chr2:25234373:C>T Detail (hg38) (DNMT3A)

Information

Genome

Assembly Position
hg19 chr2:25,457,242-25,457,242 View the variant detail on this assembly version.
hg38 chr2:25,234,373-25,234,373

HGVS

Type Transcript Protein
RefSeq NM_175629.2:c.2645G>A NP_783328.1:p.Arg882His
NM_022552.4:c.2645G>A NP_072046.2:p.Arg882His
NM_153759.3:c.2078G>A NP_715640.2:p.Arg693His
Summary

MGeND

Clinical significance Pathogenic
Variant entry 1
GWAS entry
Disease area statistics Show details

Frequency

JP HGVD:<0.001
ToMMo:<0.001
NCBN:[No Data.]
NCBN(Hondo):[No Data.]
NCBN(Ryukyu):[No Data.]
East asia ExAC:<0.001

Prediction

ClinVar

Clinical Significance Conflicting classifications of pathogenicity
Review star
Show details
Links
Type Database ID Link
Gene MIM 602769 OMIM
HGNC 2978 HGNC
Ensembl ENSG00000119772 Ensembl
NCBI NCBI
Gene Cards Gene Cards
OncoKB OncoKB
Type Database ID Link
Variant TogoVar tgv6177328 TogoVar
COSMIC COSM442676 COSMIC
MONDO
Disease area statistics
MGeND
Clinical significance Last evaluated Condition Origin Submission ID Submitter Institute Citation Comment Image
Pathogenic other germline MGS000001
(TMGS000138) 		Kenjiro Kosaki Keio University
ClinVar
Clinical significance Last evaluated Review status Condition Origin Links
Likely pathogenic 2016-05-31 no assertion criteria provided lung adenocarcinoma somatic Detail
Pathogenic Likely pathogenic 2023-06-08 no assertion criteria provided acute myeloid leukemia germline somatic Detail
Likely pathogenic 2016-05-31 no assertion criteria provided myelodysplastic syndrome somatic Detail
Pathogenic Likely pathogenic 2022-10-10 criteria provided, multiple submitters, no conflicts not provided germline Detail
Pathogenic 2024-01-17 criteria provided, multiple submitters, no conflicts Tatton-Brown-Rahman overgrowth syndrome germline unknown Detail
Pathogenic 2022-10-06 criteria provided, single submitter Inborn genetic diseases germline Detail
Likely pathogenic 2021-07-10 criteria provided, single submitter germline Detail
Uncertain significance 2022-05-04 criteria provided, single submitter not specified germline Detail
Pathogenic no assertion criteria provided Clonal Cytopenia of Undetermined Significance somatic Detail
Likely pathogenic 2020-08-11 criteria provided, single submitter intellectual disability germline Detail
not provided no assertion provided DNMT3A-related disorder de novo Detail
CIViC
[No Data.]
DisGeNET
Score Disease name Description Source Pubmed Links
0.560 Leukemia, Myelocytic, Acute To determine whether mutant IDH enzymes are valid targets for cancer therapy, we... BeFree 25795706 Detail
0.018 Leukemia, Myelocytic, Acute To determine whether mutant IDH enzymes are valid targets for cancer therapy, we... BeFree 25795706 Detail
0.018 Leukemia, Myelocytic, Acute The R882H DNMT3A mutation associated with AML dominantly inhibits wild-type DNMT... BeFree 24656771 Detail
0.001 Leukemogenesis Moreover, DNMT3A-R882H increased the CDK1 protein level and enhanced cell-cycle ... BeFree 24497509 Detail
Annotation

Annotations

DescrptionSourceLinks
NM_022552.5(DNMT3A):c.2645G>A (p.Arg882His) AND Lung adenocarcinoma ClinVar Detail
NM_022552.5(DNMT3A):c.2645G>A (p.Arg882His) AND Acute myeloid leukemia ClinVar Detail
NM_022552.5(DNMT3A):c.2645G>A (p.Arg882His) AND Myelodysplastic syndrome ClinVar Detail
NM_022552.5(DNMT3A):c.2645G>A (p.Arg882His) AND not provided ClinVar Detail
NM_022552.5(DNMT3A):c.2645G>A (p.Arg882His) AND Tatton-Brown-Rahman overgrowth syndrome ClinVar Detail
NM_022552.5(DNMT3A):c.2645G>A (p.Arg882His) AND Inborn genetic diseases ClinVar Detail
NM_022552.5(DNMT3A):c.2645G>A (p.Arg882His) AND Abnormality of the nervous system ClinVar Detail
NM_022552.5(DNMT3A):c.2645G>A (p.Arg882His) AND not specified ClinVar Detail
NM_022552.5(DNMT3A):c.2645G>A (p.Arg882His) AND Clonal Cytopenia of Undetermined Significance ClinVar Detail
NM_022552.5(DNMT3A):c.2645G>A (p.Arg882His) AND Intellectual disability ClinVar Detail
NM_022552.5(DNMT3A):c.2645G>A (p.Arg882His) AND DNMT3A-related disorder ClinVar Detail
To determine whether mutant IDH enzymes are valid targets for cancer therapy, we created a mouse mod... DisGeNET Detail
To determine whether mutant IDH enzymes are valid targets for cancer therapy, we created a mouse mod... DisGeNET Detail
The R882H DNMT3A mutation associated with AML dominantly inhibits wild-type DNMT3A by blocking its a... DisGeNET Detail
Moreover, DNMT3A-R882H increased the CDK1 protein level and enhanced cell-cycle activity, thereby co... DisGeNET Detail

Overlapped Transcript Coordinates

Gene Transcript ID Exon Number Chromosome Start Stop Type Amino Mutation Transcript Position Links

Overlapped Transcript

Gene Transcript ID Chromosome Start Stop Links
Gene
-
dbSNP
rs147001633 dbSNP
Genome
hg38
Position
chr2:25,234,373-25,234,373
Variant Type
snv
Reference Allele
C
Alternative Allele
T
Filtering Status (HGVD)
PASS
# of samples (HGVD)
1208
Mean of sample read depth (HGVD)
73.84
Standard deviation of sample read depth (HGVD)
30.60
Number of reference allele (HGVD)
2415
Number of alternative allele (HGVD)
1
Allele Frequency (HGVD)
4.139072847682119E-4
Gene Symbol (HGVD)
DNMT3A
ToMMo VCF FILTER column value (ToMMo 8.3KJPN Allele Frequency Panel(v20200831))
PASS
Total VCF ID column value (ToMMo 8.3KJPN Allele Frequency Panel(v20200831))
rs147001633
Allele frequency, for each ALT allele (ToMMo 8.3KJPN Allele Frequency Panel(v20200831))
0.0006
Allele count in genotypes, for each ALT allele (ToMMo 8.3KJPN Allele Frequency Panel(v20200831))
10
Total number of alleles in called genotypes (ToMMo 8.3KJPN Allele Frequency Panel(v20200831))
16760
Homozygous Counts in All Race (ExAC)
0
East Asian Chromosome Counts (ExAC)
8648
East Asian Allele Counts (ExAC)
6
East Asian Heterozygous Counts (ExAC)
6
East Asian Homozygous Counts (ExAC)
0
East Asian Allele Frequency (ExAC)
6.938020351526364E-4
Chromosome Counts in All Race (ExAC)
121122
Allele Counts in All Race (ExAC)
66
Heterozygous Counts in All Race (ExAC)
66
Allele Frequency in All Race (ExAC)
5.449051369693367E-4
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