chr2:47429881:C>T Detail (hg38) (MSH2)

Information

Genome

Assembly Position
hg19 chr2:47,657,020-47,657,020 View the variant detail on this assembly version.
hg38 chr2:47,429,881-47,429,881

HGVS

Type Transcript Protein
RefSeq NM_000251.2:c.1216C>T NP_000242.1:p.Arg406Ter
NM_001258281.1:c.1018C>T NP_001245210.1:p.Arg340Ter
Ensemble ENST00000233146.7:c.1216C>T ENST00000233146.7:p.Arg406Ter
Summary

MGeND

Clinical significance Pathogenic
Variant entry 2
GWAS entry
Disease area statistics Show details

Frequency

JP HGVD:<0.001
ToMMo:[No Data.]
NCBN:[No Data.]
NCBN(Hondo):[No Data.]
NCBN(Ryukyu):[No Data.]
East asia ExAC:[No Data.]

Prediction

ClinVar

Clinical Significance Pathogenic
Review star
Show details
Links
Type Database ID Link
Gene MIM 609309 OMIM
HGNC 7325 HGNC
Ensembl ENSG00000095002 Ensembl
NCBI NCBI
Gene Cards Gene Cards
OncoKB OncoKB
Type Database ID Link
Variant TogoVar
COSMIC COSM26100 COSMIC
MONDO
Disease area statistics
MGeND
Clinical significance Last evaluated Condition Origin Submission ID Submitter Institute Citation Comment Image
Pathogenic 2021/11/22 endometrium germline MGS000029
(TMGS000133) 		Hitoshi Nakagama National Cancer Center Japan
Pathogenic 2021/11/22 lynch syndrome germline MGS000029
(TMGS000133) 		Hitoshi Nakagama National Cancer Center Japan
ClinVar
Clinical significance Last evaluated Review status Condition Origin Links
Pathogenic 2023-05-17 criteria provided, multiple submitters, no conflicts Lynch syndrome 1 germline unknown Detail
Pathogenic 2013-09-05 reviewed by expert panel Lynch syndrome germline Detail
Pathogenic 2022-03-18 criteria provided, multiple submitters, no conflicts Hereditary cancer-predisposing syndrome germline Detail
Pathogenic 2021-10-05 criteria provided, multiple submitters, no conflicts not provided germline unknown Detail
Pathogenic 2024-01-30 criteria provided, single submitter Hereditary nonpolyposis colorectal neoplasms germline Detail
Pathogenic 2017-05-31 no assertion criteria provided Carcinoma of colon germline unknown Detail
Pathogenic 2018-10-31 criteria provided, single submitter Muir-Torré syndrome,Mismatch repair cancer syndrome 1,Lynch syndrome 1 unknown Detail
Pathogenic 2018-10-31 criteria provided, single submitter Muir-Torré syndrome,Mismatch repair cancer syndrome 1,Lynch syndrome 1 unknown Detail
Pathogenic 2018-10-31 criteria provided, single submitter Muir-Torré syndrome,Mismatch repair cancer syndrome 1,Lynch syndrome 1 unknown Detail
Pathogenic 2021-07-01 no assertion criteria provided Gastric cancer germline Detail
CIViC
[No Data.]
DisGeNET
Score Disease name Description Source Pubmed Links
0.332 Hereditary Nonpolyposis Colorectal Cancer NA CLINVAR Detail
0.320 Colorectal cancer, hereditary nonpolyposis, type 1 NA CLINVAR Detail
0.121 Neoplastic Syndromes, Hereditary NA CLINVAR Detail
Annotation

Annotations

DescrptionSourceLinks
NM_000251.3(MSH2):c.1216C>T (p.Arg406Ter) AND Lynch syndrome 1 ClinVar Detail
NM_000251.3(MSH2):c.1216C>T (p.Arg406Ter) AND Lynch syndrome ClinVar Detail
NM_000251.3(MSH2):c.1216C>T (p.Arg406Ter) AND Hereditary cancer-predisposing syndrome ClinVar Detail
NM_000251.3(MSH2):c.1216C>T (p.Arg406Ter) AND not provided ClinVar Detail
NM_000251.3(MSH2):c.1216C>T (p.Arg406Ter) AND Hereditary nonpolyposis colorectal neoplasms ClinVar Detail
NM_000251.3(MSH2):c.1216C>T (p.Arg406Ter) AND Carcinoma of colon ClinVar Detail
NM_000251.3(MSH2):c.1216C>T (p.Arg406Ter) AND multiple conditions ClinVar Detail
NM_000251.3(MSH2):c.1216C>T (p.Arg406Ter) AND multiple conditions ClinVar Detail
NM_000251.3(MSH2):c.1216C>T (p.Arg406Ter) AND multiple conditions ClinVar Detail
NM_000251.3(MSH2):c.1216C>T (p.Arg406Ter) AND Gastric cancer ClinVar Detail
NA DisGeNET Detail
NA DisGeNET Detail
NA 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
rs63751108 dbSNP
Genome
hg38
Position
chr2:47,429,881-47,429,881
Variant Type
snv
Reference Allele
C
Alternative Allele
T
Filtering Status (HGVD)
PASS
Filtering Status (HGVD)
LowQual
# of samples (HGVD)
958
Mean of sample read depth (HGVD)
23.38
Standard deviation of sample read depth (HGVD)
21.18
Number of reference allele (HGVD)
1914
Number of alternative allele (HGVD)
1
Allele Frequency (HGVD)
5.221932114882506E-4
Gene Symbol (HGVD)
MSH2
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