chr2:48030646:C>G Detail (hg19) (MSH6, FBXO11)
Information
Genome
| Assembly | Position |
|---|---|
| hg19 | chr2:48,030,646-48,030,646 |
| hg38 | chr2:47,803,507-47,803,507 View the variant detail on this assembly version. |
HGVS
| Type | Transcript | Protein |
|---|---|---|
| RefSeq | ||
| Ensemble | ENST00000405808.5:c.169+4688G>C |
| Type | Transcript | Protein |
|---|---|---|
| RefSeq | NM_001281492.1:c.2870C>G | NP_001268421.1:p.Pro957Arg |
| NM_000179.2:c.3260C>G | NP_000170.1:p.Pro1087Arg | |
| Ensemble | ENST00000540021.6:c.2870C>G | ENST00000540021.6:p.Pro957Arg |
Summary
MGeND
| Clinical significance |
not provided
|
| Variant entry | 7 |
| 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 | |
Disease area statistics
MGeND
| Clinical significance | Last evaluated | Condition | Origin | Submission ID | Submitter | Institute | Citation | Comment | Image |
|---|---|---|---|---|---|---|---|---|---|
|
not provided
|
pyloric antrum |
not provided
|
MGS000042
(TMGS000093) |
Hitoshi Nakagama | National Cancer Center Japan | ||||
|
not provided
|
caecum |
not provided
|
MGS000042
(TMGS000093) |
Hitoshi Nakagama | National Cancer Center Japan | ||||
|
not provided
|
extrahepatic bile duct |
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 |
ClinVar
| Clinical significance | Last evaluated | Review status | Condition | Origin | Links |
|---|---|---|---|---|---|
Uncertain significance
|
2023-11-20 | criteria provided, multiple submitters, no conflicts | Lynch syndrome |
germline
unknown
|
Detail |
Conflicting interpretations of pathogenicity
|
2023-02-27 | criteria provided, conflicting interpretations | Hereditary cancer-predisposing syndrome |
germline
|
Detail |
Likely benign
|
2024-01-24 | criteria provided, single submitter | Hereditary nonpolyposis colorectal neoplasms |
germline
|
Detail |
|
Conflicting interpretations of pathogenicity
|
2020-10-26 | criteria provided, conflicting interpretations | not provided |
germline
unknown
|
Detail |
|
Uncertain significance
|
2018-10-31 | criteria provided, single submitter | Lynch syndrome 5,endometrial carcinoma,Mismatch repair cancer syndrome 1 |
unknown
|
Detail |
|
Uncertain significance
|
2018-10-31 | criteria provided, single submitter | Lynch syndrome 5,endometrial carcinoma,Mismatch repair cancer syndrome 1 |
unknown
|
Detail |
|
Uncertain significance
|
2018-10-31 | criteria provided, single submitter | Lynch syndrome 5,endometrial carcinoma,Mismatch repair cancer syndrome 1 |
unknown
|
Detail |
|
Uncertain significance
|
2022-03-24 | criteria provided, single submitter | Breast and/or ovarian cancer |
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
| Descrption | Source | Links |
|---|---|---|
| NM_000179.3(MSH6):c.3260C>G (p.Pro1087Arg) AND Lynch syndrome | ClinVar | Detail |
| NM_000179.3(MSH6):c.3260C>G (p.Pro1087Arg) AND Hereditary cancer-predisposing syndrome | ClinVar | Detail |
| NM_000179.3(MSH6):c.3260C>G (p.Pro1087Arg) AND Hereditary nonpolyposis colorectal neoplasms | ClinVar | Detail |
| NM_000179.3(MSH6):c.3260C>G (p.Pro1087Arg) AND not provided | ClinVar | Detail |
| NM_000179.3(MSH6):c.3260C>G (p.Pro1087Arg) AND multiple conditions | ClinVar | Detail |
| NM_000179.3(MSH6):c.3260C>G (p.Pro1087Arg) AND multiple conditions | ClinVar | Detail |
| NM_000179.3(MSH6):c.3260C>G (p.Pro1087Arg) AND multiple conditions | ClinVar | Detail |
| NM_000179.3(MSH6):c.3260C>G (p.Pro1087Arg) AND Breast and/or ovarian cancer | 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
- hg19
- Position
- chr2:48,030,646-48,030,646
- Variant Type
- snv
- Reference Allele
- C
- Alternative Allele
- G
- 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))
- 0.0002
- Allele count in genotypes, for each ALT allele (ToMMo 8.3KJPN Allele Frequency Panel(v20200831))
- 3
- 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)
- 0
- East Asian Heterozygous Counts (ExAC)
- 0
- East Asian Homozygous Counts (ExAC)
- 0
- East Asian Allele Frequency (ExAC)
- 0.0
- Chromosome Counts in All Race (ExAC)
- 121364
- Allele Counts in All Race (ExAC)
- 5
- Heterozygous Counts in All Race (ExAC)
- 5
- Homozygous Counts in All Race (ExAC)
- 0
- Allele Frequency in All Race (ExAC)
- 4.1198378431824927E-5
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