NM_000535.7(PMS2):c.283T>C (p.Phe95Leu) AND not provided

Germline classification:: Uncertain significance (1 submission)
Last evaluated:: Feb 9, 2017
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:: RCV000588167.1

Allele description [Variation Report for NM_000535.7(PMS2):c.283T>C (p.Phe95Leu)]

NM_000535.7(PMS2):c.283T>C (p.Phe95Leu)

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.283T>C (p.Phe95Leu)

HGVS:

NC_000007.14:g.6003760A>G
NG_008466.1:g.10347T>C
NM_000535.7:c.283T>CMANE SELECT
NM_001322003.2:c.-123T>C
NM_001322004.2:c.-123T>C
NM_001322005.2:c.-123T>C
NM_001322006.2:c.283T>C
NM_001322007.2:c.35+212T>C
NM_001322008.2:c.35+212T>C
NM_001322009.2:c.-123T>C
NM_001322010.2:c.-123T>C
NM_001322011.2:c.-602T>C
NM_001322012.2:c.-602T>C
NM_001322013.2:c.-123T>C
NM_001322014.2:c.283T>C
NM_001322015.2:c.-202T>C
NP_000526.2:p.Phe95Leu
NP_001308935.1:p.Phe95Leu
NP_001308943.1:p.Phe95Leu
LRG_161t1:c.283T>C
LRG_161:g.10347T>C
NC_000007.13:g.6043391A>G
NM_000535.5:c.283T>C
NR_136154.1:n.370T>C

Protein change:

F95L

Links:

dbSNP: rs1554304717

NCBI 1000 Genomes Browser:

rs1554304717

Molecular consequence:

NM_001322003.2:c.-123T>C - 5 prime UTR variant - [Sequence Ontology: SO:0001623]
NM_001322004.2:c.-123T>C - 5 prime UTR variant - [Sequence Ontology: SO:0001623]
NM_001322005.2:c.-123T>C - 5 prime UTR variant - [Sequence Ontology: SO:0001623]
NM_001322009.2:c.-123T>C - 5 prime UTR variant - [Sequence Ontology: SO:0001623]
NM_001322010.2:c.-123T>C - 5 prime UTR variant - [Sequence Ontology: SO:0001623]
NM_001322011.2:c.-602T>C - 5 prime UTR variant - [Sequence Ontology: SO:0001623]
NM_001322012.2:c.-602T>C - 5 prime UTR variant - [Sequence Ontology: SO:0001623]
NM_001322013.2:c.-123T>C - 5 prime UTR variant - [Sequence Ontology: SO:0001623]
NM_001322015.2:c.-202T>C - 5 prime UTR variant - [Sequence Ontology: SO:0001623]
NM_001322007.2:c.35+212T>C - intron variant - [Sequence Ontology: SO:0001627]
NM_001322008.2:c.35+212T>C - intron variant - [Sequence Ontology: SO:0001627]
NM_000535.7:c.283T>C - missense variant - [Sequence Ontology: SO:0001583]
NM_001322006.2:c.283T>C - missense variant - [Sequence Ontology: SO:0001583]
NM_001322014.2:c.283T>C - missense variant - [Sequence Ontology: SO:0001583]
NR_136154.1:n.370T>C - non-coding transcript variant - [Sequence Ontology: SO:0001619]

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
SCV000697356	Women's Health and Genetics/Laboratory Corporation of America, LabCorp	criteria provided, single submitter (LabCorp Variant Classification Summary - May 2015)	Uncertain significance (Feb 9, 2017)	germline	clinical testing	LabCorp Variant Classification Summary - May 2015.docx Citation Link

Submission Accession

Submitter

Review Status
(Assertion method)

Clinical Significance
(Last evaluated)

Origin

Method

Citations

SCV000697356

Women's Health and Genetics/Laboratory Corporation of America, LabCorp

criteria provided, single submitter

(LabCorp Variant Classification Summary - May 2015)

Uncertain significance
(Feb 9, 2017)

germline

clinical testing

LabCorp Variant Classification Summary - May 2015.docx

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 Women's Health and Genetics/Laboratory Corporation of America, LabCorp, SCV000697356.1

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

Description

Variant summary: The PMS2 c.283T>C (p.Phe95Leu) variant involves the alteration of a conserved nucleotide. 3/4 in silico tools predict a damaging outcome for this substitution (SNPs&GO not captured due to low reliability index). This variant is absent in 114434 control chromosomes. The variant of interest has not, to our knowledge, been reported in affected individuals via publications and/or reputable databases/clinical diagnostic laboratories; nor evaluated for functional impact by in vivo/vitro studies. Because of the absence of clinical information and the lack of functional studies, the variant is classified as a variant of uncertain significance (VUS) until additional information becomes available.

#	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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