NM_000535.7(PMS2):c.2156del (p.Gln719fs) AND not provided

Germline classification:: Pathogenic (2 submissions)
Last evaluated:: May 26, 2017
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:: RCV000482434.5

Allele description [Variation Report for NM_000535.7(PMS2):c.2156del (p.Gln719fs)]

NM_000535.7(PMS2):c.2156del (p.Gln719fs)

Gene:

PMS2:PMS1 homolog 2, mismatch repair system component [Gene - OMIM - HGNC]

Variant type:

Deletion

Cytogenetic location:

7p22.1

Genomic location:

Preferred name:

NM_000535.7(PMS2):c.2156del (p.Gln719fs)

HGVS:

NC_000007.14:g.5982842del
NG_008466.1:g.31265del
NM_000535.7:c.2156delMANE SELECT
NM_001322003.2:c.1751del
NM_001322004.2:c.1751del
NM_001322005.2:c.1751del
NM_001322006.2:c.2000del
NM_001322007.2:c.1838del
NM_001322008.2:c.1838del
NM_001322009.2:c.1751del
NM_001322010.2:c.1595del
NM_001322011.2:c.1223del
NM_001322012.2:c.1223del
NM_001322013.2:c.1583del
NM_001322014.2:c.2156del
NM_001322015.2:c.1847del
NP_000526.2:p.Gln719fs
NP_001308932.1:p.Gln584fs
NP_001308933.1:p.Gln584fs
NP_001308934.1:p.Gln584fs
NP_001308935.1:p.Gln667fs
NP_001308936.1:p.Gln613fs
NP_001308937.1:p.Gln613fs
NP_001308938.1:p.Gln584fs
NP_001308939.1:p.Gln532fs
NP_001308940.1:p.Gln408fs
NP_001308941.1:p.Gln408fs
NP_001308942.1:p.Gln528fs
NP_001308943.1:p.Gln719fs
NP_001308944.1:p.Gln616fs
LRG_161t1:c.2156del
LRG_161:g.31265del
NC_000007.13:g.6022473del
NM_000535.5:c.2156delA
NM_000535.6:c.2156delA
NR_136154.1:n.2243del
p.Q719Rfs*6

Protein change:

Q408fs

Links:

dbSNP: rs786201062

NCBI 1000 Genomes Browser:

rs786201062

Molecular consequence:

NM_000535.7:c.2156del - frameshift variant - [Sequence Ontology: SO:0001589]
NM_001322003.2:c.1751del - frameshift variant - [Sequence Ontology: SO:0001589]
NM_001322004.2:c.1751del - frameshift variant - [Sequence Ontology: SO:0001589]
NM_001322005.2:c.1751del - frameshift variant - [Sequence Ontology: SO:0001589]
NM_001322006.2:c.2000del - frameshift variant - [Sequence Ontology: SO:0001589]
NM_001322007.2:c.1838del - frameshift variant - [Sequence Ontology: SO:0001589]
NM_001322008.2:c.1838del - frameshift variant - [Sequence Ontology: SO:0001589]
NM_001322009.2:c.1751del - frameshift variant - [Sequence Ontology: SO:0001589]
NM_001322010.2:c.1595del - frameshift variant - [Sequence Ontology: SO:0001589]
NM_001322011.2:c.1223del - frameshift variant - [Sequence Ontology: SO:0001589]
NM_001322012.2:c.1223del - frameshift variant - [Sequence Ontology: SO:0001589]
NM_001322013.2:c.1583del - frameshift variant - [Sequence Ontology: SO:0001589]
NM_001322014.2:c.2156del - frameshift variant - [Sequence Ontology: SO:0001589]
NM_001322015.2:c.1847del - frameshift variant - [Sequence Ontology: SO:0001589]
NR_136154.1:n.2243del - non-coding transcript variant - [Sequence Ontology: SO:0001619]

Condition(s)

Synonyms:: none provided
Identifiers:: MedGen: C3661900

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Chlorocebus sabaeus isolate 1994-021 Contig9.15486, whole genome shotgun sequenc...
Chlorocebus sabaeus isolate 1994-021 Contig9.15486, whole genome shotgun sequence
gi|501820002|gb|AQIB01073256.1||gnl AQIB01|Contig9.15486

Nucleotide

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Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV000565837	GeneDx	criteria provided, single submitter (GeneDx Variant Classification (06012015))	Pathogenic (Jan 19, 2017)	germline	clinical testing	Citation Link,
SCV000806200	PreventionGenetics, part of Exact Sciences	criteria provided, single submitter (ACMG Guidelines, 2015)	Pathogenic (May 26, 2017)	germline	clinical testing	PubMed (1) [See all records that cite this PMID]

Submission Accession

Submitter

Review Status
(Assertion method)

Clinical Significance
(Last evaluated)

Origin

Method

Citations

SCV000565837

GeneDx

criteria provided, single submitter

(GeneDx Variant Classification (06012015))

Pathogenic
(Jan 19, 2017)

germline

clinical testing

Citation Link,

SCV000806200

PreventionGenetics, part of Exact Sciences

criteria provided, single submitter

(ACMG Guidelines, 2015)

Pathogenic
(May 26, 2017)

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	unknown	not provided	not provided	not provided	not provided	not provided	clinical testing
not provided	germline	yes	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

Details of each submission

From GeneDx, SCV000565837.5

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

Description

This deletion of one nucleotide in PMS2 is denoted c.2156delA at the cDNA level and p.Gln719ArgfsX6 (Q719RfsX6) at the protein level. The normal sequence, with the base that is deleted in brackets, is CTCC[delA]GGGGC. The deletion causes a frameshift, which changes a Glutamine to an Arginine at codon 719, and creates a premature stop codon at position 6 of the new reading frame. This variant is predicted to cause loss of normal protein function through either protein truncation or nonsense-mediated mRNA decay. PMS2 c.2156delA has been reported in association with Lynch syndrome (Suerink 2015). We consider this variant to be pathogenic.

#	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 PreventionGenetics, part of Exact Sciences, SCV000806200.1

#	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

Last Updated: Aug 11, 2024

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