chr10:129708019:C>T Detail (hg38) (MGMT)

Information

Genome

Assembly Position
hg19 chr10:131,506,283-131,506,283 View the variant detail on this assembly version.
hg38 chr10:129,708,019-129,708,019

HGVS

Type Transcript Protein
RefSeq NM_002412.4:c.343C>T NP_002403.2:p.Leu115Phe
Ensemble ENST00000306010.8:c.343C>T ENST00000306010.8:p.Leu115Phe
ENST00000651593.1:c.250C>T ENST00000651593.1:p.Leu84Phe
Summary

MGeND

Clinical significance
Variant entry
GWAS entry
Disease area statistics Show details

Frequency

JP HGVD:0.153
ToMMo:0.149
NCBN:[No Data.]
NCBN(Hondo):[No Data.]
NCBN(Ryukyu):[No Data.]
East asia ExAC:0.097

Prediction

ClinVar

Clinical Significance
Review star [No Data.]
Show details
Links
Type Database ID Link
Gene MIM 156569 OMIM
HGNC 7059 HGNC
Ensembl ENSG00000170430 Ensembl
NCBI NCBI
Gene Cards Gene Cards
OncoKB OncoKB
Type Database ID Link
Variant TogoVar tgv41118841 TogoVar
COSMIC
MONDO
Disease area statistics
[No Data.]
MGeND
[No Data.]
ClinVar
[No Data.]
CIViC
[No Data.]
DisGeNET
Score Disease name Description Source Pubmed Links
0.011 colorectal cancer We observed a positive association between the PARP codon 940 Lys/Arg and Arg/Ar... BeFree 18006925 Detail
0.008 Glioma In the single-locus analysis, six single-nucleotide polymorphisms [ERCC1 3' untr... BeFree 19124499 Detail
0.003 Malignant tumor of colon We observed a positive association between the PARP codon 940 Lys/Arg and Arg/Ar... BeFree 18006925 Detail
0.007 prostate carcinoma We found that the XRCC1-Arg399Gln AA and the MGMT-Leu84Phe CT+TT genotypes were ... BeFree 16030105 Detail
0.012 Glioma In the single-locus analysis, six single-nucleotide polymorphisms [ERCC1 3' untr... BeFree 19124499 Detail
0.009 Malignant neoplasm of esophagus Lack of influence of MGMT codon Leu84Phe and codon Ileu143Val polymorphisms on e... BeFree 22994708 Detail
<0.001 Malignant tumor of colon We observed a positive association between the PARP codon 940 Lys/Arg and Arg/Ar... BeFree 18006925 Detail
0.002 esophageal carcinoma Lack of influence of MGMT codon Leu84Phe and codon Ileu143Val polymorphisms on e... BeFree 22994708 Detail
0.003 colon carcinoma We observed a positive association between the PARP codon 940 Lys/Arg and Arg/Ar... BeFree 18006925 Detail
0.014 colorectal carcinoma O6-methylguanine-DNA methyltransferase Leu84Phe and Ile143Val polymorphisms and ... BeFree 16633920 Detail
0.028 Malignant neoplasm of lung MGMT Leu84Phe gene polymorphism and lung cancer risk: a meta-analysis. BeFree 24390665 Detail
0.033 colorectal cancer We observed a positive association between the PARP codon 940 Lys/Arg and Arg/Ar... BeFree 18006925 Detail
<0.001 colon carcinoma We observed a positive association between the PARP codon 940 Lys/Arg and Arg/Ar... BeFree 18006925 Detail
0.005 diffuse large B-cell lymphoma After stratification by major NHL histological subtypes, MGMT (rs12917) modified... BeFree 22430443 Detail
0.012 colorectal cancer Our results suggest that the common Leu84Phe and Ile143Val polymorphisms in MGMT... BeFree 16633920 Detail
0.004 colorectal carcinoma Our results suggest that the common Leu84Phe and Ile143Val polymorphisms in MGMT... BeFree 16633920 Detail
<0.001 Rectal Carcinoma We observed a positive association between the PARP codon 940 Lys/Arg and Arg/Ar... BeFree 18006925 Detail
0.021 Cancer of Head and Neck Pooling data and DNA specimens from three case-control studies in western Washin... BeFree 16030112 Detail
0.003 Glioma In the single-locus analysis, six single-nucleotide polymorphisms [ERCC1 3' untr... BeFree 19124499 Detail
0.033 colorectal cancer O6-methylguanine-DNA methyltransferase Leu84Phe and Ile143Val polymorphisms and ... BeFree 16633920 Detail
0.009 Malignant neoplasm of prostate We found that the XRCC1-Arg399Gln AA and the MGMT-Leu84Phe CT+TT genotypes were ... BeFree 16030105 Detail
0.003 Lymphoma, Follicular After stratification by major NHL histological subtypes, MGMT (rs12917) modified... BeFree 22430443 Detail
0.012 Esophageal Neoplasms Lack of influence of MGMT codon Leu84Phe and codon Ileu143Val polymorphisms on e... BeFree 22994708 Detail
0.001 prostate carcinoma We found that the XRCC1-Arg399Gln AA and the MGMT-Leu84Phe CT+TT genotypes were ... BeFree 16030105 Detail
0.012 Cancer of Head and Neck Pooling data and DNA specimens from three case-control studies in western Washin... BeFree 16030112 Detail
0.003 colorectal carcinoma We observed a positive association between the PARP codon 940 Lys/Arg and Arg/Ar... BeFree 18006925 Detail
<0.001 Rectal Carcinoma We observed a positive association between the PARP codon 940 Lys/Arg and Arg/Ar... BeFree 18006925 Detail
0.014 colorectal carcinoma We observed a positive association between the PARP codon 940 Lys/Arg and Arg/Ar... BeFree 18006925 Detail
0.047 Malignant neoplasm of prostate We found that the XRCC1-Arg399Gln AA and the MGMT-Leu84Phe CT+TT genotypes were ... BeFree 16030105 Detail
0.006 Carcinoma of lung MGMT Leu84Phe gene polymorphism and lung cancer risk: a meta-analysis. BeFree 24390665 Detail
0.010 colorectal carcinoma In the present study, we investigated the role in colorectal cancer of single-nu... BeFree 18006925 Detail
0.030 colorectal cancer In the present study, we investigated the role in colorectal cancer of single-nu... BeFree 18006925 Detail
0.058 colorectal cancer In the present study, we investigated the role in colorectal cancer of single-nu... BeFree 18006925 Detail
0.013 colorectal carcinoma In the present study, we investigated the role in colorectal cancer of single-nu... BeFree 18006925 Detail
0.007 Malignant neoplasm of stomach Polymorphic variants of base excision repair (APE1-D148E, XRCC1-R194W, XRCC1-R39... BeFree 20817763 Detail
0.002 stomach carcinoma Polymorphic variants of base excision repair (APE1-D148E, XRCC1-R194W, XRCC1-R39... BeFree 20817763 Detail
0.006 stomach carcinoma Polymorphic variants of base excision repair (APE1-D148E, XRCC1-R194W, XRCC1-R39... BeFree 20817763 Detail
0.009 stomach carcinoma Polymorphic variants of base excision repair (APE1-D148E, XRCC1-R194W, XRCC1-R39... BeFree 20817763 Detail
0.006 colorectal carcinoma In the present study, we investigated the role in colorectal cancer of single-nu... BeFree 18006925 Detail
0.013 Malignant neoplasm of stomach Polymorphic variants of base excision repair (APE1-D148E, XRCC1-R194W, XRCC1-R39... BeFree 20817763 Detail
0.003 stomach carcinoma Polymorphic variants of base excision repair (APE1-D148E, XRCC1-R194W, XRCC1-R39... BeFree 20817763 Detail
0.010 Malignant neoplasm of stomach Polymorphic variants of base excision repair (APE1-D148E, XRCC1-R194W, XRCC1-R39... BeFree 20817763 Detail
0.005 stomach carcinoma Polymorphic variants of base excision repair (APE1-D148E, XRCC1-R194W, XRCC1-R39... BeFree 20817763 Detail
0.012 Malignant neoplasm of stomach Polymorphic variants of base excision repair (APE1-D148E, XRCC1-R194W, XRCC1-R39... BeFree 20817763 Detail
0.007 Malignant neoplasm of stomach Polymorphic variants of base excision repair (APE1-D148E, XRCC1-R194W, XRCC1-R39... BeFree 20817763 Detail
0.062 colorectal cancer In the present study, we investigated the role in colorectal cancer of single-nu... BeFree 18006925 Detail
0.003 Lymphoma, Follicular The following genotypes in combination with hair dye use before 1980 were associ... BeFree 25178586 Detail
0.008 Lymphoma, Follicular The following genotypes in combination with hair dye use before 1980 were associ... BeFree 25178586 Detail
0.003 Lymphoma, Follicular The following genotypes in combination with hair dye use before 1980 were associ... BeFree 25178586 Detail
0.003 Lymphoma, Follicular The following genotypes in combination with hair dye use before 1980 were associ... BeFree 25178586 Detail
0.003 Lymphoma, Follicular The following genotypes in combination with hair dye use before 1980 were associ... BeFree 25178586 Detail
0.003 Lymphoma, Follicular The following genotypes in combination with hair dye use before 1980 were associ... BeFree 25178586 Detail
0.003 Lymphoma, Follicular The following genotypes in combination with hair dye use before 1980 were associ... BeFree 25178586 Detail
<0.001 colorectal carcinoma In conclusion, this meta-analysis suggests that the PARP-1 rs1136410: T &gt; C p... BeFree 24203816 Detail
0.014 colorectal carcinoma In conclusion, this meta-analysis suggests that the PARP-1 rs1136410: T &gt; C p... BeFree 24203816 Detail
0.011 Glioma Interestingly, the risk for glioma was dramatically increased in ionizing radiat... BeFree 19124499 Detail
0.176 Glioma Interestingly, the risk for glioma was dramatically increased in ionizing radiat... BeFree 19124499 Detail
0.011 Glioma We found that SNPs rs3212986 (odds ratio [OR] = 1.35 (1.08-1.68), P = .008), rs1... BeFree 24500421 Detail
0.012 Glioma We found that SNPs rs3212986 (odds ratio [OR] = 1.35 (1.08-1.68), P = .008), rs1... BeFree 24500421 Detail
0.033 colorectal cancer In conclusion, this meta-analysis suggests that the PARP-1 rs1136410: T &gt; C p... BeFree 24203816 Detail
<0.001 colorectal cancer In conclusion, this meta-analysis suggests that the PARP-1 rs1136410: T &gt; C p... BeFree 24203816 Detail
Annotation

Annotations

DescrptionSourceLinks
We observed a positive association between the PARP codon 940 Lys/Arg and Arg/Arg genotypes and colo... DisGeNET Detail
In the single-locus analysis, six single-nucleotide polymorphisms [ERCC1 3' untranslated region (UTR... DisGeNET Detail
We observed a positive association between the PARP codon 940 Lys/Arg and Arg/Arg genotypes and colo... DisGeNET Detail
We found that the XRCC1-Arg399Gln AA and the MGMT-Leu84Phe CT+TT genotypes were associated with an i... DisGeNET Detail
In the single-locus analysis, six single-nucleotide polymorphisms [ERCC1 3' untranslated region (UTR... DisGeNET Detail
Lack of influence of MGMT codon Leu84Phe and codon Ileu143Val polymorphisms on esophageal cancer ris... DisGeNET Detail
We observed a positive association between the PARP codon 940 Lys/Arg and Arg/Arg genotypes and colo... DisGeNET Detail
Lack of influence of MGMT codon Leu84Phe and codon Ileu143Val polymorphisms on esophageal cancer ris... DisGeNET Detail
We observed a positive association between the PARP codon 940 Lys/Arg and Arg/Arg genotypes and colo... DisGeNET Detail
O6-methylguanine-DNA methyltransferase Leu84Phe and Ile143Val polymorphisms and risk of colorectal c... DisGeNET Detail
MGMT Leu84Phe gene polymorphism and lung cancer risk: a meta-analysis. DisGeNET Detail
We observed a positive association between the PARP codon 940 Lys/Arg and Arg/Arg genotypes and colo... DisGeNET Detail
We observed a positive association between the PARP codon 940 Lys/Arg and Arg/Arg genotypes and colo... DisGeNET Detail
After stratification by major NHL histological subtypes, MGMT (rs12917) modified the association bet... DisGeNET Detail
Our results suggest that the common Leu84Phe and Ile143Val polymorphisms in MGMT influence risk of c... DisGeNET Detail
Our results suggest that the common Leu84Phe and Ile143Val polymorphisms in MGMT influence risk of c... DisGeNET Detail
We observed a positive association between the PARP codon 940 Lys/Arg and Arg/Arg genotypes and colo... DisGeNET Detail
Pooling data and DNA specimens from three case-control studies in western Washington State, North Ca... DisGeNET Detail
In the single-locus analysis, six single-nucleotide polymorphisms [ERCC1 3' untranslated region (UTR... DisGeNET Detail
O6-methylguanine-DNA methyltransferase Leu84Phe and Ile143Val polymorphisms and risk of colorectal c... DisGeNET Detail
We found that the XRCC1-Arg399Gln AA and the MGMT-Leu84Phe CT+TT genotypes were associated with an i... DisGeNET Detail
After stratification by major NHL histological subtypes, MGMT (rs12917) modified the association bet... DisGeNET Detail
Lack of influence of MGMT codon Leu84Phe and codon Ileu143Val polymorphisms on esophageal cancer ris... DisGeNET Detail
We found that the XRCC1-Arg399Gln AA and the MGMT-Leu84Phe CT+TT genotypes were associated with an i... DisGeNET Detail
Pooling data and DNA specimens from three case-control studies in western Washington State, North Ca... DisGeNET Detail
We observed a positive association between the PARP codon 940 Lys/Arg and Arg/Arg genotypes and colo... DisGeNET Detail
We observed a positive association between the PARP codon 940 Lys/Arg and Arg/Arg genotypes and colo... DisGeNET Detail
We observed a positive association between the PARP codon 940 Lys/Arg and Arg/Arg genotypes and colo... DisGeNET Detail
We found that the XRCC1-Arg399Gln AA and the MGMT-Leu84Phe CT+TT genotypes were associated with an i... DisGeNET Detail
MGMT Leu84Phe gene polymorphism and lung cancer risk: a meta-analysis. DisGeNET Detail
In the present study, we investigated the role in colorectal cancer of single-nucleotide polymorphis... DisGeNET Detail
In the present study, we investigated the role in colorectal cancer of single-nucleotide polymorphis... DisGeNET Detail
In the present study, we investigated the role in colorectal cancer of single-nucleotide polymorphis... DisGeNET Detail
In the present study, we investigated the role in colorectal cancer of single-nucleotide polymorphis... DisGeNET Detail
Polymorphic variants of base excision repair (APE1-D148E, XRCC1-R194W, XRCC1-R399Q and OGG1-S326C), ... DisGeNET Detail
Polymorphic variants of base excision repair (APE1-D148E, XRCC1-R194W, XRCC1-R399Q and OGG1-S326C), ... DisGeNET Detail
Polymorphic variants of base excision repair (APE1-D148E, XRCC1-R194W, XRCC1-R399Q and OGG1-S326C), ... DisGeNET Detail
Polymorphic variants of base excision repair (APE1-D148E, XRCC1-R194W, XRCC1-R399Q and OGG1-S326C), ... DisGeNET Detail
In the present study, we investigated the role in colorectal cancer of single-nucleotide polymorphis... DisGeNET Detail
Polymorphic variants of base excision repair (APE1-D148E, XRCC1-R194W, XRCC1-R399Q and OGG1-S326C), ... DisGeNET Detail
Polymorphic variants of base excision repair (APE1-D148E, XRCC1-R194W, XRCC1-R399Q and OGG1-S326C), ... DisGeNET Detail
Polymorphic variants of base excision repair (APE1-D148E, XRCC1-R194W, XRCC1-R399Q and OGG1-S326C), ... DisGeNET Detail
Polymorphic variants of base excision repair (APE1-D148E, XRCC1-R194W, XRCC1-R399Q and OGG1-S326C), ... DisGeNET Detail
Polymorphic variants of base excision repair (APE1-D148E, XRCC1-R194W, XRCC1-R399Q and OGG1-S326C), ... DisGeNET Detail
Polymorphic variants of base excision repair (APE1-D148E, XRCC1-R194W, XRCC1-R399Q and OGG1-S326C), ... DisGeNET Detail
In the present study, we investigated the role in colorectal cancer of single-nucleotide polymorphis... DisGeNET Detail
The following genotypes in combination with hair dye use before 1980 were associated with FL risk: B... DisGeNET Detail
The following genotypes in combination with hair dye use before 1980 were associated with FL risk: B... DisGeNET Detail
The following genotypes in combination with hair dye use before 1980 were associated with FL risk: B... DisGeNET Detail
The following genotypes in combination with hair dye use before 1980 were associated with FL risk: B... DisGeNET Detail
The following genotypes in combination with hair dye use before 1980 were associated with FL risk: B... DisGeNET Detail
The following genotypes in combination with hair dye use before 1980 were associated with FL risk: B... DisGeNET Detail
The following genotypes in combination with hair dye use before 1980 were associated with FL risk: B... DisGeNET Detail
In conclusion, this meta-analysis suggests that the PARP-1 rs1136410: T &gt; C polymorphism is a sus... DisGeNET Detail
In conclusion, this meta-analysis suggests that the PARP-1 rs1136410: T &gt; C polymorphism is a sus... DisGeNET Detail
Interestingly, the risk for glioma was dramatically increased in ionizing radiation exposure individ... DisGeNET Detail
Interestingly, the risk for glioma was dramatically increased in ionizing radiation exposure individ... DisGeNET Detail
We found that SNPs rs3212986 (odds ratio [OR] = 1.35 (1.08-1.68), P = .008), rs13181 (OR = 1.18 (1.0... DisGeNET Detail
We found that SNPs rs3212986 (odds ratio [OR] = 1.35 (1.08-1.68), P = .008), rs13181 (OR = 1.18 (1.0... DisGeNET Detail
In conclusion, this meta-analysis suggests that the PARP-1 rs1136410: T &gt; C polymorphism is a sus... DisGeNET Detail
In conclusion, this meta-analysis suggests that the PARP-1 rs1136410: T &gt; C polymorphism is a sus... 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
-
Genome
hg38
Position
chr10:129,708,019-129,708,019
Variant Type
snv
Reference Allele
C
Alternative Allele
T
Filtering Status (HGVD)
PASS
# of samples (HGVD)
1206
Mean of sample read depth (HGVD)
92.87
Standard deviation of sample read depth (HGVD)
45.76
Number of reference allele (HGVD)
2043
Number of alternative allele (HGVD)
369
Allele Frequency (HGVD)
0.15298507462686567
Gene Symbol (HGVD)
MGMT
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))
rs12917
Allele frequency, for each ALT allele (ToMMo 8.3KJPN Allele Frequency Panel(v20200831))
0.1489
Allele count in genotypes, for each ALT allele (ToMMo 8.3KJPN Allele Frequency Panel(v20200831))
2496
Total number of alleles in called genotypes (ToMMo 8.3KJPN Allele Frequency Panel(v20200831))
16760
East Asian Chromosome Counts (ExAC)
8646
East Asian Allele Counts (ExAC)
835
East Asian Heterozygous Counts (ExAC)
757
East Asian Homozygous Counts (ExAC)
39
East Asian Allele Frequency (ExAC)
0.0965764515382836
Chromosome Counts in All Race (ExAC)
121158
Allele Counts in All Race (ExAC)
17209
Heterozygous Counts in All Race (ExAC)
14513
Homozygous Counts in All Race (ExAC)
1348
Allele Frequency in All Race (ExAC)
0.14203766981957444
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