NM_000535.7(PMS2):c.118A>G (p.Lys40Glu) AND not provided

Germline classification:: Uncertain significance (1 submission)
Last evaluated:: Jul 3, 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:: RCV003477617.1

Allele description [Variation Report for NM_000535.7(PMS2):c.118A>G (p.Lys40Glu)]

NM_000535.7(PMS2):c.118A>G (p.Lys40Glu)

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.118A>G (p.Lys40Glu)

HGVS:

NC_000007.14:g.6005937T>C
NG_008466.1:g.8170A>G
NG_050738.1:g.1687T>C
NM_000535.7:c.118A>GMANE SELECT
NM_001322003.2:c.-288A>G
NM_001322004.2:c.-242-1879A>G
NM_001322005.2:c.-288A>G
NM_001322006.2:c.118A>G
NM_001322007.2:c.-98A>G
NM_001322008.2:c.-52-1879A>G
NM_001322009.2:c.-288A>G
NM_001322010.2:c.-242-1879A>G
NM_001322011.2:c.-767A>G
NM_001322012.2:c.-767A>G
NM_001322013.2:c.-288A>G
NM_001322014.2:c.118A>G
NM_001322015.2:c.-367A>G
NP_000526.2:p.Lys40Glu
NP_001308935.1:p.Lys40Glu
NP_001308943.1:p.Lys40Glu
LRG_161t1:c.118A>G
LRG_161:g.8170A>G
NC_000007.13:g.6045568T>C
NM_000535.5:c.118A>G
NM_000535.6:c.118A>G
NR_136154.1:n.205A>G
p.K40E

Protein change:

K40E

Links:

dbSNP: rs786202542

NCBI 1000 Genomes Browser:

rs786202542

Molecular consequence:

NM_001322003.2:c.-288A>G - 5 prime UTR variant - [Sequence Ontology: SO:0001623]
NM_001322005.2:c.-288A>G - 5 prime UTR variant - [Sequence Ontology: SO:0001623]
NM_001322007.2:c.-98A>G - 5 prime UTR variant - [Sequence Ontology: SO:0001623]
NM_001322009.2:c.-288A>G - 5 prime UTR variant - [Sequence Ontology: SO:0001623]
NM_001322011.2:c.-767A>G - 5 prime UTR variant - [Sequence Ontology: SO:0001623]
NM_001322012.2:c.-767A>G - 5 prime UTR variant - [Sequence Ontology: SO:0001623]
NM_001322013.2:c.-288A>G - 5 prime UTR variant - [Sequence Ontology: SO:0001623]
NM_001322015.2:c.-367A>G - 5 prime UTR variant - [Sequence Ontology: SO:0001623]
NM_001322004.2:c.-242-1879A>G - intron variant - [Sequence Ontology: SO:0001627]
NM_001322008.2:c.-52-1879A>G - intron variant - [Sequence Ontology: SO:0001627]
NM_001322010.2:c.-242-1879A>G - intron variant - [Sequence Ontology: SO:0001627]
NM_000535.7:c.118A>G - missense variant - [Sequence Ontology: SO:0001583]
NM_001322006.2:c.118A>G - missense variant - [Sequence Ontology: SO:0001583]
NM_001322014.2:c.118A>G - missense variant - [Sequence Ontology: SO:0001583]
NR_136154.1:n.205A>G - 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
SCV004218942	Quest Diagnostics Nichols Institute San Juan Capistrano	criteria provided, single submitter (Quest Diagnostics criteria)	Uncertain significance (Jul 3, 2023)	unknown	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

SCV004218942

Quest Diagnostics Nichols Institute San Juan Capistrano

criteria provided, single submitter

(Quest Diagnostics criteria)

Uncertain significance
(Jul 3, 2023)

unknown

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

Citations

PubMed

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 Quest Diagnostics Nichols Institute San Juan Capistrano, SCV004218942.1

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

Description

This variant has not been reported in the published literature. The frequency of this variant in the general population, 0.000087 (3/34478 chromosomes (Genome Aggregation Database, http://gnomad.broadinstitute.org)), is uninformative in the assessment of its pathogenicity. 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 damaging. 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: May 1, 2024

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