NM_000179.3(MSH6):c.540T>C (p.Asp180=) AND Lynch syndrome

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:: RCV000030275.15

Allele description [Variation Report for NM_000179.3(MSH6):c.540T>C (p.Asp180=)]

NM_000179.3(MSH6):c.540T>C (p.Asp180=)

Gene:

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

Variant type:

single nucleotide variant

Cytogenetic location:

2p16.3

Genomic location:

Preferred name:

NM_000179.3(MSH6):c.540T>C (p.Asp180=)

HGVS:

NC_000002.12:g.47795976T>C
NG_007111.1:g.17830T>C
NM_000179.3:c.540T>CMANE SELECT
NM_001281492.2:c.238-2635T>C
NM_001281493.2:c.-279-2635T>C
NM_001281494.2:c.-363T>C
NP_000170.1:p.Asp180=
NP_000170.1:p.Asp180=
LRG_219t1:c.540T>C
LRG_219:g.17830T>C
LRG_219p1:p.Asp180=
NC_000002.11:g.48023115T>C
NM_000179.2:c.540T>C
NM_001281493.1:c.-279-2635T>C
NP_000170.1:p.(=)
c.540T>C
p.D180D

Links:

dbSNP: rs1800935

NCBI 1000 Genomes Browser:

rs1800935

Molecular consequence:

NM_001281494.2:c.-363T>C - 5 prime UTR variant - [Sequence Ontology: SO:0001623]
NM_001281492.2:c.238-2635T>C - intron variant - [Sequence Ontology: SO:0001627]
NM_001281493.2:c.-279-2635T>C - intron variant - [Sequence Ontology: SO:0001627]
NM_000179.3:c.540T>C - synonymous variant - [Sequence Ontology: SO:0001819]

Observations:

Condition(s)

Name:: Lynch syndrome
Identifiers:: MONDO: MONDO:0005835; MedGen: C4552100

Recent activity

Clear Turn Off Turn On

Your browsing activity is empty.

Activity recording is turned off.

Turn recording back on

Help

Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV000052942	Women's Health and Genetics/Laboratory Corporation of America, LabCorp	criteria provided, single submitter (LabCorp Variant Classification Summary - May 2015)	benign (Aug 18, 2011)	germline	curation, clinical testing	PubMed (1) [See all records that cite this PMID] Citation Link,
SCV000108224	International Society for Gastrointestinal Hereditary Tumours (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

SCV000052942

Women's Health and Genetics/Laboratory Corporation of America, LabCorp

criteria provided, single submitter

(LabCorp Variant Classification Summary - May 2015)

benign
(Aug 18, 2011)

germline

curation, clinical testing

PubMed (1)
[See all records that cite this PMID]

Citation Link,

SCV000108224

International Society for Gastrointestinal Hereditary Tumours (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	yes	1	not provided	not provided	not provided	not provided	curation
not provided	germline	unknown	26	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

Details of each submission

From Women's Health and Genetics/Laboratory Corporation of America, LabCorp, SCV000052942.2

#	Ethnicity	Individuals	Chromosomes Tested	Family History	Method	Citations
1	not provided	not provided	not provided	not provided	curation	PubMed (1)
2	not provided	not provided	not provided	not provided	clinical testing	PubMed (1)
3	not provided	not provided	not provided	not provided	clinical testing	PubMed (1)
4	not provided	not provided	not provided	not provided	clinical testing	PubMed (1)
5	not provided	not provided	not provided	not provided	clinical testing	PubMed (1)
6	not provided	not provided	not provided	not provided	clinical testing	PubMed (1)
7	not provided	not provided	not provided	not provided	clinical testing	PubMed (1)
8	not provided	not provided	not provided	not provided	clinical testing	PubMed (1)
9	not provided	not provided	not provided	not provided	clinical testing	PubMed (1)
10	not provided	not provided	not provided	not provided	clinical testing	PubMed (1)
11	not provided	not provided	not provided	not provided	clinical testing	PubMed (1)
12	not provided	not provided	not provided	not provided	clinical testing	PubMed (1)
13	not provided	not provided	not provided	not provided	clinical testing	PubMed (1)
14	not provided	not provided	not provided	not provided	clinical testing	PubMed (1)
15	not provided	not provided	not provided	not provided	clinical testing	PubMed (1)
16	not provided	not provided	not provided	not provided	clinical testing	PubMed (1)
17	not provided	not provided	not provided	not provided	clinical testing	PubMed (1)
18	not provided	not provided	not provided	not provided	clinical testing	PubMed (1)
19	not provided	not provided	not provided	not provided	clinical testing	PubMed (1)
20	not provided	not provided	not provided	not provided	clinical testing	PubMed (1)
21	not provided	not provided	not provided	not provided	clinical testing	PubMed (1)
22	not provided	not provided	not provided	not provided	clinical testing	PubMed (1)
23	not provided	not provided	not provided	not provided	clinical testing	PubMed (1)
24	not provided	not provided	not provided	not provided	clinical testing	PubMed (1)
25	not provided	not provided	not provided	not provided	clinical testing	PubMed (1)
26	not provided	not provided	not provided	not provided	clinical testing	PubMed (1)
27	not provided	not provided	not provided	not provided	clinical testing	PubMed (1)

Description

Converted during submission to Benign.

#	Sample				Method		Observation
#	Origin	Affected	Number tested	Tissue	Purpose	Method	Individuals	Allele frequency	Families	Co-occurrences
1	germline	yes	not provided	Blood	assert pathogenicity		not provided	not provided	not provided	not provided
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
10	germline	unknown	not provided	Blood	assert pathogenicity		not provided	not provided	not provided	See 10
11	germline	unknown	not provided	Blood	assert pathogenicity		not provided	not provided	not provided	See 11
12	germline	unknown	not provided	Blood	assert pathogenicity		not provided	not provided	not provided	See 12
13	germline	unknown	not provided	Blood	assert pathogenicity		not provided	not provided	not provided	See 13
14	germline	unknown	not provided	Blood	assert pathogenicity		not provided	not provided	not provided	See 14
15	germline	unknown	not provided	Blood	assert pathogenicity		not provided	not provided	not provided	See 15
16	germline	unknown	not provided	Blood	assert pathogenicity		not provided	not provided	not provided	See 16
17	germline	unknown	not provided	Blood	assert pathogenicity		not provided	not provided	not provided	See 17
18	germline	unknown	not provided	Blood	assert pathogenicity		not provided	not provided	not provided	See 18
19	germline	unknown	not provided	Blood	assert pathogenicity		not provided	not provided	not provided	See 19
20	germline	unknown	not provided	Blood	assert pathogenicity		not provided	not provided	not provided	See 20
21	germline	unknown	not provided	Blood	assert pathogenicity		not provided	not provided	not provided	See 21
22	germline	unknown	not provided	Blood	assert pathogenicity		not provided	not provided	not provided	See 22
23	germline	unknown	not provided	Blood	assert pathogenicity		not provided	not provided	not provided	See 23
24	germline	unknown	not provided	Blood	assert pathogenicity		not provided	not provided	not provided	See 24
25	germline	unknown	not provided	Blood	assert pathogenicity		not provided	not provided	not provided	See 25
26	germline	unknown	not provided	Blood	assert pathogenicity		not provided	not provided	not provided	See 26
27	germline	unknown	not provided	Blood	assert pathogenicity		not provided	not provided	not provided	See 27

Co-occurrences

#	Zygosity	Alleles	Number of Observations
2	SingleHeterozygote	MSH6:c.3438+14A>T, MSH6:c.276A>G, MSH6:c.186C>A	1
3	SingleHeterozygote	MSH6:c.276A>G, MSH6:c.186C>A, MSH6:c.3438+14A>T, MSH6:c.276A>G, MSH6:c.186C>A, MSH6:c.3438+14A>T	1
4	Homozygote	MSH6:c.642C>T, MSH6:c.3438+14A>T, MSH6:c.276A>G, MSH6:c.186C>A	1
5	Homozygote	MSH2:c.2006-6T>C, MSH2:c.1661+12G>A, MSH6:c.3438+14A>T, MSH6:c.276A>G, MSH6:c.186C>A	1
6	SingleHeterozygote	MLH1:c.1668-19A>G, MSH6:c.642C>T	1
7	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.642C>T	1
8	SingleHeterozygote	MSH6:c.276A>G, MSH6:c.186C>A, MSH6:c.3438+14A>T, MSH6:c.276A>G, MSH6:c.186C>A, MSH6:c.3438+14A>T	1
9	SingleHeterozygote	MSH6:c.3438+14A>T, MSH6:c.276A>G, MSH6:c.186C>A	1
10	SingleHeterozygote	MLH1:c.1668-19A>G, MSH2:c.211+9C>G, MSH2:c.1661+12G>A, MSH2:c.1077-80G>A, MSH2:c.1077-69_1143del136, MSH6:c.276A>G, MSH6:c.186C>A, MSH6:c.3438+14A>T	1
11	SingleHeterozygote	MLH1:c.1668-19A>G, MLH1:c.655A>G, MSH2:c.211+9C>G, MSH6:c.642C>T	1
12	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.642C>T, MSH6:c.3438+14A>T	1
13	SingleHeterozygote	MLH1:c.1668-19A>G, MLH1:c.655A>G, MSH2:c.211+9C>G, MSH6:c.3438+14A>T, MSH6:c.3246G>T, MSH6:c.276A>G, MSH6:c.186C>A	1
14	Homozygote	MSH6:c.3438+14A>T, MSH6:c.276A>G, MSH6:c.186C>A	1
15	SingleHeterozygote	MLH1:c.1668-19A>G, MLH1:c.655A>G, MSH6:c.642C>T, MSH6:c.116G>A	1
16	Homozygote	MLH1:c.1668-19A>G, MLH1:c.655A>G, MSH6:c.642C>T, MSH6:c.3647-35_3647-34insTTTGTTCTAATTCCTTT, MSH6:c.3438+14A>T, MSH6:c.276A>G, MSH6:c.186C>A	1
17	SingleHeterozygote	MLH1:c.1896+17T>C, MSH2:c.211+9C>G, MSH2:c.1661+12G>A, MSH2:c.1511-9A>T, MSH6:c.642C>T, MSH6:c.116G>A	1
18	SingleHeterozygote	MSH2:c.211+9C>G, MSH2:c.2006-6T>C, MSH2:c.1661+12G>A, MSH2:c.965G>A, MSH6:c.3438+14A>T, MSH6:c.276A>G, MSH6:c.186C>A	1
19	SingleHeterozygote	MLH1:c.1668-19A>G, MLH1:c.655A>G, MSH2:c.2006-6T>C, MSH2:c.1661+12G>A, MSH6:c.276A>G, MSH6:c.186C>A, MSH6:c.3438+14A>T	1
20	SingleHeterozygote	MLH1:c.1668-19A>G, MLH1:c.655A>G, MSH6:c.3438+14A>T, MSH6:c.276A>G, MSH6:c.2253T>C	1
21	SingleHeterozygote	MLH1:c.1668-19A>G, MLH1:c.655A>G, MSH2:c.211+9C>G, MSH6:c.3438+14A>T, MSH6:c.276A>G, MSH6:c.186C>A, MSH6:c.116G>A	1
22	SingleHeterozygote	MSH6:c.3438+14A>T, MSH6:c.276A>G, MSH6:c.186C>A, MSH6:c.116G>A	1
23	SingleHeterozygote	MSH6:c.642C>T	1
24	SingleHeterozygote	MLH1:c.1558+14G>A, MLH1:c.1039-8T>A, MSH2:c.211+9C>G, MSH2:c.1661+12G>A, MSH2:c.1666T>C, MSH6:c.276A>G, MSH6:c.186C>A, MSH6:c.3438+14A>T, MSH6:c.975A>G	1
25	SingleHeterozygote	MLH1:c.1668-19A>G, MLH1:c.655A>G, MSH6:c.3438+14A>T, MSH6:c.276A>G, MSH6:c.186C>A, MSH6:c.116G>A	1
26	SingleHeterozygote	MLH1:c.1668-19A>G, MLH1:c.655A>G, MSH2:c.211+9C>G, MSH2:c.2006-6T>C, MSH2:c.1661+12G>A, MSH2:c.1077-10T>C, MSH6:c.3438+14A>T, MSH6:c.276A>G, MSH6:c.186C>A	1
27	SingleHeterozygote	MSH6:c.3438+14A>T, MSH6:c.276A>G, MSH6:c.186C>A, MSH6:c.116G>A	1

From International Society for Gastrointestinal Hereditary Tumours (InSiGHT), SCV000108224.3

#	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: Apr 20, 2024

ClinVar

Relating variation to medicine