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NM_000535.7(PMS2):c.1688_1689delinsAG (p.Arg563Gln) AND Hereditary cancer-predisposing syndrome

Germline classification:
Likely benign (2 submissions)
Last evaluated:
Sep 13, 2021
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:
RCV000132456.10

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:
1

Condition(s)

Name:
Hereditary cancer-predisposing syndrome
Synonyms:
Neoplastic Syndromes, Hereditary; Tumor predisposition; Cancer predisposition; See all synonyms [MedGen]
Identifiers:
MONDO: MONDO:0015356; MeSH: D009386; MedGen: C0027672

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Assertion and evidence details

Help
Submission AccessionSubmitterReview Status
(Assertion method)		Clinical Significance
(Last evaluated)		OriginMethodCitations
SCV000187550Ambry Genetics
criteria provided, single submitter

(Ambry General Variant Classification Scheme_2022)		Likely benign
(May 5, 2021) 		germlineclinical testing

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

Citation Link,

SCV000902632Color Diagnostics, LLC DBA Color Health
criteria provided, single submitter

(ACMG Guidelines, 2015)		Likely benign
(Sep 13, 2021) 		germlineclinical testing

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

Help

Summary from all submissions

EthnicityOriginAffectedIndividualsFamiliesChromosomes testedNumber TestedFamily historyMethod
not providedgermlineunknown1not providednot provided1not providedclinical testing

Citations

PubMed

Clinical genetic testing outcome with multi-gene panel in Asian patients with multiple primary cancers.

Chan GHJ, Ong PY, Low JJH, Kong HL, Ow SGW, Tan DSP, Lim YW, Lim SE, Lee SC.

Oncotarget. 2018 Jul 17;9(55):30649-30660. doi: 10.18632/oncotarget.25769.

PubMed [citation]
PMID:
30093976
PMCID:
PMC6078133

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 Ambry Genetics, SCV000187550.7

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1not provided1not providednot providedclinical testing PubMed (1)

Description

This alteration is classified as likely benign based on a combination of the following: population frequency, intact protein function, lack of segregation with disease, co-occurrence, RNA analysis, in silico models, amino acid conservation, lack of disease association in case-control studies, and/or the mechanism of disease or impacted region is inconsistent with a known cause of pathogenicity.

#SampleMethodObservation
OriginAffectedNumber testedTissuePurposeMethodIndividualsAllele frequencyFamiliesCo-occurrences
1germlineunknown1not providednot provided1not providednot providednot provided

From Color Diagnostics, LLC DBA Color Health, SCV000902632.2

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1not providednot providednot providednot providedclinical testing PubMed (1)
#SampleMethodObservation
OriginAffectedNumber testedTissuePurposeMethodIndividualsAllele frequencyFamiliesCo-occurrences
1germlineunknownnot providednot providednot providednot providednot providednot providednot provided

Last Updated: Apr 15, 2024