NM_000535.7(PMS2):c.2069A>G (p.Lys690Arg) AND Hereditary nonpolyposis colorectal neoplasms

Germline classification:: Uncertain significance (1 submission)
Last evaluated:: Jun 23, 2021
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:: RCV001854742.6

Allele description [Variation Report for NM_000535.7(PMS2):c.2069A>G (p.Lys690Arg)]

NM_000535.7(PMS2):c.2069A>G (p.Lys690Arg)

Gene:

PMS2:PMS1 homolog 2, mismatch repair system component [Gene - OMIM - HGNC]

Variant type:

single nucleotide variant

Cytogenetic location:

7p22.1

Genomic location:

Preferred name:

NM_000535.7(PMS2):c.2069A>G (p.Lys690Arg)

HGVS:

NC_000007.14:g.5982929T>C
NG_008466.1:g.31178A>G
NM_000535.7:c.2069A>GMANE SELECT
NM_001322003.2:c.1664A>G
NM_001322004.2:c.1664A>G
NM_001322005.2:c.1664A>G
NM_001322006.2:c.1913A>G
NM_001322007.2:c.1751A>G
NM_001322008.2:c.1751A>G
NM_001322009.2:c.1664A>G
NM_001322010.2:c.1508A>G
NM_001322011.2:c.1136A>G
NM_001322012.2:c.1136A>G
NM_001322013.2:c.1496A>G
NM_001322014.2:c.2069A>G
NM_001322015.2:c.1760A>G
NP_000526.2:p.Lys690Arg
NP_001308932.1:p.Lys555Arg
NP_001308933.1:p.Lys555Arg
NP_001308934.1:p.Lys555Arg
NP_001308935.1:p.Lys638Arg
NP_001308936.1:p.Lys584Arg
NP_001308937.1:p.Lys584Arg
NP_001308938.1:p.Lys555Arg
NP_001308939.1:p.Lys503Arg
NP_001308940.1:p.Lys379Arg
NP_001308941.1:p.Lys379Arg
NP_001308942.1:p.Lys499Arg
NP_001308943.1:p.Lys690Arg
NP_001308944.1:p.Lys587Arg
LRG_161t1:c.2069A>G
LRG_161:g.31178A>G
NC_000007.13:g.6022560T>C
NM_000535.5:c.2069A>G
NR_136154.1:n.2156A>G

Protein change:

K379R

Links:

dbSNP: rs876661164

NCBI 1000 Genomes Browser:

rs876661164

Molecular consequence:

NM_000535.7:c.2069A>G - missense variant - [Sequence Ontology: SO:0001583]
NM_001322003.2:c.1664A>G - missense variant - [Sequence Ontology: SO:0001583]
NM_001322004.2:c.1664A>G - missense variant - [Sequence Ontology: SO:0001583]
NM_001322005.2:c.1664A>G - missense variant - [Sequence Ontology: SO:0001583]
NM_001322006.2:c.1913A>G - missense variant - [Sequence Ontology: SO:0001583]
NM_001322007.2:c.1751A>G - missense variant - [Sequence Ontology: SO:0001583]
NM_001322008.2:c.1751A>G - missense variant - [Sequence Ontology: SO:0001583]
NM_001322009.2:c.1664A>G - missense variant - [Sequence Ontology: SO:0001583]
NM_001322010.2:c.1508A>G - missense variant - [Sequence Ontology: SO:0001583]
NM_001322011.2:c.1136A>G - missense variant - [Sequence Ontology: SO:0001583]
NM_001322012.2:c.1136A>G - missense variant - [Sequence Ontology: SO:0001583]
NM_001322013.2:c.1496A>G - missense variant - [Sequence Ontology: SO:0001583]
NM_001322014.2:c.2069A>G - missense variant - [Sequence Ontology: SO:0001583]
NM_001322015.2:c.1760A>G - missense variant - [Sequence Ontology: SO:0001583]
NR_136154.1:n.2156A>G - 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
SCV002304015	Labcorp Genetics (formerly Invitae), Labcorp	criteria provided, single submitter (Invitae Variant Classification Sherloc (09022015))	Uncertain significance (Jun 23, 2021)	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

SCV002304015

Labcorp Genetics (formerly Invitae), Labcorp

criteria provided, single submitter

(Invitae Variant Classification Sherloc (09022015))

Uncertain significance
(Jun 23, 2021)

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 Labcorp Genetics (formerly Invitae), Labcorp, SCV002304015.3

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

Description

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 PMS2 protein function. ClinVar contains an entry for this variant (Variation ID: 234688). This variant has not been reported in the literature in individuals affected with PMS2-related conditions. The frequency data for this variant in the population databases (ExAC) is considered unreliable due to the presence of homologous sequence, such as pseudogenes or paralogs, in the genome. This sequence change replaces lysine with arginine at codon 690 of the PMS2 protein (p.Lys690Arg). The lysine residue is moderately conserved and there is a small physicochemical difference between lysine and arginine. Algorithms developed to predict the effect of sequence changes on RNA splicing suggest that this variant may create or strengthen a splice site. 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: Sep 29, 2024

ClinVar

Relating variation to medicine