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	5091
Gene name	Pyruvate carboxylase
Gene symbol	PC
Synonyms (NCBI Gene)	PCB
Chromosome	11
Chromosome location	11q13.2
Summary	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

Show/Hide all (38)

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

Show/Hide all (9)

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

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

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

1408

Show/Hide Causal Diseases (5)

Phenotype Name	Clinical Significance	dbSNP ID	RCV Accession
Causal Diseases associated with Pathogenic or Likely Pathogenic variants in ClinVar
Congenital lactic acidosis	Pathogenic	rs1591117575	RCV001003597
Global developmental delay	Pathogenic	rs1407756066	RCV001255416
Pyruvate carboxylase deficiency	Pathogenic; Likely pathogenic	rs1230803568, rs2135822173, rs2135785399, rs2135789146, rs2135790424, rs2135795582, rs2135800153, rs2135803326, rs766242199, rs2135917452, rs1482845179, rs2135822119, rs2135805611, rs1555015018, rs2135798857 View all (143 more)	RCV001332612 RCV001377234 RCV001388927 RCV001384114 RCV001380678 RCV001383937 RCV001380178 RCV001390025 RCV001383248 RCV001386564 RCV001542480 RCV001774754 RCV001774756 RCV001774758 RCV001774759 RCV001784799 RCV001782570 RCV001899258 RCV001928241 RCV001941742 RCV001904462 RCV001995264 RCV002043993 RCV001921439 RCV001944424 RCV001927018 RCV001995696 RCV001939586 RCV001951184 RCV001951152 RCV001956371 RCV001949368 RCV001914904 RCV002048351 RCV001935982 RCV001983485 RCV002249120 RCV002254835 RCV002283739 RCV000002175 RCV000002176 RCV000002177 RCV000002178 RCV000002179 RCV000002182 RCV000002183 RCV002309599 RCV002309615 RCV002309686 RCV002309823 RCV002309929 RCV002309992 RCV002308015 RCV002308040 RCV002308128 RCV002308135 RCV002308186 RCV002308190 RCV002309018 RCV002309072 RCV002309117 RCV002309177 RCV002309192 RCV002309310 RCV002309380 RCV002309426 RCV002309464 RCV002309475 RCV002309477 RCV002309491 RCV002309505 RCV002306881 RCV002306917 RCV002306920 RCV002307025 RCV002307089 RCV002307240 RCV002307323 RCV002310177 RCV002310201 RCV002310415 RCV002310473 RCV002310562 RCV002308441 RCV003062414 RCV003087326 RCV003120052 RCV002630229 RCV002630811 RCV000675135 RCV002861433 RCV003011114 RCV003005068 RCV002999782 RCV003020020 RCV003476618 RCV003476619 RCV003476620 RCV003476621 RCV003476622 RCV003476623 RCV003476624 RCV003476625 RCV003476626 RCV003476627 RCV003476628 RCV003476629 RCV003476630 RCV003476631 RCV003476632 RCV003476633 RCV003498807 RCV003498199 RCV003498883 RCV003499655 RCV003500002 RCV003497388 RCV003499975 RCV003498548 RCV003498333 RCV003499503 RCV003604047 RCV003604248 RCV003604316 RCV003604611 RCV003604626 RCV003604954 RCV003605045 RCV003866362 RCV004574439 RCV004574440 RCV004574441 RCV004574442 RCV004574443 RCV004574444 RCV004574445 RCV000020384 RCV003811121 RCV000020391 RCV004586455 RCV004586456 RCV000504155 RCV000516896 RCV000576201 RCV000670716 RCV000670028 RCV000672343 RCV000670832 RCV000672699 RCV000669751 RCV000666561 RCV000667975 RCV000698019 RCV000779075 RCV000988582 RCV001196289 RCV001222498 RCV001208930 RCV001214966 RCV001254095 RCV001261600
Thrombophilia due to protein C deficiency, autosomal dominant	Likely pathogenic; Pathogenic	rs766242199	RCV005912635
Thrombophilia due to protein C deficiency, autosomal recessive	Likely pathogenic; Pathogenic	rs766242199	RCV005912635

Show/Hide Unknown Diseases (18)

Phenotype Name	Clinical Significance	dbSNP ID	RCV Accession
Unknown Diseases with uncertain, conflicting, or no pathogenic evidence in ClinVar
-	no classification for the single variant	rs760108147	-
Acute myeloid leukemia	Benign; Conflicting classifications of pathogenicity	rs45560936, rs111858832	RCV005886742 RCV005893007
Cervical cancer	Uncertain significance; Benign	rs756621649, rs45560936	RCV005924266 RCV005886744
Cholangiocarcinoma	Conflicting classifications of pathogenicity	rs147945506	RCV005892147
Clear cell carcinoma of kidney	Conflicting classifications of pathogenicity	rs147945506	RCV005892145
Gastric cancer	Benign; Likely benign; Uncertain significance	rs45560936, rs759066494, rs573667993	RCV005886747 RCV005871215 RCV005893006
Hepatocellular carcinoma	Benign	rs45625436	RCV005904311
Malignant tumor of esophagus	Benign	rs45560936, rs45625436	RCV005886743 RCV005904312
Malignant tumor of urinary bladder	Conflicting classifications of pathogenicity	rs147945506	RCV005892143
Nonpapillary renal cell carcinoma	Conflicting classifications of pathogenicity	rs147945506	RCV005892144
Ovarian serous cystadenocarcinoma	Conflicting classifications of pathogenicity	rs111858832	RCV005893008
PC-related disorder	Likely benign; Benign; Conflicting classifications of pathogenicity	rs747244374, rs187166676, rs768625636, rs910028001, rs751541124, rs58032722, rs776840589, rs375925670, rs148281644, rs200030109, rs112719219, rs144583275, rs139717038, rs1945471519, rs201796252 View all (19 more)	RCV003963262 RCV003938692 RCV003900495 RCV003946179 RCV003965892 RCV003931291 RCV003911127 RCV003973716 RCV003907649 RCV003895221 RCV003906428 RCV003977887 RCV003930296 RCV003967054 RCV003897696 RCV003950029 RCV003912626 RCV003902592 RCV003957911 RCV004757263 RCV004757276 RCV003955524 RCV003918572 RCV003968101 RCV003968194 RCV003940789 RCV003940832 RCV003975750 RCV004757332 RCV003895626 RCV003970578 RCV003913177 RCV003903086 RCV003933208
Sarcoma	Benign	rs45560936	RCV005886746
Thymoma	Benign; Uncertain significance	rs45560936, rs139540331, rs45625436	RCV005886749 RCV005892142 RCV005904313
Thyroid cancer, nonmedullary, 1	Conflicting classifications of pathogenicity	rs147945506	RCV005892146
Uterine carcinosarcoma	Benign	rs45560936	RCV005886748
Uterine corpus endometrial carcinoma	Benign	rs45560936	RCV005886750
Uveal melanoma	Benign	rs45560936	RCV005886745

Show/Hide Text Mining Associations (70)

Disease Name	Relationship Type	References
Associations from Text MiningDisease 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)