NM_000535.7(PMS2):c.1106A>G (p.Lys369Arg) AND not provided

Germline classification:: Uncertain significance (1 submission)
Last evaluated:: Feb 21, 2020
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:: RCV001753256.2

Allele description [Variation Report for NM_000535.7(PMS2):c.1106A>G (p.Lys369Arg)]

NM_000535.7(PMS2):c.1106A>G (p.Lys369Arg)

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.1106A>G (p.Lys369Arg)

HGVS:

NC_000007.14:g.5989838T>C
NG_008466.1:g.24269A>G
NM_000535.7:c.1106A>GMANE SELECT
NM_001322003.2:c.701A>G
NM_001322004.2:c.701A>G
NM_001322005.2:c.701A>G
NM_001322006.2:c.988+2135A>G
NM_001322007.2:c.788A>G
NM_001322008.2:c.788A>G
NM_001322009.2:c.701A>G
NM_001322010.2:c.583+2135A>G
NM_001322011.2:c.173A>G
NM_001322012.2:c.173A>G
NM_001322013.2:c.533A>G
NM_001322014.2:c.1106A>G
NM_001322015.2:c.797A>G
NP_000526.2:p.Lys369Arg
NP_001308932.1:p.Lys234Arg
NP_001308933.1:p.Lys234Arg
NP_001308934.1:p.Lys234Arg
NP_001308936.1:p.Lys263Arg
NP_001308937.1:p.Lys263Arg
NP_001308938.1:p.Lys234Arg
NP_001308940.1:p.Lys58Arg
NP_001308941.1:p.Lys58Arg
NP_001308942.1:p.Lys178Arg
NP_001308943.1:p.Lys369Arg
NP_001308944.1:p.Lys266Arg
LRG_161t1:c.1106A>G
LRG_161:g.24269A>G
NC_000007.13:g.6029469T>C
NM_000535.5:c.1106A>G
NR_136154.1:n.1193A>G

Protein change:

K178R

Links:

dbSNP: rs2128747431

NCBI 1000 Genomes Browser:

rs2128747431

Molecular consequence:

NM_001322006.2:c.988+2135A>G - intron variant - [Sequence Ontology: SO:0001627]
NM_001322010.2:c.583+2135A>G - intron variant - [Sequence Ontology: SO:0001627]
NM_000535.7:c.1106A>G - missense variant - [Sequence Ontology: SO:0001583]
NM_001322003.2:c.701A>G - missense variant - [Sequence Ontology: SO:0001583]
NM_001322004.2:c.701A>G - missense variant - [Sequence Ontology: SO:0001583]
NM_001322005.2:c.701A>G - missense variant - [Sequence Ontology: SO:0001583]
NM_001322007.2:c.788A>G - missense variant - [Sequence Ontology: SO:0001583]
NM_001322008.2:c.788A>G - missense variant - [Sequence Ontology: SO:0001583]
NM_001322009.2:c.701A>G - missense variant - [Sequence Ontology: SO:0001583]
NM_001322011.2:c.173A>G - missense variant - [Sequence Ontology: SO:0001583]
NM_001322012.2:c.173A>G - missense variant - [Sequence Ontology: SO:0001583]
NM_001322013.2:c.533A>G - missense variant - [Sequence Ontology: SO:0001583]
NM_001322014.2:c.1106A>G - missense variant - [Sequence Ontology: SO:0001583]
NM_001322015.2:c.797A>G - missense variant - [Sequence Ontology: SO:0001583]
NR_136154.1:n.1193A>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
SCV002007216	GeneDx	criteria provided, single submitter (GeneDx Variant Classification Process June 2021)	Uncertain significance (Feb 21, 2020)	germline	clinical testing	Citation Link

Submission Accession

Submitter

Review Status
(Assertion method)

Clinical Significance
(Last evaluated)

Origin

Method

Citations

SCV002007216

GeneDx

criteria provided, single submitter

(GeneDx Variant Classification Process June 2021)

Uncertain significance
(Feb 21, 2020)

germline

clinical testing

Citation Link

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

Details of each submission

From GeneDx, SCV002007216.2

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

Description

Not observed in large population cohorts (Lek 2016); In silico analysis supports that this missense variant does not alter protein structure/function; 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

Last Updated: Dec 24, 2023

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