SDHC

gene
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Also known as CYB560cybL

Summary

SDHC (succinate dehydrogenase complex subunit C, HGNC:10682) is a protein-coding gene on chromosome 1q23.3, encoding Succinate dehydrogenase cytochrome b560 subunit, mitochondrial (Q99643). 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). It is a common-essential gene (DepMap: required in 92.0% of cancer cell lines) and haploinsufficient (ClinGen: sufficient evidence).

This gene encodes one of four nuclear-encoded subunits that comprise succinate dehydrogenase, also known as mitochondrial complex II, a key enzyme complex of the tricarboxylic acid cycle and aerobic respiratory chains of mitochondria. The encoded protein is one of two integral membrane proteins that anchor other subunits of the complex, which form the catalytic core, to the inner mitochondrial membrane. There are several related pseudogenes for this gene on different chromosomes. Mutations in this gene have been associated with paragangliomas. Alternatively spliced transcript variants have been described.

Source: NCBI Gene 6391 — RefSeq curated summary.

At a glance

  • Gene–disease (curated): hereditary pheochromocytoma-paraganglioma (Definitive, ClinGen) — +6 more curated relationships
  • GWAS associations: 2
  • Clinical variants (ClinVar): 1,010 total — 69 pathogenic, 32 likely-pathogenic
  • Phenotypes (HPO): 144
  • Cancer dependency (DepMap): dependent in 92.0% of screened cell lines (common-essential)
  • Dosage sensitivity (ClinGen): haploinsufficiency sufficient evidence, triplosensitivity no evidence
  • MANE Select transcript: NM_003001

Identifiers

Gene identifiers

FieldValue
HGNC IDHGNC:10682
Approved symbolSDHC
Namesuccinate dehydrogenase complex subunit C
Location1q23.3
Locus typegene with protein product
StatusApproved
AliasesCYB560, cybL
Ensembl geneENSG00000143252
Ensembl biotypeprotein_coding
OMIM602413
Entrez6391

Gene structure

Transcript identifiers

Ensembl transcripts: 15 — 13 protein_coding, 2 nonsense_mediated_decay

ENST00000342751, ENST00000367975, ENST00000392169, ENST00000432287, ENST00000470743, ENST00000504963, ENST00000513009, ENST00000515731, ENST00000714063, ENST00000714064, ENST00000714065, ENST00000714066, ENST00000893929, ENST00000893930, ENST00000893931

RefSeq mRNA: 12 — MANE Select: NM_003001 NM_001035511, NM_001035512, NM_001035513, NM_001278172, NM_001407115, NM_001407116, NM_001407117, NM_001407118, NM_001407119, NM_001407120, NM_001407121, NM_003001

CCDS: CCDS1230, CCDS41431, CCDS41432, CCDS44263, CCDS60330

Canonical transcript exons

ENST00000367975 — 6 exons

ExonStartEnd
ENSE00001931697161362329161363206
ENSE00003505683161323614161323670
ENSE00003545898161328396161328497
ENSE00003689529161340594161340655
ENSE00003901936161314381161314425
ENSE00004022699161356677161356840

Expression profiles

Bgee: expression breadth ubiquitous, 134 present calls, max score 98.82.

FANTOM5 (CAGE): breadth ubiquitous, TPM avg 65.4202 / max 409.0594, expressed in 1823 samples.

FANTOM5 promoters (1 alternative TSS)

Promoter IDTPM avgSamples expressed
624165.42021823

Top tissues by expression

134 total, by Bgee expression score (0-100, higher = more expressed):

TissueAnatomy IDExpression scoreQuality
islet of LangerhansUBERON:000000698.82gold quality
right adrenal gland cortexUBERON:003582798.72gold quality
right adrenal glandUBERON:000123398.71gold quality
adult mammalian kidneyUBERON:000008298.48gold quality
left adrenal glandUBERON:000123498.48gold quality
left adrenal gland cortexUBERON:003582598.35gold quality
rectumUBERON:000105298.21gold quality
adrenal glandUBERON:000236998.19gold quality
smooth muscle tissueUBERON:000113598.06gold quality
duodenumUBERON:000211498.06gold quality
heart left ventricleUBERON:000208498.01gold quality
right lobe of liverUBERON:000111497.88gold quality
gastrocnemiusUBERON:000138897.84gold quality
mucosa of transverse colonUBERON:000499197.83gold quality
liverUBERON:000210797.68gold quality
hindlimb stylopod muscleUBERON:000425297.61gold quality
esophagus mucosaUBERON:000246997.59gold quality
monocyteCL:000057697.58gold quality
apex of heartUBERON:000209897.55gold quality
heartUBERON:000094897.53gold quality
leukocyteCL:000073897.48gold quality
kidneyUBERON:000211397.40gold quality
right atrium auricular regionUBERON:000663197.39gold quality
muscle of legUBERON:000138397.36gold quality
endometriumUBERON:000129597.35gold quality
skeletal muscle tissueUBERON:000113497.21gold quality
metanephros cortexUBERON:001053397.20gold quality
esophagusUBERON:000104397.19gold quality
substantia nigraUBERON:000203897.19gold quality
colonic epitheliumUBERON:000039797.17gold quality

Single-cell (SCXA)

Detected in 2 experiment(s), a significant marker in 1.

ExperimentMarker?Max mean expression
E-ANND-3yes14.48
E-GEOD-36552no79.64

Regulation

Is transcription factor: no

Upstream regulators (CollecTRI, top): EGR2, NFKBIB, NFYA

miRNA regulators (miRDB)

100 targeting SDHC, top 30 by miRDB confidence (max_score; target_count = how many genes the miRNA targets in total — lower means more specific):

miRNAMax scoreAvg scoremiRNA target_count
HSA-MIR-4476100.0068.182030
HSA-MIR-6876-5P100.0067.682126
HSA-MIR-366299.9973.825684
HSA-MIR-3692-3P99.9870.272139
HSA-MIR-4725-3P99.9669.532520
HSA-MIR-6780B-5P99.9669.602562
HSA-MIR-568899.9673.234504
HSA-MIR-495-3P99.9672.814197
HSA-MIR-548AA99.9670.643753
HSA-MIR-548AP-3P99.9670.643753
HSA-MIR-548T-3P99.9670.643753
HSA-MIR-141-3P99.9472.792421
HSA-MIR-200A-3P99.9472.682420
HSA-MIR-7-1-3P99.9171.534384
HSA-MIR-7-2-3P99.9171.404394
HSA-MIR-568099.9169.833421
HSA-MIR-627-3P99.9071.423316
HSA-MIR-153-5P99.8973.866317
HSA-MIR-380-3P99.8970.181978
HSA-MIR-427199.8868.322244
HSA-MIR-3121-3P99.8271.963630
HSA-MIR-323A-3P99.7970.301739
HSA-MIR-4668-5P99.7970.583782
HSA-MIR-807699.7868.521170
HSA-MIR-57799.7869.132479
HSA-MIR-129999.7771.242389
HSA-MIR-467999.7669.191229
HSA-MIR-92A-2-5P99.7567.012164
HSA-MIR-674599.7465.331321
HSA-MIR-442899.7366.411733

Functional genomics

ClinGen dosage: haploinsufficiency 3 (sufficient evidence), triplosensitivity 0 (no evidence). ClinGen Gene Dosage Map DepMap (CRISPR cell-line fitness): dependent in 92.0% of screened cell lines, common-essential.

Literature-anchored findings (GeneRIF, showing 40)

  • Prevalence of SDHB, SDHC, and SDHD germline mutations in clinic patients with head and neck paragangliomas (PMID:11897817)
  • Review. Succinate dehydrogenase catalyses a step in the Krebs tricarboxylic-acid cycle. Inherited heterozygous mutations in the gene encoding this enzyme causes a predisposition to inherited neoplasia syndromes. (PMID:12612654)
  • A splice donor site mutation in SDHC is associates with autosomal dominant malignant and catecholamine-producing paraganglioma (PMID:12658451)
  • description of a large deletion in a complex II gene and confirmation of the role of SDHC in familial and sporadic paragangliomas (PMID:15342702)
  • Mutant protein in transgenic mice generates oxidative stress and can contribute to nuclear DNA damage, mutagenesis, and ultimately, tumorigenesis (PMID:15665296)
  • A possible role for SDH polymorphism as susceptibility/disease modifying factors in familial and sporadic medullary thyroid carcinomas was shown. (PMID:16322339)
  • Germline mutations of SDHC play a minor role in sporadic head and neck paraganglioma. (PMID:16405730)
  • investigated 11 patients with the dyad of ‘paraganglioma and gastric stromal sarcoma’; in eight, from 7 unrelated families, the GISTs were caused by germline mutations of the genes encoding subunits B, C, or D (the SDHB, SDHC and SDHD genes, respectively) (PMID:17667967)
  • familial gastrointestinal stromal tumors may be caused by mutations of the succinate dehydrogenase subunit genes SDHB, SDHC, and SDHD, and abdominal paragangliomas associated with gastrointestinal tumors may be caused uniquely by SDHC mutations (PMID:17804857)
  • Gene deletions of SDHD and SDHC represent a substantial proportion of all mutations, and must be considered in paraganglioma patients shown to be negative for mutations by sequencing. (PMID:19546167)
  • no clear association was found between gene variants involved in oxygen sensing and chemoresponsiveness, although some mutations in the SDHB and SDHD genes deserve further investigations in a larger population. (PMID:19768395)
  • Approximately 15% of all pheochromocytomas or paragangliomas are associated with germline SDH mutation. (PMID:20236688)
  • Case Report: present a 32-year-old man with a familial SDHC mutation who manifests synchronous paragangliomas of the carotid body and the thoracic aortopulmonary window. (PMID:21106325)
  • mammalian cells over expressing mutations in SDHC demonstrate low-dose/low-LET radiation sensitization that is mediated by increased levels of O*- and HO. (PMID:21268708)
  • Biallelic inactivation of the SDHC gene may represent a new pathway of pathogenesis of syndromic and nonsyndromic renal cell carcinoma, perhaps of both clear cell and papillary histologies (PMID:22351710)
  • No SDHC mutation were found in patients with sporadic paraganglioma. (PMID:22566194)
  • Tumor DNA mutation screening of the SDHx, VHL, and RET genes and LOH analyses of the SDHx and VHL genes were performed for pheochromocytoma. (PMID:22573489)
  • Studies indicate that an array of tumor syndromes caused by complex II-associated mutations in genes SDHA, SDHB, SDHC, SDHD, SDHAF1 and SDHAF2 have been identified over a decade. (PMID:23174333)
  • Overall, 9 of the 34 patients with KIT/PDGFRA wild-type GIST carried mutations in one of the four subunits of the SDH complex (six patients in SDHA, two in SDHB, one in SDHC (PMID:23612575)
  • SDH deficiency may promote tumorigenesis through accumulation of succinate and inhibition of dioxygenase enzymes. Inhibition of TET activity may, in turn, alter global DNA methylation and gene expression in SDH-deficient tumors. (PMID:23743927)
  • this study reports the first patient affected by malignant paraganglioma and< moreover, it reports two more unrelated patients with the same genotype and very different clinical presentations. (PMID:24423348)
  • Thoracic paragangliomas are common in patients with SDHC mutations, and imaging of this area should be included in surveillance of mutation carriers. (PMID:24758179)
  • these data suggest epigenetic inactivation of the SDHC gene locus with functional impairment of the SDHC as a plausible alternate mechanism of tumorigenesis in Carney Triad (PMID:24859990)
  • Variant in rs3935401 in the 3’ untranslated region of SDHC is associated with hepatocellular carcinoma. (PMID:25081338)
  • The discovery of SDHC epimutation provides a unifying explanation for the pathogenesis of SDH-deficient gastrointestinal stromal tumors. (PMID:25540324)
  • Both germline and somatic SDHx mutations/variants occur in sporadic differentiated thyroid cancer (DTC) but are very rare in sporadic breast cancer, and overall loss of SDHx gene expression is a signature of DTC (PMID:25694510)
  • Loss of the SDHC gene is associated with metastatic sympathetic paraganglioma. (PMID:26162468)
  • This study strengthens the etiological association of SDH genes with pituitary neoplasia, renal tumorigenesis, and gastric gastrointestinal stromal tumors. Also, pancreatic neuroendocrine tumor falls within the SDH-related tumor spectrum. (PMID:26259135)
  • significant association with overall survival were confirmed for SDHC gene, SDHD gene and FH gene … SDHC gene and FH gene were the primary factors contributing to the different overall survival time of colorectal carcinoma (PMID:26377099)
  • According to international guidelines, SDHB, SDHC, and SDHD genetic testing were performed in this patient, but not SDHA, which would have been prescribed only after surgery, in case of SDHA negative immunohistochemistry (PMID:26490314)
  • This report provides evidence that SDHC promoter methylation can cause Paragangliomas due to SDHC inactivation (PMID:26652933)
  • For classification, tumors were characterized by SDHA, B, C, or D (SDHX) mutations and other genetic and epigenetic alterations, including presence of mutations in germline (PMID:27011036)
  • SDH-deficient gastrointestinal stromal tumors (GISTs) account for approximately 8% of gastric GISTs and are associated with a high rate of distant metastasis, regardless of conventional risk category. (PMID:27340750)
  • Heterozygous germline deletions of up to 104 kb in size were identified in SDHB, SDHC, SDHD and flanking genes in 20 paraganglioma-pheochromocytoma patients. The exact breakpoint could be determined in 16 paraganglioma-pheochromocytoma patients of which 15 were novel deletions (PMID:27485256)
  • 31% of the paragangliomas in the French Canadian can be explained by the SDHC mutation (c.397C>T, p.[Arg133Ter]). (PMID:27700540)
  • Targeted analysis of DNA methylation array revealed the mesenchymal stem cells in infants born to obese mothers had hypermethylation in genes regulating Fatty Acid Oxidation (PRKAG2, ACC2, CPT1A, SDHC) and corresponding lower mRNA content of these genes. Moreover, mesenchymal stem cells methylation was positively correlated with infant adiposity. (PMID:29107296)
  • SDHC Promoter hypermethylation is associated with Parasympathetic Paragangliomas. (PMID:29126304)
  • Specific genotype-tumour risk associations provides a basis for novel investigative strategies into succinate dehydrogenase-related mechanisms of tumourigenesis and the development of personalised management for SDHB/SDHC/SDHD mutation carriers (PMID:29386252)
  • Low SDHC expression is associated with growth and metastasis of hepatocellular carcinoma. (PMID:31278950)
  • Variant type is associated with disease characteristics in SDHB, SDHC and SDHD-linked phaeochromocytoma-paraganglioma. (PMID:31492822)

Cross-species orthologs

5 orthologs

OrganismSymbolGene ID
danio_reriosdhcENSDARG00000038608
mus_musculusSdhcENSMUSG00000058076
rattus_norvegicusSdhcENSRNOG00000003163
drosophila_melanogasterSdhCLFBGN0037860
caenorhabditis_elegansWBGENE00003225

Protein

Protein identifiers

Succinate dehydrogenase cytochrome b560 subunit, mitochondrialQ99643 (reviewed: Q99643)

Alternative names: Integral membrane protein CII-3, Malate dehydrogenase [quinone] cytochrome b560 subunit, QPs-1, Succinate dehydrogenase complex subunit C, Succinate-ubiquinone oxidoreductase cytochrome B large subunit

All UniProt accessions (8): Q99643, A0A087WZU7, A0A0S2Z4B7, A0A0S2Z4C9, A0AAQ5BH99, A0AAQ5BHB5, A0AAQ5BHE7, D6RBX6

UniProt curated annotations — full annotation on UniProt →

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). SDH also oxidizes malate to the non-canonical enol form of oxaloacetate, enol-oxaloacetate. Enol-oxaloacetate, which is a potent inhibitor of the succinate dehydrogenase activity, is further isomerized into keto-oxaloacetate.

Subunit / interactions. 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.

Disease relevance. Pheochromocytoma/paraganglioma syndrome 3 (PPGL3) [MIM:605373] A form of pheochromocytoma/paraganglioma syndrome, a tumor predisposition syndrome characterized by the development of neuroendocrine tumors, usually in adulthood. Pheochromocytomas are catecholamine-producing tumors that arise from chromaffin cells in the adrenal medulla. Paragangliomas develop from sympathetic paraganglia in the thorax, abdomen, and pelvis, as well as from parasympathetic paraganglia in the head and neck. PPGL3 inheritance is autosomal dominant. The disease is caused by variants affecting the gene represented in this entry. Paraganglioma and gastric stromal sarcoma (PGGSS) [MIM:606864] 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. The disease is caused by variants affecting the gene represented in this entry.

Cofactor. The heme b is bound between the two transmembrane subunits SDHC and SDHD.

Pathway. Carbohydrate metabolism; tricarboxylic acid cycle.

Similarity. Belongs to the cytochrome b560 family.

Isoforms (5)

UniProt IDNamesCanonical?
Q99643-11yes
Q99643-22
Q99643-33, CII-3b
Q99643-44
Q99643-55

RefSeq proteins (12): NP_001030588, NP_001030589, NP_001030590, NP_001265101, NP_001394044, NP_001394045, NP_001394046, NP_001394047, NP_001394048, NP_001394049, NP_001394050, NP_002992* (*=MANE)

Domains & families (InterPro)

IDNameType
IPR000701SuccDH_FuR_B_TM-suFamily
IPR014314Succ_DH_cytb556Family
IPR018495Succ_DH_cyt_bsu_CSConserved_site
IPR034804SQR/QFR_C/DHomologous_superfamily

Pfam: PF01127

Enzyme classification (BRENDA):

  • EC 1.3.5.1 — succinate dehydrogenase (BRENDA: 80 organisms, 226 substrates, 192 inhibitors, 145 Km, 115 kcat entries)

Substrate kinetics (BRENDA)

28 substrates with measured Km, best-characterized 15. Km ranges are aggregated across organisms/conditions.

SubstrateKm (mM)Measurements
SUCCINATE0.0015–2039
UBIQUINONE0.0005–0.226
FUMARATE0.005–0.45514
2,3-DIMETHOXY-5-METHYL-6-DECYL-1,4-BENZOQUINONE0.0034–0.0189
REDUCED PLUMBAGIN0.11–0.199
UBIQUINONE-20.0002–0.01149
MENAQUINOL0.0009–0.00548
PHENAZINE METHOSULFATE0.11–0.483
UBIQUINONE-10.0016–0.023
2,6-DICHLOROPHENOL INDOPHENOL0.003–0.0072
CALDARIELLAQUINONE0.06–0.182
MENAQUINONE0.0018–0.0042
OXIDIZED 2,6-DICHLOROPHENOLINDOPHENOL0.0654–0.0892
2,3-DIMETHOXY-5-METHYL-1,4-BENZOQUINONE0.0031
2,3-DIMETHYL-1,4-NAPHTHOHYDROQUINONE0.121

UniProt features (19 total): helix 5, topological domain 4, splice variant 3, transmembrane region 3, transit peptide 1, chain 1, turn 1, binding site 1

Structure

Experimental structures (PDB)

2 structures.

PDBMethodResolution (Å)
9KC4ELECTRON MICROSCOPY2.65
8GS8ELECTRON MICROSCOPY2.86

Predicted structure (AlphaFold)

ModelpLDDTFraction very-high
AF-Q99643-F191.050.77

Functional residue map

Curated UniProt residues grouped by drug-discovery relevance — catalytic, ligand-binding, modification, and mutation-validated positions. Source: UniProtKB sequence features.

Ligand- & substrate-binding residues (1): 127 (axial binding residue)

Function

Pathways and Gene Ontology

Reactome pathways

5 pathways

IDPathway
R-HSA-611105Respiratory electron transport
R-HSA-71403Citric acid cycle (TCA cycle)
R-HSA-9854311Maturation of TCA enzymes and regulation of TCA cycle
R-HSA-1428517Aerobic respiration and respiratory electron transport
R-HSA-1430728Metabolism

MSigDB gene sets: 520 (showing top): MODULE_93, MORF_RAB5A, GOMF_OXIDOREDUCTASE_ACTIVITY_ACTING_ON_THE_CH_CH_GROUP_OF_DONORS, GOBP_ORGANOPHOSPHATE_METABOLIC_PROCESS, GOBP_NUCLEOSIDE_PHOSPHATE_BIOSYNTHETIC_PROCESS, MORF_PSMC2, GOBP_ORGANOPHOSPHATE_BIOSYNTHETIC_PROCESS, GOBP_CARBOHYDRATE_DERIVATIVE_METABOLIC_PROCESS, GOBP_NUCLEOBASE_CONTAINING_SMALL_MOLECULE_METABOLIC_PROCESS, GOBP_GENERATION_OF_PRECURSOR_METABOLITES_AND_ENERGY, GCM_RING1, GOBP_ATP_BIOSYNTHETIC_PROCESS, MORF_ATOX1, GOBP_OXIDATIVE_PHOSPHORYLATION, GOBP_CARBOHYDRATE_DERIVATIVE_BIOSYNTHETIC_PROCESS

GO Biological Process (4): tricarboxylic acid cycle (GO:0006099), mitochondrial electron transport, succinate to ubiquinone (GO:0006121), aerobic respiration (GO:0009060), proton motive force-driven mitochondrial ATP synthesis (GO:0042776)

GO Molecular Function (4): electron transfer activity (GO:0009055), heme binding (GO:0020037), metal ion binding (GO:0046872), protein binding (GO:0005515)

GO Cellular Component (4): mitochondrion (GO:0005739), mitochondrial inner membrane (GO:0005743), membrane (GO:0016020), respiratory chain complex II (succinate dehydrogenase) (GO:0045273)

Reactome top-level categories

Rollup of top-3 pathways:

CategoryPathways
Aerobic respiration and respiratory electron transport2
Citric acid cycle (TCA cycle)1
Metabolism1

GO top-level categories

Rollup of top GO terms by namespace:

CategoryTerms
aerobic respiration1
primary metabolic process1
aerobic electron transport chain1
mitochondrial ATP synthesis coupled electron transport1
cellular respiration1
mitochondrion1
oxidative phosphorylation1
proton motive force-driven ATP synthesis1
molecular_function1
tetrapyrrole binding1
cation binding1
binding1
cytoplasm1
intracellular membrane-bounded organelle1
organelle inner membrane1
mitochondrial membrane1
cellular anatomical structure1
membrane protein complex1
respiratory chain complex1
oxidoreductase complex1

Protein interactions and networks

STRING

5189 interactions, top by confidence (×1000):

Protein AProtein BPartner UniProtScore
SDHCSDHAP31040999
SDHCSDHAF2Q9NX18999
SDHCSDHDO14521999
SDHCSDHBP21912999
SDHCF5H5T6F5H5T6993
SDHCSDHAF1A6NFY7922
SDHCTMEM127O75204903
SDHCMMUTP22033880
SDHCMT-CYBP00156868
SDHCGAPDHP00354838
SDHCRETP07949827
SDHCPDGFRAP16234776
SDHCACTBP02570765
SDHCTIMM8BQ9Y5J9734
SDHCKITP10721733

IntAct

39 interactions, top by confidence:

ABTypeScore
PRKCASDHCpsi-mi:“MI:0915”(physical association)0.560
YWHAGSDHCpsi-mi:“MI:0915”(physical association)0.560
SETDB1SDHCpsi-mi:“MI:0915”(physical association)0.560
KAT5SDHCpsi-mi:“MI:0915”(physical association)0.560
LMO3SDHCpsi-mi:“MI:0915”(physical association)0.560
IMPDH1BCAT2psi-mi:“MI:0914”(association)0.530
SDHCDHODHpsi-mi:“MI:0915”(physical association)0.400
MDM2SDHCpsi-mi:“MI:0915”(physical association)0.370
SDHCARHGDIApsi-mi:“MI:0915”(physical association)0.370
SDHCXRCC6psi-mi:“MI:0915”(physical association)0.370
SDHDTNNC2psi-mi:“MI:0914”(association)0.350
SLC25A5psi-mi:“MI:0914”(association)0.350
CLPPNDUFA4psi-mi:“MI:2364”(proximity)0.270
DCTN1KIF2Apsi-mi:“MI:2364”(proximity)0.270
FBF1CCDC85Cpsi-mi:“MI:2364”(proximity)0.270
OFD1PSMD14psi-mi:“MI:2364”(proximity)0.270
POC5PSMD14psi-mi:“MI:2364”(proximity)0.270
AKT1SDHCpsi-mi:“MI:2364”(proximity)0.270
BRAFSDHCpsi-mi:“MI:2364”(proximity)0.270

BioGRID (50): SDHC (Affinity Capture-RNA), SDHC (Co-fractionation), SDHC (Co-fractionation), SDHC (Co-fractionation), SDHC (Co-fractionation), SDHC (Proximity Label-MS), SDHC (Proximity Label-MS), SDHC (Proximity Label-MS), SDHC (Proximity Label-MS), SDHC (Affinity Capture-MS), SDHC (Negative Genetic), SDHC (Positive Genetic), SDHC (Negative Genetic), SDHC (Negative Genetic), SDHC (Negative Genetic)

ESM2 similar proteins: A8WT26, B5FVB8, D0VWV4, O01578, O62215, O74471, O74882, O75964, P04039, P13619, P19511, P33421, P35720, P37298, P38857, P40086, P41955, P41956, P53311, P70097, P92506, P92507, Q04487, Q06236, Q08749, Q10361, Q28852, Q3ZCG2, Q5RFH0, Q6CFW6, Q6CXR8, Q6DGM2, Q6FJJ0, Q6PDU7, Q750S6, Q759E9, Q7SGY6, Q8T2T5, Q8WSR2, Q949R9

Diamond homologs: D0VWV4, O74882, P33421, P35720, P35721, P41085, P41955, P41956, P48934, P48935, P70097, P80478, P80481, P92506, Q1RHB5, Q4UKC1, Q59659, Q68XP1, Q8T2T5, Q92J99, Q99643, Q9CZB0, Q04487, P0DKI0, P0DKI1, Q84VK7, P63725, P63726, P69054, P69055

SIGNOR signaling

2 interactions.

AEffectBMechanism
SDHC“form complex”“Succinate dehydrogenase-Mitochondrial respiratory chain complex II”binding

Enriched among interaction partners

Reactome pathways and GO biological processes over-represented among this gene’s 29 IntAct physical interaction partners (hypergeometric vs the genome-wide background, BH-FDR, gene-set size 15–500, ranked by fold). A functional readout of the neighbourhood — distinct from this gene’s own memberships above, and biased toward well-studied / hub proteins, so read it as themes rather than proof.

Reactome pathways:

PathwayPartnersFoldFDR
Cell Cycle68.7×6e-03

Disease & clinical

Clinical variants and AI predictions

ClinVar

1010 variants total. Per-class counts are floors (≥ shown; pagination cap):

ClassificationCount (floor)
Pathogenic69
Likely pathogenic32
Uncertain significance455
Likely benign228
Benign83

Top pathogenic / likely-pathogenic (30)

Variant IDHGVSClassification
1040338NC_000001.10:g.(?161293394)(161293470_?)delPathogenic
1069194NM_003001.5(SDHC):c.250_251del (p.Leu84fs)Pathogenic
1072500NM_003001.5(SDHC):c.124del (p.Trp42fs)Pathogenic
1072825NC_000001.10:g.(?161310374)(161310455_?)delPathogenic
1076621NC_000001.10:g.(?161332109)(161332308_?)delPathogenic
1076622NC_000001.10:g.(?161326457)(161332308_?)delPathogenic
1443862NC_000001.10:g.(?161310374)(161332308_?)delPathogenic
1456907NM_003001.5(SDHC):c.214del (p.Arg72fs)Pathogenic
1744549NM_003001.5(SDHC):c.118del (p.Arg40fs)Pathogenic
1767917NM_003001.5(SDHC):c.97_98dup (p.Ala34fs)Pathogenic
183753NM_003001.5(SDHC):c.397C>T (p.Arg133Ter)Pathogenic
189840NM_003001.5(SDHC):c.6del (p.Ala3fs)Pathogenic
1999178NM_003001.5(SDHC):c.21-1G>APathogenic
2036254NM_003001.5(SDHC):c.220dup (p.Thr74fs)Pathogenic
2036721NM_003001.5(SDHC):c.288dup (p.Glu97Ter)Pathogenic
2055039NM_003001.5(SDHC):c.1A>C (p.Met1Leu)Pathogenic
229958NM_003001.5(SDHC):c.376dup (p.Tyr126fs)Pathogenic
239456NM_003001.3(SDHC):c.406-?_*2318+?delPathogenic
2424599NC_000001.10:g.(?161298176)(161298297_?)delPathogenic
2424601NC_000001.10:g.(?161284158)(161284225_?)delPathogenic
2442323NM_003001.5(SDHC):c.49del (p.His17fs)Pathogenic
2573281NM_003001.5(SDHC):c.107_108del (p.Glu36fs)Pathogenic
2573308NM_003001.5(SDHC):c.177C>A (p.Tyr59Ter)Pathogenic
2637552NM_003001.5(SDHC):c.248_251del (p.Ser83fs)Pathogenic
2943040NM_003001.5(SDHC):c.2T>C (p.Met1Thr)Pathogenic
2950878NM_003001.5(SDHC):c.61C>T (p.Gln21Ter)Pathogenic
2954043NM_003001.5(SDHC):c.143_144insTGGCCGGGCGCGGTGGCTCACGCCTGTAATCCCAGCACTTTGGGAGGCCGAGGCGGGCGGATCACGANNNNNNNNNNAAAAAAAAAAAAAAAAAAAAAAGAATATAGGTTC (p.Ser48_Asn49insGlyArgAlaArgTrpLeuThrProValIleProAlaLeuTrpGluAlaGluAlaGlyGlySerArgXaaXaaXaaXaaLysLysLysLysLysLysLysAsnIleGlySer)Pathogenic
3148693NM_003001.5(SDHC):c.204dup (p.Ile69fs)Pathogenic
3223027NM_003001.5(SDHC):c.183G>A (p.Trp61Ter)Pathogenic
3247756NC_000001.10:g.(?161284196)(161284215_?)delPathogenic

SpliceAI

1065 predictions. Top by Δscore:

VariantEffectΔscore
1:161323667:GAAA:Gdonor_gain1.0000
1:161328394:A:AGacceptor_gain1.0000
1:161328395:G:GGacceptor_gain1.0000
1:161328395:GTGCT:Gacceptor_gain1.0000
1:161340588:TTACA:Tacceptor_loss1.0000
1:161340589:TACA:Tacceptor_loss1.0000
1:161340590:ACAG:Aacceptor_loss1.0000
1:161340591:CA:Cacceptor_loss1.0000
1:161340592:A:ACacceptor_loss1.0000
1:161340592:A:AGacceptor_gain1.0000
1:161340592:AGTT:Aacceptor_gain1.0000
1:161340592:AGTTG:Aacceptor_gain1.0000
1:161340593:G:GCacceptor_gain1.0000
1:161340593:GTT:Gacceptor_gain1.0000
1:161340593:GTTG:Gacceptor_gain1.0000
1:161340593:GTTGG:Gacceptor_gain1.0000
1:161356675:AGG:Aacceptor_gain1.0000
1:161356676:GGG:Gacceptor_gain1.0000
1:161362440:G:GTdonor_gain1.0000
1:161314444:G:GTdonor_gain0.9900
1:161323612:A:AGacceptor_gain0.9900
1:161323613:G:GGacceptor_gain0.9900
1:161323613:GACAC:Gacceptor_gain0.9900
1:161323671:G:GGdonor_gain0.9900
1:161340593:GT:Gacceptor_gain0.9900
1:161340653:CAGG:Cdonor_loss0.9900
1:161340654:AGGT:Adonor_loss0.9900
1:161340656:G:Adonor_loss0.9900
1:161340657:T:Gdonor_loss0.9900
1:161356782:C:Gdonor_gain0.9900

AlphaMissense

1087 scored. Top likely-pathogenic:

VariantProtein changeam_pathogenicity
1:161356835:C:GH134D0.992
1:161340649:A:CS79R0.990
1:161340651:T:AS79R0.990
1:161340651:T:GS79R0.990
1:161362332:T:AW137R0.990
1:161362332:T:CW137R0.990
1:161328439:T:CF41L0.989
1:161328441:C:AF41L0.989
1:161328441:C:GF41L0.989
1:161362336:A:CD138A0.989
1:161340629:G:CR72P0.988
1:161356814:C:GH127D0.988
1:161362334:G:CW137C0.988
1:161362334:G:TW137C0.988
1:161356811:T:GY126D0.986
1:161356825:T:AN130K0.985
1:161356825:T:GN130K0.985
1:161356826:G:TG131W0.985
1:161356833:G:CR133P0.985
1:161340628:C:AR72S0.984
1:161362336:A:TD138V0.984
1:161356803:C:GP123R0.983
1:161340625:C:GH71D0.981
1:161362335:G:CD138H0.981
1:161356692:G:AG86D0.980
1:161356826:G:AG131R0.980
1:161356826:G:CG131R0.980
1:161356816:T:AH127Q0.979
1:161356816:T:GH127Q0.979
1:161356820:T:AW129R0.979

dbSNP variants (sampled 300 via entrez): RS1000003724 (1:161331644 G>A), RS1000054039 (1:161375202 G>C), RS1000138851 (1:161359469 C>T), RS1000157895 (1:161349980 G>A), RS1000178927 (1:161356301 G>A), RS1000228570 (1:161351471 A>G), RS1000238232 (1:161314686 C>G,T), RS1000252441 (1:161355962 G>A,T), RS1000284347 (1:161326239 G>A), RS1000398132 (1:161369334 C>T), RS1000466627 (1:161321135 T>A), RS1000560965 (1:161337761 G>A), RS1000561761 (1:161319975 A>G), RS1000596617 (1:161355594 G>A), RS1000646888 (1:161342644 G>A)

Disease associations

OMIM: gene MIM:602413 | disease phenotypes: MIM:605373, MIM:606764, MIM:168000, MIM:606864, MIM:171300, MIM:158350, MIM:167000, MIM:604287

GenCC curated gene-disease

DiseaseClassificationInheritance
pheochromocytoma/paraganglioma syndrome 3DefinitiveAutosomal dominant
hereditary pheochromocytoma-paragangliomaDefinitiveAutosomal dominant
gastrointestinal stromal tumorStrongAutosomal dominant
Carney-Stratakis syndromeStrongAutosomal dominant
renal cell carcinomaModerateAutosomal dominant
Cowden diseaseSupportiveAutosomal dominant

ClinGen Gene-Disease Validity (2)

Expert-panel classifications — Definitive > Strong > Moderate > Limited > Disputed > Refuted.

DiseaseClassificationInheritance
hereditary pheochromocytoma-paragangliomaDefinitiveAD
mitochondrial diseaseNo Known Disease RelationshipUD

Mondo (13): pheochromocytoma/paraganglioma syndrome 3 (MONDO:0011544), gastrointestinal stromal tumor (MONDO:0011719), hereditary neoplastic syndrome (MONDO:0015356), hereditary pheochromocytoma-paraganglioma (MONDO:0017366), Carney-Stratakis syndrome (MONDO:0011740), pheochromocytoma (MONDO:0008233), Cowden disease (MONDO:0016063), breast cancer (MONDO:0007254), ovarian cancer (MONDO:0008170), Carney triad (MONDO:0011424), neuroblastoma (MONDO:0005072), rhabdomyosarcoma (MONDO:0005212), renal cell carcinoma (MONDO:0005086)

Orphanet (9): Inherited cancer-predisposing syndrome (Orphanet:140162), Hereditary pheochromocytoma-paraganglioma (Orphanet:29072), Gastrointestinal stromal tumor (Orphanet:44890), Carney-Stratakis syndrome (Orphanet:97286), Cowden syndrome (Orphanet:201), Rare ovarian cancer (Orphanet:213500), Carney triad (Orphanet:139411), Neuroblastoma (Orphanet:635), Rhabdomyosarcoma (Orphanet:780)

HPO phenotypes

144 total (30 of 144 shown, HPO-id order):

HPOTerm
HP:0000006Autosomal dominant inheritance
HP:0000036Abnormal penis morphology
HP:0000077Abnormality of the kidney
HP:0000093Proteinuria
HP:0000096Glomerular sclerosis
HP:0000130Abnormality of the uterus
HP:0000158Macroglossia
HP:0000218High palate
HP:0000221Furrowed tongue
HP:0000256Macrocephaly
HP:0000360Tinnitus
HP:0000365Hearing impairment
HP:0000405Conductive hearing impairment
HP:0000518Cataract
HP:0000526Aniridia
HP:0000545Myopia
HP:0000717Autism
HP:0000740Episodic paroxysmal anxiety
HP:0000767Pectus excavatum
HP:0000771Gynecomastia
HP:0000790Hematuria
HP:0000820Abnormality of the thyroid gland
HP:0000822Hypertension
HP:0000853Goiter
HP:0000953Hyperpigmentation of the skin
HP:0000975Hyperhidrosis
HP:0000980Pallor
HP:0000982Palmoplantar keratoderma
HP:0000988Skin rash
HP:0000995Melanocytic nevus

GWAS associations

2 associations (top):

StudyTraitp-value
GCST001523_16Visceral adipose tissue adjusted for BMI8.000000e-06
GCST005352_1Paclitaxel disposition in epithelial ovarian cancer3.000000e-06

EFO canonical traits (1, from GWAS)

EFO IDTrait name
EFO:0004340body mass index

MeSH disease descriptors (11)

DescriptorNameTree numbers
D002292Carcinoma, Renal CellC04.557.470.200.025.390; C04.588.945.947.535.160; C12.050.351.937.820.535.160; C12.050.351.968.419.473.160; C12.200.758.820.750.160; C12.200.777.419.473.160; C12.900.820.535.160; C12.950.419.473.160; C12.950.983.535.160
D046152Gastrointestinal Stromal TumorsC04.557.450.565.370; C06.301.371.308; C06.405.249.308
D006223Hamartoma Syndrome, MultipleC04.445.435; C04.651.435; C04.700.435; C16.320.700.435
D009386Neoplastic Syndromes, HereditaryC04.700; C16.320.700
D009447NeuroblastomaC04.557.465.625.600.590.650.550; C04.557.470.670.590.650.550; C04.557.580.625.600.590.650.550
D010051Ovarian NeoplasmsC04.588.322.455; C12.050.351.500.056.630.705; C12.050.351.937.418.685; C12.100.250.056.630.705; C12.900.418.685; C19.344.410; C19.391.630.705
D010673PheochromocytomaC04.557.465.625.650.700.725; C04.557.580.625.650.700.725
D012208RhabdomyosarcomaC04.557.450.590.550.660; C04.557.450.795.550.660
C565803Carney Triad (supp.)
C564650Carney-Stratakis Syndrome (supp.)
C565335Paragangliomas 3 (supp.)

Drugs & pharmacology

Drug and pharmacology data

Is drug target: no

PharmGKB: 1 entry (VIP=true, CPIC=false)

CTD chemical–gene interactions

45 total (human), top 30 by PubMed support.

ChemicalActions (top 5)PubMed papers
Quercetindecreases expression3
bisphenol Aaffects expression, increases expression, decreases reaction, increases abundance2
Acetaminophendecreases expression2
Atrazinedecreases expression2
Cisplatindecreases expression, increases expression2
Cyclosporinedecreases expression2
Aflatoxin B1decreases expression, decreases methylation2
aristolochic acid Iincreases expression1
TAK-243decreases sumoylation1
ginger extractdecreases reaction, increases abundance, increases expression1
lasiocarpinedecreases expression1
triphenyl phosphateaffects expression1
4-chlorobiphenyldecreases expression1
chlortolurondecreases expression1
beta-lapachoneincreases expression1
sodium arseniteincreases abundance, affects cotreatment, decreases expression1
cobaltous chloridedecreases expression1
beta-methylcholineaffects expression1
di-n-butylphosphoric acidaffects expression1
JP8 aviation fuelaffects expression1
corosolic aciddecreases expression1
K 7174decreases expression1
pluronic block copolymer p85decreases expression1
Bortezomibdecreases expression1
Arsenic Trioxideincreases expression1
Arsenicdecreases expression, increases abundance, affects cotreatment1
Benzo(a)pyreneaffects methylation1
Cannabidiolincreases expression1
Curcuminaffects binding1
Doxorubicinaffects expression1

Clinical trials (associated diseases)

597 trials via MONDO — disease-level, not drug-specific.

TrialPhaseStatusTitle
NCT00414765PHASE4COMPLETEDAldesleukin in Participants With Metastatic Renal Cell Carcinoma or Metastatic Melanoma
NCT00777504PHASE4UNKNOWNStudy to the Optimal Duration of Therapy With Oral Angiogenesis Inhibitors
NCT00930345PHASE4TERMINATEDBiological, Pathological and Imagery Markers in the First-line Treatment of Metastatic Clear-cell Renal Cell Carcinoma
NCT01206764PHASE4COMPLETEDA Trial of Everolimis in Patients With Advanced Renal Cell Carcinoma.
NCT01266837PHASE4COMPLETEDOpen Label, Single Arm Trial to Characterize Patients With Metastatic RCC Treated With Everolimus After Failure of the First VEGF-targeted Therapy (MARC-2)
NCT02056587PHASE4COMPLETEDEverolimus in Patients With Metastatic Renal Cell Carcinoma Following Progression on Prior Bevacizumab Treatment
NCT02338570PHASE4TERMINATEDOutcome-related Factors in Patients With Metastatic Renal Cell Carcinoma Treated With Everolimus (ORCHIDEE)
NCT02596035PHASE4COMPLETEDAn Investigational Immuno-therapy Safety Trial of Nivolumab in Patients With Advanced or Metastatic Renal Cell Carcinoma
NCT02982954PHASE4COMPLETEDA Study to Evaluate the Safety of Nivolumab and Ipilimumab in Subjects With Previously Untreated Advanced or Metastatic Renal Cell Cancer
NCT05949424PHASE4UNKNOWNOPTI - DOSE: Optimal Dosing of Oral Anticancer Drugs in Older Adults
NCT07028125PHASE4RECRUITINGDigital Monitoring of Self-reported Symptoms by Patients Treated With Cabozantinib Plus Nivolumab for Advanced Clear-cell Renal Carcinoma
NCT07405086PHASE4RECRUITINGMorning Versus Afternoon Administration of Immunotherapy for the Treatment of Advanced or Metastatic Solid Tumors, The Knight SHIFT Study
NCT00171977PHASE4COMPLETEDPost-Marketing Clinical Study of Postoperative Adjuvant Therapy With Imatinib Mesylate in Patients With Gastrointestinal Stromal Tumors (GIST)
NCT00510354PHASE4COMPLETEDTreatment of Patients With Everolimus and Imatinib Mesylate Who Have Progressive Gastro Intestinal Stromal Tumors (GIST) and Are Resistant to Imatinib Mesylate
NCT00756509PHASE4COMPLETEDTreatment of Patients With Metastatic or Unresectable Gastrointestinal Stromal Tumors in First Line With Nilotinib
NCT02800330PHASE4COMPLETEDThe Effects of the Proton Pump Inhibitor Esomeprazole on the Bioavailability of Regorafenib
NCT04825574PHASE4COMPLETEDStudy for Patients Previously Treated in Avapritinib Clinical Trials
NCT00033904PHASE3COMPLETEDSurvival Study Of Oncophage® vs. Observation In Patients With Kidney Cancer
NCT00126178PHASE3TERMINATEDClinical Trial Studying a Personalized Cancer Vaccine in Patients With Non-metastatic Kidney Cancer
NCT00291369PHASE3COMPLETEDCytokines in Patients With Metastatic Renal Cell Carcinoma of Intermediate Prognosis
NCT00410124PHASE3COMPLETEDRAD001 Plus Best Supportive Care (BSC) Versus BSC Plus Placebo in Patients With Metastatic Carcinoma of the Kidney Which Has Progressed After Treatment With Sorafenib and/or Sunitinib
NCT00474786PHASE3COMPLETEDTemsirolimus Versus Sorafenib As Second-Line Therapy In Patients With Advanced RCC Who Have Failed First-Line Sunitinib
NCT00478114PHASE3COMPLETEDEfficacy and Safety of Sorafenib in Advanced Renal Cell Carcinoma (RCC)
NCT00606632PHASE3COMPLETEDPre-surgical Detection of Clear Cell Renal Cell Carcinoma (ccRCC) Using Radiolabeled G250-Antibody
NCT00606866PHASE3COMPLETEDMRI Study of BAY 43-9006 in Metastatic Renal Cell Carcinoma
NCT00631371PHASE3COMPLETEDStudy Comparing Bevacizumab + Temsirolimus vs. Bevacizumab + Interferon-Alfa In Advanced Renal Cell Carcinoma Subjects
NCT00732914PHASE3COMPLETEDSequential Study to Treat Renal Cell Carcinoma
NCT00869011PHASE3UNKNOWNExercise for Patients With Renal Cell Cancer Receiving Sunitinib
NCT00930033PHASE3COMPLETEDClinical Trial to Assess the Importance of Nephrectomy
NCT01030783PHASE3COMPLETEDA Study to Compare Tivozanib (AV-951) to Sorafenib in Subjects With Advanced Renal Cell Carcinoma
NCT01076010PHASE3COMPLETEDAn Extension Treatment Protocol for Subjects Who Have Participated in a Study of Tivozanib Versus Sorafenib in Kidney Carcinoma (Protocol AV-951-09-301).
NCT01198158PHASE3TERMINATEDEverolimus With or Without Bevacizumab in Treating Patients With Advanced Kidney Cancer That Progressed After First-Line Therapy
NCT01223027PHASE3COMPLETEDStudy of Dovitinib Versus Sorafenib in Patients With Metastatic Renal Cell Carcinoma
NCT01224288PHASE3ACTIVE_NOT_RECRUITINGDynamic Contrast Enhancement Computed Tomography for Evaluating Tumor Perfusion in Patients With Metastatic Renal Cell Carcinoma Receiving Targeted Therapies: Renal Cell Carcinoma (RCC) Scramble
NCT01235962PHASE3COMPLETEDA Study to Evaluate Pazopanib as an Adjuvant Treatment for Localized Renal Cell Carcinoma (RCC)
NCT01265810PHASE3COMPLETEDCaphosol in Oral Mucositis Due to Targeted Therapy
NCT01265901PHASE3COMPLETEDIMA901 in Patients Receiving Sunitinib for Advanced/Metastatic Renal Cell Carcinoma
NCT01481870PHASE3UNKNOWNComparison of Sequential Therapies With Sunitinib and Sorafenib in Advanced Renal Cell Carcinoma
NCT01582672PHASE3TERMINATEDPhase 3 Trial of Autologous Dendritic Cell Immunotherapy Plus Standard Treatment of Advanced Renal Cell Carcinoma
NCT01613846PHASE3COMPLETEDPhase III Sequential Open-label Study to Evaluate the Efficacy and Safety of Sorafenib Followed by Pazopanib Versus Pazopanib Followed by Sorafenib in the Treatment of Advanced / Metastatic Renal Cell Carcinoma (SWITCH-II)