NM_000179.3(MSH6):c.116G>A (p.Gly39Glu) AND not provided

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

Germline classification:: Benign (3 submissions)
Last evaluated:: Nov 30, 2023
Review status:: 2 stars out of maximum of 4 stars
criteria provided, multiple submitters, no conflicts

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:: RCV000034489.26

Allele description

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)

Synonyms:: none provided
Identifiers:: MedGen: C3661900

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Virus
Virus
Animal metagenomes enriched for circular DNA viruses

BioProject
DERA deoxyribose-phosphate aldolase [Homo sapiens]
DERA deoxyribose-phosphate aldolase [Homo sapiens]
Gene ID:51071

Gene

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Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV000043349	Biesecker Lab/Clinical Genomics Section, National Institutes of Health - ClinSeq	no assertion criteria provided	no known pathogenicity (Jul 13, 2012)	germline	research	PubMed (1) [See all records that cite this PMID]
SCV000604270	ARUP Laboratories, Molecular Genetics and Genomics, ARUP Laboratories	criteria provided, single submitter (ARUP Molecular Germline Variant Investigation Process 2024)	Benign (Nov 30, 2023)	germline	clinical testing	Citation Link,
SCV001892538	GeneDx	criteria provided, single submitter (GeneDx Variant Classification Process June 2021)	Benign (Mar 3, 2015)	germline	clinical testing	Citation Link

Submission Accession

Submitter

Review Status
(Assertion method)

Clinical Significance
(Last evaluated)

Origin

Method

Citations

SCV000043349

Biesecker Lab/Clinical Genomics Section, National Institutes of Health - ClinSeq

no assertion criteria provided

no known pathogenicity
(Jul 13, 2012)

germline

research

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

SCV000604270

ARUP Laboratories, Molecular Genetics and Genomics, ARUP Laboratories

criteria provided, single submitter

(ARUP Molecular Germline Variant Investigation Process 2024)

Benign
(Nov 30, 2023)

germline

clinical testing

Citation Link,

SCV001892538

GeneDx

criteria provided, single submitter

(GeneDx Variant Classification Process June 2021)

Benign
(Mar 3, 2015)

germline

clinical testing

Citation Link

Help

Summary from all submissions

Ethnicity	Origin	Affected	Individuals	Families	Chromosomes tested	Number Tested	Family history	Method
not provided	germline	yes	not provided	not provided	not provided	not provided	not provided	clinical testing
not provided	germline	unknown	not provided	not provided	not provided	not provided	not provided	clinical testing
not provided	germline	no	118	not provided	not provided	347	not provided	research

Citations

PubMed

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

Details of each submission

From Biesecker Lab/Clinical Genomics Section, National Institutes of Health - ClinSeq, SCV000043349.1

#	Ethnicity	Individuals	Chromosomes Tested	Family History	Method	Citations
1	not provided	118	not provided	not provided	research	PubMed (1)

Description

The study set was not selected for affection status in relation to any cancer. Pathogenicity categories were based on literature curation. See PubMed ID:22703879 for details.

Description

Converted during submission to Benign.

#	Sample				Method		Observation
#	Origin	Affected	Number tested	Tissue	Purpose	Method	Individuals	Allele frequency	Families	Co-occurrences
1	germline	no	347	not provided	discovery		118	not provided	not provided	not provided

From ARUP Laboratories, Molecular Genetics and Genomics, ARUP Laboratories, SCV000604270.10

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

#	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 GeneDx, SCV001892538.1

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

Description

This variant is associated with the following publications: (PMID: 24622885, 29442465, 28932927, 27153395, 18523027, 19582761, 24689082, 22949387, 19685280, 22703879)

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

Last Updated: Sep 16, 2024

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