GO:0005749 mitochondrial respiratory chain complex II, succinate dehydrogenase complex (ubiquinone)
GO:0016020 membrane
GO:0016021 integral component of membrane


-  Descriptions from all associated GenBank mRNAs
  LF385377 - JP 2014500723-A/192880: Polycomb-Associated Non-Coding RNAs.
MA620954 - JP 2018138019-A/192880: Polycomb-Associated Non-Coding RNAs.
BC015188 - Homo sapiens succinate dehydrogenase complex, subunit D, integral membrane protein, mRNA (cDNA clone MGC:14593 IMAGE:4279214), complete cds.
BC071755 - Homo sapiens succinate dehydrogenase complex, subunit D, integral membrane protein, mRNA (cDNA clone MGC:88308 IMAGE:4774525), complete cds.
BC015992 - Homo sapiens succinate dehydrogenase complex, subunit D, integral membrane protein, mRNA (cDNA clone MGC:27158 IMAGE:4292983), complete cds.
BC005263 - Homo sapiens succinate dehydrogenase complex, subunit D, integral membrane protein, mRNA (cDNA clone MGC:12303 IMAGE:3930691), complete cds.
BC022350 - Homo sapiens succinate dehydrogenase complex, subunit D, integral membrane protein, mRNA (cDNA clone MGC:23820 IMAGE:4275516), complete cds.
AK075360 - Homo sapiens cDNA PSEC0046 fis, clone NT2RP1001027, highly similar to Succinate dehydrogenase [ubiquinone] cytochrome b small subunit, mitochondrial precursor.
AB006202 - Homo sapiens mRNA for cytochrome b small subunit of complex II, complete cds.
BC012603 - Homo sapiens succinate dehydrogenase complex, subunit D, integral membrane protein, mRNA (cDNA clone MGC:13599 IMAGE:4108104), complete cds.
BC070307 - Homo sapiens succinate dehydrogenase complex, subunit D, integral membrane protein, mRNA (cDNA clone MGC:88307 IMAGE:4277540), complete cds.
BC071756 - Homo sapiens succinate dehydrogenase complex, subunit D, integral membrane protein, mRNA (cDNA clone MGC:88309 IMAGE:6450992), complete cds.
BC009574 - Homo sapiens succinate dehydrogenase complex, subunit D, integral membrane protein, mRNA (cDNA clone MGC:14562 IMAGE:4063808), complete cds.
JD176201 - Sequence 157225 from Patent EP1572962.
CR456932 - Homo sapiens full open reading frame cDNA clone RZPDo834C0116D for gene SDHD, succinate dehydrogenase complex, subunit D, integral membrane protein; complete cds, incl. stopcodon.
KU178325 - Homo sapiens succinate dehydrogenase complex subunit D integral membrane protein isoform 1 (SDHD) mRNA, partial cds.
KU178326 - Homo sapiens succinate dehydrogenase complex subunit D integral membrane protein isoform 2 (SDHD) mRNA, complete cds, alternatively spliced.
BT007238 - Homo sapiens succinate dehydrogenase complex, subunit D, integral membrane protein mRNA, complete cds.
DQ892701 - Synthetic construct Homo sapiens clone IMAGE:100005331; FLH263578.01X; RZPDo839B1078D succinate dehydrogenase complex, subunit D, integral membrane protein (SDHD) gene, encodes complete protein.
DQ896292 - Synthetic construct Homo sapiens clone IMAGE:100010752; FLH192994.01L; RZPDo839B0868D succinate dehydrogenase complex, subunit D, integral membrane protein (SDHD) gene, encodes complete protein.
CU675071 - Synthetic construct Homo sapiens gateway clone IMAGE:100016718 5' read SDHD mRNA.
KJ892121 - Synthetic construct Homo sapiens clone ccsbBroadEn_01515 SDHD gene, encodes complete protein.
KJ897535 - Synthetic construct Homo sapiens clone ccsbBroadEn_06929 SDHD gene, encodes complete protein.
KR710196 - Synthetic construct Homo sapiens clone CCSBHm_00010294 SDHD (SDHD) mRNA, encodes complete protein.
KR710197 - Synthetic construct Homo sapiens clone CCSBHm_00010307 SDHD (SDHD) mRNA, encodes complete protein.
KR710198 - Synthetic construct Homo sapiens clone CCSBHm_00010315 SDHD (SDHD) mRNA, encodes complete protein.
KR710199 - Synthetic construct Homo sapiens clone CCSBHm_00010327 SDHD (SDHD) mRNA, encodes complete protein.
JD268719 - Sequence 249743 from Patent EP1572962.
JD550226 - Sequence 531250 from Patent EP1572962.
JD378447 - Sequence 359471 from Patent EP1572962.
JD378446 - Sequence 359470 from Patent EP1572962.
JD162574 - Sequence 143598 from Patent EP1572962.
JD282499 - Sequence 263523 from Patent EP1572962.
JD193517 - Sequence 174541 from Patent EP1572962.
JD262910 - Sequence 243934 from Patent EP1572962.
JD262911 - Sequence 243935 from Patent EP1572962.
JD020964 - Sequence 1988 from Patent EP1572962.
JD082142 - Sequence 63166 from Patent EP1572962.
JD305765 - Sequence 286789 from Patent EP1572962.
JD305783 - Sequence 286807 from Patent EP1572962.
JD305591 - Sequence 286615 from Patent EP1572962.

-  Biochemical and Signaling Pathways
  KEGG - Kyoto Encyclopedia of Genes and Genomes
hsa00020 - Citrate cycle (TCA cycle)
hsa00190 - Oxidative phosphorylation
hsa01100 - Metabolic pathways
hsa05010 - Alzheimer's disease
hsa05012 - Parkinson's disease
hsa05016 - Huntington's disease

BioCyc Knowledge Library
PWY66-398 - TCA cycle
PWY66-407 - superpathway of conversion of glucose to acetyl CoA and entry into the TCA cycle

BioCarta from NCI Cancer Genome Anatomy Project
h_etcPathway - Electron Transport Reaction in Mitochondria

Reactome (by CSHL, EBI, and GO)

Protein O14521 (Reactome details) participates in the following event(s):

R-HSA-163213 Transfer of electrons through the succinate dehydrogenase complex
R-HSA-70994 Succinate <=> Fumarate (with FAD redox reaction on enzyme)
R-HSA-611105 Respiratory electron transport
R-HSA-163200 Respiratory electron transport, ATP synthesis by chemiosmotic coupling, and heat production by uncoupling proteins.
R-HSA-71403 Citric acid cycle (TCA cycle)
R-HSA-1428517 The citric acid (TCA) cycle and respiratory electron transport
R-HSA-71406 Pyruvate metabolism and Citric Acid (TCA) cycle
R-HSA-1430728 Metabolism

-  Other Names for This Gene
  Alternate Gene Symbols: A6ND90, B3KQQ8, DHSD_HUMAN, ENST00000375549.1, ENST00000375549.2, ENST00000375549.3, ENST00000375549.4, ENST00000375549.5, ENST00000375549.6, ENST00000375549.7, NR_077060, O14521, Q53XW5, Q6IRW2, SDH4, uc001pmz.1, uc001pmz.2, uc001pmz.3, uc001pmz.4, uc001pmz.5, uc001pmz.6
UCSC ID: ENST00000375549.8
RefSeq Accession: NM_003002
Protein: O14521 (aka DHSD_HUMAN)
CCDS: CCDS31678.1

-  GeneReviews for This Gene
  GeneReviews article(s) related to gene SDHD:
paragangliomas (Hereditary Paraganglioma-Pheochromocytoma Syndromes)

-  Methods, Credits, and Use Restrictions
  Click here for details on how this gene model was made and data restrictions if any.