chr2:47803507:C>A Detail (hg38) (MSH6, FBXO11)

Information

Genome

Assembly Position
hg19 chr2:48,030,646-48,030,646 View the variant detail on this assembly version.
hg38 chr2:47,803,507-47,803,507

HGVS

Type Transcript Protein
RefSeq
Ensemble ENST00000405808.5:c.169+4688G>T
Type Transcript Protein
RefSeq NM_000179.2:c.3260C>A NP_000170.1:p.Pro1087His
NM_001281492.1:c.2870C>A NP_001268421.1:p.Pro957His
Ensemble ENST00000234420.11:c.3260C>A ENST00000234420.11:p.Pro1087His
Summary

MGeND

Clinical significance
Variant entry
GWAS entry
Disease area statistics Show details

Frequency

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

Prediction

ClinVar

Clinical Significance Conflicting classifications of pathogenicity
Review star
Show details
Links
Type Database ID Link
Gene MIM 607871 OMIM
HGNC 13590 HGNC
Ensembl ENSG00000138081 Ensembl
NCBI NCBI
Gene Cards Gene Cards
OncoKB OncoKB
Type Database ID Link
Variant TogoVar tgv6795821 TogoVar
COSMIC
MONDO
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 tgv6795821 TogoVar
COSMIC
MONDO
Disease area statistics
[No Data.]
MGeND
[No Data.]
ClinVar
Clinical significance Last evaluated Review status Condition Origin Links
Conflicting interpretations of pathogenicity 2023-05-02 criteria provided, conflicting interpretations Hereditary cancer-predisposing syndrome germline Detail
Uncertain significance 2023-08-15 criteria provided, multiple submitters, no conflicts not specified germline unknown Detail
Likely benign 2024-01-27 criteria provided, single submitter Hereditary nonpolyposis colorectal neoplasms germline Detail
Conflicting interpretations of pathogenicity 2023-08-14 criteria provided, conflicting interpretations not provided germline unknown Detail
Uncertain significance 2021-02-09 criteria provided, single submitter Mismatch repair cancer syndrome 1 unknown Detail
Uncertain significance 2020-01-17 criteria provided, single submitter Lynch syndrome 5 germline Detail
Uncertain significance 2024-02-05 criteria provided, single submitter Lynch syndrome germline Detail
Uncertain significance 2023-06-14 criteria provided, single submitter MSH6-related disorder germline Detail
CIViC
[No Data.]
DisGeNET
Score Disease name Description Source Pubmed Links
0.277 Hereditary Nonpolyposis Colorectal Cancer We recreated three MSH6 variants found in suspected Lynch syndrome families, MSH... BeFree 24040339 Detail
Annotation

Annotations

DescrptionSourceLinks
NM_000179.3(MSH6):c.3260C>A (p.Pro1087His) AND Hereditary cancer-predisposing syndrome ClinVar Detail
NM_000179.3(MSH6):c.3260C>A (p.Pro1087His) AND not specified ClinVar Detail
NM_000179.3(MSH6):c.3260C>A (p.Pro1087His) AND Hereditary nonpolyposis colorectal neoplasms ClinVar Detail
NM_000179.3(MSH6):c.3260C>A (p.Pro1087His) AND not provided ClinVar Detail
NM_000179.3(MSH6):c.3260C>A (p.Pro1087His) AND Mismatch repair cancer syndrome 1 ClinVar Detail
NM_000179.3(MSH6):c.3260C>A (p.Pro1087His) AND Lynch syndrome 5 ClinVar Detail
NM_000179.3(MSH6):c.3260C>A (p.Pro1087His) AND Lynch syndrome ClinVar Detail
NM_000179.3(MSH6):c.3260C>A (p.Pro1087His) AND MSH6-related disorder ClinVar Detail
We recreated three MSH6 variants found in suspected Lynch syndrome families, MSH6-P1087R, MSH6-R1095... 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
rs63750753 dbSNP
Genome
hg38
Position
chr2:47,803,507-47,803,507
Variant Type
snv
Reference Allele
C
Alternative Allele
A
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))
rs63750753
Allele frequency, for each ALT allele (ToMMo 8.3KJPN Allele Frequency Panel(v20200831))
0.0004
Allele count in genotypes, for each ALT allele (ToMMo 8.3KJPN Allele Frequency Panel(v20200831))
7
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)
4
East Asian Heterozygous Counts (ExAC)
4
East Asian Homozygous Counts (ExAC)
0
East Asian Allele Frequency (ExAC)
4.6242774566473987E-4
Chromosome Counts in All Race (ExAC)
121364
Allele Counts in All Race (ExAC)
18
Heterozygous Counts in All Race (ExAC)
18
Homozygous Counts in All Race (ExAC)
0
Allele Frequency in All Race (ExAC)
1.4831416235456973E-4
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