chr2:48023107:C>T Detail (hg19) (MSH6, FBXO11)

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Summary
Information
Links
Disease area statistics
MGeND
ClinVar
CIViC
DisGeNET
Annotation
Genome browser

Information

Genome

Assembly	Position
hg19	chr2:48,023,107-48,023,107
hg38	chr2:47,795,968-47,795,968 View the variant detail on this assembly version.

HGVS

FBXO11
MSH6

Type	Transcript	Protein
RefSeq
Ensemble	ENST00000405808.5:c.170-6528G>A

Type	Transcript	Protein
RefSeq	NM_000179.2:c.532C>T	NP_000170.1:p.Arg178Cys
	NM_001281492.1:c.238-2643C>T
Ensemble	ENST00000455383.6:c.235C>T	ENST00000455383.6:p.Arg79Cys
	ENST00000234420.11:c.532C>T	ENST00000234420.11:p.Arg178Cys
	ENST00000420813.6:c.235C>T	ENST00000420813.6:p.Arg79Cys
	ENST00000540021.6:c.238-2643C>T
	ENST00000411819.2:c.235C>T	ENST00000411819.2:p.Arg79Cys
	ENST00000652107.1:c.235C>T	ENST00000652107.1:p.Arg79Cys
	ENST00000673637.1:c.235C>T	ENST00000673637.1:p.Arg79Cys
	ENST00000700000.1:c.532C>T	ENST00000700000.1:p.Arg178Cys
	ENST00000700002.1:c.532C>T	ENST00000700002.1:p.Arg178Cys
	ENST00000700004.2:c.532C>T	ENST00000700004.2:p.Arg178Cys

Summary

MGeND

Clinical significance	Benign Uncertain significance not provided other
Variant entry	86
GWAS entry
Disease area statistics	Show details

Frequency

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

Prediction

ClinVar

Clinical Significance	Conflicting classifications of pathogenicity
Review star
Show details

Links

FBXO11
MSH6

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	tgv6793678	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	tgv6793678	TogoVar
	COSMIC
	MONDO

Disease area statistics

MGeND

Clinical significance	Last evaluated	Condition	Origin	Submission ID	Submitter	Institute
Uncertain significance		colorectal cancer	germline	MGS000060 (TMGS000107)	Hitoshi Nakagama	National Cancer Center Japan
Uncertain significance		Endometrial cancer	germline	MGS000060 (TMGS000107)	Hitoshi Nakagama	National Cancer Center Japan
Uncertain significance	2018/10/13	juvenile polyposis syndrome	germline	MGS000029 (TMGS000133)	Hitoshi Nakagama	National Cancer Center Japan
Uncertain significance	2018/10/13	colon, unspecified	germline	MGS000029 (TMGS000133)	Hitoshi Nakagama	National Cancer Center Japan
other		Carcinoma of pancreas (disorder)	unknown	MGS000021 (TMGS000080)	Manabu Muto	Kyoto University
Uncertain significance		Biliary	germline	MGS000038 (TMGS000091)	Manabu Muto Ichiro Kinoshita	Kyoto University Department of Medical Oncology Faculty of Medicine and Graduate School of Medicine Hokkaido University
other		Adenocarcinoma of sigmoid colon (disorder)	unknown	MGS000025 (TMGS000084)	Manabu Muto	Kyoto University
Benign	2021/03/19	control	germline	MGS000047 (TMGS000111)	Yukihide Momozawa Koichi Matsuda	RIKEN The University of Tokyo
Benign	2021/03/19	Colorectal	germline	MGS000050 (TMGS000114)	Yukihide Momozawa Koichi Matsuda	RIKEN The University of Tokyo
Benign	2021/03/19	pancreatic	germline	MGS000051 (TMGS000115)	Yukihide Momozawa Koichi Matsuda	RIKEN The University of Tokyo
Benign		Centenarian	germline	MGS000068 (TMGS000140)	Kenjiro Kosaki	Keio University
not provided		stomach, unspecified	not provided	MGS000042 (TMGS000093)	Hitoshi Nakagama	National Cancer Center Japan
not provided		ascending colon	not provided	MGS000042 (TMGS000093)	Hitoshi Nakagama	National Cancer Center Japan
not provided		transverse colon	not provided	MGS000042 (TMGS000093)	Hitoshi Nakagama	National Cancer Center Japan
not provided		colon, unspecified	not provided	MGS000042 (TMGS000093)	Hitoshi Nakagama	National Cancer Center Japan
not provided		tail of pancreas	not provided	MGS000042 (TMGS000093)	Hitoshi Nakagama	National Cancer Center Japan
not provided		ill-defined sites within the digestive system	not provided	MGS000042 (TMGS000093)	Hitoshi Nakagama	National Cancer Center Japan
not provided		bronchus or lung, unspecified	not provided	MGS000042 (TMGS000093)	Hitoshi Nakagama	National Cancer Center Japan

Past history: no past history; Family history: colorectal; Histological type: adenocarcinoma; Anatomic site of CRC: left-side colon and rectum; (1)
Past history: no past history; Family history: pancreatic; Histological type: adenocarcinoma; Anatomic site of CRC: right-side colon; (1)
Past history: no past history; Family history: bileduct; Histological type: adenocarcinoma; Anatomic site of CRC: left-side colon and rectum; (1)
Past history: no past history; Family history: no family history; Histological type: adenocarcinoma; Anatomic site of CRC: left-side colon and rectum; (4)
Past history: no past history; Family history: gastric; Histological type: adenocarcinoma; Anatomic site of CRC: left-side colon and rectum; (1)
Past history: no past history; Family history: liver; Histological type: adenocarcinoma; Anatomic site of CRC: left-side colon and rectum; (1)
Past history: no past history; Family history: no family history; Histological type: NA; Anatomic site of CRC: left-side colon and rectum; (2)
Past history: no past history; Family history: no family history; Histological type: adenocarcinoma; Anatomic site of CRC: right-side colon; (4)
Past history: no past history; Family history: prostate; Histological type: others; Anatomic site of CRC: left-side colon and rectum; (1)
Past history: no past history; Family history: breast and colorectal; Histological type: adenocarcinoma; Anatomic site of CRC: left-side colon and rectum; (2)
Past history: gastric; Family history: no family history; Histological type: adenocarcinoma; Anatomic site of CRC: left-side colon and rectum; (1)
Past history: no past history; Family history: lung; Histological type: adenocarcinoma; Anatomic site of CRC: right-side colon; (1)
Past history: gastric; Family history: gastric and lung; Histological type: adenocarcinoma; Anatomic site of CRC: left-side colon and rectum; (1)
Past history: no past history; Family history: lung; Histological type: adenocarcinoma; Anatomic site of CRC: NA; (1)
Past history: no past history; Family history: gastric; Histological type: adenocarcinoma; Anatomic site of CRC: right-side colon; (1)
Past history: no past history; Family history: gastric and lung; Histological type: adenocarcinoma; Anatomic site of CRC: left-side colon and rectum; (1)
Past history: prostate; Family history: no family history; Histological type: adenocarcinoma; Anatomic site of CRC: right-side colon; (1)
Past history: lung; Family history: no family history; Histological type: adenocarcinoma; Anatomic site of CRC: NA; (1)
Past history: no past history; Family history: lung; Histological type: adenocarcinoma; Anatomic site of CRC: left-side colon and rectum; (1)
Past history: no past history; Family history: colorectal and lung; Histological type: adenocarcinoma; Anatomic site of CRC: NA; (1)

ClinVar

Clinical significance	Last evaluated	Review status	Condition	Origin	Links
Uncertain significance	2023-08-24	criteria provided, multiple submitters, no conflicts	not provided	germline unknown	Detail
Conflicting interpretations of pathogenicity	2023-10-25	criteria provided, conflicting interpretations	Hereditary cancer-predisposing syndrome	germline	Detail
Benign	2024-01-10	criteria provided, single submitter	Hereditary nonpolyposis colorectal neoplasms	germline	Detail
Uncertain significance	2018-11-23	criteria provided, single submitter	not specified	germline	Detail
Uncertain significance	2019-05-28	criteria provided, single submitter	Lynch syndrome 5	unknown	Detail
Uncertain significance	2019-05-01	criteria provided, single submitter	hereditary breast ovarian cancer syndrome	germline	Detail
Uncertain significance	2023-10-19	criteria provided, single submitter	endometrial carcinoma	unknown	Detail
Uncertain significance	2023-12-18	criteria provided, single submitter	Lynch syndrome	germline	Detail

CIViC

[No Data.]

DisGeNET

[No Data.]

Annotation

Annotations

Descrption	Source	Links
NM_000179.3(MSH6):c.532C>T (p.Arg178Cys) AND not provided	ClinVar	Detail
NM_000179.3(MSH6):c.532C>T (p.Arg178Cys) AND Hereditary cancer-predisposing syndrome	ClinVar	Detail
NM_000179.3(MSH6):c.532C>T (p.Arg178Cys) AND Hereditary nonpolyposis colorectal neoplasms	ClinVar	Detail
NM_000179.3(MSH6):c.532C>T (p.Arg178Cys) AND not specified	ClinVar	Detail
NM_000179.3(MSH6):c.532C>T (p.Arg178Cys) AND Lynch syndrome 5	ClinVar	Detail
NM_000179.3(MSH6):c.532C>T (p.Arg178Cys) AND Hereditary breast ovarian cancer syndrome	ClinVar	Detail
NM_000179.3(MSH6):c.532C>T (p.Arg178Cys) AND Endometrial carcinoma	ClinVar	Detail
NM_000179.3(MSH6):c.532C>T (p.Arg178Cys) AND Lynch syndrome	ClinVar	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: rs730881813 dbSNP
Genome: hg19
Position: chr2:48,023,107-48,023,107
Variant Type: snv
Reference Allele: C
Alternative Allele: T
Filtering Status (HGVD): PASS
Filtering Status (HGVD): LowQual
# of samples (HGVD): 1195
Mean of sample read depth (HGVD): 39.62
Standard deviation of sample read depth (HGVD): 19.66
Number of reference allele (HGVD): 2389
Number of alternative allele (HGVD): 1
Allele Frequency (HGVD): 4.1841004184100416E-4
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)): rs730881813
Allele frequency, for each ALT allele (ToMMo 8.3KJPN Allele Frequency Panel(v20200831)): 0.0008
Allele count in genotypes, for each ALT allele (ToMMo 8.3KJPN Allele Frequency Panel(v20200831)): 13
Total number of alleles in called genotypes (ToMMo 8.3KJPN Allele Frequency Panel(v20200831)): 16760

Genome browser

chr2:48023107:C>T Detail (hg19) (MSH6, FBXO11)

Genome

HGVS

MGeND

Frequency

Prediction

ClinVar

Clinical information of patient(s) with this variant provided by the submitter(s)

Clinical information of patient(s) with this variant provided by the submitter(s)

Clinical information of patient(s) with this variant provided by the submitter(s)

Image provided by the submitter

Annotations

Overlapped Transcript Coordinates

Overlapped Transcript