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

Gene Gene SNPs miRNA Transcription factors Gene ontology Other IDs Protein Pathways Associated diseases
Entrez ID Entrez Gene ID - the GENE ID in NCBI Gene database.	5091
Gene name Gene Name - the full gene name approved by the HGNC.	Pyruvate carboxylase
Gene symbol Gene Symbol - the official gene symbol approved by the HGNC.	PC
Synonyms (NCBI Gene) Gene synonyms aliases	PCB
Chromosome Chromosome number	11
Chromosome location Chromosomal Location - indicates the cytogenetic location of the gene or region on the chromosome.	11q13.2
Summary Summary of gene provided in NCBI Entrez Gene.	This gene encodes pyruvate carboxylase, which requires biotin and ATP to catalyse the carboxylation of pyruvate to oxaloacetate. The active enzyme is a homotetramer arranged in a tetrahedron which is located exclusively in the mitochondrial matrix. Pyruva

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SNP ID	Visualize variation	Clinical significance	Consequence
rs2229745	G>A	Benign, conflicting-interpretations-of-pathogenicity	Synonymous variant, coding sequence variant
rs28940589	C>T	Pathogenic	Coding sequence variant, missense variant
rs28940590	C>A	Pathogenic	Coding sequence variant, missense variant
rs28940591	A>C,G	Pathogenic	Coding sequence variant, missense variant, genic upstream transcript variant
rs113994141	G>A	Pathogenic	Genic upstream transcript variant, coding sequence variant, missense variant
rs113994142	A>C,G,T	Uncertain-significance, pathogenic, likely-pathogenic	Genic upstream transcript variant, coding sequence variant, missense variant
rs113994143	G>A	Pathogenic	Genic upstream transcript variant, coding sequence variant, missense variant
rs113994144	T>C,G	Pathogenic	Missense variant, coding sequence variant
rs113994145	C>T	Pathogenic, pathogenic-likely-pathogenic	Missense variant, coding sequence variant
rs113994146	G>T	Pathogenic	Coding sequence variant, stop gained
rs113994147	G>A	Pathogenic	Missense variant, coding sequence variant
rs113994148	AG>-	Pathogenic	Frameshift variant, coding sequence variant
rs119103242	C>A,T	Pathogenic	Coding sequence variant, missense variant
rs144583275	G>A,T	Likely-pathogenic, benign, uncertain-significance	Coding sequence variant, stop gained, genic upstream transcript variant, synonymous variant
rs200030109	C>A	Uncertain-significance, likely-pathogenic	Coding sequence variant, missense variant, genic upstream transcript variant
rs568925019	C>T	Likely-pathogenic	Coding sequence variant, missense variant
rs748620956	GCCC>-	Uncertain-significance, conflicting-interpretations-of-pathogenicity	Intron variant, genic upstream transcript variant
rs755640269	C>A,T	Likely-pathogenic	Splice donor variant, genic upstream transcript variant
rs756355930	AC>-	Pathogenic	Coding sequence variant, frameshift variant
rs760108147	C>A,T	Likely-pathogenic	Missense variant, coding sequence variant
rs763433647	A>G	Likely-pathogenic	Splice donor variant, genic upstream transcript variant
rs768514713	G>A,C	Pathogenic	Coding sequence variant, stop gained, genic upstream transcript variant, missense variant
rs769177104	C>T	Likely-pathogenic, conflicting-interpretations-of-pathogenicity	Coding sequence variant, genic upstream transcript variant, missense variant
rs796052029	C>T	Likely-pathogenic	Missense variant, coding sequence variant
rs796052030	G>A,T	Pathogenic	Missense variant, coding sequence variant, genic upstream transcript variant
rs796052032	G>A	Uncertain-significance, likely-pathogenic	Missense variant, coding sequence variant
rs928225163	G>A,C	Pathogenic	Genic upstream transcript variant, coding sequence variant, missense variant
rs1057520687	A>G	Uncertain-significance, likely-pathogenic	Genic upstream transcript variant, coding sequence variant, missense variant
rs1057524862	C>T	Likely-pathogenic	Genic upstream transcript variant, coding sequence variant, missense variant
rs1064796030	T>-	Likely-pathogenic	Genic upstream transcript variant, coding sequence variant, frameshift variant
rs1555013840	->ATCA	Likely-pathogenic	Coding sequence variant, frameshift variant
rs1555014332	AC>T	Likely-pathogenic	Coding sequence variant, frameshift variant
rs1555014957	C>A	Pathogenic	Coding sequence variant, missense variant
rs1555025823	C>T	Likely-pathogenic	Splice donor variant, genic upstream transcript variant
rs1565209327	->A	Pathogenic	Coding sequence variant, frameshift variant
rs1565245427	GCTC>-	Pathogenic	Coding sequence variant, frameshift variant, genic upstream transcript variant
rs1591117575	T>A	Pathogenic	Coding sequence variant, missense variant
rs1591186383	T>C	Likely-pathogenic	Genic upstream transcript variant, coding sequence variant, missense variant

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miRTarBase ID	miRNA	Experiments	Reference
MIRT017539	hsa-miR-335-5p	Microarray	18185580
MIRT045724	hsa-miR-125a-5p	CLASH	23622248
MIRT1216229	hsa-miR-1909	CLIP-seq
MIRT1216230	hsa-miR-3153	CLIP-seq
MIRT2062453	hsa-miR-1538	CLIP-seq
MIRT2062454	hsa-miR-3667-3p	CLIP-seq
MIRT2062455	hsa-miR-4297	CLIP-seq
MIRT2062456	hsa-miR-4745-3p	CLIP-seq
MIRT2290881	hsa-miR-31	CLIP-seq

Transcription factors

Show/Hide all(2)

Transcription factor	Regulation	Reference
AR	Activation	18497079
MAFA	Activation	17149590

Show/Hide all(36)

GO ID	Ontology	Definition	Evidence	Reference
GO:0000166	Function	Nucleotide binding	IEA
GO:0003824	Function	Catalytic activity	IEA
GO:0004736	Function	Pyruvate carboxylase activity	EXP	12437512
GO:0004736	Function	Pyruvate carboxylase activity	IBA
GO:0004736	Function	Pyruvate carboxylase activity	IEA
GO:0004736	Function	Pyruvate carboxylase activity	IMP	9585002
GO:0004736	Function	Pyruvate carboxylase activity	TAS	7918683
GO:0005515	Function	Protein binding	IPI	23861867, 34547241
GO:0005524	Function	ATP binding	IEA
GO:0005524	Function	ATP binding	TAS	8048912
GO:0005737	Component	Cytoplasm	IDA	23861867, 34547241
GO:0005739	Component	Mitochondrion	HTP	34800366
GO:0005739	Component	Mitochondrion	IBA
GO:0005739	Component	Mitochondrion	IDA	16729965
GO:0005739	Component	Mitochondrion	IEA
GO:0005759	Component	Mitochondrial matrix	IEA
GO:0005759	Component	Mitochondrial matrix	TAS
GO:0005829	Component	Cytosol	IDA
GO:0005829	Component	Cytosol	IEA
GO:0005829	Component	Cytosol	TAS
GO:0006094	Process	Gluconeogenesis	IBA
GO:0006094	Process	Gluconeogenesis	IEA
GO:0006094	Process	Gluconeogenesis	TAS
GO:0006629	Process	Lipid metabolic process	IEA
GO:0006739	Process	NADP+ metabolic process	IDA	34547241
GO:0009374	Function	Biotin binding	IEA
GO:0009374	Function	Biotin binding	TAS	8048912
GO:0010629	Process	Negative regulation of gene expression	IMP	23861867
GO:0016874	Function	Ligase activity	IEA
GO:0019074	Process	Viral RNA genome packaging	IMP	23861867
GO:0019076	Process	Viral release from host cell	IMP	23861867
GO:0019674	Process	NAD+ metabolic process	IDA	34547241
GO:0042802	Function	Identical protein binding	IPI	18297087, 34547241
GO:0044281	Process	Small molecule metabolic process	IEA
GO:0044794	Process	Host-mediated activation of viral process	IMP	23861867
GO:0046872	Function	Metal ion binding	IEA

MIM	HGNC	e!Ensembl
608786	8636	ENSG00000173599

Protein

UniProt ID

P11498

Protein name

Pyruvate carboxylase, mitochondrial (EC 6.4.1.1) (Pyruvic carboxylase) (PCB)

Protein function

Pyruvate carboxylase catalyzes a 2-step reaction, involving the ATP-dependent carboxylation of the covalently attached biotin in the first step and the transfer of the carboxyl group to pyruvate in the second. Catalyzes in a tissue specific mann

PDB

3BG3 , 3BG9 , 7WTA , 7WTB , 7WTC , 7WTD , 7WTE , 8HWL , 8J7O , 8XL9

Family and domains

Pfam

Accession	ID	Position in sequence	Description	Type
PF00289	Biotin_carb_N	36 → 146	Biotin carboxylase, N-terminal domain	Domain
PF02786	CPSase_L_D2	151 → 360	Carbamoyl-phosphate synthase L chain, ATP binding domain	Domain
PF02785	Biotin_carb_C	375 → 483	Biotin carboxylase C-terminal domain	Domain
PF00682	HMGL-like	563 → 837	HMGL-like	Domain
PF02436	PYC_OADA	861 → 1061	Conserved carboxylase domain	Domain
PF00364	Biotin_lipoyl	1110 → 1177	Biotin-requiring enzyme	Domain

Sequence

MLKFRTVHGGLRLLGIRRTSTAPAASPNVRRLEYKPIKKVMVANRGEIAIRVFRACTELG
IRTVAIYSEQDTGQMHRQKADEAYLIGRGLAPVQAYLHIPDIIKVAKENNVDAVHPGYGF
LSERADFAQACQDAGVRFIGPSPEVVRKMGDKVEARAIAIAAGVPVVPGTDAPITSLHEA
HEFSNTYGFPIIFKAAYGGGGRGMRVVHSYEELEENYTRAYSEALAAFGNGALFVEKFIE
KPRHIEVQILGDQYGNILHLYERDCSIQRRHQKVVEIAPAAHLDPQLRTRLTSDSVKLAK
QVGYENAGTVEFLVDRHGKHYFIEVNSRLQVEHTVTEEITDVDLVHAQIHVAEGRSLPDL
GLRQENIRINGCAIQCRVTTEDPARSFQPDTGRIEVFRSGEGMGIRLDNASAFQGAVISP
HYDSLLVKVIAHGKDHPTAATKMSRALAEFRVRGVKTNIAFLQNVLNNQQFLAGTVDTQF
IDENPELFQLRPAQNRAQKLLHYLGHVMVNGPTTPIPVKASPSPTDPVVPAVPIGPPPAG
FRDILLREGPEGFARAVRNHPGLLLMDTTFRDAHQSLLATRVRTHDLKKIAPYVAHNFSK
LFSMENWGGATFDVAMRFLYECPWRRLQELRELIPNIPFQMLLRGANAVGYTNYPDNVVF
KFCEVAKENGMDVFRVFDSLNYLPNMLLGMEAAGSAGGVVEAAISYTGDVADPSRTKYSL
QYYMGLAEELVRAGTHILCIKDMAGLLKPTACTMLVSSLRDRFPDLPLHIHTHDTSGAGV
AAMLACAQAGADVVDVAADSMSGMTSQPSMGALVACTRGTPLDTEVPMERVFDYSEYWEG
ARGLYAAFDCTATMKSGNSDVYENEIPGGQYTNLHFQAHSMGLGSKFKEVKKAYVEANQM
LGDLIKVTPSSKIVGDLAQFMVQNGLSRAEAEAQAEELSFPRSVVEFLQGYIGVPHGGFP
EPFRSKVLKDLPRVEGRPGASLPPLDLQALEKELVDRHGEEVTPEDVLSAAMYPDVFAHF
KDFTATFGPLDSLNTRLFLQGPKIAEEFEVELERGKTLHIKALAVSDLNRAGQRQVFFEL
NGQLRSILVKDTQAMKEMHFHPKALKDVKGQIGAPMPGKVIDIKVVAGAKVAKGQPLCVL
SAMKMETVVTSPMEGTVRKVHVTKDMTLEGDDLILEIE

Sequence length

1178

Interactions

View interactions

	KEGG		Reactome
	Citrate cycle (TCA cycle) Pyruvate metabolism Metabolic pathways Carbon metabolism Biosynthesis of amino acids		Biotin transport and metabolism Defective HLCS causes multiple carboxylase deficiency Gluconeogenesis

Show/Hide Causal Diseases (2)

Disease merge term	Disease name	dbSNP ID	References
Causal Diseases caused by PATHOGENIC or LIKELY PATHOGENIC variants from ClinVar only
Congenital lactic acidosis	congenital lactic acidosis	rs1591117575	N/A
Pyruvate Dehydrogenase Deficiency	Pyruvate carboxylase deficiency	rs1555014957, rs28940591, rs1555014332, rs113994143, rs756355930, rs2135813862, rs1555013840, rs119103242, rs1555025823, rs1565209327, rs144583275, rs113994145, rs763433647, rs113994146, rs1565245427 View all (7 more)	N/A

Show/Hide Unknown Diseases (4)

Disease merge term	Disease name	Evidence	References	Source
Unknown Includes: (1) ClinVar NON-pathogenic variants (Uncertain, Benign, Conflicting, VUS), (2) GenCC associations, (3) GWAS associations, (4) CBGDA evidence-based associations. NOTE: Diseases with pathogenic evidence are excluded to avoid conflicts.
Bipolar Disorder	Bipolar disorder, Bipolar I disorder	N/A	N/A	GWAS
Insomnia	Insomnia	N/A	N/A	GWAS
Lung adenocarcinoma	Familial squamous cell lung carcinoma	N/A	N/A	GWAS
Pyruvate Carboxylase Deficiency Disease	pyruvate carboxylase deficiency, infantile form, pyruvate carboxylase deficiency, severe neonatal type, pyruvate carboxylase deficiency, benign type	N/A	N/A	GenCC

Show/Hide Text Mining Associations (70)

Disease Name	Relationship Type	References
Associations from Text Mining Disease associations identified through Pubtator
Acute On Chronic Liver Failure	Associate	20070500, 20848146, 29065883
Alzheimer Disease	Associate	25410733, 31026621
Astrocytoma	Associate	36662405
Attention Deficit and Disruptive Behavior Disorders	Associate	25410733
Biotin deficiency	Associate	15623830
Blood Coagulation Disorders	Associate	11697723, 25651845
Blood Coagulation Disorders	Stimulate	36991043
Blood Coagulation Disorders Inherited	Associate	33864376
Breast Neoplasms	Associate	26070193, 27890529, 27936456, 29024812, 31874204, 34715905, 34857895, 35799892, 39684297
Breast Neoplasms	Stimulate	39742384
Carcinogenesis	Associate	21403838, 39684297
Carcinoma Hepatocellular	Associate	17900245, 18803358, 28902288, 31033235
Cataract	Stimulate	23781296
Cerebral Cortical Thinning	Associate	31026621
Chemical and Drug Induced Liver Injury	Associate	20848146, 28902288, 29408943
Citrullinemia	Associate	6424438
Cognition Disorders	Associate	36374219
Congenital Hyperinsulinism	Associate	23869231
Death	Associate	20848146, 36864098
Diabetes Mellitus	Inhibit	19296078
Diabetes Mellitus Type 2	Associate	19296078
Fibrosis	Associate	25788186, 28902288, 3771795
Frailty	Associate	36864098
Genetic Diseases Inborn	Associate	11697723, 23986205
Glaucoma Angle Closure	Associate	22096540
Glioblastoma	Associate	36662405
Glioma	Associate	25243911, 30283018, 33947134
Hepatitis B	Associate	18803358, 20070500
Hepatitis B Chronic	Associate	17900245, 20070500, 25788186, 26577140
Hepatitis Viral Human	Associate	28376292
Hyperammonemia	Associate	6424438
Hyperlysinemias	Associate	6424438
Immunologic Deficiency Syndromes	Stimulate	36991043
Intracranial Aneurysm	Associate	40103236
Kartagener Syndrome	Associate	37873728
Kidney Neoplasms	Associate	34543281
Liver Cirrhosis	Associate	20070500, 26577140, 28376292, 28902288
Liver Diseases	Associate	25788186
Liver Failure	Associate	28376292
Lung Injury	Associate	3371278
Lupus Nephritis	Associate	37583695
Lymphatic Metastasis	Stimulate	34857895
Measles	Associate	9878618
Meningioma	Associate	36662405
Metabolic Diseases	Associate	35843982
Mitochondrial Diseases	Stimulate	32923630
Neoplasm Metastasis	Associate	35149585
Neoplasms	Associate	19558692, 23409034, 23613812, 26070193, 31874204, 33177242, 35149585, 36662405, 39684297
Neurodegenerative Diseases	Associate	31026621, 32923630
Neurologic Manifestations	Associate	36864098
Niemann Pick Disease Type C	Associate	35159129
Non alcoholic Fatty Liver Disease	Associate	23931760
Obesity	Associate	35163195
Obesity Morbid	Associate	29457027
Oligodendroglioma	Associate	36662405
Ovarian Neoplasms	Associate	33177242, 34609082
Perinatal Death	Associate	37873728
Plaque Amyloid	Inhibit	31026621
Prostatitis	Associate	20138246
Protein C Deficiency	Inhibit	15978099, 25651845
Protein S Deficiency	Associate	11697723
Purpura Thrombocytopenic Idiopathic	Associate	28415913
Pyruvate Carboxylase Deficiency Disease	Associate	12437512, 21403838, 37484962, 37873728, 6424438
Rheumatic Diseases	Associate	32620913
Sarcoidosis	Stimulate	3371278
Spondyloepiphyseal Dysplasia Tarda Autosomal Recessive	Associate	23019651
Squamous Cell Carcinoma of Head and Neck	Associate	20537188
Thromboembolism	Associate	23986205
Venous Thromboembolism	Associate	11697723, 23986205, 25651845
Venous Thrombosis	Associate	15978099

PC (pyruvate carboxylase)