NM_000179.2(MSH6):c.642C>T (p.Tyr214=) AND Lynch syndrome

This record was updated by the submitter. Please see the current version.

Germline classification:: Benign (2 submissions)
Last evaluated:: Sep 5, 2013
Review status:: 3 stars out of maximum of 4 stars
reviewed by expert panel

Somatic classification of clinical impact:: None
Review status:: (0/4) 0 stars out of maximum of 4 stars
no assertion criteria provided

Somatic classification of oncogenicity:: None
Review status:: (0/4) 0 stars out of maximum of 4 stars
no assertion criteria provided

Record status:: current
Accession:: RCV000030277.3

Allele description

NM_000179.2(MSH6):c.642C>T (p.Tyr214=)

Gene:

MSH6:mutS homolog 6 [Gene - OMIM - HGNC]

Variant type:

single nucleotide variant

Cytogenetic location:

2p16.3

Genomic location:

Preferred name:

NM_000179.2(MSH6):c.642C>T (p.Tyr214=)

HGVS:

NC_000002.12:g.47798625C>T
NG_007111.1:g.20479C>T
NM_000179.2:c.642C>T
NM_001281493.1:c.-265C>T
NP_000170.1:p.Tyr214=
LRG_219t1:c.642C>T
LRG_219:g.20479C>T
LRG_219p1:p.Tyr214=
NC_000002.11:g.48025764C>T
NP_000170.1:p.(=)
c.642C>T
p.Y214Y

Links:

dbSNP: rs1800937

GMAF:

0.0286(T), 1800937

NCBI 1000 Genomes Browser:

rs1800937

Allele Frequency:

0.0691, GO-ESP

Molecular consequence:

NM_001281493.1:c.-265C>T - 5 prime UTR variant - [Sequence Ontology: SO:0001623]
NM_000179.2:c.642C>T - synonymous variant - [Sequence Ontology: SO:0001819]

Observations:

Condition(s)

Name:: Lynch syndrome (HNPCC)
Synonyms:: Hereditary nonpolyposis colon cancer
Identifiers:: MedGen: C1333990; OMIM: PS120435

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Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV000052944	LabCorp	criteria provided, single submitter (LabCorp Variant Classification Summary - May 2015)	benign (Aug 18, 2011)	germline	clinical testing	PubMed (3) [See all records that cite these PMIDs] 15805151, 10537275, 10699937 Citation Link,
SCV000108237	InSiGHT	reviewed by expert panel (Guidelines v1.9)	no known pathogenicity (Sep 5, 2013)	germline	research	Citation Link

Submission Accession

Submitter

Review Status
(Assertion method)

Clinical Significance
(Last evaluated)

Origin

Method

Citations

SCV000052944

LabCorp

criteria provided, single submitter

(LabCorp Variant Classification Summary - May 2015)

benign
(Aug 18, 2011)

germline

clinical testing

PubMed (3)
[See all records that cite these PMIDs]

Citation Link,

SCV000108237

InSiGHT

reviewed by expert panel

(Guidelines v1.9)

no known pathogenicity
(Sep 5, 2013)

germline

research

Citation Link

Help

Summary from all submissions

Ethnicity	Origin	Affected	Individuals	Families	Chromosomes tested	Number Tested	Family history	Method
not provided	germline	unknown	9	not provided	not provided	not provided	not provided	clinical testing, research

Citations

PubMed

No MSH6 germline mutations in breast cancer families with colorectal and/or endometrial cancer.

Vahteristo P, Ojala S, Tamminen A, Tommiska J, Sammalkorpi H, Kiuru-Kuhlefelt S, Eerola H, Aaltonen LA, Aittomäki K, Nevanlinna H.

J Med Genet. 2005 Apr;42(4):e22.

PubMed [citation]

PMID:: 15805151
PMCID:: PMC1736038

Germ-line msh6 mutations in colorectal cancer families.

Kolodner RD, Tytell JD, Schmeits JL, Kane MF, Gupta RD, Weger J, Wahlberg S, Fox EA, Peel D, Ziogas A, Garber JE, Syngal S, Anton-Culver H, Li FP.

Cancer Res. 1999 Oct 15;59(20):5068-74.

PubMed [citation]

PMID:: 10537275

See all PubMed Citations (3)

Details of each submission

From LabCorp, SCV000052944.1

#	Ethnicity	Individuals	Chromosomes Tested	Family History	Method	Citations
1	not provided	not provided	not provided	not provided	clinical testing	PubMed (3)
2	not provided	not provided	not provided	not provided	clinical testing	PubMed (3)
3	not provided	not provided	not provided	not provided	clinical testing	PubMed (3)
4	not provided	not provided	not provided	not provided	clinical testing	PubMed (3)
5	not provided	not provided	not provided	not provided	clinical testing	PubMed (3)
6	not provided	not provided	not provided	not provided	clinical testing	PubMed (3)
7	not provided	not provided	not provided	not provided	clinical testing	PubMed (3)
8	not provided	not provided	not provided	not provided	clinical testing	PubMed (3)
9	not provided	not provided	not provided	not provided	clinical testing	PubMed (3)

#	Sample				Method		Observation
#	Origin	Affected	Number tested	Tissue	Purpose	Method	Individuals	Allele frequency	Families	Co-occurrences
1	germline	unknown	not provided	Blood	assert pathogenicity		not provided	not provided	not provided	See 1
2	germline	unknown	not provided	Blood	assert pathogenicity		not provided	not provided	not provided	See 2
3	germline	unknown	not provided	Blood	assert pathogenicity		not provided	not provided	not provided	See 3
4	germline	unknown	not provided	Blood	assert pathogenicity		not provided	not provided	not provided	See 4
5	germline	unknown	not provided	Blood	assert pathogenicity		not provided	not provided	not provided	See 5
6	germline	unknown	not provided	Blood	assert pathogenicity		not provided	not provided	not provided	See 6
7	germline	unknown	not provided	Blood	assert pathogenicity		not provided	not provided	not provided	See 7
8	germline	unknown	not provided	Blood	assert pathogenicity		not provided	not provided	not provided	See 8
9	germline	unknown	not provided	Blood	assert pathogenicity		not provided	not provided	not provided	See 9

Co-occurrences

#	Zygosity	Alleles	Number of Observations
1	SingleHeterozygote	MSH6:c.3438+14A>T, MSH6:c.276A>G, MSH6:c.186C>A, MSH6:c.540T>C	1
2	SingleHeterozygote	MLH1:c.1668-19A>G, MSH6:c.540T>C	1
3	Homozygote	MLH1:c.1668-19A>G, MLH1:c.655A>G, MSH2:c.211+9C>G, MSH2:c.1661+12G>A, MSH2:c.1511-9A>T, MSH6:c.540T>C	1
4	SingleHeterozygote	MLH1:c.1668-19A>G, MLH1:c.655A>G, MSH2:c.211+9C>G, MSH6:c.540T>C	1
5	SingleHeterozygote	MSH2:c.211+9C>G, MSH2:c.2006-6T>C, MSH2:c.1661+12G>A, MSH2:c.1030C>T, MSH2:c.211+9C>G, MSH2:c.2006-6T>C, MSH2:c.1661+12G>A, MSH2:c.1030C>T, MSH6:c.540T>C, MSH6:c.3438+14A>T	1
6	SingleHeterozygote	MLH1:c.1668-19A>G, MLH1:c.655A>G, MSH6:c.540T>C, MSH6:c.116G>A	1
7	SingleHeterozygote	MLH1:c.1668-19A>G, MLH1:c.655A>G, MSH6:c.3647-35_3647-34insTTTGTTCTAATTCCTTT, MSH6:c.3438+14A>T, MSH6:c.276A>G, MSH6:c.186C>A, MSH6:c.540T>C	1
8	SingleHeterozygote	MLH1:c.1896+17T>C, MSH2:c.211+9C>G, MSH2:c.1661+12G>A, MSH2:c.1511-9A>T, MSH6:c.540T>C, MSH6:c.116G>A	1
9	SingleHeterozygote	MSH6:c.540T>C	1

From InSiGHT, SCV000108237.2

#	Ethnicity	Individuals	Chromosomes Tested	Family History	Method	Citations
1	not provided	not provided	not provided	not provided	research	not provided

Description

MAF >1%

#	Sample				Method		Observation
#	Origin	Affected	Number tested	Tissue	Purpose	Method	Individuals	Allele frequency	Families	Co-occurrences
1	germline	unknown	not provided	not provided	not provided		not provided	not provided	not provided	not provided

Last Updated: Nov 13, 2016

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