chr3:37067240:T>A Detail (hg19) (MLH1)

Information

Genome

Assembly Position
hg19 chr3:37,067,240-37,067,240
hg38 chr3:37,025,749-37,025,749 View the variant detail on this assembly version.

HGVS

Type Transcript Protein
RefSeq NM_001258274.1:c.428T>A NP_001245203.1:p.Val143Asp
NM_001167617.1:c.857T>A NP_001161089.1:p.Val286Asp
NM_001167618.1:c.428T>A NP_001161090.1:p.Val143Asp
Summary

MGeND

Clinical significance Benign not provided
Variant entry 677
GWAS entry
Disease area statistics Show details

Frequency

JP HGVD:0.035
ToMMo:0.033
NCBN:[No Data.]
NCBN(Hondo):[No Data.]
NCBN(Ryukyu):[No Data.]
East asia ExAC:0.039

Prediction

ClinVar

Clinical Significance Benign
Review star
Show details
Links
Type Database ID Link
Gene MIM 120436 OMIM
HGNC 7127 HGNC
Ensembl ENSG00000076242 Ensembl
NCBI NCBI
Gene Cards Gene Cards
OncoKB OncoKB
Type Database ID Link
Variant TogoVar tgv12069518 TogoVar
COSMIC COSM26085 COSMIC
MONDO
Disease area statistics
MGeND
Clinical significance Last evaluated Condition Origin Submission ID Submitter Institute Citation Comment Image
Benign 2020/04/20 upper third of oesophagus not provided MGS000041
(TMGS000094)
Hitoshi Nakagama National Cancer Center Japan
Benign 2020/04/20 middle third of oesophagus not provided MGS000041
(TMGS000094)
Hitoshi Nakagama National Cancer Center Japan
Benign 2020/04/20 lower third of oesophagus not provided MGS000041
(TMGS000094)
Hitoshi Nakagama National Cancer Center Japan
Benign 2020/04/20 oesophagus, unspecified not provided MGS000041
(TMGS000094)
Hitoshi Nakagama National Cancer Center Japan
Benign 2020/04/20 fundus of stomach not provided MGS000041
(TMGS000094)
Hitoshi Nakagama National Cancer Center Japan
Benign 2020/04/20 body of stomach not provided MGS000041
(TMGS000094)
Hitoshi Nakagama National Cancer Center Japan
Benign 2020/04/20 pyloric antrum not provided MGS000041
(TMGS000094)
Hitoshi Nakagama National Cancer Center Japan
Benign 2020/04/20 stomach, unspecified not provided MGS000041
(TMGS000094)
Hitoshi Nakagama National Cancer Center Japan
Benign 2020/04/20 caecum not provided MGS000041
(TMGS000094)
Hitoshi Nakagama National Cancer Center Japan
Benign 2020/04/20 appendix not provided MGS000041
(TMGS000094)
Hitoshi Nakagama National Cancer Center Japan
Benign 2020/04/20 transverse colon not provided MGS000041
(TMGS000094)
Hitoshi Nakagama National Cancer Center Japan
Benign 2020/04/20 descending colon not provided MGS000041
(TMGS000094)
Hitoshi Nakagama National Cancer Center Japan
Benign 2020/04/20 colon, unspecified not provided MGS000041
(TMGS000094)
Hitoshi Nakagama National Cancer Center Japan
Benign 2020/04/20 malignant neoplasm of rectosigmoid junction not provided MGS000041
(TMGS000094)
Hitoshi Nakagama National Cancer Center Japan
Benign 2020/04/20 malignant neoplasm of rectum not provided MGS000041
(TMGS000094)
Hitoshi Nakagama National Cancer Center Japan
Benign 2020/04/20 anal canal not provided MGS000041
(TMGS000094)
Hitoshi Nakagama National Cancer Center Japan
Benign 2020/04/20 intrahepatic bile duct carcinoma not provided MGS000041
(TMGS000094)
Hitoshi Nakagama National Cancer Center Japan
Benign 2020/04/20 extrahepatic bile duct not provided MGS000041
(TMGS000094)
Hitoshi Nakagama National Cancer Center Japan
Benign 2020/04/20 ampulla of vater not provided MGS000041
(TMGS000094)
Hitoshi Nakagama National Cancer Center Japan
Benign 2020/04/20 head of pancreas not provided MGS000041
(TMGS000094)
Hitoshi Nakagama National Cancer Center Japan
Benign 2020/04/20 tail of pancreas not provided MGS000041
(TMGS000094)
Hitoshi Nakagama National Cancer Center Japan
Benign 2020/04/20 ill-defined sites within the digestive system not provided MGS000041
(TMGS000094)
Hitoshi Nakagama National Cancer Center Japan
Benign 2020/04/20 bronchus or lung, unspecified not provided MGS000041
(TMGS000094)
Hitoshi Nakagama National Cancer Center Japan
not provided prostate cancer germline MGS000060
(TMGS000107)
Hitoshi Nakagama National Cancer Center Japan
not provided gastric cancer germline MGS000060
(TMGS000107)
Hitoshi Nakagama National Cancer Center Japan
not provided pancreas cancer germline MGS000060
(TMGS000107)
Hitoshi Nakagama National Cancer Center Japan
not provided Endometrial cancer germline MGS000060
(TMGS000107)
Hitoshi Nakagama National Cancer Center Japan
not provided cancer germline MGS000060
(TMGS000107)
Hitoshi Nakagama National Cancer Center Japan
not provided Ovarian cancer germline MGS000060
(TMGS000107)
Hitoshi Nakagama National Cancer Center Japan
not provided colorectal cancer germline MGS000060
(TMGS000107)
Hitoshi Nakagama National Cancer Center Japan
Benign Centenarian germline MGS000068
(TMGS000140)
Kenjiro Kosaki Keio University
Benign 2020/04/20 other somatic MGS000039
(TMGS000092)
Hitoshi Nakagama National Cancer Center Japan 29659903
Benign 2020/04/20 stomach cancer somatic MGS000039
(TMGS000092)
Hitoshi Nakagama National Cancer Center Japan 29659903
Benign 2020/04/20 other somatic MGS000039
(TMGS000092)
Hitoshi Nakagama National Cancer Center Japan 29659903
Benign 2020/04/20 lung cancer somatic MGS000039
(TMGS000092)
Hitoshi Nakagama National Cancer Center Japan 29659903
Benign 2020/04/20 other somatic MGS000039
(TMGS000092)
Hitoshi Nakagama National Cancer Center Japan 29659903
Benign 2020/04/20 breast cancer somatic MGS000039
(TMGS000092)
Hitoshi Nakagama National Cancer Center Japan 29659903
Benign 2020/04/20 middle third of oesophagus not provided MGS000042
(TMGS000093)
Hitoshi Nakagama National Cancer Center Japan
Benign 2020/04/20 lower third of oesophagus not provided MGS000042
(TMGS000093)
Hitoshi Nakagama National Cancer Center Japan
Benign 2020/04/20 oesophagus, unspecified not provided MGS000042
(TMGS000093)
Hitoshi Nakagama National Cancer Center Japan
Benign 2020/04/20 fundus of stomach not provided MGS000042
(TMGS000093)
Hitoshi Nakagama National Cancer Center Japan
Benign 2020/04/20 body of stomach not provided MGS000042
(TMGS000093)
Hitoshi Nakagama National Cancer Center Japan
Benign 2020/04/20 pyloric antrum not provided MGS000042
(TMGS000093)
Hitoshi Nakagama National Cancer Center Japan
Benign 2020/04/20 stomach, unspecified not provided MGS000042
(TMGS000093)
Hitoshi Nakagama National Cancer Center Japan
Benign 2020/04/20 small intestine, unspecified not provided MGS000042
(TMGS000093)
Hitoshi Nakagama National Cancer Center Japan
Benign 2020/04/20 caecum not provided MGS000042
(TMGS000093)
Hitoshi Nakagama National Cancer Center Japan
Benign 2020/04/20 appendix not provided MGS000042
(TMGS000093)
Hitoshi Nakagama National Cancer Center Japan
Benign 2020/04/20 ascending colon not provided MGS000042
(TMGS000093)
Hitoshi Nakagama National Cancer Center Japan
Benign 2020/04/20 transverse colon not provided MGS000042
(TMGS000093)
Hitoshi Nakagama National Cancer Center Japan
Benign 2020/04/20 descending colon not provided MGS000042
(TMGS000093)
Hitoshi Nakagama National Cancer Center Japan
Benign 2020/04/20 sigmoid colon not provided MGS000042
(TMGS000093)
Hitoshi Nakagama National Cancer Center Japan
Benign 2020/04/20 colon, unspecified not provided MGS000042
(TMGS000093)
Hitoshi Nakagama National Cancer Center Japan
Benign 2020/04/20 malignant neoplasm of rectosigmoid junction not provided MGS000042
(TMGS000093)
Hitoshi Nakagama National Cancer Center Japan
Benign 2020/04/20 malignant neoplasm of rectum not provided MGS000042
(TMGS000093)
Hitoshi Nakagama National Cancer Center Japan
Benign 2020/04/20 anal canal not provided MGS000042
(TMGS000093)
Hitoshi Nakagama National Cancer Center Japan
Benign 2020/04/20 intrahepatic bile duct carcinoma not provided MGS000042
(TMGS000093)
Hitoshi Nakagama National Cancer Center Japan
Benign 2020/04/20 malignant neoplasm of gallbladder not provided MGS000042
(TMGS000093)
Hitoshi Nakagama National Cancer Center Japan
Benign 2020/04/20 extrahepatic bile duct not provided MGS000042
(TMGS000093)
Hitoshi Nakagama National Cancer Center Japan
Benign 2020/04/20 ampulla of vater not provided MGS000042
(TMGS000093)
Hitoshi Nakagama National Cancer Center Japan
Benign 2020/04/20 head of pancreas not provided MGS000042
(TMGS000093)
Hitoshi Nakagama National Cancer Center Japan
Benign 2020/04/20 body of pancreas not provided MGS000042
(TMGS000093)
Hitoshi Nakagama National Cancer Center Japan
Benign 2020/04/20 tail of pancreas not provided MGS000042
(TMGS000093)
Hitoshi Nakagama National Cancer Center Japan
Benign 2020/04/20 ill-defined sites within the digestive system not provided MGS000042
(TMGS000093)
Hitoshi Nakagama National Cancer Center Japan
Benign 2020/04/20 bronchus or lung, unspecified not provided MGS000042
(TMGS000093)
Hitoshi Nakagama National Cancer Center Japan
ClinVar
Clinical significance Last evaluated Review status Condition Origin Links
Benign 2023-11-01 criteria provided, single submitter not provided germline Detail
Benign 2013-09-05 reviewed by expert panel Lynch syndrome germline Detail
Benign 2023-08-15 criteria provided, multiple submitters, no conflicts not specified germline Detail
Benign 2020-05-27 criteria provided, multiple submitters, no conflicts Hereditary cancer-predisposing syndrome germline Detail
Benign 2014-07-24 no assertion criteria provided Lynch syndrome 1 germline Detail
Likely pathogenic 2015-07-14 no assertion criteria provided gastric adenocarcinoma somatic Detail
Likely pathogenic 2015-07-14 no assertion criteria provided lung adenocarcinoma somatic Detail
Benign Likely benign 2023-07-07 criteria provided, multiple submitters, no conflicts Colorectal cancer, hereditary nonpolyposis, type 2 germline unknown Detail
Likely benign 2022-05-10 criteria provided, single submitter Muir-Torré syndrome,Colorectal cancer, hereditary nonpolyposis, type 2,Mismatch repair cancer syndrome 1 unknown Detail
Likely benign 2022-05-10 criteria provided, single submitter Muir-Torré syndrome,Colorectal cancer, hereditary nonpolyposis, type 2,Mismatch repair cancer syndrome 1 unknown Detail
Likely benign 2022-05-10 criteria provided, single submitter Muir-Torré syndrome,Colorectal cancer, hereditary nonpolyposis, type 2,Mismatch repair cancer syndrome 1 unknown Detail
Benign 2024-02-01 criteria provided, single submitter Hereditary nonpolyposis colorectal neoplasms germline Detail
Benign no assertion criteria provided bile duct cancer unknown Detail
Benign 2022-02-08 criteria provided, single submitter Breast and/or ovarian cancer germline Detail
CIViC
[No Data.]
DisGeNET
Score Disease name Description Source Pubmed Links
0.022 Malignant neoplasm of breast Seven single nucleotide polymorphisms (SNPs) (rs3856806 in PPARG, rs7014346 in P... BeFree 24338422 Detail
0.008 breast carcinoma Seven single nucleotide polymorphisms (SNPs) (rs3856806 in PPARG, rs7014346 in P... BeFree 24338422 Detail
0.082 colorectal carcinoma In a search for germline mutations in the DNA mismatch repair genes hMSH2 and hM... BeFree 9526167 Detail
0.063 colorectal carcinoma In a search for germline mutations in the DNA mismatch repair genes hMSH2 and hM... BeFree 9526167 Detail
0.017 stomach carcinoma A new familial gastric cancer-related gene polymorphism: T1151A in the mismatch ... BeFree 20177793 Detail
0.160 colorectal cancer In a search for germline mutations in the DNA mismatch repair genes hMSH2 and hM... BeFree 9526167 Detail
0.144 colorectal cancer In a search for germline mutations in the DNA mismatch repair genes hMSH2 and hM... BeFree 9526167 Detail
0.025 Malignant neoplasm of stomach A new familial gastric cancer-related gene polymorphism: T1151A in the mismatch ... BeFree 20177793 Detail
Annotation

Annotations

DescrptionSourceLinks
NM_000249.4(MLH1):c.1151T>A (p.Val384Asp) AND not provided ClinVar Detail
NM_000249.4(MLH1):c.1151T>A (p.Val384Asp) AND Lynch syndrome ClinVar Detail
NM_000249.4(MLH1):c.1151T>A (p.Val384Asp) AND not specified ClinVar Detail
NM_000249.4(MLH1):c.1151T>A (p.Val384Asp) AND Hereditary cancer-predisposing syndrome ClinVar Detail
NM_000249.4(MLH1):c.1151T>A (p.Val384Asp) AND Lynch syndrome 1 ClinVar Detail
NM_000249.4(MLH1):c.1151T>A (p.Val384Asp) AND Gastric adenocarcinoma ClinVar Detail
NM_000249.4(MLH1):c.1151T>A (p.Val384Asp) AND Lung adenocarcinoma ClinVar Detail
NM_000249.4(MLH1):c.1151T>A (p.Val384Asp) AND Colorectal cancer, hereditary nonpolyposis, type 2 ClinVar Detail
NM_000249.4(MLH1):c.1151T>A (p.Val384Asp) AND multiple conditions ClinVar Detail
NM_000249.4(MLH1):c.1151T>A (p.Val384Asp) AND multiple conditions ClinVar Detail
NM_000249.4(MLH1):c.1151T>A (p.Val384Asp) AND multiple conditions ClinVar Detail
NM_000249.4(MLH1):c.1151T>A (p.Val384Asp) AND Hereditary nonpolyposis colorectal neoplasms ClinVar Detail
NM_000249.4(MLH1):c.1151T>A (p.Val384Asp) AND Bile duct cancer ClinVar Detail
NM_000249.4(MLH1):c.1151T>A (p.Val384Asp) AND Breast and/or ovarian cancer ClinVar Detail
Seven single nucleotide polymorphisms (SNPs) (rs3856806 in PPARG, rs7014346 in POU5F1P1, rs989902 in... DisGeNET Detail
Seven single nucleotide polymorphisms (SNPs) (rs3856806 in PPARG, rs7014346 in POU5F1P1, rs989902 in... DisGeNET Detail
In a search for germline mutations in the DNA mismatch repair genes hMSH2 and hMLH1 in Chinese patie... DisGeNET Detail
In a search for germline mutations in the DNA mismatch repair genes hMSH2 and hMLH1 in Chinese patie... DisGeNET Detail
A new familial gastric cancer-related gene polymorphism: T1151A in the mismatch repair gene hMLH1. DisGeNET Detail
In a search for germline mutations in the DNA mismatch repair genes hMSH2 and hMLH1 in Chinese patie... DisGeNET Detail
In a search for germline mutations in the DNA mismatch repair genes hMSH2 and hMLH1 in Chinese patie... DisGeNET Detail
A new familial gastric cancer-related gene polymorphism: T1151A in the mismatch repair gene hMLH1. 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
rs63750447 dbSNP
Genome
hg19
Position
chr3:37,067,240-37,067,240
Variant Type
snv
Reference Allele
T
Alternative Allele
A
Filtering Status (HGVD)
PASS
# of samples (HGVD)
1210
Mean of sample read depth (HGVD)
112.95
Standard deviation of sample read depth (HGVD)
53.09
Number of reference allele (HGVD)
2336
Number of alternative allele (HGVD)
84
Allele Frequency (HGVD)
0.03471074380165289
Gene Symbol (HGVD)
MLH1
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))
rs63750447
Allele frequency, for each ALT allele (ToMMo 8.3KJPN Allele Frequency Panel(v20200831))
0.0333
Allele count in genotypes, for each ALT allele (ToMMo 8.3KJPN Allele Frequency Panel(v20200831))
558
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)
333
East Asian Heterozygous Counts (ExAC)
327
East Asian Homozygous Counts (ExAC)
3
East Asian Allele Frequency (ExAC)
0.03851492019430951
Chromosome Counts in All Race (ExAC)
121288
Allele Counts in All Race (ExAC)
337
Heterozygous Counts in All Race (ExAC)
331
Homozygous Counts in All Race (ExAC)
3
Allele Frequency in All Race (ExAC)
0.00277851065233164
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