NM_000179.3(MSH6):c.161G>A (p.Gly54Glu) AND Hereditary nonpolyposis colorectal neoplasms

Germline classification:: Uncertain significance (1 submission)
Last evaluated:: Nov 25, 2023
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:: RCV003594849.1

Allele description [Variation Report for NM_000179.3(MSH6):c.161G>A (p.Gly54Glu)]

NM_000179.3(MSH6):c.161G>A (p.Gly54Glu)

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.161G>A (p.Gly54Glu)

HGVS:

NC_000002.12:g.47783394G>A
NG_007111.1:g.5248G>A
NG_166733.1:g.17G>A
NM_000179.3:c.161G>AMANE SELECT
NM_001281492.2:c.161G>A
NM_001281493.2:c.-576G>A
NM_001406795.1:c.161G>A
NM_001406796.1:c.161G>A
NM_001406797.1:c.-38+163G>A
NM_001406798.1:c.161G>A
NM_001406799.1:c.-168G>A
NM_001406800.1:c.161G>A
NM_001406801.1:c.-38+163G>A
NM_001406802.1:c.161G>A
NM_001406803.1:c.161G>A
NM_001406804.1:c.106G>A
NM_001406805.1:c.-38+163G>A
NM_001406806.1:c.-69+163G>A
NM_001406807.1:c.-768G>A
NM_001406808.1:c.161G>A
NM_001406809.1:c.161G>A
NM_001406811.1:c.-576G>A
NM_001406812.1:c.-423G>A
NM_001406813.1:c.161G>A
NM_001406814.1:c.-834G>A
NM_001406815.1:c.-280+163G>A
NM_001406816.1:c.-379G>A
NM_001406817.1:c.161G>A
NM_001407362.1:c.161G>A
NP_000170.1:p.Gly54Glu
NP_000170.1:p.Gly54Glu
NP_001268421.1:p.Gly54Glu
NP_001393724.1:p.Gly54Glu
NP_001393725.1:p.Gly54Glu
NP_001393727.1:p.Gly54Glu
NP_001393729.1:p.Gly54Glu
NP_001393731.1:p.Gly54Glu
NP_001393732.1:p.Gly54Glu
NP_001393733.1:p.Gly36Ser
NP_001393737.1:p.Gly54Glu
NP_001393738.1:p.Gly54Glu
NP_001393742.1:p.Gly54Glu
NP_001393746.1:p.Gly54Glu
NP_001394291.1:p.Gly54Glu
LRG_219t1:c.161G>A
LRG_219:g.5248G>A
LRG_219p1:p.Gly54Glu
NC_000002.11:g.48010533G>A
NM_000179.2:c.161G>A
NR_176256.1:n.250G>A
NR_176257.1:n.250G>A
NR_176258.1:n.250G>A
NR_176259.1:n.250G>A
NR_176260.1:n.250G>A
NR_176261.1:n.250G>A

Protein change:

G36S

Molecular consequence:

NM_001281493.2:c.-576G>A - 5 prime UTR variant - [Sequence Ontology: SO:0001623]
NM_001406799.1:c.-168G>A - 5 prime UTR variant - [Sequence Ontology: SO:0001623]
NM_001406807.1:c.-768G>A - 5 prime UTR variant - [Sequence Ontology: SO:0001623]
NM_001406811.1:c.-576G>A - 5 prime UTR variant - [Sequence Ontology: SO:0001623]
NM_001406812.1:c.-423G>A - 5 prime UTR variant - [Sequence Ontology: SO:0001623]
NM_001406814.1:c.-834G>A - 5 prime UTR variant - [Sequence Ontology: SO:0001623]
NM_001406816.1:c.-379G>A - 5 prime UTR variant - [Sequence Ontology: SO:0001623]
NM_001406797.1:c.-38+163G>A - intron variant - [Sequence Ontology: SO:0001627]
NM_001406801.1:c.-38+163G>A - intron variant - [Sequence Ontology: SO:0001627]
NM_001406805.1:c.-38+163G>A - intron variant - [Sequence Ontology: SO:0001627]
NM_001406806.1:c.-69+163G>A - intron variant - [Sequence Ontology: SO:0001627]
NM_001406815.1:c.-280+163G>A - intron variant - [Sequence Ontology: SO:0001627]
NM_000179.3:c.161G>A - missense variant - [Sequence Ontology: SO:0001583]
NM_001281492.2:c.161G>A - missense variant - [Sequence Ontology: SO:0001583]
NM_001406795.1:c.161G>A - missense variant - [Sequence Ontology: SO:0001583]
NM_001406796.1:c.161G>A - missense variant - [Sequence Ontology: SO:0001583]
NM_001406798.1:c.161G>A - missense variant - [Sequence Ontology: SO:0001583]
NM_001406800.1:c.161G>A - missense variant - [Sequence Ontology: SO:0001583]
NM_001406802.1:c.161G>A - missense variant - [Sequence Ontology: SO:0001583]
NM_001406803.1:c.161G>A - missense variant - [Sequence Ontology: SO:0001583]
NM_001406804.1:c.106G>A - missense variant - [Sequence Ontology: SO:0001583]
NM_001406808.1:c.161G>A - missense variant - [Sequence Ontology: SO:0001583]
NM_001406809.1:c.161G>A - missense variant - [Sequence Ontology: SO:0001583]
NM_001406813.1:c.161G>A - missense variant - [Sequence Ontology: SO:0001583]
NM_001406817.1:c.161G>A - missense variant - [Sequence Ontology: SO:0001583]
NM_001407362.1:c.161G>A - missense variant - [Sequence Ontology: SO:0001583]
NR_176256.1:n.250G>A - non-coding transcript variant - [Sequence Ontology: SO:0001619]
NR_176257.1:n.250G>A - non-coding transcript variant - [Sequence Ontology: SO:0001619]
NR_176258.1:n.250G>A - non-coding transcript variant - [Sequence Ontology: SO:0001619]
NR_176259.1:n.250G>A - non-coding transcript variant - [Sequence Ontology: SO:0001619]
NR_176261.1:n.250G>A - non-coding transcript variant - [Sequence Ontology: SO:0001619]

Condition(s)

Name:: Hereditary nonpolyposis colorectal neoplasms
Identifiers:: MeSH: D003123; MedGen: C0009405

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Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV004251844	Invitae	criteria provided, single submitter (Invitae Variant Classification Sherloc (09022015))	Uncertain significance (Nov 25, 2023)	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

SCV004251844

Invitae

criteria provided, single submitter

(Invitae Variant Classification Sherloc (09022015))

Uncertain significance
(Nov 25, 2023)

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

Citations

PubMed

Sherloc: a comprehensive refinement of the ACMG-AMP variant classification criteria.

Nykamp K, Anderson M, Powers M, Garcia J, Herrera B, Ho YY, Kobayashi Y, Patil N, Thusberg J, Westbrook M; Invitae Clinical Genomics Group., Topper S.

Genet Med. 2017 Oct;19(10):1105-1117. doi: 10.1038/gim.2017.37. Epub 2017 May 11. Erratum in: Genet Med. 2020 Jan;22(1):240. doi: 10.1038/s41436-019-0624-9.

PubMed [citation]

PMID:: 28492532
PMCID:: PMC5632818

Details of each submission

From Invitae, SCV004251844.1

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

Description

This sequence change replaces glycine, which is neutral and non-polar, with glutamic acid, which is acidic and polar, at codon 54 of the MSH6 protein (p.Gly54Glu). This variant is not present in population databases (gnomAD no frequency). This variant has not been reported in the literature in individuals affected with MSH6-related conditions. Advanced modeling of protein sequence and biophysical properties (such as structural, functional, and spatial information, amino acid conservation, physicochemical variation, residue mobility, and thermodynamic stability) performed at Invitae indicates that this missense variant is not expected to disrupt MSH6 protein function with a negative predictive value of 95%. In summary, the available evidence is currently insufficient to determine the role of this variant in disease. Therefore, it has been classified as a Variant of Uncertain Significance.

#	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: Feb 20, 2024

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