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Phenotypic Information (metabolism pathway, cancer, disease, phenome) | |
Gene-Gene Network Information: Co-Expression Network, Interacting Genes & KEGG | |
Gene Summary for SDHD |
Basic gene info. | Gene symbol | SDHD |
Gene name | succinate dehydrogenase complex, subunit D, integral membrane protein | |
Synonyms | CBT1|CII-4|CWS3|PGL|PGL1|QPs3|SDH4|cybS | |
Cytomap | UCSC genome browser: 11q23 | |
Genomic location | chr11 :111957570-111966518 | |
Type of gene | protein-coding | |
RefGenes | NM_001276503.1, NM_001276504.1,NM_001276506.1,NM_003002.3,NR_077060.1, | |
Ensembl id | ENSG00000204370 | |
Description | succinate dehydrogenase [ubiquinone] cytochrome b small subunit, mitochondrialsuccinate-ubiquinone oxidoreductase cytochrome b small subunitsuccinate-ubiquinone reductase membrane anchor subunit | |
Modification date | 20141219 | |
dbXrefs | MIM : 602690 | |
HGNC : HGNC | ||
Ensembl : ENSG00000204370 | ||
HPRD : 04069 | ||
Vega : OTTHUMG00000166997 | ||
Protein | UniProt: O14521 go to UniProt's Cross Reference DB Table | |
Expression | CleanEX: HS_SDHD | |
BioGPS: 6392 | ||
Gene Expression Atlas: ENSG00000204370 | ||
The Human Protein Atlas: ENSG00000204370 | ||
Pathway | NCI Pathway Interaction Database: SDHD | |
KEGG: SDHD | ||
REACTOME: SDHD | ||
ConsensusPathDB | ||
Pathway Commons: SDHD | ||
Metabolism | MetaCyc: SDHD | |
HUMANCyc: SDHD | ||
Regulation | Ensembl's Regulation: ENSG00000204370 | |
miRBase: chr11 :111,957,570-111,966,518 | ||
TargetScan: NM_001276503 | ||
cisRED: ENSG00000204370 | ||
Context | iHOP: SDHD | |
cancer metabolism search in PubMed: SDHD | ||
UCL Cancer Institute: SDHD | ||
Assigned class in ccmGDB | A - This gene has a literature evidence and it belongs to cancer gene. | |
References showing role of SDHD in cancer cell metabolism | 1. Baysal BE (2003) On the association of succinate dehydrogenase mutations with hereditary paraganglioma. Trends in Endocrinology & Metabolism 14: 453-459. go to article 2. Puissegur M, Mazure N, Bertero T, Pradelli L, Grosso S, et al. (2011) miR-210 is overexpressed in late stages of lung cancer and mediates mitochondrial alterations associated with modulation of HIF-1 activity. Cell Death & Differentiation 18: 465-478. go to article |
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Phenotypic Information for SDHD(metabolism pathway, cancer, disease, phenome) |
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Cancer | CGAP: SDHD |
Familial Cancer Database: SDHD |
* This gene is included in those cancer gene databases. |
Oncogene 1 | Significant driver gene in |
cf) number; DB name 1 Oncogene; http://nar.oxfordjournals.org/content/35/suppl_1/D721.long, 2 Tumor Suppressor gene; https://bioinfo.uth.edu/TSGene/, 3 Cancer Gene Census; http://www.nature.com/nrc/journal/v4/n3/abs/nrc1299.html, 4 CancerGenes; http://nar.oxfordjournals.org/content/35/suppl_1/D721.long, 5 Network of Cancer Gene; http://ncg.kcl.ac.uk/index.php, 1Therapeutic Vulnerabilities in Cancer; http://cbio.mskcc.org/cancergenomics/statius/ |
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REACTOME_PYRUVATE_METABOLISM_AND_CITRIC_ACID_TCA_CYCLE |
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OMIM | 114900; phenotype. 168000; phenotype. 171300; phenotype. 602690; gene. 606864; phenotype. 615106; phenotype. |
Orphanet | 100093; Carcinoid tumor and carcinoid syndrome. 201; Cowden syndrome. 29072; Hereditary pheochromocytoma-paraganglioma. 3208; Isolated succinate-CoQ reductase deficiency. 97286; Carney-Stratakis syndrome. |
Disease | KEGG Disease: SDHD |
MedGen: SDHD (Human Medical Genetics with Condition) | |
ClinVar: SDHD | |
Phenotype | MGI: SDHD (International Mouse Phenotyping Consortium) |
PhenomicDB: SDHD |
Mutations for SDHD |
* Under tables are showing count per each tissue to give us broad intuition about tissue specific mutation patterns.You can go to the detailed page for each mutation database's web site. |
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- Statistics for Tissue and Mutation type | Top |
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- For Inter-chromosomal Variations |
There's no inter-chromosomal structural variation. |
- For Intra-chromosomal Variations |
* Intra-chromosomal variantions includes 'intrachromosomal amplicon to amplicon', 'intrachromosomal amplicon to non-amplified dna', 'intrachromosomal deletion', 'intrachromosomal fold-back inversion', 'intrachromosomal inversion', 'intrachromosomal tandem duplication', 'Intrachromosomal unknown type', 'intrachromosomal with inverted orientation', 'intrachromosomal with non-inverted orientation'. |
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Sample | Symbol_a | Chr_a | Start_a | End_a | Symbol_b | Chr_b | Start_b | End_b |
prostate | SDHD | chr11 | 111963712 | 111963712 | chr11 | 115734775 | 115734775 |
cf) Tissue number; Tissue name (1;Breast, 2;Central_nervous_system, 3;Haematopoietic_and_lymphoid_tissue, 4;Large_intestine, 5;Liver, 6;Lung, 7;Ovary, 8;Pancreas, 9;Prostate, 10;Skin, 11;Soft_tissue, 12;Upper_aerodigestive_tract) |
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* From mRNA Sanger sequences, Chitars2.0 arranged chimeric transcripts. This table shows SDHD related fusion information. |
ID | Head Gene | Tail Gene | Accession | Gene_a | qStart_a | qEnd_a | Chromosome_a | tStart_a | tEnd_a | Gene_a | qStart_a | qEnd_a | Chromosome_a | tStart_a | tEnd_a |
AA213804 | SDHD | 1 | 198 | 11 | 111965577 | 111965774 | XIRP2 | 199 | 309 | 2 | 168106959 | 168107074 |
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There's no copy number variation information in COSMIC data for this gene. |
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Stat. for Non-Synonymous SNVs (# total SNVs=13) | (# total SNVs=5) |
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(# total SNVs=0) | (# total SNVs=0) |
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* When you move the cursor on each content, you can see more deailed mutation information on the Tooltip. Those are primary_site,primary_histology,mutation(aa),pubmedID. |
GRCh37 position | Mutation(aa) | Unique sampleID count |
chr11:111958593-111958593 | p.R22Q | 3 |
chr11:111965590-111965590 | p.A126S | 1 |
chr11:111959622-111959622 | p.T67T | 1 |
chr11:111965680-111965680 | p.L156M | 1 |
chr11:111959626-111959626 | p.E69K | 1 |
chr11:111965691-111965691 | p.L159L | 1 |
chr11:111959628-111959628 | p.E69E | 1 |
chr11:111965693-111965693 | p.*160L | 1 |
chr11:111957641-111957641 | p.L4F | 1 |
chr11:111959637-111959637 | p.V72V | 1 |
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Point Mutation/ Tissue ID | 1 | 2 | 3 | 4 | 5 | 6 | 7 | 8 | 9 | 10 | 11 | 12 | 13 | 14 | 15 | 16 | 17 | 18 | 19 | 20 |
# sample | 2 | 1 |   | 4 |   |   |   |   | 1 |   |   | 3 |   |   |   |   | 1 |   | 1 | 4 |
# mutation | 2 | 1 |   | 4 |   |   |   |   | 1 |   |   | 3 |   |   |   |   | 1 |   | 1 | 4 |
nonsynonymous SNV |   |   |   | 4 |   |   |   |   | 1 |   |   | 2 |   |   |   |   |   |   | 1 | 3 |
synonymous SNV | 2 | 1 |   |   |   |   |   |   |   |   |   | 1 |   |   |   |   | 1 |   |   | 1 |
cf) Tissue ID; Tissue type (1; BLCA[Bladder Urothelial Carcinoma], 2; BRCA[Breast invasive carcinoma], 3; CESC[Cervical squamous cell carcinoma and endocervical adenocarcinoma], 4; COAD[Colon adenocarcinoma], 5; GBM[Glioblastoma multiforme], 6; Glioma Low Grade, 7; HNSC[Head and Neck squamous cell carcinoma], 8; KICH[Kidney Chromophobe], 9; KIRC[Kidney renal clear cell carcinoma], 10; KIRP[Kidney renal papillary cell carcinoma], 11; LAML[Acute Myeloid Leukemia], 12; LUAD[Lung adenocarcinoma], 13; LUSC[Lung squamous cell carcinoma], 14; OV[Ovarian serous cystadenocarcinoma ], 15; PAAD[Pancreatic adenocarcinoma], 16; PRAD[Prostate adenocarcinoma], 17; SKCM[Skin Cutaneous Melanoma], 18:STAD[Stomach adenocarcinoma], 19:THCA[Thyroid carcinoma], 20:UCEC[Uterine Corpus Endometrial Carcinoma]) |
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* We represented just top 10 SNVs. When you move the cursor on each content, you can see more deailed mutation information on the Tooltip. Those are primary_site, primary_histology, mutation(aa), pubmedID. |
Genomic Position | Mutation(aa) | Unique sampleID count |
chr11:111958593 | p.R22Q,SDHD | 2 |
chr11:111959647 | p.L37H,SDHD | 1 |
chr11:111959648 | p.L38L,SDHD | 1 |
chr11:111959652 | p.S50C,SDHD | 1 |
chr11:111957641 | p.A58A,SDHD | 1 |
chr11:111959687 | p.G69W,SDHD | 1 |
chr11:111959712 | p.L117M,SDHD | 1 |
chr11:111958662 | p.L120L,SDHD | 1 |
chr11:111965564 | p.L4F,SDHD | 1 |
chr11:111958687 | p.G45E,SDHD | 1 |
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* Copy number data were extracted from TCGA using R package TCGA-Assembler. The URLs of all public data files on TCGA DCC data server were gathered on Jan-05-2015. Function ProcessCNAData in TCGA-Assembler package was used to obtain gene-level copy number value which is calculated as the average copy number of the genomic region of a gene. |
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cf) Tissue ID[Tissue type]: BLCA[Bladder Urothelial Carcinoma], BRCA[Breast invasive carcinoma], CESC[Cervical squamous cell carcinoma and endocervical adenocarcinoma], COAD[Colon adenocarcinoma], GBM[Glioblastoma multiforme], Glioma Low Grade, HNSC[Head and Neck squamous cell carcinoma], KICH[Kidney Chromophobe], KIRC[Kidney renal clear cell carcinoma], KIRP[Kidney renal papillary cell carcinoma], LAML[Acute Myeloid Leukemia], LUAD[Lung adenocarcinoma], LUSC[Lung squamous cell carcinoma], OV[Ovarian serous cystadenocarcinoma ], PAAD[Pancreatic adenocarcinoma], PRAD[Prostate adenocarcinoma], SKCM[Skin Cutaneous Melanoma], STAD[Stomach adenocarcinoma], THCA[Thyroid carcinoma], UCEC[Uterine Corpus Endometrial Carcinoma] |
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Gene Expression for SDHD |
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* CCLE gene expression data were extracted from CCLE_Expression_Entrez_2012-10-18.res: Gene-centric RMA-normalized mRNA expression data. |
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* Normalized gene expression data of RNASeqV2 was extracted from TCGA using R package TCGA-Assembler. The URLs of all public data files on TCGA DCC data server were gathered at Jan-05-2015. Only eight cancer types have enough normal control samples for differential expression analysis. (t test, adjusted p<0.05 (using Benjamini-Hochberg FDR)) |
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* This plots show the correlation between CNV and gene expression. |
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Gene-Gene Network Information |
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* Co-Expression network figures were drawn using R package igraph. Only the top 20 genes with the highest correlations were shown. Red circle: input gene, orange circle: cell metabolism gene, sky circle: other gene |
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ALG9,ARCN1,ATP5L,C11orf57,CWF19L2,DDX10,DLAT, EI24,NPAT,PTS,PUS3,RBM7,REXO2,RPS25, SDHD,STT3A,TMEM123,UBE4A,USP28,ZPR1,ZW10 | ACAT1,ATPAF1,MPC1,DLD,GHITM,GNPAT,GPN3, HADHB,MRPS36,NDUFB5,PDHX,PHYH,PPP3CB,PRDX3, RRAGD,SDHB,SDHD,SNRNP27,SUCLA2,VBP1,VDAC2 | ||||
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ATP5F1,ATP5G3,ATP5L,ATP5O,C14orf142,COX7A2,MRPL21, MRPL35,MRPS22,NDUFB5,NDUFS3,SAR1B,SDHB,SDHD, SUCLG1,TIMM8B,TMEM126A,TMEM126B,TMX2,TOMM22,UQCRC2 | ATG5,ATP5C1,ATP5F1,ATP5O,TMEM251,C14orf142,C3orf38, COX7A2,FAM96A,HINT1,MRPL13,MRPS36,NDUFB5,NXT2, ORC4,PDZD11,PPCS,SDHB,SDHD,TXNL1,UQCRC2 |
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* Co-Expression network figures were drawn using R package igraph. Only the top 20 genes with the highest correlations were shown. Red circle: input gene, orange circle: cell metabolism gene, sky circle: other gene |
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Pharmacological Information for SDHD |
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DB Category | DB Name | DB's ID and Url link |
Organism-specific databases | PharmGKB | PA35608; -. |
Organism-specific databases | CTD | 6392; -. |
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* Gene Centered Interaction Network. |
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* Drug Centered Interaction Network. |
DrugBank ID | Target Name | Drug Groups | Generic Name | Drug Centered Network | Drug Structure |
DB00139 | succinate dehydrogenase complex, subunit D, integral membrane protein | approved; nutraceutical | Succinic acid | ![]() | ![]() |
DB00756 | succinate dehydrogenase complex, subunit D, integral membrane protein | approved | Hexachlorophene | ![]() | ![]() |
DB04141 | succinate dehydrogenase complex, subunit D, integral membrane protein | experimental | 2-Hexyloxy-6-Hydroxymethyl-Tetrahydro-Pyran-3,4,5-Triol | ![]() | ![]() |
DB08689 | succinate dehydrogenase complex, subunit D, integral membrane protein | experimental | UBIQUINONE-1 | ![]() | ![]() |
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Cross referenced IDs for SDHD |
* We obtained these cross-references from Uniprot database. It covers 150 different DBs, 18 categories. http://www.uniprot.org/help/cross_references_section |
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