chr3:37012077:A>G Detail (hg38) (MLH1)

Information

Genome

Assembly Position
hg19 chr3:37,053,568-37,053,568 View the variant detail on this assembly version.
hg38 chr3:37,012,077-37,012,077

HGVS

Type Transcript Protein
RefSeq NM_000249.3:c.655A>G NP_000240.1:p.Ile219Val
NM_001167617.1:c.361A>G NP_001161089.1:p.Ile121Val
NM_001167618.1:c.-69A>G
Summary

MGeND

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

Frequency

JP HGVD:0.056
ToMMo:0.050
NCBN:[No Data.]
NCBN(Hondo):[No Data.]
NCBN(Ryukyu):[No Data.]
East asia ExAC:0.022

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 tgv12068685 TogoVar
COSMIC COSM1131469 COSMIC
MONDO
Disease area statistics
MGeND
Clinical significance Last evaluated Condition Origin Submission ID Submitter Institute Citation Comment Image
Benign Centenarian germline MGS000068
(TMGS000140) 		Kenjiro Kosaki Keio University
ClinVar
Clinical significance Last evaluated Review status Condition Origin Links
Benign 2013-09-05 reviewed by expert panel Lynch syndrome germline Detail
Benign 2023-11-30 criteria provided, multiple submitters, no conflicts not provided germline Detail
Benign 2014-06-24 criteria provided, multiple submitters, no conflicts not specified germline unknown Detail
Benign 2020-01-10 criteria provided, multiple submitters, no conflicts Hereditary cancer-predisposing syndrome germline Detail
Benign 2017-08-18 criteria provided, single submitter Lynch syndrome 1 germline Detail
Benign 2023-07-07 criteria provided, multiple submitters, no conflicts Colorectal cancer, hereditary nonpolyposis, type 2 germline Detail
Benign 2024-02-01 criteria provided, single submitter Hereditary nonpolyposis colorectal neoplasms germline Detail
Benign no assertion criteria provided germline Detail
CIViC
[No Data.]
DisGeNET
Score Disease name Description Source Pubmed Links
0.085 Malignant neoplasm of breast Using data/samples collected from the first 752 Caucasians and 141 African-Ameri... BeFree 18701435 Detail
0.008 breast carcinoma Using data/samples collected from the first 752 Caucasians and 141 African-Ameri... BeFree 18701435 Detail
0.015 Malignant neoplasm of breast Using data/samples collected from the first 752 Caucasians and 141 African-Ameri... BeFree 18701435 Detail
0.011 breast carcinoma Using data/samples collected from the first 752 Caucasians and 141 African-Ameri... BeFree 18701435 Detail
0.002 adenoma In a Minnesota-based case-control study of individuals with adenomas (N=401), hy... BeFree 16771955 Detail
0.002 breast carcinoma Using data/samples collected from the first 752 Caucasians and 141 African-Ameri... BeFree 18701435 Detail
0.009 Malignant neoplasm of breast Using data/samples collected from the first 752 Caucasians and 141 African-Ameri... BeFree 18701435 Detail
0.019 Malignant neoplasm of breast Using data/samples collected from the first 752 Caucasians and 141 African-Ameri... BeFree 18701435 Detail
0.001 breast carcinoma Using data/samples collected from the first 752 Caucasians and 141 African-Ameri... BeFree 18701435 Detail
0.004 breast carcinoma Using data/samples collected from the first 752 Caucasians and 141 African-Ameri... BeFree 18701435 Detail
<0.001 polyps In a Minnesota-based case-control study of individuals with adenomas (N=401), hy... BeFree 16771955 Detail
0.018 breast carcinoma Using data/samples collected from the first 752 Caucasians and 141 African-Ameri... BeFree 18701435 Detail
<0.001 Hyperplastic Polyp In a Minnesota-based case-control study of individuals with adenomas (N=401), hy... BeFree 16771955 Detail
0.023 Malignant neoplasm of breast Using data/samples collected from the first 752 Caucasians and 141 African-Ameri... BeFree 18701435 Detail
0.013 Malignant neoplasm of breast Using data/samples collected from the first 752 Caucasians and 141 African-Ameri... BeFree 18701435 Detail
0.002 breast carcinoma Using data/samples collected from the first 752 Caucasians and 141 African-Ameri... BeFree 18701435 Detail
0.013 polyps In a Minnesota-based case-control study of individuals with adenomas (N=401), hy... BeFree 16771955 Detail
0.098 Malignant neoplasm of breast Using data/samples collected from the first 752 Caucasians and 141 African-Ameri... BeFree 18701435 Detail
<0.001 Polyp of large intestine In a Minnesota-based case-control study of individuals with adenomas (N=401), hy... BeFree 16771955 Detail
0.015 Malignant neoplasm of ovary When the analyses were restricted to serous type ovarian cancer, two SNPs showed... BeFree 18723338 Detail
<0.001 Hereditary pancreatitis Second, the samples from Finnish hereditary prostate cancer (HPC) families were ... BeFree 16963262 Detail
0.329 Hereditary Nonpolyposis Colorectal Cancer Evaluation of MLH1 I219V polymorphism in unrelated South American individuals su... BeFree 23060557 Detail
0.329 Hereditary Nonpolyposis Colorectal Cancer The approach was validated by transfecting cDNA of wild-type (WT) MLH1, cDNAs be... BeFree 16982745 Detail
0.012 ulcerative colitis Evaluation of the MLH1 I219V alteration in DNA mismatch repair activity and ulce... BeFree 18200512 Detail
0.020 colon carcinoma Statistically significant interactions were observed between: MLH1 -93G&gt;A and... BeFree 18523027 Detail
0.332 Hereditary Nonpolyposis Colorectal Cancer To evaluate the mutL homolog 1 (MLH1) I219V polymorphism in 124 unrelated South ... BeFree 23060557 Detail
0.003 Malignant neoplasm of ovary When the analyses were restricted to serous type ovarian cancer, two SNPs showed... BeFree 18723338 Detail
0.002 ovarian carcinoma When the analyses were restricted to serous type ovarian cancer, two SNPs showed... BeFree 18723338 Detail
0.010 ovarian carcinoma When the analyses were restricted to serous type ovarian cancer, two SNPs showed... BeFree 18723338 Detail
0.012 ulcerative colitis I219V polymorphism in hMLH1 gene in patients affected with ulcerative colitis. BeFree 19371218 Detail
0.005 breast carcinoma We observed two two-way SNP-SNP interactions (APEX1-rs1130409 and RPAP1-rs229738... BeFree 23755158 Detail
0.059 Malignant neoplasm of breast We observed two two-way SNP-SNP interactions (APEX1-rs1130409 and RPAP1-rs229738... BeFree 23755158 Detail
<0.001 breast carcinoma We observed two two-way SNP-SNP interactions (APEX1-rs1130409 and RPAP1-rs229738... BeFree 23755158 Detail
0.022 Malignant neoplasm of breast We observed two two-way SNP-SNP interactions (APEX1-rs1130409 and RPAP1-rs229738... BeFree 23755158 Detail
<0.001 Malignant neoplasm of breast We observed two two-way SNP-SNP interactions (APEX1-rs1130409 and RPAP1-rs229738... BeFree 23755158 Detail
0.008 breast carcinoma We observed two two-way SNP-SNP interactions (APEX1-rs1130409 and RPAP1-rs229738... BeFree 23755158 Detail
0.021 breast carcinoma We observed two two-way SNP-SNP interactions (APEX1-rs1130409 and RPAP1-rs229738... BeFree 23755158 Detail
0.019 Malignant neoplasm of breast We observed two two-way SNP-SNP interactions (APEX1-rs1130409 and RPAP1-rs229738... BeFree 23755158 Detail
Annotation

Annotations

DescrptionSourceLinks
NM_000249.4(MLH1):c.655A>G (p.Ile219Val) AND Lynch syndrome ClinVar Detail
NM_000249.4(MLH1):c.655A>G (p.Ile219Val) AND not provided ClinVar Detail
NM_000249.4(MLH1):c.655A>G (p.Ile219Val) AND not specified ClinVar Detail
NM_000249.4(MLH1):c.655A>G (p.Ile219Val) AND Hereditary cancer-predisposing syndrome ClinVar Detail
NM_000249.4(MLH1):c.655A>G (p.Ile219Val) AND Lynch syndrome 1 ClinVar Detail
NM_000249.4(MLH1):c.655A>G (p.Ile219Val) AND Colorectal cancer, hereditary nonpolyposis, type 2 ClinVar Detail
NM_000249.4(MLH1):c.655A>G (p.Ile219Val) AND Hereditary nonpolyposis colorectal neoplasms ClinVar Detail
NM_000249.4(MLH1):c.655A>G (p.Ile219Val) AND Malignant tumor of breast ClinVar Detail
Using data/samples collected from the first 752 Caucasians and 141 African-Americans in an ongoing c... DisGeNET Detail
Using data/samples collected from the first 752 Caucasians and 141 African-Americans in an ongoing c... DisGeNET Detail
Using data/samples collected from the first 752 Caucasians and 141 African-Americans in an ongoing c... DisGeNET Detail
Using data/samples collected from the first 752 Caucasians and 141 African-Americans in an ongoing c... DisGeNET Detail
In a Minnesota-based case-control study of individuals with adenomas (N=401), hyperplastic polyps (N... DisGeNET Detail
Using data/samples collected from the first 752 Caucasians and 141 African-Americans in an ongoing c... DisGeNET Detail
Using data/samples collected from the first 752 Caucasians and 141 African-Americans in an ongoing c... DisGeNET Detail
Using data/samples collected from the first 752 Caucasians and 141 African-Americans in an ongoing c... DisGeNET Detail
Using data/samples collected from the first 752 Caucasians and 141 African-Americans in an ongoing c... DisGeNET Detail
Using data/samples collected from the first 752 Caucasians and 141 African-Americans in an ongoing c... DisGeNET Detail
In a Minnesota-based case-control study of individuals with adenomas (N=401), hyperplastic polyps (N... DisGeNET Detail
Using data/samples collected from the first 752 Caucasians and 141 African-Americans in an ongoing c... DisGeNET Detail
In a Minnesota-based case-control study of individuals with adenomas (N=401), hyperplastic polyps (N... DisGeNET Detail
Using data/samples collected from the first 752 Caucasians and 141 African-Americans in an ongoing c... DisGeNET Detail
Using data/samples collected from the first 752 Caucasians and 141 African-Americans in an ongoing c... DisGeNET Detail
Using data/samples collected from the first 752 Caucasians and 141 African-Americans in an ongoing c... DisGeNET Detail
In a Minnesota-based case-control study of individuals with adenomas (N=401), hyperplastic polyps (N... DisGeNET Detail
Using data/samples collected from the first 752 Caucasians and 141 African-Americans in an ongoing c... DisGeNET Detail
In a Minnesota-based case-control study of individuals with adenomas (N=401), hyperplastic polyps (N... DisGeNET Detail
When the analyses were restricted to serous type ovarian cancer, two SNPs showed marginal significan... DisGeNET Detail
Second, the samples from Finnish hereditary prostate cancer (HPC) families were used for the screeni... DisGeNET Detail
Evaluation of MLH1 I219V polymorphism in unrelated South American individuals suspected of having Ly... DisGeNET Detail
The approach was validated by transfecting cDNA of wild-type (WT) MLH1, cDNAs bearing two previously... DisGeNET Detail
Evaluation of the MLH1 I219V alteration in DNA mismatch repair activity and ulcerative colitis. DisGeNET Detail
Statistically significant interactions were observed between: MLH1 -93G&gt;A and smoking (MSI-negati... DisGeNET Detail
To evaluate the mutL homolog 1 (MLH1) I219V polymorphism in 124 unrelated South American individuals... DisGeNET Detail
When the analyses were restricted to serous type ovarian cancer, two SNPs showed marginal significan... DisGeNET Detail
When the analyses were restricted to serous type ovarian cancer, two SNPs showed marginal significan... DisGeNET Detail
When the analyses were restricted to serous type ovarian cancer, two SNPs showed marginal significan... DisGeNET Detail
I219V polymorphism in hMLH1 gene in patients affected with ulcerative colitis. DisGeNET Detail
We observed two two-way SNP-SNP interactions (APEX1-rs1130409 and RPAP1-rs2297381; MLH1-rs1799977 an... DisGeNET Detail
We observed two two-way SNP-SNP interactions (APEX1-rs1130409 and RPAP1-rs2297381; MLH1-rs1799977 an... DisGeNET Detail
We observed two two-way SNP-SNP interactions (APEX1-rs1130409 and RPAP1-rs2297381; MLH1-rs1799977 an... DisGeNET Detail
We observed two two-way SNP-SNP interactions (APEX1-rs1130409 and RPAP1-rs2297381; MLH1-rs1799977 an... DisGeNET Detail
We observed two two-way SNP-SNP interactions (APEX1-rs1130409 and RPAP1-rs2297381; MLH1-rs1799977 an... DisGeNET Detail
We observed two two-way SNP-SNP interactions (APEX1-rs1130409 and RPAP1-rs2297381; MLH1-rs1799977 an... DisGeNET Detail
We observed two two-way SNP-SNP interactions (APEX1-rs1130409 and RPAP1-rs2297381; MLH1-rs1799977 an... DisGeNET Detail
We observed two two-way SNP-SNP interactions (APEX1-rs1130409 and RPAP1-rs2297381; MLH1-rs1799977 an... 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
rs1799977 dbSNP
Genome
hg38
Position
chr3:37,012,077-37,012,077
Variant Type
snv
Reference Allele
A
Alternative Allele
G
Filtering Status (HGVD)
PASS
# of samples (HGVD)
1191
Mean of sample read depth (HGVD)
36.30
Standard deviation of sample read depth (HGVD)
21.08
Number of reference allele (HGVD)
2248
Number of alternative allele (HGVD)
134
Allele Frequency (HGVD)
0.056255247691015954
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))
rs1799977
Allele frequency, for each ALT allele (ToMMo 8.3KJPN Allele Frequency Panel(v20200831))
0.0504
Allele count in genotypes, for each ALT allele (ToMMo 8.3KJPN Allele Frequency Panel(v20200831))
845
Total number of alleles in called genotypes (ToMMo 8.3KJPN Allele Frequency Panel(v20200831))
16760
East Asian Chromosome Counts (ExAC)
8650
East Asian Allele Counts (ExAC)
191
East Asian Heterozygous Counts (ExAC)
187
East Asian Homozygous Counts (ExAC)
2
East Asian Allele Frequency (ExAC)
0.02208092485549133
Chromosome Counts in All Race (ExAC)
121236
Allele Counts in All Race (ExAC)
28192
Heterozygous Counts in All Race (ExAC)
20186
Homozygous Counts in All Race (ExAC)
4003
Allele Frequency in All Race (ExAC)
0.2325381899765746
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