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:

Elsevier Inc. S-adenosylhomocysteine <--> homocysteine 5-methyl-THF ---> THF Cbl Mtr remethylation pathway of homocysteine metabolism - cobalamin dependent 5-methyl-THF homocysteine adenosine S-adenosylmethionine Bhmt Mtrr Mthfr Ahcy transsulfuration pathway of homocysteine metabolism methionine dimethylglycine THF dimethylglycine ---| Bhmt S-adenosylmethionine ---| remethylation pathway of homocysteine metabolism - cobalamin dependent S-adenosylmethionine --+> transsulfuration pathway of homocysteine metabolism betaine S-adenosylhomocysteine homocysteine ---> cysteine, donwstream metabolites S-adenosylhomocysteine ---> adenosine betaine ---> dimethylglycine Mtrr ---> Mtr cysteine, donwstream metabolites folate cycle metabolic pathway folate mediated one-carbon metabolic pathway methionine cycle/metabolic pathway remethylation pathway of homocysteine metabolism - cobalamin independent, betaine dependent S-adenosylmethionine ---> S-adenosylhomocysteine homocysteine ---> methionine
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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:10402751
RGD:7242426
RGD:7242428
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:10402751
RGD:7242427
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:10402751
RGD:7242427

Pathway Gene Annotations

Disease Annotations Associated with Genes in the homocysteine metabolic pathway
Disease TermsGene Symbols
abdominal aortic aneurysmMthfr
abetalipoproteinemiaDnmt1
Abortion, HabitualMthfr
ACANTHOCYTOSISDnmt1
acute kidney failureMthfr
acute myeloid leukemiaDnmt1 , Mthfr
Acute PainComt
adenocarcinomaDnmt1
AlbuminuriaMthfr
alcohol use disorderComt
Alcoholic Fatty LiverDnmt1 , Pemt
allergic hypersensitivity diseaseMthfr
alopeciaMthfr
alopecia areataDnmt1
Alzheimer's diseaseMthfr , Pcmt1 , Pnmt
amino acid metabolic disorderAhcy , Gamt
amphetamine abuseComt
amyotrophic lateral sclerosisMthfr
anemiaMthfr
angle-closure glaucomaMthfr
Animal Disease ModelsAhcy
Animal Mammary NeoplasmsComt
anxiety disorderDnmt1
Aortic CoarctationMthfr
Aortic InjuriesPcmt1
aphthous stomatitisMthfr
Arsenic PoisoningAs3mt , Mthfr
Arterial Occlusive DiseasesMthfr
asthmaCarm1 , Dnmt1 , Hnmt , Mthfr , Prmt1 , Prmt3 , Prmt5
astrocytomaPcmt1
AtaxiaDnmt1
atherosclerosisMthfr
atopic dermatitisHnmt
attention deficit hyperactivity disorderAs3mt , Comt , Mthfr
autism spectrum disorderComt
autistic disorderAsmt , Comt , Mthfr , Setdb1
Autoimmune DiseasesDnmt1
autosomal dominant cerebellar ataxia, deafness and narcolepsyDnmt1
B- and T-cell mixed leukemiaDot1l
B-Cell Chronic Lymphocytic LeukemiaMthfr
Beckwith-Wiedemann syndromeDnmt1
Binge DrinkingDnmt1
bipolar disorderComt , Mthfr
Birth WeightAs3mt
brain infarctionHnmt
Brain InjuriesComt , Dnmt1
brain ischemiaMthfr
Breast NeoplasmsCarm1 , Comt , Dnmt1 , Mthfr
Bronchial HyperreactivityHnmt
bronchiolo-alveolar adenocarcinomaDnmt1
Budd-Chiari syndromeMthfr
bulimia nervosaComt
CarcinogenesisDnmt1
carcinomaDnmt1
cardiovascular system diseaseMthfr
carotid stenosisMthfr
CatalepsyComt
cataractMthfr
cerebellar ataxiaDnmt1
cerebral creatine deficiency syndromeGamt
cerebral infarctionMthfr
cervix uteri carcinoma in situMthfr
Chemical and Drug Induced Liver InjuryMthfr
Child Behavior DisordersComt
cholangiocarcinomaMthfr
choline deficiency diseaseDnmt1
choreatic diseaseDnmt1
Chromosome 17, Trisomy 17p11 2Pemt
Chronic HepatitisGnmt
chronic kidney diseaseMthfr
chronic myeloid leukemiaDnmt1 , Mthfr
clear cell renal cell carcinomaDnmt1 , Mthfr
cleft lipMthfr
clubfootMthfr
Cocaine-Related DisordersComt , Prmt6
cognitive disorderComt
Colonic NeoplasmsDnmt1 , Mthfr
Colorectal NeoplasmsDnmt1 , Mthfr
congenital heart diseaseDnmt1 , Mthfr
congestive heart failureDnmt1 , Pcmt1
Conotruncal Cardiac DefectsMthfr
ContusionsPnmt
coronary artery diseaseMthfr
Coronary DiseaseMthfr
coronary restenosisMthfr
Crohn's diseaseMthfr
Deglutition DisordersDnmt1
dementiaDnmt1
Developmental DisabilitiesAs3mt
dextro-looped transposition of the great arteriesMthfr
Diabetes Mellitus, Experimental Comt , Mthfr , Pemt , Pnmt
diabetic angiopathyMthfr
Diabetic NephropathiesMthfr , Prmt1
diabetic retinopathyMthfr
diffuse large B-cell lymphomaMthfr
DiGeorge syndromeComt
dilated cardiomyopathyComt
dilated cardiomyopathy 1ADot1l
disease of mental healthComt
Down syndromeHnmt , Mthfr
drug allergyHnmt
Drug EruptionsMthfr
Drug-Induced DyskinesiaComt
Drug-Related Side Effects and Adverse ReactionsMthfr
DysarthriaDnmt1
end stage renal failureMthfr
Endometrial NeoplasmsComt , Dnmt1 , Mthfr
Endometrioid CarcinomasDnmt1
endometriosisDnmt1
endometriosis of uterusDnmt1
essential hypertensionPnmt
essential tremorHnmt
eumycotic mycetomaComt
Experimental ArthritisAhcy , Dnmt1
Experimental Autoimmune EncephalomyelitisComt
Experimental Liver NeoplasmsPemt
eye diseaseMthfr
factor VIII deficiencyMthfr
familial hypertrophic cardiomyopathyComt
FatigueComt
fatty liver diseaseMthfr
Female InfertilityMthfr
Fetal Growth RetardationComt , Dnmt1
fibromyalgiaComt
follicular lymphomaMthfr
Gastrointestinal DiseasesMthfr
gastrointestinal stromal tumorMthfr
genetic diseaseAhcy
Glandular and Epithelial NeoplasmsAs3mt
glomerulonephritisMthfr
glycine N-methyltransferase deficiencyGnmt
Graft vs Host DiseaseMthfr
Graves' diseaseDnmt1 , Mthfr
guanidinoacetate methyltransferase deficiencyGamt
Hearing LossDnmt1 , Mthfr
Hearing Loss, Cisplatin-Induced, Susceptibility ToComt
Hearing Loss, SuddenMthfr
Hematologic NeoplasmsMthfr
hematopoietic system diseaseMthfr
hepatitisGnmt
hepatocellular adenomaCarm1
hepatocellular carcinomaCarm1 , Comt , Dnmt1 , Gnmt
hereditary sensory neuropathyDnmt1
hereditary sensory neuropathy type 1EDnmt1
homocystinuriaMthfr
Huntington's diseaseHnmt , Setdb1
HyperalgesiaComt , Dnmt1
hyperhomocysteinemiaAhcy , Gnmt , Mthfr
hypermethioninemiaAhcy , Gnmt
hypermethioninemia with deficiency of S-adenosylhomocysteine hydrolaseAhcy
hypertensionAhcy , Comt , Pnmt
hyperthyroidismMthfr
hypoglycemiaPnmt
hypopituitarismMthfr
hypothyroidismMthfr
HypoxiaAhcy
inflammatory bowel diseaseMthfr
inherited blood coagulation diseaseMthfr
intellectual disabilityGamt
intracranial sinus thrombosisMthfr
ischemiaMthfr
kidney diseaseMthfr
kidney failureMthfr
Kuhnt-Junius degenerationMthfr
Leigh diseaseGamt
leiomyomaComt
LeukoencephalopathiesMthfr
leukopeniaMthfr
Leydig cell tumorPrmt5
liver benign neoplasmGnmt , Mthfr
liver cirrhosisDnmt1
liver diseaseMthfr
long QT syndromeAhcy
Lung NeoplasmsDnmt1 , Mthfr , Setdb1
lung small cell carcinomaMthfr
Lymphatic MetastasisComt
lymphomaMthfr
male infertilityMthfr
malignant gliomaPcmt1 , Setdb1
malignant mesotheliomaSetdb1
MalnutritionMthfr
Maxillofacial AbnormalitiesMthfr
medulloblastomaDnmt1
melanomaSetdb1
Memory DisordersComt
Meniere's diseaseMthfr
mental depressionMthfr
Mental Retardation, Autosomal Recessive 51Hnmt
Methylenetetrahydrofolate Reductase DeficiencyMthfr
Microsatellite InstabilityMthfr
Microvascular AnginaMthfr
middle cerebral artery infarctionDnmt1
migraineMthfr
migraine with auraMthfr
mitochondrial complex I deficiencyGamt
Mthfr Deficiency, Thermolabile TypeMthfr
mucoepidermoid carcinomaDnmt1
mucositisMthfr
multiple myelomaMthfr
multiple sclerosisPnmt
Musculoskeletal PainComt
myeloid neoplasmMthfr
myelomeningoceleMthfr
myocardial infarctionMthfr
NecrosisMthfr
Neoplasm InvasivenessDnmt1
Neoplasm MetastasisMthfr
nephroblastomaMthfr
nephrosclerosisMthfr
nervous system diseaseMthfr
neural tube defectMthfr
Neural Tube Defect, Folate-SensitiveMthfr
neutropeniaMthfr
non-arteritic anterior ischemic optic neuropathyMthfr
non-Hodgkin lymphomaMthfr
obesityComt
obsessive-compulsive disorderComt
open-angle glaucomaMthfr
Oral Lichen PlanusDnmt1
oral squamous cell carcinomaMthfr
osteonecrosisMthfr
osteosarcomaMthfr
Ovarian NeoplasmsComt , Dnmt1
PainComt
pancreatic cancerMthfr
pancreatic ductal carcinomaDnmt1
Pancreatic Intraepithelial NeoplasiaDnmt1
panic disorderComt
Parkinson's diseaseHnmt
Parkinsonian DisordersComt
peripheral artery diseaseMthfr
Peritoneal FibrosisDnmt1
pheochromocytomaComt
Pick's diseaseHnmt
polycystic ovary syndromeComt
pre-eclampsiaComt
precursor lymphoblastic lymphoma/leukemiaMthfr
prostate adenocarcinomaDnmt1
prostate cancerMthfr
prostate carcinoma in situCarm1 , Dnmt1
Prostatic NeoplasmsCarm1 , Comt , Dnmt1 , Gnmt , Mthfr , Setdb1
psoriasisCarm1 , Comt
pulmonary embolismMthfr
pyridoxine deficiency anemiaAhcy
rectal neoplasmMthfr
renal artery diseaseMthfr
renal cell carcinomaComt , Mthfr , Nnmt
Reperfusion InjuryPnmt
retinal diseaseMthfr
retinal vein occlusionMthfr
Rett syndromeSetdb1
RhabdomyolysisAhcy
rheumatoid arthritisDnmt1 , Mthfr
rhinitisHnmt
schizophreniaComt , Dnmt1 , Hnmt , Mthfr , Setdb1
Schizophrenia Spectrum and Other Psychotic DisordersComt
seminomaPrmt5
sickle cell anemiaMthfr
skin diseaseMthfr
Skin/Hair/Eye Pigmentation, Variation In, 9Ahcy
Smith-Magenis syndromePnmt
spina bifidaMthfr , Pcmt1
spinal cord diseaseMthfr
squamous cell carcinomaMthfr
Stomach NeoplasmsDnmt1 , Mthfr
StrokeMthfr
systemic lupus erythematosusDnmt1
Temporomandibular Joint DisordersComt
tetralogy of FallotMthfr
thrombocytopeniaMthfr
thrombophiliaMthfr
thrombosisMthfr
Thrombotic MicroangiopathiesMthfr
thyrotoxicosisMthfr
transitional cell carcinomaMthfr
type 1 diabetes mellitusMthfr
type 2 diabetes mellitusDnmt1 , Mthfr
ulcerative colitisHnmt
uremiaComt
urinary bladder cancerAs3mt , Comt , Dnmt1 , Mthfr
urticariaHnmt
Uterine Cervical NeoplasmsDnmt1 , Mthfr
Vascular CalcificationMthfr
vascular diseaseMthfr
Venous ThromboembolismMthfr
Venous ThrombosisComt , Mthfr
visual epilepsyGamt
vitiligoComt
Wilson diseaseAhcy , Asmt
Pathway Annotations Associated with Genes in the homocysteine metabolic pathway
Pathway TermsGene Symbols
5'-end pre-mRNA capping pathwayRnmt
AGAT deficiency pathwayGamt
alkaptonuria pathwayComt , Pnmt
altered folate cycle metabolic pathwayMthfr
altered folate mediated one-carbon metabolic pathwayMthfr
androgen signaling pathwayCarm1 , Prmt1
arginine and proline metabolic pathwayGamt
aromatic L-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 pathwayComt , Pnmt
hereditary folate malabsorption pathwayMthfr
histidine metabolic pathwayHnmt , Prmt3
histidinemia 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 pathwayAhcy , Dnmt1 , Mthfr
hypermethioninemia pathwayAhcy , Dnmt1 , Mthfr
hypermethioninemia pathwayAhcy , Dnmt1 , Mthfr
hyperprolinemia type I pathwayGamt
hyperprolinemia type II pathwayGamt
lysine degradation pathwayDot1l , Setdb1 , Suv39h2
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 pathwayGamt , Gnmt
ornithine translocase deficiency pathwayGamt
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 pathwayGamt , Gnmt
selenoamino acid metabolic pathwayAhcy
steroid hormone biosynthetic pathwayComt
tryptophan metabolic pathwayAsmt
tyrosine metabolic pathwayComt , Pnmt
tyrosinemia type I 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: