chr3:129155451:C>T Detail (hg19) (MBD4)

Information

Genome

Assembly Position
hg19 chr3:129,155,451-129,155,451
hg38 chr3:129,436,608-129,436,608 View the variant detail on this assembly version.

HGVS

Type Transcript Protein
RefSeq NM_001276273.1:c.247+1200G>A
NM_001276270.1:c.1036G>A NP_001263199.1:p.Glu346Lys
NM_001276272.1:c.1036G>A NP_001263201.1:p.Glu346Lys
Summary

MGeND

Clinical significance
Variant entry
GWAS entry
Disease area statistics Show details

Frequency

JP HGVD:0.345
ToMMo:0.344
NCBN:[No Data.]
NCBN(Hondo):[No Data.]
NCBN(Ryukyu):[No Data.]
East asia ExAC:0.403

Prediction

ClinVar

Clinical Significance Benign
Review star
Show details
Links
Type Database ID Link
Gene MIM 603574 OMIM
HGNC 6919 HGNC
Ensembl ENSG00000129071 Ensembl
NCBI NCBI
Gene Cards Gene Cards
OncoKB OncoKB
Type Database ID Link
Variant TogoVar tgv14186735 TogoVar
COSMIC
MONDO
Disease area statistics
[No Data.]
MGeND
[No Data.]
ClinVar
Clinical significance Last evaluated Review status Condition Origin Links
Benign 2024-02-01 criteria provided, multiple submitters, no conflicts not provided germline Detail
CIViC
[No Data.]
DisGeNET
Score Disease name Description Source Pubmed Links
0.003 adenocarcinoma Our findings suggest that the MBD4 Glu346Lys polymorphism could be used as a mar... BeFree 16803845 Detail
<0.001 Carcinoma of lung To test this hypothesis, we examined the potential association between the MBD4 ... BeFree 16803845 Detail
0.010 Malignant neoplasm of lung To test this hypothesis, we examined the potential association between the MBD4 ... BeFree 16803845 Detail
0.005 Carcinoma of lung SNPs associated with lung cancer prognosis primarily mapped to 14 genes in diffe... BeFree 21739480 Detail
0.021 Malignant neoplasm of lung SNPs associated with lung cancer prognosis primarily mapped to 14 genes in diffe... BeFree 21739480 Detail
0.020 Carcinoma of lung SNPs associated with lung cancer prognosis primarily mapped to 14 genes in diffe... BeFree 21739480 Detail
<0.001 Carcinoma of lung SNPs associated with lung cancer prognosis primarily mapped to 14 genes in diffe... BeFree 21739480 Detail
<0.001 Carcinoma of lung SNPs associated with lung cancer prognosis primarily mapped to 14 genes in diffe... BeFree 21739480 Detail
0.214 Malignant neoplasm of lung SNPs associated with lung cancer prognosis primarily mapped to 14 genes in diffe... BeFree 21739480 Detail
0.100 Malignant neoplasm of lung SNPs associated with lung cancer prognosis primarily mapped to 14 genes in diffe... BeFree 21739480 Detail
<0.001 Carcinoma of lung SNPs associated with lung cancer prognosis primarily mapped to 14 genes in diffe... BeFree 21739480 Detail
0.010 Malignant neoplasm of lung SNPs associated with lung cancer prognosis primarily mapped to 14 genes in diffe... BeFree 21739480 Detail
0.003 Malignant neoplasm of lung SNPs associated with lung cancer prognosis primarily mapped to 14 genes in diffe... BeFree 21739480 Detail
0.014 Carcinoma of lung SNPs associated with lung cancer prognosis primarily mapped to 14 genes in diffe... BeFree 21739480 Detail
<0.001 Malignant neoplasm of lung SNPs associated with lung cancer prognosis primarily mapped to 14 genes in diffe... BeFree 21739480 Detail
<0.001 Squamous cell carcinoma of esophagus In the final model, 4 SNPs, including 2 in the coding regions (ADPRT Val762Ala a... BeFree 15205355 Detail
<0.001 Squamous cell carcinoma of esophagus In the final model, 4 SNPs, including 2 in the coding regions (ADPRT Val762Ala a... BeFree 15205355 Detail
<0.001 Squamous cell carcinoma of esophagus In the final model, 4 SNPs, including 2 in the coding regions (ADPRT Val762Ala a... BeFree 15205355 Detail
<0.001 Squamous cell carcinoma of esophagus In the final model, 4 SNPs, including 2 in the coding regions (ADPRT Val762Ala a... BeFree 15205355 Detail
0.123 Squamous cell carcinoma of esophagus In the final model, 4 SNPs, including 2 in the coding regions (ADPRT Val762Ala a... BeFree 15205355 Detail
Annotation

Annotations

DescrptionSourceLinks
NM_001276270.2(MBD4):c.1036G>A (p.Glu346Lys) AND not provided ClinVar Detail
Our findings suggest that the MBD4 Glu346Lys polymorphism could be used as a marker for genetic susc... DisGeNET Detail
To test this hypothesis, we examined the potential association between the MBD4 Glu346Lys polymorphi... DisGeNET Detail
To test this hypothesis, we examined the potential association between the MBD4 Glu346Lys polymorphi... DisGeNET Detail
SNPs associated with lung cancer prognosis primarily mapped to 14 genes in different repair pathways... DisGeNET Detail
SNPs associated with lung cancer prognosis primarily mapped to 14 genes in different repair pathways... DisGeNET Detail
SNPs associated with lung cancer prognosis primarily mapped to 14 genes in different repair pathways... DisGeNET Detail
SNPs associated with lung cancer prognosis primarily mapped to 14 genes in different repair pathways... DisGeNET Detail
SNPs associated with lung cancer prognosis primarily mapped to 14 genes in different repair pathways... DisGeNET Detail
SNPs associated with lung cancer prognosis primarily mapped to 14 genes in different repair pathways... DisGeNET Detail
SNPs associated with lung cancer prognosis primarily mapped to 14 genes in different repair pathways... DisGeNET Detail
SNPs associated with lung cancer prognosis primarily mapped to 14 genes in different repair pathways... DisGeNET Detail
SNPs associated with lung cancer prognosis primarily mapped to 14 genes in different repair pathways... DisGeNET Detail
SNPs associated with lung cancer prognosis primarily mapped to 14 genes in different repair pathways... DisGeNET Detail
SNPs associated with lung cancer prognosis primarily mapped to 14 genes in different repair pathways... DisGeNET Detail
SNPs associated with lung cancer prognosis primarily mapped to 14 genes in different repair pathways... DisGeNET Detail
In the final model, 4 SNPs, including 2 in the coding regions (ADPRT Val762Ala and MBD4 Glu346Lys) a... DisGeNET Detail
In the final model, 4 SNPs, including 2 in the coding regions (ADPRT Val762Ala and MBD4 Glu346Lys) a... DisGeNET Detail
In the final model, 4 SNPs, including 2 in the coding regions (ADPRT Val762Ala and MBD4 Glu346Lys) a... DisGeNET Detail
In the final model, 4 SNPs, including 2 in the coding regions (ADPRT Val762Ala and MBD4 Glu346Lys) a... DisGeNET Detail
In the final model, 4 SNPs, including 2 in the coding regions (ADPRT Val762Ala and MBD4 Glu346Lys) a... 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
rs140693 dbSNP
Genome
hg19
Position
chr3:129,155,451-129,155,451
Variant Type
snv
Reference Allele
C
Alternative Allele
T
Filtering Status (HGVD)
PASS
# of samples (HGVD)
1209
Mean of sample read depth (HGVD)
114.86
Standard deviation of sample read depth (HGVD)
52.45
Number of reference allele (HGVD)
1303
Number of alternative allele (HGVD)
686
Allele Frequency (HGVD)
0.34489693313222725
Gene Symbol (HGVD)
MBD4
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))
rs140693
Allele frequency, for each ALT allele (ToMMo 8.3KJPN Allele Frequency Panel(v20200831))
0.3444
Allele count in genotypes, for each ALT allele (ToMMo 8.3KJPN Allele Frequency Panel(v20200831))
5772
Total number of alleles in called genotypes (ToMMo 8.3KJPN Allele Frequency Panel(v20200831))
16760
East Asian Chromosome Counts (ExAC)
8648
East Asian Allele Counts (ExAC)
3485
East Asian Heterozygous Counts (ExAC)
2019
East Asian Homozygous Counts (ExAC)
733
East Asian Allele Frequency (ExAC)
0.4029833487511563
Chromosome Counts in All Race (ExAC)
121334
Allele Counts in All Race (ExAC)
6183
Heterozygous Counts in All Race (ExAC)
4423
Homozygous Counts in All Race (ExAC)
880
Allele Frequency in All Race (ExAC)
0.050958511216971335
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