ConVarT

ClinVar Data

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Variation ID	Allele ID	RS Number	Variant Type	Record	Alteration	Clinicial Sig.	Last Update	Phenotypes	Cytogenetic	Review Status	RCV Acc.N.

gnomAD

Frameshift Variant

Missense Variant

Splice Region Variant

Stop Gained

Synonymous Variant

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Variant ID	Transcript ID	Alteration	Annotation	Allele C.	Allele N.	Allele F.	rsNumber	Filter
2-25505261-G-T	ENST00000406659	p.Pro166His	Missense Variant	0	0	0	rs770891159
2-25505262-G-A	ENST00000406659	p.Pro166Ser	Missense Variant	0	0	0	rs778675092
2-25505262-G-T	ENST00000406659	p.Pro166Thr	Missense Variant	1	31370	0.000032	rs778675092
2-25505263-T-A	ENST00000406659	p.Ile165Ile	Synonymous Variant	0	0	0	rs745720212
2-25505270-G-T	ENST00000406659	p.Thr163Asn	Missense Variant	2	31370	0.000064	rs1220450373
2-25505284-G-A	ENST00000406659	p.Ala158Ala	Synonymous Variant	0	0	0	rs1263164315
2-25505287-T-A	ENST00000406659	p.Ala157Ala	Synonymous Variant	1	31364	0.000032	rs181544799
2-25505290-C-A	ENST00000406659	p.Gly156Gly	Synonymous Variant	0	0	0	rs776751263
2-25505291-C-T	ENST00000406659	p.Gly156Glu	Missense Variant	2	31372	0.000064	rs761905111
2-25505293-T-A	ENST00000406659	p.Pro155Pro	Synonymous Variant	2	31360	0.000064	rs1272894258	RF
2-25505296-T-A	ENST00000406659	p.Ala154Ala	Synonymous Variant	0	0	0	rs769741588
2-25505298-C-T	ENST00000406659	p.Ala154Thr	Missense Variant	0	0	0	rs1180248310
2-25505303-G-A	ENST00000406659	p.Ser152Phe	Missense Variant	1	31348	0.000032	rs773465605
2-25505311-C-T	ENST00000406659	p.Ala149Ala	Synonymous Variant	2	31358	0.000064	rs763553315
2-25505312-G-A	ENST00000406659	p.Ala149Val	Missense Variant	0	0	0	rs767055283
2-25505313-C-T	ENST00000406659	p.Ala149Thr	Missense Variant	0	0	0	rs751918466
2-25505318-G-T	ENST00000406659	p.Ala147Glu	Missense Variant	1	31368	0.000032	rs1210750462
2-25505325-C-T	ENST00000406659	p.Ala145Thr	Missense Variant	0	0	0	rs759826795
2-25505329-T-A	ENST00000406659	p.Arg143Arg	Synonymous Variant	0	0	0	rs767155995
2-25505330-C-T	ENST00000406659	p.Arg143Gln	Missense Variant	0	0	0	rs745432645

Showing 1 to 20 of 152 entries

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Post-translational Modifications (PTMs)

Methylation

Phosphorylation

Sumoylation

Ubiquitination

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Gene Name	ACC ID	PTM Type	Position	Mod-rsd	Site +/-7 Aa	Mw_kd	Site grpID
DNMT3A	Q9Y6K1	Phosphorylation	105	S105-p	EPQPEEGsPAGGQKG	101.86	3217803
DNMT3A	Q9Y6K1	Phosphorylation	138	T138-p	AVENGCCtPKEGRGA	101.86	23100108
DNMT3A	Q9Y6K1	Phosphorylation	156	T156-p	AGKEQKEtNIESMKM	101.86	23100111
DNMT3A	Q9Y6K1	Methylation	171	R171-m1	EGSRGRLrGGLGWEs	101.86	6010255
DNMT3A	Q9Y6K1	Phosphorylation	178	S178-p	rGGLGWEssLRQRPM	101.86	25289560
DNMT3A	Q9Y6K1	Phosphorylation	179	S179-p	GGLGWEssLRQRPMP	101.86	25289564
DNMT3A	Q9Y6K1	Phosphorylation	199	S199-p	AGDPYYIskRKRDEW	101.86	56668015
DNMT3A	Q9Y6K1	Ubiquitination	200	K200-ub	GDPYYIskRKRDEWL	101.86	22243505
DNMT3A	Q9Y6K1	Methylation	23	R23-m1	AAEREEDrKDGEEQE	101.86	57694812
DNMT3A	Q9Y6K1	Phosphorylation	236	S236-p	ENQGPGEsQKVEEAs	101.86	17439179
DNMT3A	Q9Y6K1	Phosphorylation	243	S243-p	sQKVEEAsPPAVQQP	101.86	7232136
DNMT3A	Q9Y6K1	Phosphorylation	255	S255-p	QQPTDPAsPTVATtP	101.86	4700048
DNMT3A	Q9Y6K1	Phosphorylation	261	T261-p	AsPTVATtPEPVGsD	101.86	4700054
DNMT3A	Q9Y6K1	Phosphorylation	267	S267-p	TtPEPVGsDAGDKNA	101.86	18910065
DNMT3A	Q9Y6K1	Ubiquitination	276	K276-ub	AGDKNATkAGDDEPE	101.86	610815790
DNMT3A	Q9Y6K1	Ubiquitination	299	K299-ub	IGELVWGkLRGFSWW	101.86	610815788
DNMT3A	Q9Y6K1	Ubiquitination	367	K367-ub	NKQPMYRkAIYEVLQ	101.86	22243508
DNMT3A	Q9Y6K1	Phosphorylation	377	S377-p	YEVLQVAsSRAGkLF	101.86	15419147
DNMT3A	Q9Y6K1	Ubiquitination	382	K382-ub	VAsSRAGkLFPVCHD	101.86	964510994
DNMT3A	Q9Y6K1	Phosphorylation	390	S390-p	LFPVCHDsDEsDTAK	101.86	17548178

Showing 1 to 20 of 34 entries

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Catalogue of Somatic Mutations in Cancer (COSMIC)

Deletion - Frameshift

Insertion - Frameshift

Substitution - Coding Silent

Substitution - Missense

Substitution - Nonsense

Unknown

Show entries

Gene Name	Transcript ID	Sample name	Primary Site	Primary Histology	Mutation ID	Mutation CDS	Mutation Aa	Mutation Desc.	FATHMM Prediction	FATHMM Score	Mutation Somatic Status	PUBMED PMID	Tumor Origin	Position
DNMT3A_ENST00000406659	ENST00000406659	P-0003505-T01-IM5	lung	carcinoma	47700406	c.234G>T	p.M78I	Substitution - Missense		.68928	Confirmed somatic variant	PMID: 28481359	primary	78
DNMT3A_ENST00000406659	ENST00000406659	P-0005823-T01-IM5	large_intestine	carcinoma	47697556	c.136C>T	p.R46W	Substitution - Missense		.60205	Confirmed somatic variant	PMID: 28481359	metastasis	46
DNMT3A_ENST00000406659	ENST00000406659	TCGA-94-8491-01	lung	carcinoma	47700102	c.321T>G	p.A107=	Substitution - coding silent		.66071	Confirmed somatic variant	PMID: N/A	primary	107
DNMT3A_ENST00000406659	ENST00000406659	P-0007961-T02-IM5	kidney	carcinoma	47698037	c.250G>A	p.A84T	Substitution - Missense	NEUTRAL	.4409	Confirmed somatic variant	PMID: 28481359	primary	84
DNMT3A_ENST00000406659	ENST00000406659	0207_CRUK_PC_0207_T1_DNA	prostate	carcinoma	47698364	c.177+5831C>G	p.?	Unknown	NEUTRAL	.13238	Confirmed somatic variant	PMID: N/A	primary	0
DNMT3A_ENST00000406659	ENST00000406659	TCGA-FU-A3HY-01	cervix	carcinoma	47696960	c.*18C>G	p.?	Unknown	NEUTRAL	.05453	Confirmed somatic variant	PMID: N/A	NS	0
DNMT3A_ENST00000406659	ENST00000406659	tumor_4147360	haematopoietic_and_lymphoid_tissue	lymphoid_neoplasm	47697828	c.72+474C>T	p.?	Unknown	NEUTRAL	.03929	Confirmed somatic variant	PMID: N/A	primary	0
DNMT3A_ENST00000406659	ENST00000406659	PD6722a	breast	carcinoma	47698746	c.73-1199G>C	p.?	Unknown	NEUTRAL	.0568	Confirmed somatic variant	PMID: N/A	primary	0
DNMT3A_ENST00000406659	ENST00000406659	ICGC_GBM48_tumor	central_nervous_system	primitive_neuroectodermal_tumour-medulloblastoma	47698955	c.178-8119G>A	p.?	Unknown	NEUTRAL	.05216	Confirmed somatic variant	PMID: N/A	primary	0
DNMT3A_ENST00000406659	ENST00000406659	RK101_C01	liver	carcinoma	47699300	c.-178+4801C>T	p.?	Unknown	NEUTRAL	.03215	Confirmed somatic variant	PMID: N/A	NS	0
DNMT3A_ENST00000406659	ENST00000406659	TMIT_IV_21	stomach	carcinoma	47696587	c.55C>T	p.R19W	Substitution - Missense		.68663	Reported in another cancer sample as somatic	PMID: 30239046	NS	19
DNMT3A_ENST00000406659	ENST00000406659	RK101_C01	liver	carcinoma	47699294	c.-177-5390C>T	p.?	Unknown	NEUTRAL	.01042	Confirmed somatic variant	PMID: N/A	NS	0
DNMT3A_ENST00000406659	ENST00000406659	ML_75_T_01	skin	carcinoma	47696733	c.-178+1129A>G	p.?	Unknown	NEUTRAL	.00374	Confirmed somatic variant	PMID: N/A	primary	0
DNMT3A_ENST00000406659	ENST00000406659	P-0002163-T01-IM3	lung	carcinoma	47698490	c.266C>G	p.P89R	Substitution - Missense	PATHOGENIC	.94216	Confirmed somatic variant	PMID: 28481359	primary	89
DNMT3A_ENST00000406659	ENST00000406659	PD6722a	breast	carcinoma	47698712	c.178-1143G>C	p.?	Unknown	NEUTRAL	.00866	Confirmed somatic variant	PMID: N/A	primary	0
DNMT3A_ENST00000406659	ENST00000406659	tumor_4139212	haematopoietic_and_lymphoid_tissue	lymphoid_neoplasm	47697056	c.73-5400G>T	p.?	Unknown	NEUTRAL	.05412	Confirmed somatic variant	PMID: N/A	primary	0
DNMT3A_ENST00000406659	ENST00000406659	EXTERN_MELA_20140526_051	skin	malignant_melanoma	47698154	c.-32C>T	p.?	Unknown	NEUTRAL	.39001	Confirmed somatic variant	PMID: 28467829	primary	0
DNMT3A_ENST00000406659	ENST00000406659	AOCS-113-1-5	ovary	carcinoma	47696967	c.177+3620C>G	p.?	Unknown	NEUTRAL	.01029	Confirmed somatic variant	PMID: N/A	NS	0
DNMT3A_ENST00000406659	ENST00000406659	8053200	pancreas	carcinoma	47697931	c.-178+500A>G	p.?	Unknown	NEUTRAL	.00049	Confirmed somatic variant	PMID: N/A	NS	0
DNMT3A_ENST00000406659	ENST00000406659	2485535	NS	malignant_melanoma	47696743	c.89A>C	p.E30A	Substitution - Missense	PATHOGENIC	.88348	Variant of unknown origin	PMID: 25886620	NS	30

Showing 1 to 20 of 182 entries

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dbSNP

Gene ID	Transcript ID	Consequence	Position	HGVSp	Impact

Protein Domains (PFAM)

Pfam Domain	Domain Name	Description	Positions	Clan	Clan Name	Organism
NO RESULT FOUND
PF00145	DNA_methylase	C-5 cytosine-specific DNA methylase	634-776	CL0063	NADP_Rossmann	Homo sapiens
PF00855	PWWP	PWWP domain	293-377	CL0049	Tudor	Homo sapiens
PF17980	ADD_DNMT3	Cysteine rich ADD domain in DNMT3	475-530	CL0390	zf-FYVE-PHD	Homo sapiens

List of the diseases from DisGeNET

Disease Name	Disease Category	DSI*	DPI**
Malignant neoplasm of breast	Neoplasms ; Skin and Connective Tissue Diseases ;	0.507	0.69
Crohn Disease	Digestive System Diseases ;	0.507	0.69
Cytopenia	N/A	0.507	0.69
Growth Disorders	Pathological Conditions, Signs and Symptoms ;	0.507	0.69
Profound Mental Retardation	Nervous System Diseases ; Pathological Conditions, Signs and Symptoms ; Behavior and Behavior Mechanisms ; Mental Disorders ;	0.507	0.69
Angioimmunoblastic Lymphadenopathy	Hemic and Lymphatic Diseases ; Immune System Diseases ;	0.507	0.69
Acute monocytic leukemia	Neoplasms ;	0.507	0.69
Leukemia, Myelocytic, Acute	Neoplasms ;	0.507	0.69
Leukemia, Myelomonocytic, Chronic	Neoplasms ; Hemic and Lymphatic Diseases ;	0.507	0.69
Acute Promyelocytic Leukemia	Neoplasms ;	0.507	0.69
Lung Neoplasms	Neoplasms ; Respiratory Tract Diseases ;	0.507	0.69
Mental Retardation, Psychosocial	Nervous System Diseases ; Pathological Conditions, Signs and Symptoms ; Behavior and Behavior Mechanisms ; Mental Disorders ;	0.507	0.69
Acute Myeloid Leukemia, M1	Neoplasms ;	0.507	0.69
Neoplasm Recurrence, Local	Neoplasms ; Pathological Conditions, Signs and Symptoms ;	0.507	0.69
Sezary Syndrome	Neoplasms ; Hemic and Lymphatic Diseases ; Immune System Diseases ;	0.507	0.69
Lymphoma, T-Cell, Cutaneous	Neoplasms ; Hemic and Lymphatic Diseases ; Immune System Diseases ;	0.507	0.69
Peripheral T-Cell Lymphoma	Neoplasms ; Hemic and Lymphatic Diseases ; Immune System Diseases ;	0.507	0.69
Crohn's disease of large bowel	Digestive System Diseases ;	0.507	0.69
Congenital anemia	N/A	0.507	0.69
Malignant neoplasm of lung	Neoplasms ; Respiratory Tract Diseases ;	0.507	0.69
Crohn's disease of the ileum	Digestive System Diseases ;	0.507	0.69
Facies	Pathological Conditions, Signs and Symptoms ;	0.507	0.69
Juvenile Myelomonocytic Leukemia	Neoplasms ; Hemic and Lymphatic Diseases ;	0.507	0.69
Granulomatous Slack Skin	Neoplasms ; Hemic and Lymphatic Diseases ; Immune System Diseases ;	0.507	0.69
Craniofacial Abnormalities	Musculoskeletal Diseases ; Congenital, Hereditary, and Neonatal Diseases and Abnormalities ;	0.507	0.69
Regional enteritis	Digestive System Diseases ;	0.507	0.69
Breast Carcinoma	Neoplasms ; Skin and Connective Tissue Diseases ;	0.507	0.69
Mental deficiency	Nervous System Diseases ; Pathological Conditions, Signs and Symptoms ; Behavior and Behavior Mechanisms ; Mental Disorders ;	0.507	0.69
IIeocolitis	Digestive System Diseases ;	0.507	0.69
Mammary Neoplasms, Human	Neoplasms ; Skin and Connective Tissue Diseases ;	0.507	0.69
Mammary Neoplasms	Neoplasms ; Skin and Connective Tissue Diseases ;	0.507	0.69
Autism Spectrum Disorders	Mental Disorders ;	0.507	0.69
Acute Myeloid Leukemia (AML-M2)	Neoplasms ;	0.507	0.69
Clear-cell metastatic renal cell carcinoma	Neoplasms ; Male Urogenital Diseases ; Female Urogenital Diseases and Pregnancy Complications ;	0.507	0.69
cocaine use	N/A	0.507	0.69
Intellectual Disability	Nervous System Diseases ; Pathological Conditions, Signs and Symptoms ; Behavior and Behavior Mechanisms ; Mental Disorders ;	0.507	0.69
TATTON-BROWN-RAHMAN SYNDROME	N/A	0.507	0.69
NO RESULT FOUND

Description:	DNA methyltransferase 3 alpha [Source:HGNC Symbol;Acc:HGNC:2978]
Synonyms:	DNMT3A2, TBRS, M.HsaIIIA
Other ID(s):	ENSG00000119772, HGNC:2978
Protein Accession Numbers:	NP_001362748, ENST00000264709.3, ENST00000406659, ENST00000380746, NP_715640, NP_001307822, ENST00000264709, ENST00000402667, NP_783329, ENST00000321117, NP_072046, NP_001307821, ENST00000380756, NP_783328
Statistics:	ClinVar(48) gnomAD(152) COSMIC(182) PTM(34)

Classification of Clinicial Significance of ClinVar Data