NM_000535.7(PMS2):c.40G>T (p.Ala14Ser) AND PMS2-related disorder

Germline classification:: Uncertain significance (1 submission)
Last evaluated:: Jan 27, 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:: RCV003417796.4

Allele description [Variation Report for NM_000535.7(PMS2):c.40G>T (p.Ala14Ser)]

NM_000535.7(PMS2):c.40G>T (p.Ala14Ser)

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.40G>T (p.Ala14Ser)

HGVS:

NC_000007.14:g.6006015C>A
NG_008466.1:g.8092G>T
NG_050738.1:g.1765C>A
NM_000535.7:c.40G>TMANE SELECT
NM_001322003.2:c.-366G>T
NM_001322004.2:c.-242-1957G>T
NM_001322005.2:c.-366G>T
NM_001322006.2:c.40G>T
NM_001322007.2:c.-176G>T
NM_001322008.2:c.-52-1957G>T
NM_001322009.2:c.-366G>T
NM_001322010.2:c.-242-1957G>T
NM_001322011.2:c.-845G>T
NM_001322012.2:c.-845G>T
NM_001322013.2:c.-366G>T
NM_001322014.2:c.40G>T
NM_001322015.2:c.-445G>T
NP_000526.2:p.Ala14Ser
NP_001308935.1:p.Ala14Ser
NP_001308943.1:p.Ala14Ser
LRG_161t1:c.40G>T
LRG_161:g.8092G>T
NC_000007.13:g.6045646C>A
NM_000535.5:c.40G>T
NM_000535.6:c.40G>T
NR_136154.1:n.127G>T

Protein change:

A14S

Links:

dbSNP: rs876661039

NCBI 1000 Genomes Browser:

rs876661039

Molecular consequence:

NM_001322003.2:c.-366G>T - 5 prime UTR variant - [Sequence Ontology: SO:0001623]
NM_001322005.2:c.-366G>T - 5 prime UTR variant - [Sequence Ontology: SO:0001623]
NM_001322007.2:c.-176G>T - 5 prime UTR variant - [Sequence Ontology: SO:0001623]
NM_001322009.2:c.-366G>T - 5 prime UTR variant - [Sequence Ontology: SO:0001623]
NM_001322011.2:c.-845G>T - 5 prime UTR variant - [Sequence Ontology: SO:0001623]
NM_001322012.2:c.-845G>T - 5 prime UTR variant - [Sequence Ontology: SO:0001623]
NM_001322013.2:c.-366G>T - 5 prime UTR variant - [Sequence Ontology: SO:0001623]
NM_001322015.2:c.-445G>T - 5 prime UTR variant - [Sequence Ontology: SO:0001623]
NM_001322004.2:c.-242-1957G>T - intron variant - [Sequence Ontology: SO:0001627]
NM_001322008.2:c.-52-1957G>T - intron variant - [Sequence Ontology: SO:0001627]
NM_001322010.2:c.-242-1957G>T - intron variant - [Sequence Ontology: SO:0001627]
NM_000535.7:c.40G>T - missense variant - [Sequence Ontology: SO:0001583]
NM_001322006.2:c.40G>T - missense variant - [Sequence Ontology: SO:0001583]
NM_001322014.2:c.40G>T - missense variant - [Sequence Ontology: SO:0001583]
NR_136154.1:n.127G>T - non-coding transcript variant - [Sequence Ontology: SO:0001619]

Condition(s)

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

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Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV004117015	PreventionGenetics, part of Exact Sciences	criteria provided, single submitter (ACMG Guidelines, 2015)	Uncertain significance (Jan 27, 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

SCV004117015

PreventionGenetics, part of Exact Sciences

criteria provided, single submitter

(ACMG Guidelines, 2015)

Uncertain significance
(Jan 27, 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, SCV004117015.1

#	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.40G>T variant is predicted to result in the amino acid substitution p.Ala14Ser. To our knowledge, this variant has not been reported in the literature or in a large population database (http://gnomad.broadinstitute.org), indicating this variant is rare. This variant is reported with uncertain significance in ClinVar (https://www.ncbi.nlm.nih.gov/clinvar/variation/234477/). 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