NM_000179.3(MSH6):c.116G>A (p.Gly39Glu) AND Lynch syndrome 1

Germline classification:: Benign (2 submissions)
Last evaluated:: Aug 18, 2017
Review status:: 1 star out of maximum of 4 stars
criteria provided, single submitter

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:: RCV000144626.10

Allele description [Variation Report for NM_000179.3(MSH6):c.116G>A (p.Gly39Glu)]

NM_000179.3(MSH6):c.116G>A (p.Gly39Glu)

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.116G>A (p.Gly39Glu)

HGVS:

NC_000002.12:g.47783349G>A
NG_007111.1:g.5203G>A
NM_000179.3:c.116G>AMANE SELECT
NM_001281492.2:c.116G>A
NM_001281493.2:c.-621G>A
NP_000170.1:p.Gly39Glu
NP_001268421.1:p.Gly39Glu
LRG_219t1:c.116G>A
LRG_219:g.5203G>A
LRG_219p1:p.Gly39Glu
NC_000002.11:g.48010488G>A
NM_000179.2:c.116G>A
P52701:p.Gly39Glu
c.116G>A
p.G39E

Protein change:

G39E

Links:

UniProtKB: P52701#VAR_004490; dbSNP: rs1042821

NCBI 1000 Genomes Browser:

rs1042821

Molecular consequence:

NM_001281493.2:c.-621G>A - 5 prime UTR variant - [Sequence Ontology: SO:0001623]
NM_000179.3:c.116G>A - missense variant - [Sequence Ontology: SO:0001583]
NM_001281492.2:c.116G>A - missense variant - [Sequence Ontology: SO:0001583]

Condition(s)

Name:: Lynch syndrome 1
Synonyms:: COLON CANCER, FAMILIAL NONPOLYPOSIS, TYPE 1; MSH2-Related Hereditary Non-Polyposis Colon Cancer; Lynch syndrome I; See all synonyms [MedGen]
Identifiers:: MONDO: MONDO:0007356; MedGen: C2936783; Orphanet: 144; OMIM: 120435

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LY6G6C lymphocyte antigen 6 family member G6C [Homo sapiens]
LY6G6C lymphocyte antigen 6 family member G6C [Homo sapiens]
Gene ID:80740

Gene
Gene Links for GEO Profiles (Select 125903537) (1)
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Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV000189953	Pathway Genomics	no assertion criteria provided	Benign (Jul 24, 2014)	germline	clinical testing	PubMed (3) [See all records that cite these PMIDs] 22949387, 22703879, 18523027 Citation Link,
SCV000611715	IntelligeneCG	criteria provided, single submitter (ACMG Guidelines, 2015)	Benign (Aug 18, 2017)	germline	clinical testing	PubMed (1) [See all records that cite this PMID]

Submission Accession

Submitter

Review Status
(Assertion method)

Clinical Significance
(Last evaluated)

Origin

Method

Citations

SCV000189953

Pathway Genomics

no assertion criteria provided

Benign
(Jul 24, 2014)

germline

clinical testing

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

Citation Link,

SCV000611715

IntelligeneCG

criteria provided, single submitter

(ACMG Guidelines, 2015)

Benign
(Aug 18, 2017)

germline

clinical testing

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

Help

Summary from all submissions

Ethnicity	Origin	Affected	Individuals	Families	Chromosomes tested	Number Tested	Family history	Method
not provided	germline	unknown	not provided	not provided	not provided	not provided	not provided	clinical testing
not provided	germline	no	not provided	not provided	not provided	not provided	not provided	clinical testing

Citations

PubMed

Calibration of multiple in silico tools for predicting pathogenicity of mismatch repair gene missense substitutions.

Thompson BA, Greenblatt MS, Vallee MP, Herkert JC, Tessereau C, Young EL, Adzhubey IA, Li B, Bell R, Feng B, Mooney SD, Radivojac P, Sunyaev SR, Frebourg T, Hofstra RM, Sijmons RH, Boucher K, Thomas A, Goldgar DE, Spurdle AB, Tavtigian SV.

Hum Mutat. 2013 Jan;34(1):255-65. doi: 10.1002/humu.22214. Epub 2012 Oct 22.

PubMed [citation]

PMID:: 22949387
PMCID:: PMC4318556

Secondary variants in individuals undergoing exome sequencing: screening of 572 individuals identifies high-penetrance mutations in cancer-susceptibility genes.

Johnston JJ, Rubinstein WS, Facio FM, Ng D, Singh LN, Teer JK, Mullikin JC, Biesecker LG.

Am J Hum Genet. 2012 Jul 13;91(1):97-108. doi: 10.1016/j.ajhg.2012.05.021. Epub 2012 Jun 14.

PubMed [citation]

PMID:: 22703879
PMCID:: PMC3397257

See all PubMed Citations (4)

Details of each submission

From Pathway Genomics, SCV000189953.1

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

From IntelligeneCG, SCV000611715.1

#	Ethnicity	Individuals	Chromosomes Tested	Family History	Method	Citations
1	not provided	not provided	not provided	not provided	clinical testing	PubMed (1)

#	Sample				Method		Observation
#	Origin	Affected	Number tested	Tissue	Purpose	Method	Individuals	Allele frequency	Families	Co-occurrences
1	germline	no	not provided	not provided	not provided		not provided	not provided	not provided	not provided

Last Updated: Jun 9, 2024

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