HOMOCYSTEINE METABOLIC PATHWAY (PW:0000398)

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Description

Homocysteine (Hcy) metabolism is at the cross-roads of several pathways; Hcy itself is a byproduct in the de novo pathway of methionine metabolic cycle. The first reaction of the methionine cycle produces S-adenosylmethionine, also known as AdoMet or SAM, which is the major methyl donor for nucleic acids, proteins, lipids and small molecules. The methyltransfer reaction, carried by a large number of methyltransferases (MTs) generates S-adenosylhomocysteine (SAH), the precursor of Hcy and also a

Pathway Diagram:

Ariadne Genomics Inc. homocysteine ---> methionine S-adenosylmethionine ---> S-adenosylhomocysteine S-adenosylmethionine S-adenosylhomocysteine Cbl Mtr Bhmt remethylation pathway of homocysteine metabolism - cobalamin independent, betaine dependent remethylation pathway of homocysteine metabolism - cobalamin dependent transsulfuration pathway of homocysteine metabolism methionine cycle/metabolic pathway folate mediated one-carbon metabolic pathway folate cycle metabolic pathway cysteine, donwstream metabolites S-adenosylmethionine ---| remethylation pathway of homocysteine metabolism - cobalamin dependent 5-methyl-THF homocysteine <--> S-adenosylhomocysteine Ahcy methionine dimethylglycine betaine homocysteine adenosine THF Mtrr Mtrr ---> Mtr dimethylglycine ---| Bhmt betaine ---> dimethylglycine S-adenosylhomocysteine ---> adenosine Mthfr homocysteine ---> cysteine, donwstream metabolites S-adenosylmethionine --+> transsulfuration pathway of homocysteine metabolism 5-methyl-THF ---> THF
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Genes in Pathway:

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homocysteine metabolic pathway term browser
Symbol Object Name JBrowse Chr Start Stop Reference
G Ahcy adenosylhomocysteinase JBrowse link 3 150,587,833 150,603,057 RGD:730275
RGD:7242426
G As3mt arsenite methyltransferase JBrowse link 1 266,482,787 266,514,570 RGD:625365
G Asmt acetylserotonin O-methyltransferase JBrowse link 12 18,521,383 18,527,036 RGD:1359073
G Carm1 coactivator-associated arginine methyltransferase 1 JBrowse link 8 22,577,723 22,622,555 RGD:1359044
G Comt catechol-O-methyltransferase JBrowse link 11 86,715,981 86,735,630 RGD:1359089
G Dnmt1 DNA methyltransferase 1 JBrowse link 8 21,922,515 21,968,495 RGD:1359078
G Dot1l DOT1 like histone lysine methyltransferase JBrowse link 7 11,786,105 11,824,742 RGD:1359080
G Gamt guanidinoacetate N-methyltransferase JBrowse link 7 12,314,848 12,317,998 RGD:1359081
G Gnmt glycine N-methyltransferase JBrowse link 9 16,565,274 16,568,626 RGD:1359070
G Hnmt histamine N-methyltransferase JBrowse link 3 905,111 937,038 RGD:1359041
G Icmt isoprenylcysteine carboxyl methyltransferase JBrowse link 5 169,475,270 169,482,031 RGD:1359083
G Mrm2 mitochondrial rRNA methyltransferase 2 JBrowse link 12 16,398,749 16,403,656 RGD:1359074
G Mthfr methylenetetrahydrofolate reductase JBrowse link 5 164,844,642 164,864,360 RGD:7242426
G Nnmt nicotinamide N-methyltransferase JBrowse link 8 52,918,437 52,938,172 RGD:1359084
G Pcmt1 protein-L-isoaspartate (D-aspartate) O-methyltransferase 1 JBrowse link 1 1,734,863 1,767,759 RGD:729481
G Pemt phosphatidylethanolamine N-methyltransferase JBrowse link 10 46,339,821 46,404,640 RGD:729486
G Pnmt phenylethanolamine-N-methyltransferase JBrowse link 10 86,340,893 86,342,501 RGD:1359087
G Prmt1 protein arginine methyltransferase 1 JBrowse link 1 100,971,132 100,980,411 RGD:1359044
G Prmt3 protein arginine methyltransferase 3 JBrowse link 1 105,113,595 105,200,253 RGD:1359044
G Prmt5 protein arginine methyltransferase 5 JBrowse link 15 33,156,508 33,165,893 RGD:1359044
G Prmt6 protein arginine methyltransferase 6 JBrowse link 2 213,173,403 213,180,721 RGD:1359044
G Rnmt RNA (guanine-7-) methyltransferase JBrowse link 18 64,084,746 64,108,246 RGD:1359071
G Setdb1 SET domain, bifurcated 1 JBrowse link 2 196,495,867 196,527,412 RGD:1359072
G Suv39h2 suppressor of variegation 3-9 homolog 2 JBrowse link 17 78,762,897 78,782,016 RGD:1359810
G Trdmt1 tRNA aspartic acid methyltransferase 1 JBrowse link 17 80,824,652 80,859,585 RGD:1359088
remethylation pathway of homocysteine metabolism - cobalamin dependent term browser
Symbol Object Name JBrowse Chr Start Stop Reference
G Mthfr methylenetetrahydrofolate reductase JBrowse link 5 164,844,642 164,864,360 RGD:7242426
G Mtr 5-methyltetrahydrofolate-homocysteine methyltransferase JBrowse link 17 66,210,444 66,295,014 RGD:1359026
RGD:7242426
G Mtrr 5-methyltetrahydrofolate-homocysteine methyltransferase reductase JBrowse link 1 37,743,089 37,774,485 RGD:1359037
RGD:7242426
remethylation pathway of homocysteine metabolism - cobalamin independent, betaine dependent term browser
Symbol Object Name JBrowse Chr Start Stop Reference
G Ahcy adenosylhomocysteinase JBrowse link 3 150,587,833 150,603,057 RGD:10402751
G Aldh7a1 aldehyde dehydrogenase 7 family, member A1 JBrowse link 18 51,619,007 51,651,267 RGD:10402751
G Bhmt betaine-homocysteine S-methyltransferase JBrowse link 2 23,236,573 23,256,158 RGD:1359026
RGD:7242426
RGD:7242428
RGD:10402751
G Chdh choline dehydrogenase JBrowse link 16 6,078,083 6,109,386 RGD:10402751
G Mat2a methionine adenosyltransferase 2A JBrowse link 4 100,297,478 100,303,047 RGD:10402751
G Mat2b methionine adenosyltransferase 2B JBrowse link 10 25,832,096 25,848,045 RGD:10402751
G Mtr 5-methyltetrahydrofolate-homocysteine methyltransferase JBrowse link 17 66,210,444 66,295,014 RGD:10402751
G Pemt phosphatidylethanolamine N-methyltransferase JBrowse link 10 46,339,821 46,404,640 RGD:10402751
transsulfuration pathway of homocysteine metabolism term browser
Symbol Object Name JBrowse Chr Start Stop Reference
G Cbs cystathionine beta synthase JBrowse link 20 10,361,987 10,386,663 RGD:1359024
RGD:7242427
RGD:10402751
G Cdo1 cysteine dioxygenase type 1 JBrowse link 18 40,702,027 40,716,901 RGD:7242427
G Csad cysteine sulfinic acid decarboxylase JBrowse link 7 143,781,520 143,810,880 RGD:7242427
G Cth cystathionine gamma-lyase JBrowse link 2 264,266,959 264,293,040 RGD:1359024
RGD:7242427
RGD:10402751

Pathway Gene Annotations

Disease Annotations Associated with Genes in the homocysteine metabolic pathway
Disease TermsGene Symbols
AbetalipoproteinemiaDnmt1
Abortion, HabitualMthfr
Acute Kidney InjuryMthfr
AdenocarcinomaDnmt1
Adenocarcinoma of LungDot1l
Adenocarcinoma, Bronchiolo-AlveolarDnmt1
Adenocarcinoma, ProstaticDnmt1
Adenoma, Liver CellCarm1
AdenomyosisDnmt1
AlbuminuriaMthfr
AlcoholismComt
AlopeciaMthfr
Alopecia AreataDnmt1
Alzheimer DiseaseHnmt , Mthfr , Pcmt1 , Pnmt
Amino Acid Metabolism, Inborn ErrorsAhcy , Gamt
Amphetamine-Related DisordersComt
Amyotrophic Lateral SclerosisMthfr
AnemiaMthfr
Anemia, Sickle CellMthfr
AnoxiaAhcy
Anxiety DisordersDnmt1
Aortic Aneurysm, AbdominalMthfr
Aortic CoarctationMthfr
Aortic InjuriesPcmt1
Arsenic PoisoningAs3mt , Mthfr
Arterial Occlusive DiseasesMthfr
Arthritis, ExperimentalAhcy , Dnmt1
Arthritis, RheumatoidDnmt1 , Mthfr
AsthmaCarm1 , Dnmt1 , Hnmt , Mthfr , Prmt1 , Prmt3 , Prmt5
AstrocytomaPcmt1
AtaxiaDnmt1
AtherosclerosisMthfr
Attention Deficit Disorder with HyperactivityAs3mt , Comt , Mthfr
Autism Spectrum DisorderComt
Autistic DisorderAsmt , Comt , Mthfr , Setdb1
Autoimmune DiseasesDnmt1
Binge DrinkingDnmt1
Bipolar DisorderComt , Mthfr
Birth WeightAs3mt
Blood Coagulation Disorders, InheritedMthfr
Brain InfarctionHnmt
Brain InjuriesComt , Dnmt1
Brain IschemiaMthfr
Breast NeoplasmsCarm1 , Comt , Dnmt1 , Mthfr
Bronchial HyperreactivityHnmt
Budd-Chiari SyndromeMthfr
CarcinogenesisDnmt1
CarcinomaDnmt1
Carcinoma, EndometrioidDnmt1
Carcinoma, HepatocellularCarm1 , Comt , Dnmt1 , Gnmt
Carcinoma, MucoepidermoidDnmt1
Carcinoma, Pancreatic DuctalDnmt1
Carcinoma, Renal CellComt , Mthfr , Nnmt
Carcinoma, Squamous CellMthfr
Carcinoma, Transitional CellMthfr
Cardiomyopathy, HypertrophicComt
Cardiomyopathy, Hypertrophic, FamilialComt
Cardiovascular DiseasesMthfr
Carotid StenosisMthfr
CatalepsyComt
CataractMthfr
Cerebellar AtaxiaDnmt1
Cerebellar Ataxia, Deafness, and NarcolepsyDnmt1
Cerebral InfarctionMthfr
Cervical Intraepithelial NeoplasiaMthfr
CholangiocarcinomaMthfr
Choline DeficiencyDnmt1
ChoreaDnmt1
Clear-Cell Metastatic Renal Cell CarcinomaMthfr
Cleft LipMthfr
ClubfootMthfr
Cocaine-Related DisordersComt
Cognition DisordersComt
Colonic NeoplasmsDnmt1 , Mthfr
Colorectal NeoplasmsDnmt1 , Mthfr
Conotruncal Cardiac DefectsMthfr
ContusionsPnmt
Coronary Artery DiseaseMthfr
Coronary DiseaseMthfr
Coronary RestenosisMthfr
Deglutition DisordersDnmt1
DementiaDnmt1
Depressive DisorderMthfr
Dermatitis, AtopicHnmt
Diabetes Mellitus, ExperimentalComt , Mthfr , Pemt , Pnmt
Diabetes Mellitus, Type 1Mthfr
Diabetes Mellitus, Type 2Dnmt1 , Mthfr
Diabetic AngiopathiesMthfr
Diabetic NephropathiesMthfr , Prmt1
Diabetic RetinopathyMthfr
DiGeorge SyndromeComt
Down SyndromeHnmt , Mthfr
Drug EruptionsMthfr
Drug HypersensitivityHnmt
Drug-Induced Liver InjuryMthfr
Drug-Related Side Effects and Adverse ReactionsMthfr
DysarthriaDnmt1
Dyskinesia, Drug-InducedComt
Endometrial NeoplasmsComt , Dnmt1 , Mthfr
EndometriosisDnmt1
Essential TremorHnmt
Eye DiseasesMthfr
FatigueComt
Fatty LiverMthfr
Fatty Liver, AlcoholicDnmt1 , Pemt
Fetal Growth RetardationComt , Dnmt1
Gastrointestinal DiseasesMthfr
Gastrointestinal Stromal TumorsMthfr
Glaucoma, Angle-ClosureMthfr
Glaucoma, Open-AngleMthfr
GliomaPcmt1 , Setdb1
GlomerulonephritisMthfr
Graft vs Host DiseaseMthfr
Graves DiseaseDnmt1 , Mthfr
Guanidinoacetate Methyltransferase DeficiencyGamt
Hearing LossDnmt1 , Mthfr
Hearing Loss, Cisplatin-Induced, Susceptibility ToComt
Hearing Loss, SuddenMthfr
Heart Defects, CongenitalDnmt1 , Mthfr
Heart FailureDnmt1 , Pcmt1
Hematologic DiseasesMthfr
Hematologic NeoplasmsMthfr
Hemophilia AMthfr
HepatitisGnmt
Hepatitis, ChronicGnmt
Hepatolenticular DegenerationAhcy , Asmt
Hereditary Sensory and Autonomic NeuropathiesDnmt1
HomocystinuriaMthfr
Huntington DiseaseHnmt , Setdb1
HyperalgesiaComt , Dnmt1
HyperhomocysteinemiaAhcy , Gnmt , Mthfr
HypermethioninemiaAhcy , Gnmt
HypersensitivityMthfr
HypertensionAhcy , Comt , Pnmt
Hypertension, EssentialPnmt
HyperthyroidismMthfr
HypoglycemiaPnmt
HypopituitarismMthfr
HypothyroidismMthfr
Infarction, Middle Cerebral ArteryDnmt1
Infertility, FemaleMthfr
Infertility, MaleMthfr
Inflammatory Bowel Disease 11Hnmt
Inflammatory Bowel DiseasesMthfr
Intellectual DisabilityGamt
IschemiaMthfr
Kidney DiseasesMthfr
Kidney Failure, ChronicMthfr
Leigh DiseaseGamt
LeiomyomaComt
Leukemia, Biphenotypic, AcuteDot1l
Leukemia, Lymphocytic, Chronic, B-CellMthfr
Leukemia, Myelogenous, Chronic, BCR-ABL PositiveDnmt1 , Mthfr
Leukemia, Myeloid, AcuteDnmt1 , Mthfr
LeukoencephalopathiesMthfr
LeukopeniaMthfr
Leydig Cell TumorPrmt5
Lichen Planus, OralDnmt1
Liver CirrhosisDnmt1
Liver DiseasesMthfr
Liver NeoplasmsGnmt , Mthfr
Liver Neoplasms, ExperimentalPemt
Lung NeoplasmsDnmt1 , Mthfr , Setdb1
Lupus Erythematosus, SystemicDnmt1
Lymphatic MetastasisComt
LymphomaMthfr
Lymphoma, FollicularMthfr
Lymphoma, Large B-Cell, DiffuseMthfr
Lymphoma, Non-HodgkinMthfr
MalnutritionMthfr
Mammary Neoplasms, AnimalComt
Maxillofacial AbnormalitiesMthfr
MedulloblastomaDnmt1
MelanomaSetdb1
Meniere DiseaseMthfr
MeningomyeloceleMthfr
Mental DisordersComt
Mental Retardation, Autosomal Recessive 51Hnmt
Mesothelioma, MalignantSetdb1
Methylenetetrahydrofolate Reductase DeficiencyMthfr
Microsatellite InstabilityMthfr
Microvascular AnginaMthfr
Migraine DisordersMthfr
Migraine with AuraMthfr
Mitochondrial Complex I DeficiencyGamt
Mthfr Deficiency, Thermolabile TypeMthfr
MucositisMthfr
Multiple MyelomaMthfr
Multiple SclerosisPnmt
Musculoskeletal PainComt
MycetomaComt
Myeloproliferative DisordersMthfr
Myocardial InfarctionMthfr
NecrosisMthfr
Neoplasm MetastasisMthfr
Neoplasms, Glandular and EpithelialAs3mt
NephrosclerosisMthfr
Nervous System DiseasesMthfr
Neural Tube Defect, Folate-SensitiveMthfr
Neural Tube DefectsMthfr
Neuropathy, Hereditary Sensory and Autonomic, Type IEDnmt1
NeutropeniaMthfr
Nonarteritic Anterior Ischemic Optic NeuropathyMthfr
ObesityComt
Obsessive-Compulsive DisorderComt
Oral Squamous Cell CarcinomaMthfr
Orofacial Cleft 1Mthfr
OsteonecrosisMthfr
OsteosarcomaMthfr
Ovarian NeoplasmsComt , Dnmt1
PainComt
Pancreatic Intraepithelial NeoplasiaDnmt1
Pancreatic NeoplasmsMthfr
Panic DisorderComt
Parkinson DiseaseHnmt
Parkinsonian DisordersComt
Peripheral Arterial DiseaseMthfr
Peritoneal FibrosisDnmt1
PheochromocytomaComt
Pick Disease of the BrainHnmt
Polycystic Ovary SyndromeComt
Precursor Cell Lymphoblastic Leukemia-LymphomaMthfr
Prostatic Intraepithelial NeoplasiaCarm1 , Dnmt1
Prostatic NeoplasmsCarm1 , Comt , Dnmt1 , Gnmt , Mthfr , Setdb1
PsoriasisCarm1 , Comt
Pulmonary EmbolismMthfr
Rectal NeoplasmsMthfr
Renal InsufficiencyMthfr
Renal Insufficiency, ChronicMthfr
Renal Vascular DiseasesMthfr
Reperfusion InjuryPnmt
Retinal DiseasesMthfr
Retinal Vein OcclusionMthfr
Rett SyndromeSetdb1
RhinitisHnmt
SchizophreniaComt , Dnmt1 , Hnmt , Mthfr , Setdb1
SeizuresGamt
SeminomaPrmt5
Sinus Thrombosis, IntracranialMthfr
Skin DiseasesMthfr
Skin/Hair/Eye Pigmentation, Variation In, 9Ahcy
Small Cell Lung CarcinomaMthfr
Smith-Magenis SyndromePnmt
Spinal Cord DiseasesMthfr
Spinal DysraphismMthfr , Pcmt1
Stomach NeoplasmsDnmt1 , Mthfr
Stomatitis, AphthousMthfr
StrokeMthfr
Temporomandibular Joint DisordersComt
Tetralogy of FallotMthfr
ThrombocytopeniaMthfr
ThrombophiliaMthfr
ThrombosisMthfr
Thrombotic MicroangiopathiesMthfr
ThyrotoxicosisMthfr
Transposition of Great VesselsMthfr
UremiaComt
Urinary Bladder NeoplasmsAs3mt , Comt , Dnmt1 , Mthfr
UrticariaHnmt
Uterine Cervical NeoplasmsDnmt1 , Mthfr
Vascular CalcificationMthfr
Vascular DiseasesMthfr
Venous ThromboembolismMthfr
Venous ThrombosisComt , Mthfr
Vitamin B 6 DeficiencyAhcy
VitiligoComt
Wet Macular DegenerationMthfr
Wilms TumorMthfr
Pathway Annotations Associated with Genes in the homocysteine metabolic pathway
Pathway TermsGene Symbols
5'-end pre-mRNA capping pathwayRnmt
alkaptonuria disease pathwayComt , Pnmt
altered folate cycle metabolic pathwayMthfr
altered folate mediated one-carbon metabolic pathwayMthfr
androgen signaling pathwayCarm1 , Prmt1
arginine and proline metabolic pathwayGamt
arginine:glycine amidinotransferase deficiency pathwayGamt
aromatic amino acid decarboxylase deficiency pathwayPnmt
catecholamine biosynthetic pathwayPnmt
choline metabolic pathwayAhcy , Pemt
creatine metabolic pathwayGamt
cysteine and methionine metabolic pathwayAhcy , Dnmt1 , Trdmt1
dihydropyrimidine dehydrogenase deficiency pathwayGamt , Gnmt
dimethylglycine dehydrogenase deficiency pathwayGamt , Gnmt
disulfiram pharmacodynamics pathwayComt , Pnmt
DNA modification pathwayDnmt1
dopamine beta hydroxylase deficiency pathwayComt , Pnmt
epinephrine biosynthetic pathwayPnmt
estrogen signaling pathwayCarm1 , Prmt1
folate cycle metabolic pathwayMthfr
folate mediated one-carbon metabolic pathwayGnmt , Mthfr
folate metabolic pathwayGnmt , Mthfr
glycerophospholipid metabolic pathwayPemt
glycine N-methyltransferase deficiency pathwayAhcy , Dnmt1 , Mthfr
glycine, serine and threonine metabolic pathwayGamt , Gnmt
guanidinoacetate methyltransferase deficiency pathwayGamt
gyrate atrophy pathwayGamt
hawkinsinuria disease pathwayComt , Pnmt
hereditary folate malabsorption disease pathwayMthfr
histidine metabolic pathwayHnmt , Prmt3
histidinemia disease pathwayHnmt , Prmt3
histone modification pathwayCarm1 , Dot1l , Prmt1 , Prmt5 , Suv39h2
homocysteine metabolic pathwayAhcy , As3mt , Asmt , Carm1 , Comt , Dnmt1 , Dot1l , Gamt , Gnmt , Hnmt , Icmt , Mrm2 , Mthfr , Nnmt , Pcmt1 , Pemt , Pnmt , Prmt1 , Prmt3 , Prmt5 , Prmt6 , Rnmt , Setdb1 , Suv39h2 , Trdmt1
homocystinuria disease pathwayAhcy , Dnmt1 , Mthfr
hypermethioninemia disease pathwayAhcy , Dnmt1 , Mthfr
hyperornithinemia-hyperammonemia-homocitrullinemia syndrome pathwayGamt
hyperprolinemia disease pathwayGamt
hyperprolinemia type II disease pathwayGamt
lysine degradation pathwayDot1l , Setdb1 , Suv39h2
methionine adenosyltransferase deficiency pathwayAhcy , Dnmt1 , Mthfr
methionine cycle/metabolic pathwayAhcy , As3mt , Asmt , Carm1 , Comt , Dnmt1 , Dot1l , Gamt , Gnmt , Hnmt , Icmt , Mrm2 , Mthfr , Nnmt , Pcmt1 , Pemt , Pnmt , Prmt1 , Prmt3 , Prmt5 , Prmt6 , Rnmt , Setdb1 , Suv39h2 , Trdmt1
methotrexate pharmacodynamics pathwayMthfr
methylenetetrahydrofolate reductase deficiency pathwayAhcy , Dnmt1 , Mthfr
monoterpenoid biosynthetic pathwayNnmt
mRNA decay pathwayRnmt
niacin metabolic pathwayNnmt
nonketotic hyperglycinemia disease pathwayGamt , Gnmt
Nonketotic hyperglycinemia disease pathwayGamt , Gnmt
p53 signaling pathwayPrmt5
phenytoin pharmacodynamics pathwayComt
prolidase deficiency pathwayGamt
remethylation pathway of homocysteine metabolism - cobalamin dependentMthfr
remethylation pathway of homocysteine metabolism - cobalamin independent, betaine dependentAhcy , Pemt
RNA transport pathwayPrmt5
sarcosinemia disease pathwayGamt , Gnmt
selenoamino acid metabolic pathwayAhcy
steroid hormone biosynthetic pathwayComt
tryptophan metabolic pathwayAsmt
tyrosine metabolic pathwayComt , Pnmt
tyrosinemia type I disease pathwayComt , Pnmt
Wnt signaling, non-canonical pathwaySetdb1
Phenotype Annotations Associated with Genes in the homocysteine metabolic pathway

References Associated with the homocysteine metabolic pathway:

Ontology Path Diagram:

paths to the root

Import into Pathway Studio: