NM_000535.7(PMS2):c.1131G>A (p.Leu377=) AND not provided

Germline classification:: Uncertain significance (1 submission)
Last evaluated:: Mar 23, 2016
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:: RCV000766528.1

Allele description [Variation Report for NM_000535.7(PMS2):c.1131G>A (p.Leu377=)]

NM_000535.7(PMS2):c.1131G>A (p.Leu377=)

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.1131G>A (p.Leu377=)

HGVS:

NC_000007.14:g.5989813C>T
NG_008466.1:g.24294G>A
NM_000535.7:c.1131G>AMANE SELECT
NM_001322003.2:c.726G>A
NM_001322004.2:c.726G>A
NM_001322005.2:c.726G>A
NM_001322006.2:c.988+2160G>A
NM_001322007.2:c.813G>A
NM_001322008.2:c.813G>A
NM_001322009.2:c.726G>A
NM_001322010.2:c.583+2160G>A
NM_001322011.2:c.198G>A
NM_001322012.2:c.198G>A
NM_001322013.2:c.558G>A
NM_001322014.2:c.1131G>A
NM_001322015.2:c.822G>A
NP_000526.2:p.Leu377=
NP_001308932.1:p.Leu242=
NP_001308933.1:p.Leu242=
NP_001308934.1:p.Leu242=
NP_001308936.1:p.Leu271=
NP_001308937.1:p.Leu271=
NP_001308938.1:p.Leu242=
NP_001308940.1:p.Leu66=
NP_001308941.1:p.Leu66=
NP_001308942.1:p.Leu186=
NP_001308943.1:p.Leu377=
NP_001308944.1:p.Leu274=
LRG_161t1:c.1131G>A
LRG_161:g.24294G>A
NC_000007.13:g.6029444C>T
NM_000535.5:c.1131G>A
NM_000535.6:c.1131G>A
NR_136154.1:n.1218G>A
p.Leu377Leu

Links:

dbSNP: rs1064794687

NCBI 1000 Genomes Browser:

rs1064794687

Molecular consequence:

NM_001322006.2:c.988+2160G>A - intron variant - [Sequence Ontology: SO:0001627]
NM_001322010.2:c.583+2160G>A - intron variant - [Sequence Ontology: SO:0001627]
NR_136154.1:n.1218G>A - non-coding transcript variant - [Sequence Ontology: SO:0001619]
NM_000535.7:c.1131G>A - synonymous variant - [Sequence Ontology: SO:0001819]
NM_001322003.2:c.726G>A - synonymous variant - [Sequence Ontology: SO:0001819]
NM_001322004.2:c.726G>A - synonymous variant - [Sequence Ontology: SO:0001819]
NM_001322005.2:c.726G>A - synonymous variant - [Sequence Ontology: SO:0001819]
NM_001322007.2:c.813G>A - synonymous variant - [Sequence Ontology: SO:0001819]
NM_001322008.2:c.813G>A - synonymous variant - [Sequence Ontology: SO:0001819]
NM_001322009.2:c.726G>A - synonymous variant - [Sequence Ontology: SO:0001819]
NM_001322011.2:c.198G>A - synonymous variant - [Sequence Ontology: SO:0001819]
NM_001322012.2:c.198G>A - synonymous variant - [Sequence Ontology: SO:0001819]
NM_001322013.2:c.558G>A - synonymous variant - [Sequence Ontology: SO:0001819]
NM_001322014.2:c.1131G>A - synonymous variant - [Sequence Ontology: SO:0001819]
NM_001322015.2:c.822G>A - synonymous variant - [Sequence Ontology: SO:0001819]

Condition(s)

Synonyms:: none provided
Identifiers:: MedGen: C3661900

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Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV000569727	GeneDx	criteria provided, single submitter (GeneDx Variant Classification (06012015))	Uncertain significance (Mar 23, 2016)	germline	clinical testing	Citation Link

Submission Accession

Submitter

Review Status
(Assertion method)

Clinical Significance
(Last evaluated)

Origin

Method

Citations

SCV000569727

GeneDx

criteria provided, single submitter

(GeneDx Variant Classification (06012015))

Uncertain significance
(Mar 23, 2016)

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	yes	not provided	not provided	not provided	not provided	not provided	clinical testing

Details of each submission

From GeneDx, SCV000569727.4

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

Description

This variant is denoted PMS2 c.1131G>A at the DNA level. This variant is silent at the coding level, preserving a Leucine at codon 377. It is not predicted to cause abnormal splicing. This variant has not, to our knowledge, been published in the literature as being pathogenic or benign. PMS2 c.1131G>A was not observed in approximately 6,500 individuals of European and African American ancestry in the NHLBI Exome Sequencing Project, indicating it is not a common benign variant in these populations. The nucleotide which is altered, a guanine (G) at base 1131, is conserved in mammals. Based on currently available information, it is unclear whether PMS2 c.1131G>A is a pathogenic or benign variant. We consider it to be a variant of uncertain significance.

#	Sample				Method		Observation
#	Origin	Affected	Number tested	Tissue	Purpose	Method	Individuals	Allele frequency	Families	Co-occurrences
1	germline	yes	not provided	not provided	not provided		not provided	not provided	not provided	not provided

Last Updated: Sep 29, 2024

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