Gene Gene information from NCBI Gene database.
Entrez ID 1786
Gene name DNA methyltransferase 1
Gene symbol DNMT1
Synonyms (NCBI Gene)
ADCADNAIMCXXC9DNMTHSN1EMCMTm.HsaI
Chromosome 19
Chromosome location 19p13.2
Summary This gene encodes an enzyme that transfers methyl groups to cytosine nucleotides of genomic DNA. This protein is the major enzyme responsible for maintaining methylation patterns following DNA replication and shows a preference for hemi-methylated DNA. Me
SNPs SNP information provided by dbSNP.
23
SNP ID Visualize variation Clinical significance Consequence
rs62621089 G>A Likely-benign, conflicting-interpretations-of-pathogenicity, uncertain-significance Coding sequence variant, missense variant
rs141856197 G>A Conflicting-interpretations-of-pathogenicity Synonymous variant, coding sequence variant
rs143904813 G>A Likely-benign, conflicting-interpretations-of-pathogenicity, benign Synonymous variant, coding sequence variant
rs143925123 G>A,C Conflicting-interpretations-of-pathogenicity Synonymous variant, coding sequence variant
rs144685297 G>A Conflicting-interpretations-of-pathogenicity 5 prime UTR variant, synonymous variant, coding sequence variant
miRNA miRNA information provided by mirtarbase database.
157
miRTarBase ID miRNA Experiments Reference
MIRT000020 hsa-miR-148a-3p Luciferase reporter assay 20146264
MIRT004456 hsa-miR-152-3p Luciferase reporter assay 20146264
MIRT000020 hsa-miR-148a-3p qRT-PCRLuciferase reporter assayWestern blot 20483747
MIRT000020 hsa-miR-148a-3p qRT-PCRLuciferase reporter assayWestern blot 20483747
MIRT000020 hsa-miR-148a-3p qRT-PCRLuciferase reporter assayWestern blot 20483747
Transcription factors Transcription factors information provided by TRRUST V2 database.
16
Transcription factor Regulation Reference
APC Repression 12538344
DMAP1 Unknown 20864525
E2F1 Repression 24502362
EP300 Activation 19275888
HBP1 Repression 23249948
Gene ontology (GO) Gene Ontology (GO) annotations describing the biological processes, molecular functions, and cellular components associated with a gene.
55
GO ID Ontology Definition Evidence Reference
GO:0000122 Process Negative regulation of transcription by RNA polymerase II IEA
GO:0000122 Process Negative regulation of transcription by RNA polymerase II TAS 10888872
GO:0000792 Component Heterochromatin IEA
GO:0001674 Component Female germ cell nucleus IEA
GO:0003677 Function DNA binding IBA
Other IDs Other IDs provides unique identifiers for this gene in OMIM, HGNC, and Ensembl databases.
MIM HGNC e!Ensembl
126375 2976 ENSG00000130816
Protein Protein information from UniProt database.
UniProt ID Unique identifier for the protein in the UniProt database. Click to view detailed protein information.
P26358
Protein name DNA (cytosine-5)-methyltransferase 1 (Dnmt1) (EC 2.1.1.37) (CXXC-type zinc finger protein 9) (DNA methyltransferase HsaI) (DNA MTase HsaI) (M.HsaI) (MCMT)
Protein function Methylates CpG residues. Preferentially methylates hemimethylated DNA. Associates with DNA replication sites in S phase maintaining the methylation pattern in the newly synthesized strand, that is essential for epigenetic inheritance. Associates
PDB 3EPZ , 3PTA , 3SWR , 4WXX , 4YOC , 4Z96 , 4Z97 , 5WVO , 5YDR , 6K3A , 6L1F , 6X9I , 6X9J , 6X9K , 7SFC , 7SFD , 7SFE , 7SFF , 7SFG , 7XI9 , 7XIB , 8V9U , 8XQC
Family and domains

Pfam

Accession ID Position in sequence Description Type
PF06464 DMAP_binding 16 105 DMAP1-binding Domain Domain
PF12047 DNMT1-RFD 399 534 Cytosine specific DNA methyltransferase replication foci domain Domain
PF02008 zf-CXXC 645 691 CXXC zinc finger domain Domain
PF01426 BAH 755 880 BAH domain Domain
PF01426 BAH 931 1100 BAH domain Domain
PF00145 DNA_methylase 1139 1594 C-5 cytosine-specific DNA methylase Domain
Tissue specificity TISSUE SPECIFICITY: Ubiquitous; highly expressed in fetal tissues, heart, kidney, placenta, peripheral blood mononuclear cells, and expressed at lower levels in spleen, lung, brain, small intestine, colon, liver, and skeletal muscle. Isoform 2 is less exp
Sequence
MPARTAPARVPTLAVPAISLPDDVRRRLKDLERDSLTEKECVKEKLNLLHEFLQTEIKNQ
LCDLETKLRKEELSEEGYLAKVKSLLNKDLSLENGAHAYNREVNG
RLENGNQARSEARRV
GMADANSPPKPLSKPRTPRRSKSDGEAKPEPSPSPRITRKSTRQTTITSHFAKGPAKRKP
QEESERAKSDESIKEEDKDQDEKRRRVTSRERVARPLPAEEPERAKSGTRTEKEEERDEK
EEKRLRSQTKEPTPKQKLKEEPDREARAGVQADEDEDGDEKDEKKHRSQPKDLAAKRRPE
EKEPEKVNPQISDEKDEDEKEEKRRKTTPKEPTEKKMARAKTVMNSKTHPPKCIQCGQYL
DDPDLKYGQHPPDAVDEPQMLTNEKLSIFDANESGFESYEALPQHKLTCFSVYCKHGHLC
PIDTGLIEKNIELFFSGSAKPIYDDDPSLEGGVNGKNLGPINEWWITGFDGGEKALIGFS
TSFAEYILMDPSPEYAPIFGLMQEKIYISKIVVEFLQSNSDSTYEDLINKIETT
VPPSGL
NLNRFTEDSLLRHAQFVVEQVESYDEAGDSDEQPIFLTPCMRDLIKLAGVTLGQRRAQAR
RQTIRHSTREKDRGPTKATTTKLVYQIFDTFFAEQIEKDDREDKENAFKRRRCGVCEVCQ
QPECGKCKACKDMVKFGGSGRSKQACQERRC
PNMAMKEADDDEEVDDNIPEMPSPKKMHQ
GKKKKQNKNRISWVGEAVKTDGKKSYYKKVCIDAETLEVGDCVSVIPDDSSKPLYLARVT
ALWEDSSNGQMFHAHWFCAGTDTVLGATSDPLELFLVDECEDMQLSYIHSKVKVIYKAPS
ENWAMEGGMDPESLLEGDDGKTYFYQLWYDQDYARFESPP
KTQPTEDNKFKFCVSCARLA
EMRQKEIPRVLEQLEDLDSRVLYYSATKNGILYRVGDGVYLPPEAFTFNIKLSSPVKRPR
KEPVDEDLYPEHYRKYSDYIKGSNLDAPEPYRIGRIKEIFCPKKSNGRPNETDIKIRVNK
FYRPENTHKSTPASYHADINLLYWSDEEAVVDFKAVQGRCTVEYGEDLPECVQVYSMGGP
NRFYFLEAYNAKSKSFEDPP
NHARSPGNKGKGKGKGKGKPKSQACEPSEPEIEIKLPKLR
TLDVFSGCGGLSEGFHQAGISDTLWAIEMWDPAAQAFRLNNPGSTVFTEDCNILLKLVMA
GETTNSRGQRLPQKGDVEMLCGGPPCQGFSGMNRFNSRTYSKFKNSLVVSFLSYCDYYRP
RFFLLENVRNFVSFKRSMVLKLTLRCLVRMGYQCTFGVLQAGQYGVAQTRRRAIILAAAP
GEKLPLFPEPLHVFAPRACQLSVVVDDKKFVSNITRLSSGPFRTITVRDTMSDLPEVRNG
ASALEISYNGEPQSWFQRQLRGAQYQPILRDHICKDMSALVAARMRHIPLAPGSDWRDLP
NIEVRLSDGTMARKLRYTHHDRKNGRSSSGALRGVCSCVEAGKACDPAARQFNTLIPWCL
PHTGNRHNHWAGLYGRLEWDGFFSTTVTNPEPMGKQGRVLHPEQHRVVSVRECARSQGFP
DTYRLFGNILDKHRQVGNAVPPPLAKAIGLEIKL
CMLAKARESASAKIKEEEAAKD
Sequence length 1616
Interactions View interactions
Pathways Pathway information has different metabolic/signaling pathways associated with genes.
  KEGG  Reactome
  Cysteine and methionine metabolism
Metabolic pathways
MicroRNAs in cancer
  PRC2 methylates histones and DNA
SUMOylation of DNA methylation proteins
Associated diseases Disease associations from ClinVar (causal & non-causal) and other databases (OMIM, Orphanet, GWAS, etc.).
74
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
Phenotype Name Clinical Significance dbSNP ID RCV Accession Evidence Score
Autosomal dominant cerebellar ataxia, deafness and narcolepsy Likely pathogenic; Pathogenic rs2145253354, rs199473690, rs397509391, rs397509392, rs397509393, rs2038416963 RCV002249028
RCV002283444
RCV000043631
RCV000043632
RCV000043633
View all (1 more)
★★★★★
ClinVar: Pathogenic / Likely Pathogenic (≥5 Variants)
Charcot-Marie-Tooth disease Likely pathogenic; Pathogenic rs199473690 RCV000789093
★★★★☆
ClinVar: Pathogenic / Likely Pathogenic (<5 Variants)
Hereditary sensory neuropathy-deafness-dementia syndrome Likely pathogenic; Pathogenic rs1599366421, rs2145253737, rs199473692, rs199473690, rs199473691, rs397509391, rs397509392, rs397509393 RCV001378601
RCV001385365
RCV000149568
RCV000022529
RCV000022530
View all (3 more)
★★★★★
ClinVar: Pathogenic / Likely Pathogenic (≥5 Variants)
Pituitary stalk interruption syndrome Likely pathogenic rs2038202226 RCV001257292
★★★★☆
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.
Phenotype Name Clinical Significance Source Evidence Score
Acute myeloid leukemia Likely benign; Benign ClinVar
★★☆☆☆
Found in Text Mining + Unknown/Other Associations
ANXIETY DISORDERS CTD, Disgenet
CTD, Disgenet
★★☆☆☆
Found in Text Mining + Unknown/Other Associations
ARTHRITIS, EXPERIMENTAL CTD
★★☆☆☆
Found in Text Mining + Unknown/Other Associations
ASTHMA CTD, Disgenet
CTD, Disgenet
★★☆☆☆
Found in Text Mining + Unknown/Other Associations
Associations from Text Mining Disease associations identified through text mining
Disease Name Disease (Merged) Source PMID Relationship Type Evidence Score
Acne Acne BEFREE 28814964
★☆☆☆☆
Found in Text Mining only
Acne Vulgaris Acne BEFREE 28814964
★☆☆☆☆
Found in Text Mining only
Acute lymphocytic leukemia Lymphocytic Leukemia BEFREE 25444908
★☆☆☆☆
Found in Text Mining only
Acute monocytic leukemia Monocytic Leukemia BEFREE 24085765, 25315154
★☆☆☆☆
Found in Text Mining only
Acute Promyelocytic Leukemia Promyelocytic Leukemia BEFREE 22820861
★☆☆☆☆
Found in Text Mining only
Adenocarcinoma Adenocarcinoma BEFREE 16053511, 17053888
★☆☆☆☆
Found in Text Mining only
Adenocarcinoma Adenocarcinoma LHGDN 17053888
★☆☆☆☆
Found in Text Mining only
Adenocarcinoma Adenocarcinoma CTD_human_DG 17571247
★☆☆☆☆
Found in Text Mining only
Adenocarcinoma Of Esophagus Esophageal Cancer BEFREE 24025864
★☆☆☆☆
Found in Text Mining only
Adenocarcinoma of lung (disorder) Lung adenocarcinoma BEFREE 27190263, 31194977
★☆☆☆☆
Found in Text Mining only