NM_000535.7(PMS2):c.255G>A (p.Leu85=) AND not specified

Germline classification:: Benign/Likely benign (4 submissions)
Last evaluated:: Aug 15, 2023
Review status:: 2 stars out of maximum of 4 stars
criteria provided, multiple submitters, no conflicts

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:: RCV000212839.13

Allele description [Variation Report for NM_000535.7(PMS2):c.255G>A (p.Leu85=)]

NM_000535.7(PMS2):c.255G>A (p.Leu85=)

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.255G>A (p.Leu85=)

Other names:

p.L85L:CTG>CTA

HGVS:

NC_000007.14:g.6003788C>T
NG_008466.1:g.10319G>A
NM_000535.7:c.255G>AMANE SELECT
NM_001322003.2:c.-151G>A
NM_001322004.2:c.-151G>A
NM_001322005.2:c.-151G>A
NM_001322006.2:c.255G>A
NM_001322007.2:c.35+184G>A
NM_001322008.2:c.35+184G>A
NM_001322009.2:c.-151G>A
NM_001322010.2:c.-151G>A
NM_001322011.2:c.-630G>A
NM_001322012.2:c.-630G>A
NM_001322013.2:c.-151G>A
NM_001322014.2:c.255G>A
NM_001322015.2:c.-230G>A
NP_000526.2:p.Leu85=
NP_001308935.1:p.Leu85=
NP_001308943.1:p.Leu85=
LRG_161t1:c.255G>A
LRG_161:g.10319G>A
NC_000007.13:g.6043419C>T
NM_000535.5:c.255G>A
NM_000535.6:c.255G>A
NM_000535.7:c.255G>A
NR_136154.1:n.342G>A
p.L85L

Links:

dbSNP: rs200491279

NCBI 1000 Genomes Browser:

rs200491279

Molecular consequence:

NM_001322003.2:c.-151G>A - 5 prime UTR variant - [Sequence Ontology: SO:0001623]
NM_001322004.2:c.-151G>A - 5 prime UTR variant - [Sequence Ontology: SO:0001623]
NM_001322005.2:c.-151G>A - 5 prime UTR variant - [Sequence Ontology: SO:0001623]
NM_001322009.2:c.-151G>A - 5 prime UTR variant - [Sequence Ontology: SO:0001623]
NM_001322010.2:c.-151G>A - 5 prime UTR variant - [Sequence Ontology: SO:0001623]
NM_001322011.2:c.-630G>A - 5 prime UTR variant - [Sequence Ontology: SO:0001623]
NM_001322012.2:c.-630G>A - 5 prime UTR variant - [Sequence Ontology: SO:0001623]
NM_001322013.2:c.-151G>A - 5 prime UTR variant - [Sequence Ontology: SO:0001623]
NM_001322015.2:c.-230G>A - 5 prime UTR variant - [Sequence Ontology: SO:0001623]
NM_001322007.2:c.35+184G>A - intron variant - [Sequence Ontology: SO:0001627]
NM_001322008.2:c.35+184G>A - intron variant - [Sequence Ontology: SO:0001627]
NR_136154.1:n.342G>A - non-coding transcript variant - [Sequence Ontology: SO:0001619]
NM_000535.7:c.255G>A - synonymous variant - [Sequence Ontology: SO:0001819]
NM_001322006.2:c.255G>A - synonymous variant - [Sequence Ontology: SO:0001819]
NM_001322014.2:c.255G>A - synonymous variant - [Sequence Ontology: SO:0001819]

Condition(s)

Synonyms:: AllHighlyPenetrant
Identifiers:: MedGen: CN169374

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Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV000211598	GeneDx	criteria provided, single submitter (GeneDx Variant Classification (06012015))	Benign (Aug 6, 2014)	germline	clinical testing	Citation Link,
SCV000697355	Women's Health and Genetics/Laboratory Corporation of America, LabCorp	criteria provided, single submitter (LabCorp Variant Classification Summary - May 2015)	Benign (Mar 1, 2021)	germline	clinical testing	PubMed (1) [See all records that cite this PMID] Citation Link,
SCV002072407	Genetic Services Laboratory, University of Chicago	criteria provided, single submitter (ACMG Guidelines, 2015)	Likely benign (Oct 8, 2021)	germline	clinical testing	PubMed (1) [See all records that cite this PMID]
SCV002550757	Center for Genomic Medicine, Rigshospitalet, Copenhagen University Hospital	criteria provided, single submitter (ACMG Guidelines, 2015)	Likely benign (Aug 15, 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	yes	not provided	not provided	not provided	not provided	not provided	clinical testing
not provided	germline	no	not provided	not provided	not provided	not provided	not provided	clinical testing
not provided	germline	unknown	not provided	not provided	not provided	not provided	not provided	clinical testing

Citations

PubMed

Prioritizing Variants in Complete Hereditary Breast and Ovarian Cancer Genes in Patients Lacking Known BRCA Mutations.

Caminsky NG, Mucaki EJ, Perri AM, Lu R, Knoll JH, Rogan PK.

Hum Mutat. 2016 Jul;37(7):640-52. doi: 10.1002/humu.22972. Epub 2016 Mar 18.

PubMed [citation]

PMID:: 26898890

Standards and guidelines for the interpretation of sequence variants: a joint consensus recommendation of the American College of Medical Genetics and Genomics and the Association for Molecular Pathology.

Richards S, Aziz N, Bale S, Bick D, Das S, Gastier-Foster J, Grody WW, Hegde M, Lyon E, Spector E, Voelkerding K, Rehm HL; ACMG Laboratory Quality Assurance Committee..

Genet Med. 2015 May;17(5):405-24. doi: 10.1038/gim.2015.30. Epub 2015 Mar 5.

PubMed [citation]

PMID:: 25741868
PMCID:: PMC4544753

Details of each submission

From GeneDx, SCV000211598.10

#	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 considered likely benign or benign based on one or more of the following criteria: it is a conservative change, it occurs at a poorly conserved position in the protein, it is predicted to be benign by multiple in silico algorithms, and/or has population frequency not consistent with disease.

#	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

From Women's Health and Genetics/Laboratory Corporation of America, LabCorp, SCV000697355.3

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

#	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

From Genetic Services Laboratory, University of Chicago, SCV002072407.1

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

#	Sample				Method		Observation
#	Origin	Affected	Number tested	Tissue	Purpose	Method	Individuals	Allele frequency	Families	Co-occurrences
1	germline	no	not provided	not provided	not provided		not provided	not provided	not provided	not provided

From Center for Genomic Medicine, Rigshospitalet, Copenhagen University Hospital, SCV002550757.4

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

#	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: Oct 20, 2024

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