chr2:47783349:G>A Detail (hg38) (MSH6)

Information

Genome

Assembly Position
hg19 chr2:48,010,488-48,010,488 View the variant detail on this assembly version.
hg38 chr2:47,783,349-47,783,349

HGVS

Type Transcript Protein
RefSeq NM_000179.2:c.116G>A NP_000170.1:p.Gly39Glu
NM_001281492.1:c.116G>A NP_001268421.1:p.Gly39Glu
Ensemble ENST00000234420.11:c.116G>A ENST00000234420.11:p.Gly39Glu
Summary

MGeND

Clinical significance
Variant entry
GWAS entry
Disease area statistics Show details

Frequency

JP HGVD:0.311
ToMMo:0.318
NCBN:[No Data.]
NCBN(Hondo):[No Data.]
NCBN(Ryukyu):[No Data.]
East asia ExAC:0.290

Prediction

ClinVar

Clinical Significance Benign
Review star
Show details
Links
Type Database ID Link
Gene MIM 600678 OMIM
HGNC 7329 HGNC
Ensembl ENSG00000116062 Ensembl
NCBI NCBI
Gene Cards Gene Cards
OncoKB OncoKB
Type Database ID Link
Variant TogoVar tgv6792938 TogoVar
COSMIC COSM3749667 COSMIC
MONDO
Disease area statistics
[No Data.]
MGeND
[No Data.]
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 2016-02-29 criteria provided, multiple submitters, no conflicts not specified germline unknown Detail
Benign 2019-12-11 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 Likely benign 2023-07-07 criteria provided, multiple submitters, no conflicts Lynch syndrome 5 germline unknown Detail
Benign 2024-02-01 criteria provided, single submitter Hereditary nonpolyposis colorectal neoplasms germline Detail
Benign 2019-01-01 criteria provided, single submitter breast carcinoma unknown Detail
Benign no assertion criteria provided Carcinoma of colon unknown 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
<0.001 breast carcinoma Using unconditional logistic regression we found that MLH3 (L844P, G&gt;A) polym... BeFree 19781088 Detail
0.004 breast carcinoma Using unconditional logistic regression we found that MLH3 (L844P, G&gt;A) polym... BeFree 19781088 Detail
0.006 Malignant tumor of colon The MSH6 Gly39Glu and MLH1 -93G&gt;A polymorphisms were associated with risk of ... BeFree 18523027 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
0.013 Malignant neoplasm of breast Using unconditional logistic regression we found that MLH3 (L844P, G&gt;A) polym... BeFree 19781088 Detail
0.277 Hereditary Nonpolyposis Colorectal Cancer Although the MSH6 G39E polymorphism is considered to be a biomarker of hereditar... BeFree 24622885 Detail
0.011 breast carcinoma Using data/samples collected from the first 752 Caucasians and 141 African-Ameri... BeFree 18701435 Detail
<0.001 Triple Negative Breast Neoplasms Our results suggest that TNBC was associated with 6 DNA-repair nsSNPs, ERCC4 R41... BeFree 25023197 Detail
0.003 Malignant neoplasm of breast Using unconditional logistic regression we found that MLH3 (L844P, G&gt;A) polym... BeFree 19781088 Detail
0.008 breast carcinoma Using unconditional logistic regression we found that MLH3 (L844P, G&gt;A) polym... BeFree 19781088 Detail
<0.001 breast carcinoma Using unconditional logistic regression we found that MLH3 (L844P, G&gt;A) polym... BeFree 19781088 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 Triple Negative Breast Neoplasms Our results suggest that TNBC was associated with 6 DNA-repair nsSNPs, ERCC4 R41... BeFree 25023197 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
0.006 Malignant tumor of colon MSH6 G39E polymorphism and CpG island methylator phenotype in colon cancer. BeFree 19582761 Detail
<0.001 Triple Negative Breast Neoplasms Our results suggest that TNBC was associated with 6 DNA-repair nsSNPs, ERCC4 R41... BeFree 25023197 Detail
<0.001 Hyperplastic Polyp In a Minnesota-based case-control study of individuals with adenomas (N=401), hy... BeFree 16771955 Detail
<0.001 Malignant neoplasm of breast Using unconditional logistic regression we found that MLH3 (L844P, G&gt;A) polym... BeFree 19781088 Detail
0.005 colon carcinoma MSH6 G39E polymorphism and CpG island methylator phenotype in colon cancer. BeFree 19582761 Detail
0.024 Malignant tumor of colon The MSH6 Gly39Glu and MLH1 -93G&gt;A polymorphisms were associated with risk of ... BeFree 18523027 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
<0.001 Triple Negative Breast Neoplasms Our results suggest that TNBC was associated with 6 DNA-repair nsSNPs, ERCC4 R41... BeFree 25023197 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 Malignant neoplasm of pancreas Although the MSH6 G39E polymorphism is considered to be a biomarker of hereditar... BeFree 24622885 Detail
<0.001 Triple Negative Breast Neoplasms Our results suggest that TNBC was associated with 6 DNA-repair nsSNPs, ERCC4 R41... BeFree 25023197 Detail
<0.001 Triple Negative Breast Neoplasms Our results suggest that TNBC was associated with 6 DNA-repair nsSNPs, ERCC4 R41... BeFree 25023197 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 breast Using unconditional logistic regression we found that MLH3 (L844P, G&gt;A) polym... BeFree 19781088 Detail
Annotation

Annotations

DescrptionSourceLinks
NM_000179.3(MSH6):c.116G>A (p.Gly39Glu) AND Lynch syndrome ClinVar Detail
NM_000179.3(MSH6):c.116G>A (p.Gly39Glu) AND not provided ClinVar Detail
NM_000179.3(MSH6):c.116G>A (p.Gly39Glu) AND not specified ClinVar Detail
NM_000179.3(MSH6):c.116G>A (p.Gly39Glu) AND Hereditary cancer-predisposing syndrome ClinVar Detail
NM_000179.3(MSH6):c.116G>A (p.Gly39Glu) AND Lynch syndrome 1 ClinVar Detail
NM_000179.3(MSH6):c.116G>A (p.Gly39Glu) AND Lynch syndrome 5 ClinVar Detail
NM_000179.3(MSH6):c.116G>A (p.Gly39Glu) AND Hereditary nonpolyposis colorectal neoplasms ClinVar Detail
NM_000179.3(MSH6):c.116G>A (p.Gly39Glu) AND Breast carcinoma ClinVar Detail
NM_000179.3(MSH6):c.116G>A (p.Gly39Glu) AND Carcinoma of colon ClinVar Detail
Using data/samples collected from the first 752 Caucasians and 141 African-Americans in an ongoing c... DisGeNET Detail
Using unconditional logistic regression we found that MLH3 (L844P, G&gt;A) polymorphism GA (Leu/Pro)... DisGeNET Detail
Using unconditional logistic regression we found that MLH3 (L844P, G&gt;A) polymorphism GA (Leu/Pro)... DisGeNET Detail
The MSH6 Gly39Glu and MLH1 -93G&gt;A polymorphisms were associated with risk of overall colon and MS... 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 unconditional logistic regression we found that MLH3 (L844P, G&gt;A) polymorphism GA (Leu/Pro)... DisGeNET Detail
Although the MSH6 G39E polymorphism is considered to be a biomarker of hereditary nonpolyposis color... DisGeNET Detail
Using data/samples collected from the first 752 Caucasians and 141 African-Americans in an ongoing c... DisGeNET Detail
Our results suggest that TNBC was associated with 6 DNA-repair nsSNPs, ERCC4 R415Q (rs1800067), MSH3... DisGeNET Detail
Using unconditional logistic regression we found that MLH3 (L844P, G&gt;A) polymorphism GA (Leu/Pro)... DisGeNET Detail
Using unconditional logistic regression we found that MLH3 (L844P, G&gt;A) polymorphism GA (Leu/Pro)... DisGeNET Detail
Using unconditional logistic regression we found that MLH3 (L844P, G&gt;A) polymorphism GA (Leu/Pro)... 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
Our results suggest that TNBC was associated with 6 DNA-repair nsSNPs, ERCC4 R415Q (rs1800067), MSH3... 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
MSH6 G39E polymorphism and CpG island methylator phenotype in colon cancer. DisGeNET Detail
Our results suggest that TNBC was associated with 6 DNA-repair nsSNPs, ERCC4 R415Q (rs1800067), MSH3... DisGeNET Detail
In a Minnesota-based case-control study of individuals with adenomas (N=401), hyperplastic polyps (N... DisGeNET Detail
Using unconditional logistic regression we found that MLH3 (L844P, G&gt;A) polymorphism GA (Leu/Pro)... DisGeNET Detail
MSH6 G39E polymorphism and CpG island methylator phenotype in colon cancer. DisGeNET Detail
The MSH6 Gly39Glu and MLH1 -93G&gt;A polymorphisms were associated with risk of overall colon and MS... 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
Our results suggest that TNBC was associated with 6 DNA-repair nsSNPs, ERCC4 R415Q (rs1800067), MSH3... DisGeNET Detail
Using data/samples collected from the first 752 Caucasians and 141 African-Americans in an ongoing c... DisGeNET Detail
Although the MSH6 G39E polymorphism is considered to be a biomarker of hereditary nonpolyposis color... DisGeNET Detail
Our results suggest that TNBC was associated with 6 DNA-repair nsSNPs, ERCC4 R415Q (rs1800067), MSH3... DisGeNET Detail
Our results suggest that TNBC was associated with 6 DNA-repair nsSNPs, ERCC4 R415Q (rs1800067), MSH3... DisGeNET Detail
In a Minnesota-based case-control study of individuals with adenomas (N=401), hyperplastic polyps (N... DisGeNET Detail
Using unconditional logistic regression we found that MLH3 (L844P, G&gt;A) polymorphism GA (Leu/Pro)... 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
rs1042821 dbSNP
Genome
hg38
Position
chr2:47,783,349-47,783,349
Variant Type
snv
Reference Allele
G
Alternative Allele
A
Filtering Status (HGVD)
PASS
# of samples (HGVD)
1185
Mean of sample read depth (HGVD)
127.96
Standard deviation of sample read depth (HGVD)
64.77
Number of reference allele (HGVD)
1633
Number of alternative allele (HGVD)
736
Allele Frequency (HGVD)
0.3106796116504854
Gene Symbol (HGVD)
MSH6
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))
rs1042821
Allele frequency, for each ALT allele (ToMMo 8.3KJPN Allele Frequency Panel(v20200831))
0.3178
Allele count in genotypes, for each ALT allele (ToMMo 8.3KJPN Allele Frequency Panel(v20200831))
5325
Total number of alleles in called genotypes (ToMMo 8.3KJPN Allele Frequency Panel(v20200831))
16754
Homozygous Counts in All Race (ExAC)
1894
East Asian Chromosome Counts (ExAC)
6792
East Asian Allele Counts (ExAC)
1973
East Asian Heterozygous Counts (ExAC)
1511
East Asian Homozygous Counts (ExAC)
231
East Asian Allele Frequency (ExAC)
0.29048881036513546
Chromosome Counts in All Race (ExAC)
91130
Allele Counts in All Race (ExAC)
19510
Heterozygous Counts in All Race (ExAC)
15722
Allele Frequency in All Race (ExAC)
0.2140897618786349
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