NM_000251.3(MSH2):c.2068C>A (p.Gln690Lys) AND Lynch syndrome 1

Germline classification:: Likely pathogenic (1 submission)
Last evaluated:: Aug 7, 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:: RCV003454322.1

Allele description [Variation Report for NM_000251.3(MSH2):c.2068C>A (p.Gln690Lys)]

NM_000251.3(MSH2):c.2068C>A (p.Gln690Lys)

Gene:

MSH2:mutS homolog 2 [Gene - OMIM - HGNC]

Variant type:

single nucleotide variant

Cytogenetic location:

2p21

Genomic location:

Preferred name:

NM_000251.3(MSH2):c.2068C>A (p.Gln690Lys)

HGVS:

NC_000002.12:g.47476429C>A
NG_007110.2:g.78306C>A
NM_000251.3:c.2068C>AMANE SELECT
NM_001258281.1:c.1870C>A
NM_001406631.1:c.2068C>A
NM_001406632.1:c.2068C>A
NM_001406633.1:c.2068C>A
NM_001406634.1:c.2068C>A
NM_001406635.1:c.2068C>A
NM_001406636.1:c.2035C>A
NM_001406637.1:c.2068C>A
NM_001406638.1:c.2107C>A
NM_001406639.1:c.2068C>A
NM_001406640.1:c.2068C>A
NM_001406641.1:c.2068C>A
NM_001406642.1:c.2068C>A
NM_001406643.1:c.2068C>A
NM_001406644.1:c.2068C>A
NM_001406645.1:c.2068C>A
NM_001406646.1:c.2068C>A
NM_001406647.1:c.1918C>A
NM_001406648.1:c.2068C>A
NM_001406649.1:c.1918C>A
NM_001406650.1:c.1918C>A
NM_001406651.1:c.1918C>A
NM_001406652.1:c.1918C>A
NM_001406653.1:c.2008C>A
NM_001406654.1:c.1648C>A
NM_001406656.1:c.1171C>A
NM_001406658.1:c.712C>A
NM_001406659.1:c.712C>A
NM_001406660.1:c.712C>A
NM_001406661.1:c.712C>A
NM_001406662.1:c.712C>A
NM_001406669.1:c.712C>A
NM_001406674.1:c.2068C>A
NP_000242.1:p.Gln690Lys
NP_000242.1:p.Gln690Lys
NP_001245210.1:p.Gln624Lys
NP_001393560.1:p.Gln690Lys
NP_001393561.1:p.Gln690Lys
NP_001393562.1:p.Gln690Lys
NP_001393563.1:p.Gln690Lys
NP_001393564.1:p.Gln690Lys
NP_001393565.1:p.Gln679Lys
NP_001393566.1:p.Gln690Lys
NP_001393567.1:p.Gln703Lys
NP_001393568.1:p.Gln690Lys
NP_001393569.1:p.Gln690Lys
NP_001393570.1:p.Gln690Lys
NP_001393571.1:p.Gln690Lys
NP_001393572.1:p.Gln690Lys
NP_001393573.1:p.Gln690Lys
NP_001393574.1:p.Gln690Lys
NP_001393575.1:p.Gln690Lys
NP_001393576.1:p.Gln640Lys
NP_001393577.1:p.Gln690Lys
NP_001393578.1:p.Gln640Lys
NP_001393579.1:p.Gln640Lys
NP_001393580.1:p.Gln640Lys
NP_001393581.1:p.Gln640Lys
NP_001393582.1:p.Gln670Lys
NP_001393583.1:p.Gln550Lys
NP_001393585.1:p.Gln391Lys
NP_001393587.1:p.Gln238Lys
NP_001393588.1:p.Gln238Lys
NP_001393589.1:p.Gln238Lys
NP_001393590.1:p.Gln238Lys
NP_001393591.1:p.Gln238Lys
NP_001393598.1:p.Gln238Lys
NP_001393603.1:p.Gln690Lys
LRG_218t1:c.2068C>A
LRG_218:g.78306C>A
LRG_218p1:p.Gln690Lys
NC_000002.11:g.47703568C>A
NM_000251.1:c.2068C>A
NM_000251.2:c.2068C>A
NR_176230.1:n.2104C>A
NR_176231.1:n.2104C>A
NR_176232.1:n.2104C>A
NR_176233.1:n.1946C>A
NR_176234.1:n.2104C>A
NR_176235.1:n.2104C>A
NR_176236.1:n.2104C>A
NR_176237.1:n.2104C>A
NR_176238.1:n.2237C>A
NR_176239.1:n.2104C>A
NR_176241.1:n.2104C>A
NR_176242.1:n.2104C>A
NR_176243.1:n.1954C>A
NR_176244.1:n.2104C>A
NR_176245.1:n.2104C>A
NR_176246.1:n.2104C>A
NR_176247.1:n.2104C>A
NR_176248.1:n.2104C>A
NR_176249.1:n.2334C>A
NR_176250.1:n.1844C>A

Protein change:

Q238K

Molecular consequence:

NM_000251.3:c.2068C>A - missense variant - [Sequence Ontology: SO:0001583]
NM_001258281.1:c.1870C>A - missense variant - [Sequence Ontology: SO:0001583]
NM_001406631.1:c.2068C>A - missense variant - [Sequence Ontology: SO:0001583]
NM_001406632.1:c.2068C>A - missense variant - [Sequence Ontology: SO:0001583]
NM_001406633.1:c.2068C>A - missense variant - [Sequence Ontology: SO:0001583]
NM_001406634.1:c.2068C>A - missense variant - [Sequence Ontology: SO:0001583]
NM_001406635.1:c.2068C>A - missense variant - [Sequence Ontology: SO:0001583]
NM_001406636.1:c.2035C>A - missense variant - [Sequence Ontology: SO:0001583]
NM_001406637.1:c.2068C>A - missense variant - [Sequence Ontology: SO:0001583]
NM_001406638.1:c.2107C>A - missense variant - [Sequence Ontology: SO:0001583]
NM_001406639.1:c.2068C>A - missense variant - [Sequence Ontology: SO:0001583]
NM_001406640.1:c.2068C>A - missense variant - [Sequence Ontology: SO:0001583]
NM_001406641.1:c.2068C>A - missense variant - [Sequence Ontology: SO:0001583]
NM_001406642.1:c.2068C>A - missense variant - [Sequence Ontology: SO:0001583]
NM_001406643.1:c.2068C>A - missense variant - [Sequence Ontology: SO:0001583]
NM_001406644.1:c.2068C>A - missense variant - [Sequence Ontology: SO:0001583]
NM_001406645.1:c.2068C>A - missense variant - [Sequence Ontology: SO:0001583]
NM_001406646.1:c.2068C>A - missense variant - [Sequence Ontology: SO:0001583]
NM_001406647.1:c.1918C>A - missense variant - [Sequence Ontology: SO:0001583]
NM_001406648.1:c.2068C>A - missense variant - [Sequence Ontology: SO:0001583]
NM_001406649.1:c.1918C>A - missense variant - [Sequence Ontology: SO:0001583]
NM_001406650.1:c.1918C>A - missense variant - [Sequence Ontology: SO:0001583]
NM_001406651.1:c.1918C>A - missense variant - [Sequence Ontology: SO:0001583]
NM_001406652.1:c.1918C>A - missense variant - [Sequence Ontology: SO:0001583]
NM_001406653.1:c.2008C>A - missense variant - [Sequence Ontology: SO:0001583]
NM_001406654.1:c.1648C>A - missense variant - [Sequence Ontology: SO:0001583]
NM_001406656.1:c.1171C>A - missense variant - [Sequence Ontology: SO:0001583]
NM_001406658.1:c.712C>A - missense variant - [Sequence Ontology: SO:0001583]
NM_001406659.1:c.712C>A - missense variant - [Sequence Ontology: SO:0001583]
NM_001406660.1:c.712C>A - missense variant - [Sequence Ontology: SO:0001583]
NM_001406661.1:c.712C>A - missense variant - [Sequence Ontology: SO:0001583]
NM_001406662.1:c.712C>A - missense variant - [Sequence Ontology: SO:0001583]
NM_001406669.1:c.712C>A - missense variant - [Sequence Ontology: SO:0001583]
NM_001406674.1:c.2068C>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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Mus musculus phospholipid phosphatase 1 (Plpp1), transcript variant 1, mRNA
Mus musculus phospholipid phosphatase 1 (Plpp1), transcript variant 1, mRNA
gi|545688123|ref|NM_008247.3|

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Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV004186598	Myriad Genetics, Inc.	criteria provided, single submitter (Myriad Autosomal Dominant, Autosomal Recessive and X-Linked Classification Criteria (2023))	Likely pathogenic (Aug 7, 2023)	unknown	clinical testing	PubMed (1) [See all records that cite this PMID] Citation Link

Submission Accession

Submitter

Review Status
(Assertion method)

Clinical Significance
(Last evaluated)

Origin

Method

Citations

SCV004186598

Myriad Genetics, Inc.

criteria provided, single submitter

(Myriad Autosomal Dominant, Autosomal Recessive and X-Linked Classification Criteria (2023))

Likely pathogenic
(Aug 7, 2023)

unknown

clinical testing

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

Citation Link

Help

Summary from all submissions

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

Citations

PubMed

Massively parallel functional testing of MSH2 missense variants conferring Lynch syndrome risk.

Jia X, Burugula BB, Chen V, Lemons RM, Jayakody S, Maksutova M, Kitzman JO.

Am J Hum Genet. 2021 Jan 7;108(1):163-175. doi: 10.1016/j.ajhg.2020.12.003. Epub 2020 Dec 23.

PubMed [citation]

PMID:: 33357406
PMCID:: PMC7820803

Details of each submission

From Myriad Genetics, Inc., SCV004186598.1

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

Description

This variant is considered likely pathogenic. Functional studies indicate this variant impacts protein function [PMID: 33357406]. This variant is expected to disrupt protein structure [Myriad internal data].

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

Last Updated: Jun 9, 2024

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