Gene Details | GeDiPNet - Complete Gene Info, Disease Associations & Pathways

Gene Gene information from NCBI Gene database. Gene SNPs miRNA Transcription factors Gene ontology Other IDs Protein Pathways Associated diseases
Entrez ID	8050
Gene name	Pyruvate dehydrogenase complex component X
Gene symbol	PDHX
Synonyms (NCBI Gene)	DLDBPE3BPOPDXPDHXDPDX1proX
Chromosome	11
Chromosome location	11p13
Summary	The pyruvate dehydrogenase (PDH) complex is located in the mitochondrial matrix and catalyzes the conversion of pyruvate to acetyl coenzyme A. The PDH complex thereby links glycolysis to Krebs cycle. The PDH complex contains three catalytic subunits, E1,

Show/Hide all (14)

SNP ID	Visualize variation	Clinical significance	Consequence
rs35560997	G>C	Benign, likely-benign, uncertain-significance, conflicting-interpretations-of-pathogenicity	Coding sequence variant, intron variant, missense variant
rs113309941	C>G,T	Pathogenic	Missense variant, stop gained, coding sequence variant, intron variant
rs139052284	C>A,G	Conflicting-interpretations-of-pathogenicity, uncertain-significance	Coding sequence variant, intron variant, missense variant
rs143131258	C>T	Pathogenic	Coding sequence variant, stop gained, intron variant
rs146876119	C>T	Conflicting-interpretations-of-pathogenicity, uncertain-significance	Coding sequence variant, intron variant, missense variant
rs724159829	G>A	Pathogenic	Intron variant, splice donor variant
rs724159830	G>A	Pathogenic	Splice acceptor variant
rs724159979	C>-	Pathogenic	Coding sequence variant, intron variant, frameshift variant
rs745949756	A>G	Likely-pathogenic	Coding sequence variant, missense variant
rs776567343	->C	Pathogenic	Frameshift variant, coding sequence variant, intron variant
rs912318281	G>T	Pathogenic	Coding sequence variant, stop gained
rs1057518180	->A	Pathogenic	Intron variant, coding sequence variant, frameshift variant
rs1135402725	C>T	Pathogenic	Stop gained, coding sequence variant
rs1554989996	ATGACATTAAAGTATCAGTAAATGATTTTATCATCAAGGCAGCAGCTGTTACCCTTAAA>-	Pathogenic	Coding sequence variant, frameshift variant, intron variant

Show/Hide all (96)

miRTarBase ID	miRNA	Experiments	Reference
MIRT020386	hsa-miR-29c-3p	Sequencing	20371350
MIRT030260	hsa-miR-26b-5p	Microarray	19088304
MIRT032040	hsa-miR-16-5p	Proteomics	18668040
MIRT032478	hsa-let-7b-5p	Proteomics	18668040
MIRT051324	hsa-miR-15a-5p	CLASH	23622248
MIRT047246	hsa-miR-181b-5p	CLASH	23622248
MIRT044791	hsa-miR-320a	CLASH	23622248
MIRT041546	hsa-miR-193b-3p	CLASH	23622248
MIRT041176	hsa-miR-181d-5p	CLASH	23622248
MIRT471461	hsa-miR-128-3p	PAR-CLIP	23592263
MIRT471459	hsa-miR-3681-3p	PAR-CLIP	23592263
MIRT471458	hsa-miR-216a-3p	PAR-CLIP	23592263
MIRT471457	hsa-miR-27a-3p	PAR-CLIP	23592263
MIRT471456	hsa-miR-27b-3p	PAR-CLIP	23592263
MIRT471455	hsa-miR-410-3p	PAR-CLIP	23592263
MIRT471454	hsa-miR-190a-3p	PAR-CLIP	23592263
MIRT471453	hsa-miR-513a-5p	PAR-CLIP	23592263
MIRT471461	hsa-miR-128-3p	PAR-CLIP	23592263
MIRT471459	hsa-miR-3681-3p	PAR-CLIP	23592263
MIRT471458	hsa-miR-216a-3p	PAR-CLIP	23592263
MIRT471457	hsa-miR-27a-3p	PAR-CLIP	23592263
MIRT471456	hsa-miR-27b-3p	PAR-CLIP	23592263
MIRT471455	hsa-miR-410-3p	PAR-CLIP	23592263
MIRT471454	hsa-miR-190a-3p	PAR-CLIP	23592263
MIRT471453	hsa-miR-513a-5p	PAR-CLIP	23592263
MIRT1221364	hsa-miR-1297	CLIP-seq
MIRT1221365	hsa-miR-204	CLIP-seq
MIRT1221366	hsa-miR-211	CLIP-seq
MIRT1221367	hsa-miR-2278	CLIP-seq
MIRT1221368	hsa-miR-26a	CLIP-seq
MIRT1221369	hsa-miR-26b	CLIP-seq
MIRT1221370	hsa-miR-29a	CLIP-seq
MIRT1221371	hsa-miR-29b	CLIP-seq
MIRT1221372	hsa-miR-29c	CLIP-seq
MIRT1221373	hsa-miR-3065-3p	CLIP-seq
MIRT1221374	hsa-miR-3120-3p	CLIP-seq
MIRT1221375	hsa-miR-3938	CLIP-seq
MIRT1221376	hsa-miR-4465	CLIP-seq
MIRT1221377	hsa-miR-4519	CLIP-seq
MIRT1221378	hsa-miR-4755-5p	CLIP-seq
MIRT1221379	hsa-miR-4789-5p	CLIP-seq
MIRT1221380	hsa-miR-518d-5p	CLIP-seq
MIRT1221381	hsa-miR-519b-5p	CLIP-seq
MIRT1221382	hsa-miR-519c-5p	CLIP-seq
MIRT1221383	hsa-miR-520c-5p	CLIP-seq
MIRT1221384	hsa-miR-526a	CLIP-seq
MIRT1221385	hsa-miR-623	CLIP-seq
MIRT1221386	hsa-miR-889	CLIP-seq
MIRT1221364	hsa-miR-1297	CLIP-seq
MIRT1221365	hsa-miR-204	CLIP-seq
MIRT1221366	hsa-miR-211	CLIP-seq
MIRT1221367	hsa-miR-2278	CLIP-seq
MIRT1221368	hsa-miR-26a	CLIP-seq
MIRT1221369	hsa-miR-26b	CLIP-seq
MIRT1221387	hsa-miR-299-5p	CLIP-seq
MIRT1221370	hsa-miR-29a	CLIP-seq
MIRT1221371	hsa-miR-29b	CLIP-seq
MIRT1221372	hsa-miR-29c	CLIP-seq
MIRT1221373	hsa-miR-3065-3p	CLIP-seq
MIRT1221374	hsa-miR-3120-3p	CLIP-seq
MIRT1221388	hsa-miR-3200-5p	CLIP-seq
MIRT1221375	hsa-miR-3938	CLIP-seq
MIRT1221389	hsa-miR-421	CLIP-seq
MIRT1221390	hsa-miR-4257	CLIP-seq
MIRT1221376	hsa-miR-4465	CLIP-seq
MIRT1221377	hsa-miR-4519	CLIP-seq
MIRT1221391	hsa-miR-4682	CLIP-seq
MIRT1221392	hsa-miR-4694-3p	CLIP-seq
MIRT1221393	hsa-miR-4724-3p	CLIP-seq
MIRT1221378	hsa-miR-4755-5p	CLIP-seq
MIRT1221379	hsa-miR-4789-5p	CLIP-seq
MIRT1221394	hsa-miR-4803	CLIP-seq
MIRT1221380	hsa-miR-518d-5p	CLIP-seq
MIRT1221381	hsa-miR-519b-5p	CLIP-seq
MIRT1221382	hsa-miR-519c-5p	CLIP-seq
MIRT1221383	hsa-miR-520c-5p	CLIP-seq
MIRT1221395	hsa-miR-520f	CLIP-seq
MIRT1221384	hsa-miR-526a	CLIP-seq
MIRT1221396	hsa-miR-548c-3p	CLIP-seq
MIRT1221397	hsa-miR-582-5p	CLIP-seq
MIRT1221398	hsa-miR-584	CLIP-seq
MIRT1221385	hsa-miR-623	CLIP-seq
MIRT1221386	hsa-miR-889	CLIP-seq
MIRT1221399	hsa-miR-944	CLIP-seq
MIRT1552196	hsa-miR-3609	CLIP-seq
MIRT1552197	hsa-miR-548ah	CLIP-seq
MIRT1552198	hsa-miR-548n	CLIP-seq
MIRT1552199	hsa-miR-548t	CLIP-seq
MIRT2063890	hsa-miR-337-3p	CLIP-seq
MIRT2063891	hsa-miR-3685	CLIP-seq
MIRT2063892	hsa-miR-382	CLIP-seq
MIRT2063893	hsa-miR-384	CLIP-seq
MIRT2063894	hsa-miR-4436b-5p	CLIP-seq
MIRT2063895	hsa-miR-485-3p	CLIP-seq
MIRT2292395	hsa-miR-4795-3p	CLIP-seq
MIRT2063895	hsa-miR-485-3p	CLIP-seq

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Transcription factor	Regulation	Reference
PAX6	Repression	12783165

Show/Hide all (22)

GO ID	Ontology	Definition	Evidence	Reference
GO:0004742	Function	Dihydrolipoyllysine-residue acetyltransferase activity	IDA	9242632
GO:0005515	Function	Protein binding	IPI	16263718, 16442803, 21516116, 25416956, 25525879, 28514442, 31515488, 32296183, 33961781
GO:0005654	Component	Nucleoplasm	IDA
GO:0005739	Component	Mitochondrion	HTP	34800366
GO:0005739	Component	Mitochondrion	IBA
GO:0005739	Component	Mitochondrion	IDA
GO:0005739	Component	Mitochondrion	IEA
GO:0005739	Component	Mitochondrion	NAS	24534072
GO:0005759	Component	Mitochondrial matrix	IEA
GO:0005759	Component	Mitochondrial matrix	IEA
GO:0005759	Component	Mitochondrial matrix	TAS
GO:0005886	Component	Plasma membrane	IDA
GO:0006086	Process	Pyruvate decarboxylation to acetyl-CoA	IC	9242632
GO:0006086	Process	Pyruvate decarboxylation to acetyl-CoA	IDA	24534072
GO:0006086	Process	Pyruvate decarboxylation to acetyl-CoA	IEA
GO:0006086	Process	Pyruvate decarboxylation to acetyl-CoA	ISS
GO:0016746	Function	Acyltransferase activity	IEA
GO:0045254	Component	Pyruvate dehydrogenase complex	IBA
GO:0045254	Component	Pyruvate dehydrogenase complex	IDA	9242632, 25525879
GO:0045254	Component	Pyruvate dehydrogenase complex	IEA
GO:0045254	Component	Pyruvate dehydrogenase complex	IPI	19240034
GO:0045254	Component	Pyruvate dehydrogenase complex	ISS

MIM	HGNC	e!Ensembl
608769	21350	ENSG00000110435

O00330

Protein name

Pyruvate dehydrogenase protein X component, mitochondrial (Dihydrolipoamide dehydrogenase-binding protein of pyruvate dehydrogenase complex) (E3-binding protein) (E3BP) (Lipoyl-containing pyruvate dehydrogenase complex component X) (proX)

Protein function

Required for anchoring dihydrolipoamide dehydrogenase (E3) to the dihydrolipoamide transacetylase (E2) core of the pyruvate dehydrogenase complexes of eukaryotes. This specific binding is essential for a functional PDH complex.

PDB

1ZY8 , 2DNC , 2F5Z , 2F60 , 6H60

Family and domains

Pfam

Accession	ID	Position in sequence	Description	Type
PF00364	Biotin_lipoyl	57 → 131	Biotin-requiring enzyme	Domain
PF02817	E3_binding	182 → 217	e3 binding domain	Family
PF00198	2-oxoacid_dh	272 → 501	2-oxoacid dehydrogenases acyltransferase (catalytic domain)	Domain

Sequence

MAASWRLGCDPRLLRYLVGFPGRRSVGLVKGALGWSVSRGANWRWFHSTQWLRGDPIKIL
MPSLSPTMEEGNIVKWLKKEGEAVSAGDALCEIETDKAVVTLDASDDGILAKIVVEEGSK
NIRLGSLIGLIVEEGEDWKHVEIPKDVGPPPPVSKPSEPRPSPEPQISIPVKKEHIPGTL
RFRLSPAARNILEKHSLDASQGTATGPRGIFTKEDALKLVQLKQTGKITESRPTPAPTAT
PTAPSPLQATAGPSYPRPVIPPVSTPGQPNAVGTFTEIPASNIRRVIAKRLTESKSTVPH
AYATADCDLGAVLKVRQDLVKDDIKVSVNDFIIKAAAVTLKQMPDVNVSWDGEGPKQLPF
IDISVAVATDKGLLTPIIKDAAAKGIQEIADSVKALSKKARDGKLLPEEYQGGSFSISNL
GMFGIDEFTAVINPPQACILAVGRFRPVLKLTEDEEGNAKLQQRQLITVTMSSDSRVVDD
ELATRFLKSFKANLENPIRLA

Sequence length

501

Interactions

View interactions

	KEGG		Reactome
	Metabolic pathways		Regulation of pyruvate dehydrogenase (PDH) complex Glyoxylate metabolism and glycine degradation Signaling by Retinoic Acid Pyruvate metabolism

167

Show/Hide Causal Diseases (2)

Phenotype Name	Clinical Significance	dbSNP ID	RCV Accession
Causal Diseases associated with Pathogenic or Likely Pathogenic variants in ClinVar
Pyruvate dehydrogenase E1-alpha deficiency	Likely pathogenic	rs1158194122	RCV000721986
Pyruvate dehydrogenase E3-binding protein deficiency	Likely pathogenic; Pathogenic	rs766377898, rs1554989996, rs724159828, rs724159829, rs724159830, rs724159979, rs113309941, rs1135402725, rs758020436, rs2494708862, rs2494744424, rs763473883, rs756985515, rs11539201, rs1057518180 View all (4 more)	RCV005225436 RCV000002193 RCV000002194 RCV000002195 RCV000002196 RCV000002197 RCV000002199 RCV000149582 RCV004526962 RCV002810036 RCV003148160 RCV003227587 RCV004765920 RCV003986041 RCV001782890 RCV000762841 RCV001782961 RCV005603666 RCV001197626

Show/Hide Unknown Diseases (16)

Phenotype Name	Clinical Significance	dbSNP ID	RCV Accession
Unknown Diseases with uncertain, conflicting, or no pathogenic evidence in ClinVar
Cervical cancer	Likely benign	rs114136993	RCV005915994
Cholangiocarcinoma	Benign	rs59918794	RCV005892967
Colon adenocarcinoma	Benign	rs563029223	RCV005868231
Colorectal cancer	Uncertain significance	rs146456454	RCV005895578
Familial cancer of breast	Benign	rs563029223	RCV005868230
Gastric cancer	Benign	rs563029223	RCV005868233
Hepatocellular carcinoma	Benign	rs733567	RCV005905844
Malignant tumor of esophagus	Benign	rs563029223	RCV005868232
Mitochondrial disease	Uncertain significance	rs147958676	RCV005370143
Nonpapillary renal cell carcinoma	Benign	rs59918794	RCV005892966
Ovarian serous cystadenocarcinoma	Likely benign; Uncertain significance	rs114136993, rs555691861	RCV005915995 RCV005892969
PDHX-related disorder	Likely benign; Benign; Conflicting classifications of pathogenicity	rs1397269544, rs78878052, rs34582941, rs36047324, rs35560997, rs765182974, rs200438675, rs118136428, rs151049569, rs148758785, rs199583315	RCV003921039 RCV003975125 RCV003975126 RCV004757963 RCV003925258 RCV003940151 RCV003910117 RCV003957573 RCV003970119 RCV004758034 RCV003950791
Pyruvate dehydrogenase complex deficiency	Uncertain significance; Benign	rs780153979, rs371074122	RCV000302285 RCV000362815
Thymoma	Uncertain significance	rs886048250	RCV005892970
Uterine carcinosarcoma	Benign	rs733567	RCV005905845
Uterine corpus endometrial carcinoma	Benign	rs59918794	RCV005892968

Show/Hide Text Mining Associations (18)

Disease Name	Relationship Type	References
Associations from Text MiningDisease associations identified through Pubtator
Acidosis	Associate	25087164
Acidosis Lactic	Associate	25087164
Alcohol Related Disorders	Associate	35076175
Brain Diseases	Associate	20002125
Breast Neoplasms	Associate	30012170
Cancer Pain	Associate	21194677
Cerebral Palsy	Associate	35076175
Colorectal Neoplasms	Associate	24935220
Developmental Disabilities	Associate	33092611
Esophageal Neoplasms	Associate	36889194
Gaucher Disease	Associate	26027833
Genetic Diseases Inborn	Associate	35076175
Inflammation	Associate	21194677
Intellectual Disability	Associate	25087164
Leigh Disease	Associate	30981218
Lupus Erythematosus Systemic	Associate	21194677
Pyruvate Dehydrogenase Complex Deficiency Disease	Associate	16904023, 20002125, 33092611, 40225937
Stomach Neoplasms	Associate	37800836

PDHX (pyruvate dehydrogenase complex component X)