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

Germline classification:: Likely benign (5 submissions)
Last evaluated:: Jul 1, 2024
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:: RCV000587054.34

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]

Observations:

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
SCV000806211	PreventionGenetics, part of Exact Sciences	criteria provided, single submitter (ACMG Guidelines, 2015)	Likely benign (Apr 3, 2017)	germline	clinical testing	PubMed (1) [See all records that cite this PMID]
SCV001155037	CeGaT Center for Human Genetics Tuebingen	criteria provided, single submitter (CeGaT Center For Human Genetics Tuebingen Variant Classification Criteria Version 2)	Likely benign (Jul 1, 2024)	germline	clinical testing	Citation Link,
SCV001470057	Quest Diagnostics Nichols Institute San Juan Capistrano	criteria provided, single submitter (Quest Diagnostics criteria)	Likely benign (Sep 15, 2023)	unknown	clinical testing	PubMed (2) [See all records that cite these PMIDs] 26898890, 26467025
SCV001929597	Genome Diagnostics Laboratory, University Medical Center Utrecht - VKGL Data-share Consensus See additional submitters Diagnostic Laboratory, Department of Genetics, University Medical Center Groningen	no assertion criteria provided	Likely benign	germline	clinical testing
SCV001957120	Joint Genome Diagnostic Labs from Nijmegen and Maastricht, Radboudumc and MUMC+ - VKGL Data-share Consensus See additional submitters Diagnostic Laboratory, Department of Genetics, University Medical Center Groningen	no assertion criteria provided	Likely benign	germline	clinical testing

Help

Summary from all submissions

Ethnicity	Origin	Affected	Individuals	Families	Chromosomes tested	Number Tested	Family history	Method
not provided	germline	yes	3	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
not provided	unknown	unknown	not provided	not provided	not provided	not provided	not provided	clinical testing

Citations

PubMed

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

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

See all PubMed Citations (3)

Details of each submission

From PreventionGenetics, part of Exact Sciences, SCV000806211.1

#	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	unknown	not provided	not provided	not provided		not provided	not provided	not provided	not provided

From CeGaT Center for Human Genetics Tuebingen, SCV001155037.25

#	Ethnicity	Individuals	Chromosomes Tested	Family History	Method	Citations
1	not provided	3	not provided	not provided	clinical testing	not provided

Description

PMS2: BP4

#	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		3	not provided	not provided	not provided

From Quest Diagnostics Nichols Institute San Juan Capistrano, SCV001470057.2

#	Ethnicity	Individuals	Chromosomes Tested	Family History	Method	Citations
1	not provided	not provided	not provided	not provided	clinical testing	PubMed (2)

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

From Genome Diagnostics Laboratory, University Medical Center Utrecht - VKGL Data-share Consensus, SCV001929597.1

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

#	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 Joint Genome Diagnostic Labs from Nijmegen and Maastricht, Radboudumc and MUMC+ - VKGL Data-share Consensus, SCV001957120.1

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

#	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: Aug 11, 2024

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