NM_000535.7(PMS2):c.1924G>A (p.Glu642Lys) AND not provided

Germline classification:: Uncertain significance (2 submissions)
Last evaluated:: Feb 8, 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:: RCV001539689.3

Allele description [Variation Report for NM_000535.7(PMS2):c.1924G>A (p.Glu642Lys)]

NM_000535.7(PMS2):c.1924G>A (p.Glu642Lys)

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.1924G>A (p.Glu642Lys)

HGVS:

NC_000007.14:g.5986841C>T
NG_008466.1:g.27266G>A
NM_000535.6:c.1924G>A
NM_000535.7:c.1924G>AMANE SELECT
NM_001322003.2:c.1519G>A
NM_001322004.2:c.1519G>A
NM_001322005.2:c.1519G>A
NM_001322006.2:c.1768G>A
NM_001322007.2:c.1606G>A
NM_001322008.2:c.1606G>A
NM_001322009.2:c.1519G>A
NM_001322010.2:c.1363G>A
NM_001322011.2:c.991G>A
NM_001322012.2:c.991G>A
NM_001322013.2:c.1351G>A
NM_001322014.2:c.1924G>A
NM_001322015.2:c.1615G>A
NP_000526.2:p.Glu642Lys
NP_001308932.1:p.Glu507Lys
NP_001308933.1:p.Glu507Lys
NP_001308934.1:p.Glu507Lys
NP_001308935.1:p.Glu590Lys
NP_001308936.1:p.Glu536Lys
NP_001308937.1:p.Glu536Lys
NP_001308938.1:p.Glu507Lys
NP_001308939.1:p.Glu455Lys
NP_001308940.1:p.Glu331Lys
NP_001308941.1:p.Glu331Lys
NP_001308942.1:p.Glu451Lys
NP_001308943.1:p.Glu642Lys
NP_001308944.1:p.Glu539Lys
LRG_161t1:c.1924G>A
LRG_161:g.27266G>A
NC_000007.13:g.6026472C>T
NM_000535.5:c.1924G>A
NR_136154.1:n.2011G>A

Protein change:

E331K

Links:

dbSNP: rs752772040

NCBI 1000 Genomes Browser:

rs752772040

Molecular consequence:

NM_000535.7:c.1924G>A - missense variant - [Sequence Ontology: SO:0001583]
NM_001322003.2:c.1519G>A - missense variant - [Sequence Ontology: SO:0001583]
NM_001322004.2:c.1519G>A - missense variant - [Sequence Ontology: SO:0001583]
NM_001322005.2:c.1519G>A - missense variant - [Sequence Ontology: SO:0001583]
NM_001322006.2:c.1768G>A - missense variant - [Sequence Ontology: SO:0001583]
NM_001322007.2:c.1606G>A - missense variant - [Sequence Ontology: SO:0001583]
NM_001322008.2:c.1606G>A - missense variant - [Sequence Ontology: SO:0001583]
NM_001322009.2:c.1519G>A - missense variant - [Sequence Ontology: SO:0001583]
NM_001322010.2:c.1363G>A - missense variant - [Sequence Ontology: SO:0001583]
NM_001322011.2:c.991G>A - missense variant - [Sequence Ontology: SO:0001583]
NM_001322012.2:c.991G>A - missense variant - [Sequence Ontology: SO:0001583]
NM_001322013.2:c.1351G>A - missense variant - [Sequence Ontology: SO:0001583]
NM_001322014.2:c.1924G>A - missense variant - [Sequence Ontology: SO:0001583]
NM_001322015.2:c.1615G>A - missense variant - [Sequence Ontology: SO:0001583]
NR_136154.1:n.2011G>A - non-coding transcript variant - [Sequence Ontology: SO:0001619]

Condition(s)

Synonyms:: none provided
Identifiers:: MedGen: C3661900

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Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV001757489	GeneDx	criteria provided, single submitter (GeneDx Variant Classification Process June 2021)	Uncertain significance (Aug 5, 2019)	germline	clinical testing	Citation Link,
SCV004218968	Quest Diagnostics Nichols Institute San Juan Capistrano	criteria provided, single submitter (Quest Diagnostics criteria)	Uncertain significance (Feb 8, 2023)	unknown	clinical testing	PubMed (2) [See all records that cite these PMIDs] 29570743, 26467025

Submission Accession

Submitter

Review Status
(Assertion method)

Clinical Significance
(Last evaluated)

Origin

Method

Citations

SCV001757489

GeneDx

criteria provided, single submitter

(GeneDx Variant Classification Process June 2021)

Uncertain significance
(Aug 5, 2019)

germline

clinical testing

Citation Link,

SCV004218968

Quest Diagnostics Nichols Institute San Juan Capistrano

criteria provided, single submitter

(Quest Diagnostics criteria)

Uncertain significance
(Feb 8, 2023)

unknown

clinical testing

PubMed (2)
[See all records that cite these PMIDs]

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	unknown	unknown	not provided	not provided	not provided	not provided	not provided	clinical testing

Citations

PubMed

Novel putative drivers revealed by targeted exome sequencing of advanced solid tumors.

Pannuti A, Filipovic A, Hicks C, Lefkowitz E, Ptacek T, Stebbing J, Miele L.

PLoS One. 2018;13(3):e0194790. doi: 10.1371/journal.pone.0194790.

PubMed [citation]

PMID:: 29570743
PMCID:: PMC5865730

A Standardized DNA Variant Scoring System for Pathogenicity Assessments in Mendelian Disorders.

Karbassi I, Maston GA, Love A, DiVincenzo C, Braastad CD, Elzinga CD, Bright AR, Previte D, Zhang K, Rowland CM, McCarthy M, Lapierre JL, Dubois F, Medeiros KA, Batish SD, Jones J, Liaquat K, Hoffman CA, Jaremko M, Wang Z, Sun W, Buller-Burckle A, et al.

Hum Mutat. 2016 Jan;37(1):127-34. doi: 10.1002/humu.22918. Epub 2015 Oct 29.

PubMed [citation]

PMID:: 26467025
PMCID:: PMC4737317

Details of each submission

From GeneDx, SCV001757489.1

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

Description

Not observed at a significant frequency in large population cohorts (Lek et al., 2016); Has not been previously published as pathogenic or benign to our knowledge

#	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

From Quest Diagnostics Nichols Institute San Juan Capistrano, SCV004218968.1

#	Ethnicity	Individuals	Chromosomes Tested	Family History	Method	Citations
1	not provided	not provided	not provided	not provided	clinical testing	PubMed (2)

Description

The frequency of this variant in the general population, 0.000004 (1/251284 chromosomes, http://gnomad.broadinstitute.org), is uninformative in assessment of its pathogenicity. The variant was identified along with other variants in different genes in specimens from a published study of advanced solid tumors (PMID: 29570743 (2018)). Analysis of this variant using bioinformatics tools for the prediction of the effect of amino acid changes on protein structure and function yielded predictions that this variant is benign. Based on the available information, we are unable to determine the clinical significance of this variant.

#	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: Sep 29, 2024

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