NM_000535.7(PMS2):c.235A>G (p.Asn79Asp) AND Hereditary cancer-predisposing syndrome

Germline classification:: Uncertain significance (1 submission)
Last evaluated:: Jul 23, 2014
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:: RCV002448510.2

Allele description [Variation Report for NM_000535.7(PMS2):c.235A>G (p.Asn79Asp)]

NM_000535.7(PMS2):c.235A>G (p.Asn79Asp)

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.235A>G (p.Asn79Asp)

HGVS:

NC_000007.14:g.6003987T>C
NG_008466.1:g.10120A>G
NM_000535.7:c.235A>GMANE SELECT
NM_001018040.1:c.-171A>G
NM_001322003.2:c.-171A>G
NM_001322004.2:c.-171A>G
NM_001322005.2:c.-171A>G
NM_001322006.2:c.235A>G
NM_001322007.2:c.20A>G
NM_001322008.2:c.20A>G
NM_001322009.2:c.-171A>G
NM_001322010.2:c.-171A>G
NM_001322011.2:c.-650A>G
NM_001322012.2:c.-650A>G
NM_001322013.2:c.-171A>G
NM_001322014.2:c.235A>G
NM_001322015.2:c.-250A>G
NM_001406866.1:c.421A>G
NM_001406868.1:c.235A>G
NM_001406869.1:c.235A>G
NM_001406870.1:c.235A>G
NM_001406871.1:c.235A>G
NM_001406872.1:c.235A>G
NM_001406873.1:c.235A>G
NM_001406874.1:c.235A>G
NM_001406875.1:c.-250A>G
NM_001406876.1:c.20A>G
NM_001406877.1:c.-250A>G
NM_001406878.1:c.-250A>G
NM_001406879.1:c.-250A>G
NM_001406880.1:c.-197A>G
NM_001406881.1:c.-147A>G
NM_001406882.1:c.-250A>G
NM_001406883.1:c.20A>G
NM_001406884.1:c.235A>G
NM_001406885.1:c.235A>G
NM_001406886.1:c.235A>G
NM_001406887.1:c.-171A>G
NM_001406888.1:c.-118A>G
NM_001406889.1:c.-118A>G
NM_001406890.1:c.-161A>G
NM_001406891.1:c.-171A>G
NM_001406892.1:c.-118A>G
NM_001406893.1:c.-171A>G
NM_001406894.1:c.-118A>G
NM_001406895.1:c.-118A>G
NM_001406897.1:c.-171A>G
NM_001406898.1:c.-171A>G
NM_001406899.1:c.-118A>G
NM_001406900.1:c.-147A>G
NM_001406901.1:c.20A>G
NM_001406902.1:c.20A>G
NM_001406903.1:c.20A>G
NM_001406904.1:c.-118A>G
NM_001406905.1:c.-171A>G
NM_001406906.1:c.-171A>G
NM_001406907.1:c.-118A>G
NM_001406908.1:c.-171A>G
NM_001406909.1:c.-118A>G
NM_001406910.1:c.-171A>G
NM_001406911.1:c.-171A>G
NM_001406912.1:c.235A>G
NP_000526.1:p.Asn79Asp
NP_000526.2:p.Asn79Asp
NP_001308935.1:p.Asn79Asp
NP_001308936.1:p.Lys7Arg
NP_001308937.1:p.Lys7Arg
NP_001308943.1:p.Asn79Asp
NP_001393795.1:p.Asn141Asp
NP_001393797.1:p.Asn79Asp
NP_001393798.1:p.Asn79Asp
NP_001393799.1:p.Asn79Asp
NP_001393800.1:p.Asn79Asp
NP_001393801.1:p.Asn79Asp
NP_001393802.1:p.Asn79Asp
NP_001393803.1:p.Asn79Asp
NP_001393805.1:p.Lys7Arg
NP_001393812.1:p.Lys7Arg
NP_001393813.1:p.Asn79Asp
NP_001393814.1:p.Asn79Asp
NP_001393815.1:p.Asn79Asp
NP_001393830.1:p.Lys7Arg
NP_001393831.1:p.Lys7Arg
NP_001393832.1:p.Lys7Arg
NP_001393841.1:p.Asn79Asp
LRG_161t1:c.235A>G
LRG_161:g.10120A>G
LRG_161p1:p.Asn79Asp
NC_000007.13:g.6043618T>C
NM_000535.5:c.235A>G
NR_003085.2:n.317A>G
NR_136154.1:n.322A>G

Protein change:

K7R

Molecular consequence:

NM_001322003.2:c.-171A>G - 5 prime UTR variant - [Sequence Ontology: SO:0001623]
NM_001322004.2:c.-171A>G - 5 prime UTR variant - [Sequence Ontology: SO:0001623]
NM_001322005.2:c.-171A>G - 5 prime UTR variant - [Sequence Ontology: SO:0001623]
NM_001322009.2:c.-171A>G - 5 prime UTR variant - [Sequence Ontology: SO:0001623]
NM_001322010.2:c.-171A>G - 5 prime UTR variant - [Sequence Ontology: SO:0001623]
NM_001322011.2:c.-650A>G - 5 prime UTR variant - [Sequence Ontology: SO:0001623]
NM_001322012.2:c.-650A>G - 5 prime UTR variant - [Sequence Ontology: SO:0001623]
NM_001322013.2:c.-171A>G - 5 prime UTR variant - [Sequence Ontology: SO:0001623]
NM_001322015.2:c.-250A>G - 5 prime UTR variant - [Sequence Ontology: SO:0001623]
NM_000535.7:c.235A>G - missense variant - [Sequence Ontology: SO:0001583]
NM_001322006.2:c.235A>G - missense variant - [Sequence Ontology: SO:0001583]
NM_001322007.2:c.20A>G - missense variant - [Sequence Ontology: SO:0001583]
NM_001322008.2:c.20A>G - missense variant - [Sequence Ontology: SO:0001583]
NM_001322014.2:c.235A>G - missense variant - [Sequence Ontology: SO:0001583]
NM_001406866.1:c.421A>G - missense variant - [Sequence Ontology: SO:0001583]
NM_001406868.1:c.235A>G - missense variant - [Sequence Ontology: SO:0001583]
NM_001406869.1:c.235A>G - missense variant - [Sequence Ontology: SO:0001583]
NM_001406870.1:c.235A>G - missense variant - [Sequence Ontology: SO:0001583]
NM_001406871.1:c.235A>G - missense variant - [Sequence Ontology: SO:0001583]
NM_001406872.1:c.235A>G - missense variant - [Sequence Ontology: SO:0001583]
NM_001406873.1:c.235A>G - missense variant - [Sequence Ontology: SO:0001583]
NM_001406874.1:c.235A>G - missense variant - [Sequence Ontology: SO:0001583]
NM_001406876.1:c.20A>G - missense variant - [Sequence Ontology: SO:0001583]
NM_001406883.1:c.20A>G - missense variant - [Sequence Ontology: SO:0001583]
NM_001406884.1:c.235A>G - missense variant - [Sequence Ontology: SO:0001583]
NM_001406885.1:c.235A>G - missense variant - [Sequence Ontology: SO:0001583]
NM_001406886.1:c.235A>G - missense variant - [Sequence Ontology: SO:0001583]
NM_001406901.1:c.20A>G - missense variant - [Sequence Ontology: SO:0001583]
NM_001406902.1:c.20A>G - missense variant - [Sequence Ontology: SO:0001583]
NM_001406903.1:c.20A>G - missense variant - [Sequence Ontology: SO:0001583]
NM_001406912.1:c.235A>G - missense variant - [Sequence Ontology: SO:0001583]
NR_136154.1:n.322A>G - 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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cytochrome oxidase subunit 1, partial (mitochondrion) [Hermania scabra]
cytochrome oxidase subunit 1, partial (mitochondrion) [Hermania scabra]
gi|459926690|gb|AGG84206.1|

Protein
cytochrome oxidase subunit 1, partial (mitochondrion) [Hermania indistincta]
cytochrome oxidase subunit 1, partial (mitochondrion) [Hermania indistincta]
gi|908309315|gb|AKT25680.1|

Protein

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Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV002733171	Ambry Genetics	criteria provided, single submitter (Ambry Variant Classification Scheme 2023)	Uncertain significance (Jul 23, 2014)	germline	clinical testing	Citation Link

Submission Accession

Submitter

Review Status
(Assertion method)

Clinical Significance
(Last evaluated)

Origin

Method

Citations

SCV002733171

Ambry Genetics

criteria provided, single submitter

(Ambry Variant Classification Scheme 2023)

Uncertain significance
(Jul 23, 2014)

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, SCV002733171.2

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

Description

The p.N79D variant (also known as c.235A>G), located in coding exon 3 of the PMS2 gene, results from an A to G substitution at nucleotide position 235. The asparagine at codon 79 is replaced by aspartic acid, an amino acid with highly similar properties. This variant was not reported in population based cohorts in the following databases: Database of Single Nucleotide Polymorphisms (dbSNP), NHLBI Exome Sequencing Project (ESP), and 1000 Genomes Project. In the ESP, this variant was not observed in 6489 samples (12978 alleles) with coverage at this position. To date, this alteration has been detected with an allele frequency of approximately 0.004% (greater than 23,000 alleles tested) in our clinical cohort. Based on protein sequence alignment, this amino acid position is highly conserved in available vertebrate species. In addition, this alteration is predicted to be possibly damaging but tolerated by PolyPhen and SIFT in silico analyses, respectively. Since supporting evidence is limited at this time, the clinical significance of p.N79D 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: May 1, 2024

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