NM_000535.7(PMS2):c.274A>T (p.Ile92Phe) AND Hereditary nonpolyposis colorectal neoplasms

Germline classification:: Uncertain significance (1 submission)
Last evaluated:: Oct 9, 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:: RCV001339452.7

Allele description [Variation Report for NM_000535.7(PMS2):c.274A>T (p.Ile92Phe)]

NM_000535.7(PMS2):c.274A>T (p.Ile92Phe)

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.274A>T (p.Ile92Phe)

HGVS:

NC_000007.14:g.6003769T>A
NG_008466.1:g.10338A>T
NM_000535.5:c.274A>T
NM_000535.7:c.274A>TMANE SELECT
NM_001322003.2:c.-132A>T
NM_001322004.2:c.-132A>T
NM_001322005.2:c.-132A>T
NM_001322006.2:c.274A>T
NM_001322007.2:c.35+203A>T
NM_001322008.2:c.35+203A>T
NM_001322009.2:c.-132A>T
NM_001322010.2:c.-132A>T
NM_001322011.2:c.-611A>T
NM_001322012.2:c.-611A>T
NM_001322013.2:c.-132A>T
NM_001322014.2:c.274A>T
NM_001322015.2:c.-211A>T
NP_000526.2:p.Ile92Phe
NP_001308935.1:p.Ile92Phe
NP_001308943.1:p.Ile92Phe
LRG_161t1:c.274A>T
LRG_161:g.10338A>T
NC_000007.13:g.6043400T>A
NR_136154.1:n.361A>T

Protein change:

I92F

Links:

dbSNP: rs1333262869

NCBI 1000 Genomes Browser:

rs1333262869

Molecular consequence:

NM_001322003.2:c.-132A>T - 5 prime UTR variant - [Sequence Ontology: SO:0001623]
NM_001322004.2:c.-132A>T - 5 prime UTR variant - [Sequence Ontology: SO:0001623]
NM_001322005.2:c.-132A>T - 5 prime UTR variant - [Sequence Ontology: SO:0001623]
NM_001322009.2:c.-132A>T - 5 prime UTR variant - [Sequence Ontology: SO:0001623]
NM_001322010.2:c.-132A>T - 5 prime UTR variant - [Sequence Ontology: SO:0001623]
NM_001322011.2:c.-611A>T - 5 prime UTR variant - [Sequence Ontology: SO:0001623]
NM_001322012.2:c.-611A>T - 5 prime UTR variant - [Sequence Ontology: SO:0001623]
NM_001322013.2:c.-132A>T - 5 prime UTR variant - [Sequence Ontology: SO:0001623]
NM_001322015.2:c.-211A>T - 5 prime UTR variant - [Sequence Ontology: SO:0001623]
NM_001322007.2:c.35+203A>T - intron variant - [Sequence Ontology: SO:0001627]
NM_001322008.2:c.35+203A>T - intron variant - [Sequence Ontology: SO:0001627]
NM_000535.7:c.274A>T - missense variant - [Sequence Ontology: SO:0001583]
NM_001322006.2:c.274A>T - missense variant - [Sequence Ontology: SO:0001583]
NM_001322014.2:c.274A>T - missense variant - [Sequence Ontology: SO:0001583]
NR_136154.1:n.361A>T - non-coding transcript variant - [Sequence Ontology: SO:0001619]

Condition(s)

Name:: Hereditary nonpolyposis colorectal neoplasms
Identifiers:: MeSH: D003123; MedGen: C0009405

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Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV001533195	Labcorp Genetics (formerly Invitae), Labcorp	criteria provided, single submitter (Invitae Variant Classification Sherloc (09022015))	Uncertain significance (Oct 9, 2020)	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

SCV001533195

Labcorp Genetics (formerly Invitae), Labcorp

criteria provided, single submitter

(Invitae Variant Classification Sherloc (09022015))

Uncertain significance
(Oct 9, 2020)

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

Sherloc: a comprehensive refinement of the ACMG-AMP variant classification criteria.

Nykamp K, Anderson M, Powers M, Garcia J, Herrera B, Ho YY, Kobayashi Y, Patil N, Thusberg J, Westbrook M; Invitae Clinical Genomics Group., Topper S.

Genet Med. 2017 Oct;19(10):1105-1117. doi: 10.1038/gim.2017.37. Epub 2017 May 11. Erratum in: Genet Med. 2020 Jan;22(1):240. doi: 10.1038/s41436-019-0624-9.

PubMed [citation]

PMID:: 28492532
PMCID:: PMC5632818

Details of each submission

From Labcorp Genetics (formerly Invitae), Labcorp, SCV001533195.4

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

Description

This sequence change replaces isoleucine with phenylalanine at codon 92 of the PMS2 protein (p.Ile92Phe). The isoleucine residue is weakly conserved and there is a small physicochemical difference between isoleucine and phenylalanine. In summary, the available evidence is currently insufficient to determine the role of this variant in disease. Therefore, it has been classified as a Variant of Uncertain Significance. Algorithms developed to predict the effect of missense changes on protein structure and function are either unavailable or do not agree on the potential impact of this missense change (SIFT: "Deleterious"; PolyPhen-2: "Probably Damaging"; Align-GVGD: "Class C0"). This variant has not been reported in the literature in individuals with PMS2-related conditions. This variant is not present in population databases (ExAC no frequency).

#	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

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