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Gene Gene information from NCBI Gene database.
Entrez ID 4548
Gene name 5-methyltetrahydrofolate-homocysteine methyltransferase
Gene symbol MTR
Synonyms (NCBI Gene)
HMAGMScblG
Chromosome 1
Chromosome location 1q43
Summary This gene encodes the 5-methyltetrahydrofolate-homocysteine methyltransferase. This enzyme, also known as cobalamin-dependent methionine synthase, catalyzes the final step in methionine biosynthesis. Mutations in MTR have been identified as the underlying
SNPs SNP information provided by dbSNP.
21 Show/Hide all (21)
SNP ID Visualize variation Clinical significance Consequence
rs1805087 A>G Benign, risk-factor, uncertain-significance Coding sequence variant, missense variant
rs116836001 C>G,T Conflicting-interpretations-of-pathogenicity, uncertain-significance Missense variant, coding sequence variant
rs121913578 C>T Likely-pathogenic, pathogenic, pathogenic-likely-pathogenic Missense variant, coding sequence variant
rs121913580 C>T Pathogenic Stop gained, coding sequence variant
rs121913581 G>T Pathogenic Stop gained, coding sequence variant
miRNA miRNA information provided by mirtarbase database.
921 Show/Hide all (921)
miRTarBase ID miRNA Experiments Reference
MIRT047589 hsa-miR-10a-5p CLASH 23622248
MIRT044357 hsa-miR-106b-5p CLASH 23622248
MIRT042208 hsa-miR-484 CLASH 23622248
MIRT041354 hsa-miR-193b-3p CLASH 23622248
MIRT041354 hsa-miR-193b-3p CLASH 23622248
Gene ontology (GO) Gene Ontology (GO) annotations describing the biological processes, molecular functions, and cellular components associated with a gene.
34 Show/Hide all (34)
GO ID Ontology Definition Evidence Reference
GO:0000096 Process Sulfur amino acid metabolic process TAS
GO:0005515 Function Protein binding IPI 17288554, 23825108, 27771510
GO:0005737 Component Cytoplasm IEA
GO:0005829 Component Cytosol IBA
GO:0005829 Component Cytosol TAS
Other IDs Other IDs provides unique identifiers for this gene in OMIM, HGNC, and Ensembl databases.
MIM HGNC e!Ensembl
156570 7468 ENSG00000116984
Protein Protein information from UniProt database.
UniProt ID Unique identifier for the protein in the UniProt database. Click to view detailed protein information.
Q99707
Protein name Methionine synthase (MS) (EC 2.1.1.13) (5-methyltetrahydrofolate--homocysteine methyltransferase) (Cobalamin-dependent methionine synthase) (Vitamin-B12 dependent methionine synthase)
Protein function Catalyzes the transfer of a methyl group from methylcob(III)alamin (MeCbl) to homocysteine, yielding enzyme-bound cob(I)alamin and methionine in the cytosol (PubMed:16769880, PubMed:17288554, PubMed:27771510). MeCbl is an active form of cobalami
PDB 2O2K , 4CCZ
Family and domains

Pfam

Accession ID Position in sequence Description Type
PF00809 Pterin_bind 375 → 613 Pterin binding enzyme Domain
PF02310 B12-binding 773 → 874 B12 binding domain Domain
PF02574 S-methyl_trans 31 → 338 Homocysteine S-methyltransferase Family
PF02607 B12-binding_2 671 → 748 B12 binding domain Domain
PF02965 Met_synt_B12 965 → 1246 Vitamin B12 dependent methionine synthase, activation domain Domain
Tissue specificity TISSUE SPECIFICITY: Widely expressed. Expressed at the highest levels in pancreas, heart, brain, skeletal muscle and placenta (PubMed:8968735, PubMed:8968737). Expressed at lower levels in lung, liver and kidney (PubMed:8968735, PubMed:8968737). {ECO:0000
Sequence
Sequence length 1265
Interactions View interactions
Pathways Pathway information has different metabolic/signaling pathways associated with genes.
KEGG Pathway Reactome Pathway
Cysteine and methionine metabolism Methylation
Selenocompound metabolism Sulfur amino acid metabolism
One carbon pool by folate Cobalamin (Cbl, vitamin B12) transport and metabolism
Metabolic pathways Defective MTRR causes methylmalonic aciduria and homocystinuria type cblE
Biosynthesis of amino acids Defective MTR causes methylmalonic aciduria and homocystinuria type cblG
Cobalamin transport and metabolism  
Folate transport and metabolism  
Associated diseases Disease associations from ClinVar (causal & non-causal) and other databases (OMIM, Orphanet, GWAS, etc.).
62
Evidence Score: ★☆☆☆☆  Gene-disease association found in Text Mining only ★★☆☆☆  Found in Text Mining and Unknown/Other Associations ★★★☆☆  Reported in Unknown/Other Associations across ≥2 Sources ★★★★☆  ClinVar: Pathogenic/Likely Pathogenic (<5 Variants) ★★★★★  ClinVar: Pathogenic/Likely Pathogenic (≥5 Variants)
Causal Diseases associated with Pathogenic or Likely Pathogenic variants in ClinVar
Show/Hide Causal Diseases (11)
Phenotype Name Clinical Significance dbSNP ID RCV Accession Evidence Score
Decreased methionine synthase activity Pathogenic; Likely pathogenic rs121913578, rs1190777785 RCV001003947
RCV001003946
★★★★★
★★★★☆
ClinVar: Pathogenic / Likely Pathogenic (<5 Variants)
Disorders of Intracellular Cobalamin Metabolism Pathogenic rs121913578 RCV000778974
★★★★★
★★★★☆
ClinVar: Pathogenic / Likely Pathogenic (<5 Variants)
Epilepsy Pathogenic rs121913578 RCV000162189
★★★★★
★★★★☆
ClinVar: Pathogenic / Likely Pathogenic (<5 Variants)
Homocystinuria Pathogenic; Likely pathogenic rs121913578, rs1190777785 RCV001003947
RCV001003946
★★★★★
★★★★☆
ClinVar: Pathogenic / Likely Pathogenic (<5 Variants)
Intellectual disability Likely pathogenic; Pathogenic rs1324468065 RCV005626831
★★★★★
★★★★☆
ClinVar: Pathogenic / Likely Pathogenic (<5 Variants)
Unknown / Other Associations ClinVar entries with uncertain/conflicting evidence, and associations from other databases (OMIM, Orphanet, GWAS, etc.) where the gene is not established as causal.
Show/Hide Unknown Diseases (51)
Phenotype Name Clinical Significance Source Reference Evidence Score
Acute myeloid leukemia Benign; Uncertain significance; Likely benign ClinVar —
★★★★★
★★☆☆☆
Found in Text Mining + Unknown/Other Associations
AUTISM SPECTRUM DISORDER — CTD 35663546
★★★★★
★★☆☆☆
Found in Text Mining + Unknown/Other Associations
AUTISM SPECTRUM DISORDERS — Disgenet —
★★★★★
★★☆☆☆
Found in Text Mining + Unknown/Other Associations
AUTISTIC DISORDER — Disgenet —
★★★★★
★★☆☆☆
Found in Text Mining + Unknown/Other Associations
BIPOLAR DISORDER — Disgenet —
★★★★★
★★☆☆☆
Found in Text Mining + Unknown/Other Associations
Associations from Text Mining Disease associations identified through text mining
Show/Hide Text Mining Associations (293)
Disease Name Disease (Merged) Source PMID Relationship Type Evidence Score
Acromegaly Acromegaly BEFREE 26154858
★★★★★
★☆☆☆☆
Found in Text Mining only
Acute lymphocytic leukemia Lymphocytic Leukemia BEFREE 16013960, 17454638, 19775302, 21643952, 22838948
★★★★★
★☆☆☆☆
Found in Text Mining only
Adenocarcinoma Adenocarcinoma BEFREE 15319544
★★★★★
★☆☆☆☆
Found in Text Mining only
Adenocarcinoma Of Esophagus Esophageal Cancer BEFREE 17726616
★★★★★
★☆☆☆☆
Found in Text Mining only
Adenoma Adenoma LHGDN 19124508
★★★★★
★☆☆☆☆
Found in Text Mining only
Adenoma of large intestine Colorectal adenoma BEFREE 14744749, 19124508, 22407825, 23593229, 31740010, 9886567
★★★★★
★☆☆☆☆
Found in Text Mining only
Adult Acute Lymphocytic Leukemia Lymphocytic Leukemia BEFREE 11986237, 15159311, 16013960, 17454638, 21643952, 22838948
★★★★★
★☆☆☆☆
Found in Text Mining only
Adult Diffuse Large B-Cell Lymphoma B-cell Lymphoma BEFREE 12648076
★★★★★
★☆☆☆☆
Found in Text Mining only
Alzheimer Disease Alzheimer disease Pubtator 15201366 Associate
★★★★★
★☆☆☆☆
Found in Text Mining only
Amyotrophic Lateral Sclerosis Amyotrophic Lateral Sclerosis BEFREE 28785215
★★★★★
★☆☆☆☆
Found in Text Mining only