NM_000535.7(PMS2):c.1324C>T (p.Pro442Ser) AND Hereditary cancer-predisposing syndrome

Germline classification:: Uncertain significance (1 submission)
Last evaluated:: Feb 17, 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:: RCV002379986.3

Allele description [Variation Report for NM_000535.7(PMS2):c.1324C>T (p.Pro442Ser)]

NM_000535.7(PMS2):c.1324C>T (p.Pro442Ser)

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.1324C>T (p.Pro442Ser)

HGVS:

NC_000007.14:g.5987441G>A
NG_008466.1:g.26666C>T
NM_000535.7:c.1324C>TMANE SELECT
NM_001322003.2:c.919C>T
NM_001322004.2:c.919C>T
NM_001322005.2:c.919C>T
NM_001322006.2:c.1168C>T
NM_001322007.2:c.1006C>T
NM_001322008.2:c.1006C>T
NM_001322009.2:c.919C>T
NM_001322010.2:c.763C>T
NM_001322011.2:c.391C>T
NM_001322012.2:c.391C>T
NM_001322013.2:c.751C>T
NM_001322014.2:c.1324C>T
NM_001322015.2:c.1015C>T
NP_000526.2:p.Pro442Ser
NP_001308932.1:p.Pro307Ser
NP_001308933.1:p.Pro307Ser
NP_001308934.1:p.Pro307Ser
NP_001308935.1:p.Pro390Ser
NP_001308936.1:p.Pro336Ser
NP_001308937.1:p.Pro336Ser
NP_001308938.1:p.Pro307Ser
NP_001308939.1:p.Pro255Ser
NP_001308940.1:p.Pro131Ser
NP_001308941.1:p.Pro131Ser
NP_001308942.1:p.Pro251Ser
NP_001308943.1:p.Pro442Ser
NP_001308944.1:p.Pro339Ser
LRG_161t1:c.1324C>T
LRG_161:g.26666C>T
NC_000007.13:g.6027072G>A
NM_000535.5:c.1324C>T
NR_136154.1:n.1411C>T

Protein change:

P131S

Links:

dbSNP: rs1783134322

NCBI 1000 Genomes Browser:

rs1783134322

Molecular consequence:

NM_000535.7:c.1324C>T - missense variant - [Sequence Ontology: SO:0001583]
NM_001322003.2:c.919C>T - missense variant - [Sequence Ontology: SO:0001583]
NM_001322004.2:c.919C>T - missense variant - [Sequence Ontology: SO:0001583]
NM_001322005.2:c.919C>T - missense variant - [Sequence Ontology: SO:0001583]
NM_001322006.2:c.1168C>T - missense variant - [Sequence Ontology: SO:0001583]
NM_001322007.2:c.1006C>T - missense variant - [Sequence Ontology: SO:0001583]
NM_001322008.2:c.1006C>T - missense variant - [Sequence Ontology: SO:0001583]
NM_001322009.2:c.919C>T - missense variant - [Sequence Ontology: SO:0001583]
NM_001322010.2:c.763C>T - missense variant - [Sequence Ontology: SO:0001583]
NM_001322011.2:c.391C>T - missense variant - [Sequence Ontology: SO:0001583]
NM_001322012.2:c.391C>T - missense variant - [Sequence Ontology: SO:0001583]
NM_001322013.2:c.751C>T - missense variant - [Sequence Ontology: SO:0001583]
NM_001322014.2:c.1324C>T - missense variant - [Sequence Ontology: SO:0001583]
NM_001322015.2:c.1015C>T - missense variant - [Sequence Ontology: SO:0001583]
NR_136154.1:n.1411C>T - non-coding transcript variant - [Sequence Ontology: SO:0001619]

Condition(s)

Name:: Hereditary cancer-predisposing syndrome
Synonyms:: Neoplastic Syndromes, Hereditary; Tumor predisposition; Cancer predisposition; See all synonyms [MedGen]
Identifiers:: MONDO: MONDO:0015356; MeSH: D009386; MedGen: C0027672

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KHNYN KH and NYN domain containing [Homo sapiens]
KHNYN KH and NYN domain containing [Homo sapiens]
Gene ID:23351

Gene
IFIT3 interferon induced protein with tetratricopeptide repeats 3 [Homo sapiens]
IFIT3 interferon induced protein with tetratricopeptide repeats 3 [Homo sapiens]
Gene ID:3437

Gene

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Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV002691449	Ambry Genetics	criteria provided, single submitter (Ambry Variant Classification Scheme 2023)	Uncertain significance (Feb 17, 2023)	germline	clinical testing	Citation Link

Submission Accession

Submitter

Review Status
(Assertion method)

Clinical Significance
(Last evaluated)

Origin

Method

Citations

SCV002691449

Ambry Genetics

criteria provided, single submitter

(Ambry Variant Classification Scheme 2023)

Uncertain significance
(Feb 17, 2023)

germline

clinical testing

Citation Link

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

Details of each submission

From Ambry Genetics, SCV002691449.3

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

Description

The p.P442S variant (also known as c.1324C>T), located in coding exon 11 of the PMS2 gene, results from a C to T substitution at nucleotide position 1324. The proline at codon 442 is replaced by serine, an amino acid with similar properties. This amino acid position is not well conserved in available vertebrate species. In addition, this alteration is predicted to be tolerated by in silico analysis. Since supporting evidence is limited at this time, the clinical significance of this alteration remains unclear.

#	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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