NM_000535.7(PMS2):c.55G>T (p.Asp19Tyr) AND Hereditary nonpolyposis colorectal neoplasms

Germline classification:: Uncertain significance (1 submission)
Last evaluated:: Nov 13, 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:: RCV002009549.6

Allele description [Variation Report for NM_000535.7(PMS2):c.55G>T (p.Asp19Tyr)]

NM_000535.7(PMS2):c.55G>T (p.Asp19Tyr)

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.55G>T (p.Asp19Tyr)

HGVS:

NC_000007.14:g.6006000C>A
NG_008466.1:g.8107G>T
NG_050738.1:g.1750C>A
NM_000535.7:c.55G>TMANE SELECT
NM_001322003.2:c.-351G>T
NM_001322004.2:c.-242-1942G>T
NM_001322005.2:c.-351G>T
NM_001322006.2:c.55G>T
NM_001322007.2:c.-161G>T
NM_001322008.2:c.-52-1942G>T
NM_001322009.2:c.-351G>T
NM_001322010.2:c.-242-1942G>T
NM_001322011.2:c.-830G>T
NM_001322012.2:c.-830G>T
NM_001322013.2:c.-351G>T
NM_001322014.2:c.55G>T
NM_001322015.2:c.-430G>T
NP_000526.2:p.Asp19Tyr
NP_001308935.1:p.Asp19Tyr
NP_001308943.1:p.Asp19Tyr
LRG_161t1:c.55G>T
LRG_161:g.8107G>T
NC_000007.13:g.6045631C>A
NM_000535.5:c.55G>T
NR_136154.1:n.142G>T

Protein change:

D19Y

Links:

dbSNP: rs1554306568

NCBI 1000 Genomes Browser:

rs1554306568

Molecular consequence:

NM_001322003.2:c.-351G>T - 5 prime UTR variant - [Sequence Ontology: SO:0001623]
NM_001322005.2:c.-351G>T - 5 prime UTR variant - [Sequence Ontology: SO:0001623]
NM_001322007.2:c.-161G>T - 5 prime UTR variant - [Sequence Ontology: SO:0001623]
NM_001322009.2:c.-351G>T - 5 prime UTR variant - [Sequence Ontology: SO:0001623]
NM_001322011.2:c.-830G>T - 5 prime UTR variant - [Sequence Ontology: SO:0001623]
NM_001322012.2:c.-830G>T - 5 prime UTR variant - [Sequence Ontology: SO:0001623]
NM_001322013.2:c.-351G>T - 5 prime UTR variant - [Sequence Ontology: SO:0001623]
NM_001322015.2:c.-430G>T - 5 prime UTR variant - [Sequence Ontology: SO:0001623]
NM_001322004.2:c.-242-1942G>T - intron variant - [Sequence Ontology: SO:0001627]
NM_001322008.2:c.-52-1942G>T - intron variant - [Sequence Ontology: SO:0001627]
NM_001322010.2:c.-242-1942G>T - intron variant - [Sequence Ontology: SO:0001627]
NM_000535.7:c.55G>T - missense variant - [Sequence Ontology: SO:0001583]
NM_001322006.2:c.55G>T - missense variant - [Sequence Ontology: SO:0001583]
NM_001322014.2:c.55G>T - missense variant - [Sequence Ontology: SO:0001583]
NR_136154.1:n.142G>T - non-coding transcript variant - [Sequence Ontology: SO:0001619]

Condition(s)

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

Recent activity

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Phlebiopsis gigantea strain FP-70857-Sp 28S ribosomal RNA gene, partial sequence
Phlebiopsis gigantea strain FP-70857-Sp 28S ribosomal RNA gene, partial sequence
gi|817033502|gb|KP135272.1|

Nucleotide
Phlebia tremellosa voucher ES2008-2 (GB) internal transcribed spacer 1, partial ...
Phlebia tremellosa voucher ES2008-2 (GB) internal transcribed spacer 1, partial sequence; 5.8S ribosomal RNA gene, complete sequence; and internal transcribed spacer 2, partial sequence
gi|429496730|gb|JX109859.1|

Nucleotide
Candelabrochaete africana strain FP-102987-Sp internal transcribed spacer 1, par...
Candelabrochaete africana strain FP-102987-Sp internal transcribed spacer 1, partial sequence; 5.8S ribosomal RNA gene and internal transcribed spacer 2, complete sequence; and 28S ribosomal RNA gene, partial sequence
gi|817033524|gb|KP135294.1|

Nucleotide

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Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV002288967	Labcorp Genetics (formerly Invitae), Labcorp	criteria provided, single submitter (Invitae Variant Classification Sherloc (09022015))	Uncertain significance (Nov 13, 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

SCV002288967

Labcorp Genetics (formerly Invitae), Labcorp

criteria provided, single submitter

(Invitae Variant Classification Sherloc (09022015))

Uncertain significance
(Nov 13, 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

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, SCV002288967.3

#	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 aspartic acid, which is acidic and polar, with tyrosine, which is neutral and polar, at codon 19 of the PMS2 protein (p.Asp19Tyr). This variant is not present in population databases (gnomAD no frequency). This variant has not been reported in the literature in individuals affected with PMS2-related conditions. ClinVar contains an entry for this variant (Variation ID: 1507597). Advanced modeling of protein sequence and biophysical properties (such as structural, functional, and spatial information, amino acid conservation, physicochemical variation, residue mobility, and thermodynamic stability) performed at Invitae indicates that this missense variant is expected to disrupt PMS2 protein function with a positive predictive value of 80%. 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.

#	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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