KGD4

gene
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Also known as DC47MRP-S36

Summary

KGD4 (alpha-ketoglutarate dehydrogenase subunit 4, HGNC:16631) is a protein-coding gene on chromosome 5q13.2, encoding Alpha-ketoglutarate dehydrogenase component 4 (P82909). Molecular adapter that is necessary to form a stable 2-oxoglutarate dehydrogenase enzyme complex (OGDHC). It is a selective cancer dependency (DepMap: 12.9% of cell lines).

Mammalian mitochondrial ribosomal proteins are encoded by nuclear genes and help in protein synthesis within the mitochondrion. The mitochondrial ribosome (mitoribosome) consists of a small 28S subunit and a large 39S subunit. They have an estimated 75% protein to rRNA composition compared to prokaryotic ribosomes, where this ratio is reversed. Another difference between mammalian mitoribosomes and prokaryotic ribosomes is that the latter contain a 5S rRNA. Among different species, the proteins comprising the mitoribosome differ greatly in sequence, and sometimes in biochemical properties, which prevents easy recognition by sequence homology. This gene encodes a 28S subunit protein. Pseudogenes corresponding to this gene are found on chromosomes 3p, 4q, 8p, 11q, 12q, and 20p.

Source: NCBI Gene 92259 — RefSeq curated summary.

At a glance

  • Gene–disease (curated): Leigh syndrome (Limited, GenCC)
  • Clinical variants (ClinVar): 19 total — 1 pathogenic, 1 likely-pathogenic
  • Cancer dependency (DepMap): dependent in 12.9% of screened cell lines
  • MANE Select transcript: NM_033281

Identifiers

Gene identifiers

FieldValue
HGNC IDHGNC:16631
Approved symbolKGD4
Namealpha-ketoglutarate dehydrogenase subunit 4
Location5q13.2
Locus typegene with protein product
StatusApproved
AliasesDC47, MRP-S36
Ensembl geneENSG00000134056
Ensembl biotypeprotein_coding
OMIM611996
Entrez92259

Gene structure

Transcript identifiers

Ensembl transcripts: 6 — 4 protein_coding, 2 protein_coding_CDS_not_defined

ENST00000256441, ENST00000503793, ENST00000507022, ENST00000512880, ENST00000602380, ENST00000932836

RefSeq mRNA: 1 — MANE Select: NM_033281 NM_033281

CCDS: CCDS34174

Canonical transcript exons

ENST00000256441 — 4 exons

ExonStartEnd
ENSE000010085096922920869230158
ENSE000020350586921776069217871
ENSE000035085546922820069228387
ENSE000035788886922633869226401

Expression profiles

Bgee: expression breadth ubiquitous, 139 present calls, max score 96.83.

FANTOM5 (CAGE): breadth ubiquitous, TPM avg 27.0454 / max 221.5980, expressed in 1817 samples.

FANTOM5 promoters (2 alternative TSS)

Promoter IDTPM avgSamples expressed
5683819.19361813
568397.85181748

Top tissues by expression

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

TissueAnatomy IDExpression scoreQuality
apex of heartUBERON:000209896.83gold quality
heart left ventricleUBERON:000208496.79gold quality
hindlimb stylopod muscleUBERON:000425296.39gold quality
heartUBERON:000094895.55gold quality
right atrium auricular regionUBERON:000663195.25gold quality
mucosa of transverse colonUBERON:000499194.69gold quality
gastrocnemiusUBERON:000138894.32gold quality
adult mammalian kidneyUBERON:000008294.19gold quality
muscle of legUBERON:000138394.11gold quality
skeletal muscle organUBERON:001489294.07gold quality
skeletal muscle tissueUBERON:000113493.08gold quality
kidneyUBERON:000211392.92gold quality
primary visual cortexUBERON:000243692.54gold quality
lower esophagus mucosaUBERON:003583492.42gold quality
prefrontal cortexUBERON:000045192.28gold quality
cortex of kidneyUBERON:000122592.19gold quality
transverse colonUBERON:000115792.01gold quality
endometriumUBERON:000129591.99gold quality
rectumUBERON:000105291.70gold quality
islet of LangerhansUBERON:000000691.67gold quality
muscle tissueUBERON:000238591.55gold quality
right lobe of liverUBERON:000111491.49gold quality
nucleus accumbensUBERON:000188291.36gold quality
anterior cingulate cortexUBERON:000983591.28gold quality
metanephros cortexUBERON:001053391.28gold quality
colonUBERON:000115591.21gold quality
adrenal tissueUBERON:001830391.21gold quality
duodenumUBERON:000211491.15gold quality
dorsolateral prefrontal cortexUBERON:000983491.12gold quality
substantia nigraUBERON:000203891.11gold quality

Single-cell (SCXA)

Detected in 3 experiment(s), a significant marker in 1.

ExperimentMarker?Max mean expression
E-ANND-3yes17.45
E-CURD-10no317.50
E-MTAB-6524no174.32

Regulation

Is transcription factor: no

miRNA regulators (miRDB)

64 targeting KGD4, 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-3925-3P100.0069.951237
HSA-MIR-607799.9968.042299
HSA-MIR-569699.9872.364487
HSA-MIR-1250-3P99.9670.044038
HSA-MIR-55999.9572.283609
HSA-MIR-548AB99.9571.313488
HSA-MIR-548A-5P99.9471.273482
HSA-MIR-548AD-5P99.9471.233502
HSA-MIR-548AE-5P99.9471.233502
HSA-MIR-548AK99.9471.243488
HSA-MIR-548AM-5P99.9471.243488
HSA-MIR-548AP-5P99.9471.143489
HSA-MIR-548AR-5P99.9471.283515
HSA-MIR-548AS-5P99.9471.223482
HSA-MIR-548AU-5P99.9471.243488
HSA-MIR-548AY-5P99.9471.233502
HSA-MIR-548B-5P99.9471.233502
HSA-MIR-548BB-5P99.9471.273509
HSA-MIR-548C-5P99.9471.243488
HSA-MIR-548D-5P99.9471.233502
HSA-MIR-548H-5P99.9471.243488
HSA-MIR-548I99.9471.253481
HSA-MIR-548J-5P99.9471.143489
HSA-MIR-548O-5P99.9471.243488
HSA-MIR-548W99.9471.243488
HSA-MIR-548Y99.9471.283514
HSA-MIR-548AQ-5P99.9471.343426
HSA-MIR-335-3P99.9373.364958
HSA-MIR-205-3P99.9269.923165
HSA-MIR-153-5P99.8973.866317

Functional genomics

DepMap (CRISPR cell-line fitness): dependent in 12.9% of screened cell lines.

Cross-species orthologs

4 orthologs

OrganismSymbolGene ID
danio_reriokgd4ENSDARG00000079823
mus_musculusMrps36ENSMUSG00000061474
rattus_norvegicusAC132020.1ENSRNOG00000017757
rattus_norvegicusKgd4ENSRNOG00000061213

Protein

Protein identifiers

Alpha-ketoglutarate dehydrogenase component 4P82909 (reviewed: P82909)

Alternative names: Alpha-ketoglutarate dehydrogenase subunit 4

All UniProt accessions (2): D6R941, P82909

UniProt curated annotations — full annotation on UniProt →

Function. Molecular adapter that is necessary to form a stable 2-oxoglutarate dehydrogenase enzyme complex (OGDHC). Enables the specific recruitment of E3 subunit to E2 subunit in the 2-oxoglutarate dehydrogenase complex (OGDHC).

Subunit / interactions. Component of the 2-oxoglutarate dehydrogenase complex (OGDHC), composed of OGDH (2-oxoglutarate dehydrogenase; also called E1 subunit), DLST (dihydrolipoamide succinyltransferase; also called E2 subunit) and DLD (dihydrolipoamide dehydrogenase; also called E3 subunit), and the assembly factor KGD4. Within OGDHC complex, interacts (via N-terminus) with E3 subunit and (via C-terminus) with E2 subunit.

Subcellular location. Mitochondrion.

Similarity. Belongs to the alpha-ketoglutarate dehydrogenase component 4 family.

RefSeq proteins (1): NP_150597* (*=MANE)

Domains & families (InterPro)

IDNameType
IPR020373Kgd4/YMR-31Family

UniProt features (8 total): modified residue 5, chain 1, region of interest 1, compositionally biased region 1

Structure

Experimental structures (PDB)

0 structures.

Predicted structure (AlphaFold)

ModelpLDDTFraction very-high
AF-P82909-F174.790.21

Functional residue map

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

Post-translational modifications (5): 1, 5, 49, 61, 90

Function

Pathways and Gene Ontology

Reactome pathways

14 pathways

IDPathway
R-HSA-5368286Mitochondrial translation initiation
R-HSA-5389840Mitochondrial translation elongation
R-HSA-5419276Mitochondrial translation termination
R-HSA-6783984Glycine degradation
R-HSA-9853506OGDH complex synthesizes succinyl-CoA from 2-OG
R-HSA-9937383Mitochondrial ribosome-associated quality control
R-HSA-1428517Aerobic respiration and respiratory electron transport
R-HSA-1430728Metabolism
R-HSA-389661Glyoxylate metabolism and glycine degradation
R-HSA-392499Metabolism of proteins
R-HSA-5368287Mitochondrial translation
R-HSA-71291Metabolism of amino acids and derivatives
R-HSA-71403Citric acid cycle (TCA cycle)
R-HSA-72766Translation

MSigDB gene sets: 125 (showing top): IVANOVA_HEMATOPOIESIS_LATE_PROGENITOR, LINDGREN_BLADDER_CANCER_CLUSTER_3_DN, GOBP_DICARBOXYLIC_ACID_METABOLIC_PROCESS, GOBP_GENERATION_OF_PRECURSOR_METABOLITES_AND_ENERGY, WEI_MYCN_TARGETS_WITH_E_BOX, MODULE_331, GOCC_MITOCHONDRIAL_ENVELOPE, GOBP_ORGANIC_ACID_METABOLIC_PROCESS, WONG_MITOCHONDRIA_GENE_MODULE, GOBP_CELLULAR_RESPIRATION, GOBP_2_OXOGLUTARATE_METABOLIC_PROCESS, GOCC_OXIDOREDUCTASE_COMPLEX, GOCC_TRANSFERASE_COMPLEX, GOCC_ORGANELLE_INNER_MEMBRANE, GOCC_TRICARBOXYLIC_ACID_CYCLE_HETEROMERIC_ENZYME_COMPLEX

GO Biological Process (2): tricarboxylic acid cycle (GO:0006099), 2-oxoglutarate metabolic process (GO:0006103)

GO Molecular Function (1): protein-macromolecule adaptor activity (GO:0030674)

GO Cellular Component (3): mitochondrion (GO:0005739), mitochondrial inner membrane (GO:0005743), oxoglutarate dehydrogenase complex (GO:0045252)

Reactome top-level categories

Rollup of top-8 pathways:

CategoryPathways
Mitochondrial translation4
Metabolism2
Glyoxylate metabolism and glycine degradation1
Citric acid cycle (TCA cycle)1
Metabolism of amino acids and derivatives1
Translation1
Aerobic respiration and respiratory electron transport1
Metabolism of proteins1

GO top-level categories

Rollup of top GO terms by namespace:

CategoryTerms
aerobic respiration1
primary metabolic process1
dicarboxylic acid metabolic process1
protein binding1
molecular adaptor activity1
cytoplasm1
intracellular membrane-bounded organelle1
organelle inner membrane1
mitochondrial membrane1
tricarboxylic acid cycle heteromeric enzyme complex1
alpha-ketoacid dehydrogenase complex1
transferase complex1

Protein interactions and networks

STRING

890 interactions, top by confidence (×1000):

Protein AProtein BPartner UniProtScore
KGD4MRPL42Q9Y6G3630
KGD4MTIF3Q9H2K0543
KGD4PTCD3Q96EY7534
KGD4MRPL33O75394521
KGD4MRPL16Q9NX20492
KGD4DAP3P51398466
KGD4MRPL52Q86TS9457
KGD4MRPS27Q92552444
KGD4GADD45GIP1Q8TAE8443
KGD4MRPS15P82914436
KGD4MRPL41Q8IXM3422
KGD4MRPS35P82673417
KGD4SNX30Q5VWJ9400
KGD4MSANTD4Q8NCY6398
KGD4PDHXO00330396

IntAct

40 interactions, top by confidence:

ABTypeScore
DLDPDHXpsi-mi:“MI:0914”(association)0.880
KGD4DLDpsi-mi:“MI:0914”(association)0.640
COLGALT2COL1A1psi-mi:“MI:0914”(association)0.530
HMGCLDBTpsi-mi:“MI:0914”(association)0.530
ISXMOCS3psi-mi:“MI:0914”(association)0.530
Hdac6TDGpsi-mi:“MI:0914”(association)0.350
HDAC6GLOD5psi-mi:“MI:0914”(association)0.350
HSCBRBP5psi-mi:“MI:0914”(association)0.350
ORF70PDHXpsi-mi:“MI:0914”(association)0.350
ABHD11NME4psi-mi:“MI:0914”(association)0.350
CEP135MCRIP1psi-mi:“MI:0914”(association)0.350
POC5PDHXpsi-mi:“MI:0914”(association)0.350
CEP135WWP2psi-mi:“MI:0914”(association)0.350
CEP135WDR91psi-mi:“MI:0914”(association)0.350
CHD8IGLV4-60psi-mi:“MI:0914”(association)0.350
CAPZBENAHpsi-mi:“MI:0914”(association)0.350
POLR2BPALM3psi-mi:“MI:0914”(association)0.350
POLR2KBDP1psi-mi:“MI:0914”(association)0.350
TCAIMKGD4psi-mi:“MI:0914”(association)0.350
THEM5GTPBP10psi-mi:“MI:0914”(association)0.350
COLGALT2PLOD2psi-mi:“MI:0914”(association)0.350
KGD4SPTBN2psi-mi:“MI:0914”(association)0.350
SIAH1SIAH2psi-mi:“MI:0914”(association)0.350
ESRRGTTRpsi-mi:“MI:0914”(association)0.350
OGDHLTMSB4Xpsi-mi:“MI:0914”(association)0.350
RAD23APIK3C2Apsi-mi:“MI:0914”(association)0.350
TRMT61BPRORPpsi-mi:“MI:0914”(association)0.350

BioGRID (133): MRPS36 (Affinity Capture-MS), MRPS36 (Co-fractionation), MRPS36 (Affinity Capture-MS), MRPS36 (Affinity Capture-MS), MRPS36 (Affinity Capture-MS), MRPS36 (Affinity Capture-MS), MRPS36 (Affinity Capture-MS), MRPS36 (Affinity Capture-MS), MRPS36 (Affinity Capture-MS), MRPS36 (Proximity Label-MS), MRPS36 (Proximity Label-MS), MRPS36 (Proximity Label-MS), MRPS36 (Proximity Label-MS), MRPS36 (Proximity Label-MS), MRPS36 (Proximity Label-MS)

ESM2 similar proteins: A0A7P0TBJ1, A4IG66, A8E4M4, A9JSQ8, B0BN72, C9JLW8, E1C760, O75182, P82909, P97578, Q02225, Q0P4B9, Q13541, Q1JPG0, Q28C41, Q32LE2, Q3MHI4, Q3UGS4, Q3ULM0, Q4QQM5, Q4V8E4, Q504E7, Q5BLE2, Q5DTY9, Q5U465, Q5VSY0, Q5XIG5, Q5XJS0, Q5ZIU1, Q62141, Q63068, Q68DU8, Q6GR21, Q6IEG0, Q6PCG6, Q6TYB5, Q7L4E1, Q8AVJ1, Q8BK03, Q8C6E0

Diamond homologs: P82908, P82909, Q9CQX8

SIGNOR signaling

0 interactions.

Disease & clinical

Clinical variants and AI predictions

ClinVar

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

ClassificationCount (floor)
Pathogenic1
Likely pathogenic1
Uncertain significance10
Likely benign0
Benign0

Top pathogenic / likely-pathogenic (2)

Variant IDHGVSClassification
3909971NM_033281.6(KGD4):c.42+1G>APathogenic
3909972NM_033281.6(KGD4):c.296G>C (p.Arg99Pro)Likely pathogenic

SpliceAI

321 predictions. Top by Δscore:

VariantEffectΔscore
5:69226337:GGTA:Gacceptor_gain1.0000
5:69228192:A:AGacceptor_gain1.0000
5:69228193:A:AGacceptor_gain1.0000
5:69228198:A:AGacceptor_gain1.0000
5:69228199:G:GAacceptor_gain1.0000
5:69228199:GT:Gacceptor_gain1.0000
5:69228199:GTA:Gacceptor_gain1.0000
5:69228199:GTAT:Gacceptor_gain1.0000
5:69228199:GTATC:Gacceptor_gain1.0000
5:69228266:G:GTdonor_gain1.0000
5:69228387:AGTA:Adonor_loss1.0000
5:69228388:G:Cdonor_loss1.0000
5:69228388:G:GGdonor_gain1.0000
5:69228389:T:Gdonor_loss1.0000
5:69229205:CA:Cacceptor_loss1.0000
5:69229206:A:AGacceptor_gain1.0000
5:69229206:A:Tacceptor_loss1.0000
5:69229206:AGCGT:Aacceptor_gain1.0000
5:69229207:G:GCacceptor_gain1.0000
5:69229207:GC:Gacceptor_gain1.0000
5:69229207:GCGT:Gacceptor_gain1.0000
5:69229207:GCGTG:Gacceptor_gain1.0000
5:69218431:G:GGdonor_gain0.9900
5:69226333:TTTA:Tacceptor_loss0.9900
5:69226335:TAGGT:Tacceptor_loss0.9900
5:69226336:A:Gacceptor_loss0.9900
5:69226337:G:GAacceptor_loss0.9900
5:69226337:GGT:Gacceptor_gain0.9900
5:69226397:CAATG:Cdonor_gain0.9900
5:69226398:AATGG:Adonor_loss0.9900

AlphaMissense

666 scored. Top likely-pathogenic:

VariantProtein changeam_pathogenicity
5:69228351:G:CR86S0.997
5:69228351:G:TR86S0.997
5:69226368:T:CF25L0.996
5:69226370:T:AF25L0.996
5:69226370:T:GF25L0.996
5:69228350:G:CR86T0.996
5:69226369:T:CF25S0.995
5:69226363:T:CI23T0.994
5:69226369:T:GF25C0.992
5:69228383:T:AI97N0.992
5:69228350:G:TR86M0.990
5:69229209:G:CR99P0.990
5:69229214:G:CG101R0.988
5:69228383:T:GI97S0.987
5:69229211:G:AG100R0.987
5:69229211:G:CG100R0.987
5:69229215:G:AG101D0.987
5:69226342:T:AV16D0.986
5:69226379:A:CR28S0.986
5:69226379:A:TR28S0.986
5:69229212:G:AG100E0.986
5:69226363:T:AI23K0.985
5:69217862:G:CR11S0.984
5:69217862:G:TR11S0.984
5:69228383:T:CI97T0.984
5:69226368:T:GF25V0.981
5:69229212:G:TG100V0.981
5:69217855:C:AA9D0.980
5:69228349:A:GR86G0.979
5:69217861:G:TR11M0.978

dbSNP variants (sampled 300 via entrez): RS1000109357 (5:69223982 A>G), RS1000388209 (5:69217742 T>A,C), RS1000723205 (5:69216342 C>A), RS1000922904 (5:69222048 A>G), RS1001414494 (5:69219600 A>G), RS1001509982 (5:69218113 T>C), RS1001878102 (5:69217079 G>A,C,T), RS1002169367 (5:69226011 A>G), RS1002452662 (5:69227206 G>C), RS1002478839 (5:69219363 T>C), RS1003189804 (5:69216102 C>A), RS1003243908 (5:69216474 T>G), RS1003454794 (5:69220907 A>T), RS1003781970 (5:69222189 A>G), RS1003796759 (5:69224540 C>G)

Disease associations

OMIM: gene MIM:611996 | disease phenotypes: MIM:256000

GenCC curated gene-disease

DiseaseClassificationInheritance
Leigh syndromeLimitedAutosomal recessive

Mondo (1): Leigh syndrome (MONDO:0009723)

Orphanet (1): Leigh syndrome (Orphanet:506)

HPO phenotypes

0 total (0 of 0 shown, HPO-id order):

GWAS associations

0 associations (top):

MeSH disease descriptors (1)

DescriptorNameTree numbers
D007888Leigh DiseaseC10.228.140.163.100.412; C16.320.565.189.412; C16.320.565.202.810.444; C18.452.132.100.412; C18.452.648.189.412; C18.452.648.202.810.444; C18.452.660.520

Drugs & pharmacology

Drug and pharmacology data

Is drug target: no

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

CTD chemical–gene interactions

18 total (human), top 18 by PubMed support.

ChemicalActions (top 5)PubMed papers
Acetaminophendecreases expression2
FR900359increases phosphorylation1
dicrotophosdecreases expression1
sodium arsenitedecreases expression1
perfluorooctanoic acidincreases expression1
potassium chromate(VI)decreases expression1
jinfukangdecreases expression1
Sunitinibdecreases expression1
Benzo(a)pyreneincreases methylation1
Caffeinedecreases phosphorylation1
Cisplatinincreases expression1
Ivermectindecreases expression1
Lipopolysaccharidesdecreases expression1
Smokedecreases expression1
Zincdecreases expression1
Sodium Seleniteincreases expression1
Copper Sulfatedecreases expression, increases expression1
Lactic Aciddecreases expression1

Clinical trials (associated diseases)

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

TrialPhaseStatusTitle
NCT01721733PHASE2COMPLETEDSafety and Efficacy Study of EPI-743 in Children With Leigh Syndrome
NCT02352896PHASE2COMPLETEDLong-Term Safety and Efficacy Evaluation of EPI-743 in Children With Leigh Syndrome
NCT03747328PHASE2WITHDRAWNABI-009 (Nab-sirolimus) in Patients With Genetically-confirmed Leigh or Leigh-like Syndrome
NCT06843811PHASE2ENROLLING_BY_INVITATIONSirolimus for Leigh Syndrome
NCT06990984PHASE2NOT_YET_RECRUITINGA Dose-ranging Study of TTI-0102 in Adults and Children With Leigh Syndrome Spectrum (LSS)
NCT02544217PHASE1COMPLETEDA Dose-escalating Clinical Trial With KH176
NCT04378075PHASE2/PHASE3TERMINATEDA Study to Evaluate Efficacy and Safety of Vatiquinone for Treating Mitochondrial Disease in Participants With Refractory Epilepsy
NCT01780168Not specifiedRECRUITINGThe NIH MINI Study: Metabolism, Infection, and Immunity in Inborn Errors of Metabolism
NCT01793168Not specifiedRECRUITINGRare Disease Patient Registry & Natural History Study - Coordination of Rare Diseases at Sanford
NCT01803906Not specifiedENROLLING_BY_INVITATIONTissue Sample Study for Mitochondrial Disorders
NCT03137355Not specifiedRECRUITINGThe International Registry for Leigh Syndrome
NCT05277363Not specifiedWITHDRAWNA Study of the Natural Course of SURF1 Deficiency
NCT05554835Not specifiedRECRUITINGGlobal Registry and Natural History Study for Mitochondrial Disorders
NCT06967831Not specifiedRECRUITINGDrug Repurposing for Mitochondrial Disorders Using iPSCs Derived Neural Cells
  • Associated diseases: Leigh syndrome
  • Disease cohort memberships (association, not causation — diseases whose associated-gene cohort lists this gene; a subset are also under Associated diseases): Leigh syndrome