Gene Gene information from NCBI Gene database.
Entrez ID 1788
Gene name DNA methyltransferase 3 alpha
Gene symbol DNMT3A
Synonyms (NCBI Gene)
DNMT3A2HESJASM.HsaIIIATBRS
Chromosome 2
Chromosome location 2p23.3
Summary CpG methylation is an epigenetic modification that is important for embryonic development, imprinting, and X-chromosome inactivation. Studies in mice have demonstrated that DNA methylation is required for mammalian development. This gene encodes a DNA met
SNPs SNP information provided by dbSNP.
53
SNP ID Visualize variation Clinical significance Consequence
rs144689354 G>A Likely-pathogenic, uncertain-significance Missense variant, coding sequence variant, genic downstream transcript variant, non coding transcript variant
rs147001633 C>A,G,T Likely-pathogenic, pathogenic, uncertain-significance Missense variant, coding sequence variant, genic downstream transcript variant, non coding transcript variant
rs147828672 T>C,G Likely-pathogenic Missense variant, coding sequence variant, genic downstream transcript variant, non coding transcript variant
rs149095705 G>A,C,T Likely-pathogenic Missense variant, coding sequence variant, genic downstream transcript variant, non coding transcript variant
rs370376334 G>A,C Pathogenic Stop gained, non coding transcript variant, synonymous variant, genic downstream transcript variant, coding sequence variant
miRNA miRNA information provided by mirtarbase database.
317
miRTarBase ID miRNA Experiments Reference
MIRT003029 hsa-miR-29b-3p Luciferase reporter assayWestern blotqRT-PCR 17890317
MIRT003028 hsa-miR-29c-3p Luciferase reporter assayWestern blotqRT-PCR 17890317
MIRT003021 hsa-miR-29a-3p Luciferase reporter assayWestern blotqRT-PCR 17890317
MIRT000716 hsa-miR-143-3p real time qRT-PCRLuciferase reporter assayWestern blot 19638978
MIRT000716 hsa-miR-143-3p real time qRT-PCRLuciferase reporter assayWestern blot 19638978
Transcription factors Transcription factors information provided by TRRUST V2 database.
7
Transcription factor Regulation Reference
MDM2 Activation 22733537
RB1 Repression 22733537
SALL3 Unknown 19139273
SP1 Activation 15362956
SP2 Activation 15362956
Gene ontology (GO) Gene Ontology (GO) annotations describing the biological processes, molecular functions, and cellular components associated with a gene.
71
GO ID Ontology Definition Evidence Reference
GO:0000122 Process Negative regulation of transcription by RNA polymerase II IDA 23042785
GO:0000122 Process Negative regulation of transcription by RNA polymerase II IMP 19786833
GO:0000775 Component Chromosome, centromeric region IEA
GO:0000791 Component Euchromatin IDA 12138111
GO:0000792 Component Heterochromatin IEA
Other IDs Other IDs provides unique identifiers for this gene in OMIM, HGNC, and Ensembl databases.
MIM HGNC e!Ensembl
602769 2978 ENSG00000119772
Protein Protein information from UniProt database.
UniProt ID Unique identifier for the protein in the UniProt database. Click to view detailed protein information.
Q9Y6K1
Protein name DNA (cytosine-5)-methyltransferase 3A (Dnmt3a) (EC 2.1.1.37) (Cysteine methyltransferase DNMT3A) (EC 2.1.1.-) (DNA methyltransferase HsaIIIA) (DNA MTase HsaIIIA) (M.HsaIIIA)
Protein function Required for genome-wide de novo methylation and is essential for the establishment of DNA methylation patterns during development (PubMed:12138111, PubMed:16357870, PubMed:30478443). DNA methylation is coordinated with methylation of histones (
PDB 2QRV , 3A1A , 3A1B , 3LLR , 3SVM , 4QBQ , 4QBR , 4QBS , 4U7P , 4U7T , 5YX2 , 6BRR , 6F57 , 6PA7 , 6W89 , 6W8B , 6W8D , 6W8J , 8BA5 , 8QZM , 8TDR , 8TE1 , 8TE3 , 8TE4 , 8U5H , 8UW1
Family and domains

Pfam

Accession ID Position in sequence Description Type
PF00855 PWWP 290 377 PWWP domain Domain
PF17980 ADD_DNMT3 475 530 Cysteine rich ADD domain in DNMT3 Domain
PF00145 DNA_methylase 634 776 C-5 cytosine-specific DNA methylase Domain
Tissue specificity TISSUE SPECIFICITY: Highly expressed in fetal tissues, skeletal muscle, heart, peripheral blood mononuclear cells, kidney, and at lower levels in placenta, brain, liver, colon, spleen, small intestine and lung. {ECO:0000269|PubMed:10325416}.
Sequence
MPAMPSSGPGDTSSSAAEREEDRKDGEEQEEPRGKEERQEPSTTARKVGRPGRKRKHPPV
ESGDTPKDPAVISKSPSMAQDSGASELLPNGDLEKRSEPQPEEGSPAGGQKGGAPAEGEG
AAETLPEASRAVENGCCTPKEGRGAPAEAGKEQKETNIESMKMEGSRGRLRGGLGWESSL
RQRPMPRLTFQAGDPYYISKRKRDEWLARWKREAEKKAKVIAGMNAVEENQGPGESQKVE
EASPPAVQQPTDPASPTVATTPEPVGSDAGDKNATKAGDDEPEYEDGRGFGIGELVWGKL
RGFSWWPGRIVSWWMTGRSRAAEGTRWVMWFGDGKFSVVCVEKLMPLSSFCSAFHQATYN
KQPMYRKAIYEVLQVAS
SRAGKLFPVCHDSDESDTAKAVEVQNKPMIEWALGGFQPSGPK
GLEPPEEEKNPYKEVYTDMWVEPEAAAYAPPPPAKKPRKSTAEKPKVKEIIDERTRERLV
YEVRQKCRNIEDICISCGSLNVTLEHPLFVGGMCQNCKNCFLECAYQYDD
DGYQSYCTIC
CGGREVLMCGNNNCCRCFCVECVDLLVGPGAAQAAIKEDPWNCYMCGHKGTYGLLRRRED
WPSRLQMFFANNHDQEFDPPKVYPPVPAEKRKPIRVLSLFDGIATGLLVLKDLGIQVDRY
IASEVCEDSITVGMVRHQGKIMYVGDVRSVTQKHIQEWGPFDLVIGGSPCNDLSIVNPAR
KGLYEGTGRLFFEFYRLLHDARPKEGDDRPFFWLFENVVAMGVSDKRDISRFLESN
PVMI
DAKEVSAAHRARYFWGNLPGMNRPLASTVNDKLELQECLEHGRIAKFSKVRTITTRSNSI
KQGKDQHFPVFMNEKEDILWCTEMERVFGFPVHYTDVSNMSRLARQRLLGRSWSVPVIRH
LFAPLKEYFACV
Sequence length 912
Interactions View interactions
Pathways Pathway information has different metabolic/signaling pathways associated with genes.
  KEGG  Reactome
  Cysteine and methionine metabolism
Metabolic pathways
Efferocytosis
MicroRNAs in cancer
  PRC2 methylates histones and DNA
RMTs methylate histone arginines
Associated diseases Disease associations from ClinVar categorized as Causal (Pathogenic/Likely Pathogenic) or Unknown.
723
Causal Diseases associated with Pathogenic or Likely Pathogenic variants in ClinVar
Phenotype Name Clinical Significance dbSNP ID RCV Accession
Abnormality of the nervous system Likely pathogenic; Pathogenic rs147001633 RCV001814155
Acute myeloid leukemia Likely pathogenic; Pathogenic rs1674056899, rs1313738991, rs147001633, rs377577594, rs779626155, rs757823678, rs771174392, rs759380437, rs1573338559 RCV005025733
RCV002249029
RCV000430182
RCV000429128
RCV003338604
RCV004796213
RCV000760250
RCV000760251
RCV001003799
Autism spectrum disorder Likely pathogenic; Pathogenic rs2149307214, rs1674056899, rs759747476, rs149095705 RCV001871979
RCV002226414
RCV003127441
RCV003233631
Clonal Cytopenia of Undetermined Significance Likely pathogenic; Pathogenic rs147001633 RCV003153242
Unknown Diseases with uncertain, conflicting, or no pathogenic evidence in ClinVar
Phenotype Name Clinical Significance dbSNP ID RCV Accession
Craniosynostosis syndrome Conflicting classifications of pathogenicity rs781254365 RCV005626291
Hepatocellular carcinoma - rs1166765403 RCV005931994
Hereditary pheochromocytoma and paraganglioma Conflicting classifications of pathogenicity rs760854242 RCV005909262
Malignant lymphoma, large B-cell, diffuse Benign; Conflicting classifications of pathogenicity rs10084238, rs147828672 RCV005925250
RCV003448984
Associations from Text MiningDisease associations identified through Pubtator
Disease Name Relationship Type References
Acute erythroleukemia Associate 35967966
Adenomatous Polyposis Coli Associate 21347319
Adrenal Insufficiency Associate 25126948
Adrenocortical Carcinoma Associate 25078331, 37528470
Aging Premature Associate 34210413
Alzheimer Disease Associate 26371346, 36646969
Anemia Associate 32243522, 37160316
Anemia Aplastic Associate 25139356, 26132940, 29720492, 34587721, 37087521
Aortic Aneurysm Abdominal Associate 31001930
Aortic Aneurysm Thoracic Associate 36291095