NM_000535.7(PMS2):c.2062A>G (p.Ile688Val) AND PMS2-related disorder

Germline classification:: Uncertain significance (1 submission)
Last evaluated:: Sep 8, 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:: RCV003418198.4

Allele description [Variation Report for NM_000535.7(PMS2):c.2062A>G (p.Ile688Val)]

NM_000535.7(PMS2):c.2062A>G (p.Ile688Val)

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.2062A>G (p.Ile688Val)

HGVS:

NC_000007.14:g.5982936T>C
NG_008466.1:g.31171A>G
NM_000535.7:c.2062A>GMANE SELECT
NM_001322003.2:c.1657A>G
NM_001322004.2:c.1657A>G
NM_001322005.2:c.1657A>G
NM_001322006.2:c.1906A>G
NM_001322007.2:c.1744A>G
NM_001322008.2:c.1744A>G
NM_001322009.2:c.1657A>G
NM_001322010.2:c.1501A>G
NM_001322011.2:c.1129A>G
NM_001322012.2:c.1129A>G
NM_001322013.2:c.1489A>G
NM_001322014.2:c.2062A>G
NM_001322015.2:c.1753A>G
NP_000526.2:p.Ile688Val
NP_001308932.1:p.Ile553Val
NP_001308933.1:p.Ile553Val
NP_001308934.1:p.Ile553Val
NP_001308935.1:p.Ile636Val
NP_001308936.1:p.Ile582Val
NP_001308937.1:p.Ile582Val
NP_001308938.1:p.Ile553Val
NP_001308939.1:p.Ile501Val
NP_001308940.1:p.Ile377Val
NP_001308941.1:p.Ile377Val
NP_001308942.1:p.Ile497Val
NP_001308943.1:p.Ile688Val
NP_001308944.1:p.Ile585Val
LRG_161t1:c.2062A>G
LRG_161:g.31171A>G
NC_000007.13:g.6022567T>C
NM_000535.5:c.2062A>G
NM_000535.6:c.2062A>G
NR_136154.1:n.2149A>G

Protein change:

I377V

Links:

dbSNP: rs1060503144

NCBI 1000 Genomes Browser:

rs1060503144

Molecular consequence:

NM_000535.7:c.2062A>G - missense variant - [Sequence Ontology: SO:0001583]
NM_001322003.2:c.1657A>G - missense variant - [Sequence Ontology: SO:0001583]
NM_001322004.2:c.1657A>G - missense variant - [Sequence Ontology: SO:0001583]
NM_001322005.2:c.1657A>G - missense variant - [Sequence Ontology: SO:0001583]
NM_001322006.2:c.1906A>G - missense variant - [Sequence Ontology: SO:0001583]
NM_001322007.2:c.1744A>G - missense variant - [Sequence Ontology: SO:0001583]
NM_001322008.2:c.1744A>G - missense variant - [Sequence Ontology: SO:0001583]
NM_001322009.2:c.1657A>G - missense variant - [Sequence Ontology: SO:0001583]
NM_001322010.2:c.1501A>G - missense variant - [Sequence Ontology: SO:0001583]
NM_001322011.2:c.1129A>G - missense variant - [Sequence Ontology: SO:0001583]
NM_001322012.2:c.1129A>G - missense variant - [Sequence Ontology: SO:0001583]
NM_001322013.2:c.1489A>G - missense variant - [Sequence Ontology: SO:0001583]
NM_001322014.2:c.2062A>G - missense variant - [Sequence Ontology: SO:0001583]
NM_001322015.2:c.1753A>G - missense variant - [Sequence Ontology: SO:0001583]
NR_136154.1:n.2149A>G - non-coding transcript variant - [Sequence Ontology: SO:0001619]

Condition(s)

Name:: PMS2-related disorder
Synonyms:: PMS2-related condition
Identifiers:

Recent activity

Clear Turn Off Turn On

Your browsing activity is empty.

Activity recording is turned off.

Turn recording back on

Help

Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV004106201	PreventionGenetics, part of Exact Sciences	criteria provided, single submitter (ACMG Guidelines, 2015)	Uncertain significance (Sep 8, 2023)	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

SCV004106201

PreventionGenetics, part of Exact Sciences

criteria provided, single submitter

(ACMG Guidelines, 2015)

Uncertain significance
(Sep 8, 2023)

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

Standards and guidelines for the interpretation of sequence variants: a joint consensus recommendation of the American College of Medical Genetics and Genomics and the Association for Molecular Pathology.

Richards S, Aziz N, Bale S, Bick D, Das S, Gastier-Foster J, Grody WW, Hegde M, Lyon E, Spector E, Voelkerding K, Rehm HL; ACMG Laboratory Quality Assurance Committee..

Genet Med. 2015 May;17(5):405-24. doi: 10.1038/gim.2015.30. Epub 2015 Mar 5.

PubMed [citation]

PMID:: 25741868
PMCID:: PMC4544753

Details of each submission

From PreventionGenetics, part of Exact Sciences, SCV004106201.1

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

Description

The PMS2 c.2062A>G variant is predicted to result in the amino acid substitution p.Ile688Val. To our knowledge, this variant has not been reported in the literature. This variant is reported in 0.0028% of alleles in individuals of European (Non-Finnish) descent in gnomAD (http://gnomad.broadinstitute.org/variant/7-6022567-T-C). It is interpreted as uncertain significance in ClinVar (https://preview.ncbi.nlm.nih.gov/clinvar/variation/411074/). At this time, the clinical significance of this variant is uncertain due to the absence of conclusive functional and genetic evidence.

#	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