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NM_000535.7(PMS2):c.1954A>T (p.Ile652Phe) AND Lynch syndrome

Germline classification:
Uncertain significance (1 submission)
Last evaluated:
Dec 18, 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:
RCV003995577.2

Allele description [Variation Report for NM_000535.7(PMS2):c.1954A>T (p.Ile652Phe)]

NM_000535.7(PMS2):c.1954A>T (p.Ile652Phe)

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.1954A>T (p.Ile652Phe)
HGVS:
  • NC_000007.14:g.5986811T>A
  • NG_008466.1:g.27296A>T
  • NM_000535.7:c.1954A>TMANE SELECT
  • NM_001322003.2:c.1549A>T
  • NM_001322004.2:c.1549A>T
  • NM_001322005.2:c.1549A>T
  • NM_001322006.2:c.1798A>T
  • NM_001322007.2:c.1636A>T
  • NM_001322008.2:c.1636A>T
  • NM_001322009.2:c.1549A>T
  • NM_001322010.2:c.1393A>T
  • NM_001322011.2:c.1021A>T
  • NM_001322012.2:c.1021A>T
  • NM_001322013.2:c.1381A>T
  • NM_001322014.2:c.1954A>T
  • NM_001322015.2:c.1645A>T
  • NP_000526.2:p.Ile652Phe
  • NP_001308932.1:p.Ile517Phe
  • NP_001308933.1:p.Ile517Phe
  • NP_001308934.1:p.Ile517Phe
  • NP_001308935.1:p.Ile600Phe
  • NP_001308936.1:p.Ile546Phe
  • NP_001308937.1:p.Ile546Phe
  • NP_001308938.1:p.Ile517Phe
  • NP_001308939.1:p.Ile465Phe
  • NP_001308940.1:p.Ile341Phe
  • NP_001308941.1:p.Ile341Phe
  • NP_001308942.1:p.Ile461Phe
  • NP_001308943.1:p.Ile652Phe
  • NP_001308944.1:p.Ile549Phe
  • LRG_161t1:c.1954A>T
  • LRG_161:g.27296A>T
  • NC_000007.13:g.6026442T>A
  • NM_000535.5:c.1954A>T
  • NM_000535.6:c.1954A>T
  • NR_136154.1:n.2041A>T
  • p.I652F
Protein change:
I341F
Links:
dbSNP: rs748927376
NCBI 1000 Genomes Browser:
rs748927376
Molecular consequence:
  • NM_000535.7:c.1954A>T - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001322003.2:c.1549A>T - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001322004.2:c.1549A>T - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001322005.2:c.1549A>T - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001322006.2:c.1798A>T - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001322007.2:c.1636A>T - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001322008.2:c.1636A>T - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001322009.2:c.1549A>T - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001322010.2:c.1393A>T - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001322011.2:c.1021A>T - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001322012.2:c.1021A>T - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001322013.2:c.1381A>T - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001322014.2:c.1954A>T - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001322015.2:c.1645A>T - missense variant - [Sequence Ontology: SO:0001583]
  • NR_136154.1:n.2041A>T - non-coding transcript variant - [Sequence Ontology: SO:0001619]
Observations:
9

Condition(s)

Name:
Lynch syndrome
Identifiers:
MONDO: MONDO:0005835; MedGen: C4552100

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Assertion and evidence details

Help
Submission AccessionSubmitterReview Status
(Assertion method)		Clinical Significance
(Last evaluated)		OriginMethodCitations
SCV004844109All of Us Research Program, National Institutes of Health
criteria provided, single submitter

(ACMG Guidelines, 2015)		Uncertain Significance
(Dec 18, 2023) 		germlineclinical testing

PubMed (1)
[See all records that cite this PMID]

Help

Summary from all submissions

EthnicityOriginAffectedIndividualsFamiliesChromosomes testedNumber TestedFamily historyMethod
not providedgermlineunknown9not providednot provided108544not providedclinical 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 All of Us Research Program, National Institutes of Health, SCV004844109.1

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1not provided9not providednot providedclinical testing PubMed (1)

Description

This missense variant replaces isoleucine with phenylalanine at codon 652 of the PMS2 protein. Computational prediction suggests that this variant may not impact protein structure and function (internally defined REVEL score threshold <= 0.5, PMID: 27666373). To our knowledge, functional studies have not been reported for this variant. This variant has not been reported in individuals affected with PMS2-related disorders in the literature. This variant has been identified in 9/250552 chromosomes in the general population by the Genome Aggregation Database (gnomAD). The available evidence is insufficient to determine the role of this variant in disease conclusively. Therefore, this variant is classified as a Variant of Uncertain Significance.

#SampleMethodObservation
OriginAffectedNumber testedTissuePurposeMethodIndividualsAllele frequencyFamiliesCo-occurrences
1germlineunknown108544not providednot provided9not providednot providednot provided

Last Updated: Sep 29, 2024