NM_000535.7(PMS2):c.1688_1689delinsAG (p.Arg563Gln) AND not provided

Germline classification:: Conflicting interpretations of pathogenicity (2 submissions)
Last evaluated:: Feb 1, 2024
Review status:: criteria provided, conflicting classifications

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:: RCV000587523.9

Allele description [Variation Report for NM_000535.7(PMS2):c.1688_1689delinsAG (p.Arg563Gln)]

NM_000535.7(PMS2):c.1688_1689delinsAG (p.Arg563Gln)

Gene:

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

Variant type:

Indel

Cytogenetic location:

7p22.1

Genomic location:

Preferred name:

NM_000535.7(PMS2):c.1688_1689delinsAG (p.Arg563Gln)

HGVS:

NC_000007.14:g.5987076_5987077delinsCT
NG_008466.1:g.27030_27031delinsAG
NM_000535.7:c.1688_1689delinsAGMANE SELECT
NM_001322003.2:c.1283_1284delinsAG
NM_001322004.2:c.1283_1284delinsAG
NM_001322005.2:c.1283_1284delinsAG
NM_001322006.2:c.1532_1533delinsAG
NM_001322007.2:c.1370_1371delinsAG
NM_001322008.2:c.1370_1371delinsAG
NM_001322009.2:c.1283_1284delinsAG
NM_001322010.2:c.1127_1128delinsAG
NM_001322011.2:c.755_756delinsAG
NM_001322012.2:c.755_756delinsAG
NM_001322013.2:c.1115_1116delinsAG
NM_001322014.2:c.1688_1689delinsAG
NM_001322015.2:c.1379_1380delinsAG
NP_000526.2:p.Arg563Gln
NP_001308932.1:p.Arg428Gln
NP_001308933.1:p.Arg428Gln
NP_001308934.1:p.Arg428Gln
NP_001308935.1:p.Arg511Gln
NP_001308936.1:p.Arg457Gln
NP_001308937.1:p.Arg457Gln
NP_001308938.1:p.Arg428Gln
NP_001308939.1:p.Arg376Gln
NP_001308940.1:p.Arg252Gln
NP_001308941.1:p.Arg252Gln
NP_001308942.1:p.Arg372Gln
NP_001308943.1:p.Arg563Gln
NP_001308944.1:p.Arg460Gln
LRG_161t1:c.1688_1689delGAinsAG
LRG_161:g.27030_27031delinsAG
NC_000007.13:g.6026707_6026708delinsCT
NM_000535.5:c.1688_1689delGAinsAG
NM_000535.6:c.1688_1689delGAinsAG
NR_136154.1:n.1775_1776delinsAG
p.R563Q

Protein change:

R252Q

Links:

dbSNP: rs587780725

NCBI 1000 Genomes Browser:

rs587780725

Molecular consequence:

NM_000535.7:c.1688_1689delinsAG - missense variant - [Sequence Ontology: SO:0001583]
NM_001322003.2:c.1283_1284delinsAG - missense variant - [Sequence Ontology: SO:0001583]
NM_001322004.2:c.1283_1284delinsAG - missense variant - [Sequence Ontology: SO:0001583]
NM_001322005.2:c.1283_1284delinsAG - missense variant - [Sequence Ontology: SO:0001583]
NM_001322006.2:c.1532_1533delinsAG - missense variant - [Sequence Ontology: SO:0001583]
NM_001322007.2:c.1370_1371delinsAG - missense variant - [Sequence Ontology: SO:0001583]
NM_001322008.2:c.1370_1371delinsAG - missense variant - [Sequence Ontology: SO:0001583]
NM_001322009.2:c.1283_1284delinsAG - missense variant - [Sequence Ontology: SO:0001583]
NM_001322010.2:c.1127_1128delinsAG - missense variant - [Sequence Ontology: SO:0001583]
NM_001322011.2:c.755_756delinsAG - missense variant - [Sequence Ontology: SO:0001583]
NM_001322012.2:c.755_756delinsAG - missense variant - [Sequence Ontology: SO:0001583]
NM_001322013.2:c.1115_1116delinsAG - missense variant - [Sequence Ontology: SO:0001583]
NM_001322014.2:c.1688_1689delinsAG - missense variant - [Sequence Ontology: SO:0001583]
NM_001322015.2:c.1379_1380delinsAG - missense variant - [Sequence Ontology: SO:0001583]
NR_136154.1:n.1775_1776delinsAG - non-coding transcript variant - [Sequence Ontology: SO:0001619]

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
SCV000806184	PreventionGenetics, part of Exact Sciences	criteria provided, single submitter (ACMG Guidelines, 2015)	Uncertain significance (Jan 15, 2018)	germline	clinical testing	PubMed (1) [See all records that cite this PMID]
SCV004704418	CeGaT Center for Human Genetics Tuebingen	criteria provided, single submitter (CeGaT Center For Human Genetics Tuebingen Variant Classification Criteria Version 2)	Likely benign (Feb 1, 2024)	germline	clinical testing	Citation Link

Submission Accession

Submitter

Review Status
(Assertion method)

Clinical Significance
(Last evaluated)

Origin

Method

Citations

SCV000806184

PreventionGenetics, part of Exact Sciences

criteria provided, single submitter

(ACMG Guidelines, 2015)

Uncertain significance
(Jan 15, 2018)

germline

clinical testing

PubMed (1)
[See all records that cite this PMID]

SCV004704418

CeGaT Center for Human Genetics Tuebingen

criteria provided, single submitter

(CeGaT Center For Human Genetics Tuebingen Variant Classification Criteria Version 2)

Likely benign
(Feb 1, 2024)

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	1	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

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 PreventionGenetics, part of Exact Sciences, SCV000806184.1

#	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, SCV004704418.2

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

Description

PMS2: BP1

#	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		1	not provided	not provided	not provided

Last Updated: Apr 15, 2024

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