ClinVar Genomic variation as it relates to human health
NM_000535.7(PMS2):c.1688G>T (p.Arg563Leu)
No data submitted for somatic clinical impact
No data submitted for oncogenicity
Variant Details
- Identifiers
-
NM_000535.7(PMS2):c.1688G>T (p.Arg563Leu)
Variation ID: 41705 Accession: VCV000041705.80
- Type and length
-
single nucleotide variant, 1 bp
- Location
-
Cytogenetic: 7p22.1 7: 5987077 (GRCh38) [ NCBI UCSC ] 7: 6026708 (GRCh37) [ NCBI UCSC ]
- Timeline in ClinVar
-
First in ClinVar Help The date this variant first appeared in ClinVar with each type of classification.
Last submission Help The date of the most recent submission for each type of classification for this variant.
Last evaluated Help The most recent date that a submitter evaluated this variant for each type of classification.
Germline Apr 12, 2013 Jul 15, 2024 Sep 5, 2013 - HGVS
-
Nucleotide Protein Molecular
consequenceNM_000535.7:c.1688G>T MANE Select Help Transcripts from the Matched Annotation from the NCBI and EMBL-EBI (MANE) collaboration.
NP_000526.2:p.Arg563Leu missense NM_001322003.2:c.1283G>T NP_001308932.1:p.Arg428Leu missense NM_001322004.2:c.1283G>T NP_001308933.1:p.Arg428Leu missense NM_001322005.2:c.1283G>T NP_001308934.1:p.Arg428Leu missense NM_001322006.2:c.1532G>T NP_001308935.1:p.Arg511Leu missense NM_001322007.2:c.1370G>T NP_001308936.1:p.Arg457Leu missense NM_001322008.2:c.1370G>T NP_001308937.1:p.Arg457Leu missense NM_001322009.2:c.1283G>T NP_001308938.1:p.Arg428Leu missense NM_001322010.2:c.1127G>T NP_001308939.1:p.Arg376Leu missense NM_001322011.2:c.755G>T NP_001308940.1:p.Arg252Leu missense NM_001322012.2:c.755G>T NP_001308941.1:p.Arg252Leu missense NM_001322013.2:c.1115G>T NP_001308942.1:p.Arg372Leu missense NM_001322014.2:c.1688G>T NP_001308943.1:p.Arg563Leu missense NM_001322015.2:c.1379G>T NP_001308944.1:p.Arg460Leu missense NR_136154.1:n.1775G>T non-coding transcript variant NC_000007.14:g.5987077C>A NC_000007.13:g.6026708C>A NG_008466.1:g.27030G>T LRG_161:g.27030G>T LRG_161t1:c.1688G>T LRG_161p1:p.Arg563Leu NP_000526.1:p.Arg563Leu - Protein change
- R563L, R372L, R460L, R428L, R376L, R457L, R252L, R511L
- Other names
- p.R563L:CGA>CTA
- Canonical SPDI
- NC_000007.14:5987076:C:A
-
Functional
consequence HelpThe effect of the variant on RNA or protein function, based on experimental evidence from submitters.
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Global minor allele
frequency (GMAF) HelpThe global minor allele frequency calculated by the 1000 Genomes Project. The minor allele at this location is indicated in parentheses and may be different from the allele represented by this VCV record.
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0.00300 (A)
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Allele frequency
Help
The frequency of the allele represented by this VCV record.
1000 Genomes Project 0.00300
1000 Genomes Project 30x 0.00328
Trans-Omics for Precision Medicine (TOPMed) 0.00665
NHLBI Exome Sequencing Project (ESP) Exome Variant Server 0.00800
Genes
Gene | OMIM | ClinGen Gene Dosage Sensitivity Curation |
Variation Viewer
Help
Links to Variation Viewer, a genome browser to view variation data from NCBI databases. |
Related variants | ||
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HI score
Help
The haploinsufficiency score for the gene, curated by ClinGen’s Dosage Sensitivity Curation task team. |
TS score
Help
The triplosensitivity score for the gene, curated by ClinGen’s Dosage Sensitivity Curation task team. |
Within gene
Help
The number of variants in ClinVar that are contained within this gene, with a link to view the list of variants. |
All
Help
The number of variants in ClinVar for this gene, including smaller variants within the gene and larger CNVs that overlap or fully contain the gene. |
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PMS2 | Sufficient evidence for dosage pathogenicity | No evidence available |
GRCh38 GRCh37 |
5179 | 5279 |
Conditions - Germline
Condition
Help
The condition for this variant-condition (RCV) record in ClinVar. |
Classification
Help
The aggregate germline classification for this variant-condition (RCV) record in ClinVar. The number of submissions that contribute to this aggregate classification is shown in parentheses. (# of submissions) |
Review status
Help
The aggregate review status for this variant-condition (RCV) record in ClinVar. This value is calculated by NCBI based on data from submitters. Read our rules for calculating the review status. |
Last evaluated
Help
The most recent date that a submitter evaluated this variant for the condition. |
Variation/condition record
Help
The RCV accession number, with most recent version number, for the variant-condition record, with a link to the RCV web page. |
---|---|---|---|---|
Benign/Likely benign (8) |
criteria provided, multiple submitters, no conflicts
|
Jul 1, 2024 | RCV000034620.46 | |
Likely benign (3) |
reviewed by expert panel
|
Sep 5, 2013 | RCV000076820.18 | |
Likely benign (1) |
no assertion criteria provided
|
Jul 24, 2014 | RCV000144651.11 | |
Benign/Likely benign (8) |
criteria provided, multiple submitters, no conflicts
|
Aug 15, 2023 | RCV000079105.36 | |
Benign (4) |
criteria provided, multiple submitters, no conflicts
|
Jun 25, 2021 | RCV000132121.13 | |
Conflicting interpretations of pathogenicity (9) |
criteria provided, conflicting classifications
|
Jul 7, 2023 | RCV000409245.27 | |
Benign (1) |
criteria provided, single submitter
|
Feb 1, 2024 | RCV001080515.15 | |
Benign (1) |
no assertion criteria provided
|
- | RCV001353968.10 | |
Likely benign (1) |
criteria provided, single submitter
|
Apr 13, 2021 | RCV001798065.10 | |
Benign (1) |
criteria provided, single submitter
|
Sep 12, 2022 | RCV003224115.8 |
Submissions - Germline
Classification
Help
The submitted germline classification for each SCV record. (Last evaluated) |
Review status
Help
Stars represent the review status, or the level of review supporting the submitted (SCV) record. This value is calculated by NCBI based on data from the submitter. Read our rules for calculating the review status. This column also includes a link to the submitter’s assertion criteria if provided, and the collection method. (Assertion criteria) |
Condition
Help
The condition for the classification, provided by the submitter for this submitted (SCV) record. This column also includes the affected status and allele origin of individuals observed with this variant. |
Submitter
Help
The submitting organization for this submitted (SCV) record. This column also includes the SCV accession and version number, the date this SCV first appeared in ClinVar, and the date that this SCV was last updated in ClinVar. |
More information
Help
This column includes more information supporting the classification, including citations, the comment on classification, and detailed evidence provided as observations of the variant by the submitter. |
|
---|---|---|---|---|---|
Likely benign
(Sep 05, 2013)
|
reviewed by expert panel
Method: research
|
Lynch Syndrome
Affected status: unknown
Allele origin:
germline
|
International Society for Gastrointestinal Hereditary Tumours (InSiGHT)
Accession: SCV000108307.3
First in ClinVar: Dec 19, 2013 Last updated: Dec 24, 2022
Comment:
Classified with v1.9 guidelines: https://docs.google.com/file/d/0B3JL6rP6JzhoN2EydHRVMEI1UGs
|
Comment:
Multifactorial likelihood analysis posterior probability 0.001-0.049
|
|
Likely benign
(Oct 09, 2014)
|
criteria provided, single submitter
Method: clinical testing
|
Lynch syndrome 4
Affected status: yes
Allele origin:
germline
|
Genome Diagnostics Laboratory, University Medical Center Utrecht
Study: VKGL Data-share Consensus
Accession: SCV000743780.1 First in ClinVar: Apr 09, 2018 Last updated: Apr 09, 2018 |
|
|
Likely benign
(May 28, 2019)
|
criteria provided, single submitter
Method: clinical testing
|
Lynch syndrome 4
Affected status: unknown
Allele origin:
unknown
|
Mendelics
Accession: SCV001137289.1
First in ClinVar: Jan 13, 2020 Last updated: Jan 13, 2020 |
|
|
Benign
(Jun 25, 2021)
|
criteria provided, single submitter
Method: curation
|
Hereditary cancer-predisposing syndrome
Affected status: unknown
Allele origin:
germline
|
Sema4, Sema4
Accession: SCV002530217.1
First in ClinVar: Jun 24, 2022 Last updated: Jun 24, 2022 |
|
|
Benign
(Nov 19, 2014)
|
criteria provided, single submitter
Method: clinical testing
|
Hereditary cancer-predisposing syndrome
Affected status: unknown
Allele origin:
germline
|
Color Diagnostics, LLC DBA Color Health
Accession: SCV000537373.1
First in ClinVar: Mar 24, 2015 Last updated: Mar 24, 2015 |
|
|
Benign
(Aug 22, 2013)
|
criteria provided, single submitter
Method: clinical testing
|
not specified
Affected status: unknown
Allele origin:
germline
|
Eurofins Ntd Llc (ga)
Accession: SCV000110974.8
First in ClinVar: Jan 17, 2014 Last updated: May 03, 2018 |
Number of individuals with the variant: 3
Sex: mixed
|
|
Uncertain significance
(Oct 19, 2018)
|
criteria provided, single submitter
Method: clinical testing
|
Lynch syndrome 4
Affected status: yes
Allele origin:
germline
|
Institute of Human Genetics, University of Leipzig Medical Center
Accession: SCV001428489.2
First in ClinVar: Aug 17, 2020 Last updated: Jul 31, 2021 |
|
|
Benign
(Jul 20, 2020)
|
criteria provided, single submitter
Method: clinical testing
|
not specified
Affected status: no
Allele origin:
germline
|
Genetic Services Laboratory, University of Chicago
Accession: SCV002069907.1
First in ClinVar: Jan 29, 2022 Last updated: Jan 29, 2022 |
|
|
Benign
(Oct 20, 2015)
|
criteria provided, single submitter
Method: clinical testing
|
Lynch syndrome
Affected status: unknown
Allele origin:
unknown
|
Genomic Diagnostic Laboratory, Division of Genomic Diagnostics, Children's Hospital of Philadelphia
Accession: SCV000296932.3
First in ClinVar: Oct 11, 2015 Last updated: Dec 24, 2022 |
|
|
Likely benign
(Jul 07, 2023)
|
criteria provided, single submitter
Method: clinical testing
|
Lynch syndrome 4
Affected status: yes
Allele origin:
germline
|
KCCC/NGS Laboratory, Kuwait Cancer Control Center
Accession: SCV004016591.1
First in ClinVar: Jul 29, 2023 Last updated: Jul 29, 2023 |
|
|
Benign
(May 11, 2023)
|
criteria provided, single submitter
Method: clinical testing
|
Lynch syndrome 4
Affected status: unknown
Allele origin:
unknown
|
Myriad Genetics, Inc.
Accession: SCV004044332.2
First in ClinVar: Oct 21, 2023 Last updated: Oct 28, 2023 |
Comment:
This variant is considered benign. This variant has been observed at a population frequency that is significantly greater than expected given the associated disease prevalence … (more)
This variant is considered benign. This variant has been observed at a population frequency that is significantly greater than expected given the associated disease prevalence and penetrance. (less)
|
|
Benign
(Nov 07, 2023)
|
criteria provided, single submitter
Method: clinical testing
|
not provided
Affected status: unknown
Allele origin:
germline
|
ARUP Laboratories, Molecular Genetics and Genomics, ARUP Laboratories
Accession: SCV000884396.6
First in ClinVar: May 29, 2016 Last updated: Feb 20, 2024 |
|
|
Benign
(Feb 05, 2024)
|
criteria provided, single submitter
Method: clinical testing
|
Lynch syndrome
(Autosomal dominant inheritance)
Affected status: unknown
Allele origin:
germline
|
All of Us Research Program, National Institutes of Health
Accession: SCV004844154.1
First in ClinVar: Apr 20, 2024 Last updated: Apr 20, 2024
Comment:
This study involves interpretation of variants in research participants for the purpose of population health screening. Participant phenotype was not available at the time of … (more)
This study involves interpretation of variants in research participants for the purpose of population health screening. Participant phenotype was not available at the time of variant classification. Additional details can be found in publication PMID: 35346344, PMCID: PMC8962531 (less)
|
Number of individuals with the variant: 1855
|
|
Benign
(Nov 18, 2014)
|
criteria provided, single submitter
Method: clinical testing
|
Hereditary cancer-predisposing syndrome
Affected status: unknown
Allele origin:
germline
|
Ambry Genetics
Accession: SCV000187189.8
First in ClinVar: Aug 06, 2014 Last updated: May 01, 2024 |
Comment:
This alteration is classified as benign based on a combination of the following: seen in unaffected individuals, population frequency, intact protein function, lack of segregation … (more)
This alteration is classified as benign based on a combination of the following: seen in unaffected individuals, 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. (less)
|
|
Likely benign
(Apr 25, 2016)
|
criteria provided, single submitter
Method: clinical testing
|
not specified
Affected status: unknown
Allele origin:
germline
|
Laboratory for Molecular Medicine, Mass General Brigham Personalized Medicine
Accession: SCV000540066.1
First in ClinVar: Jun 28, 2015 Last updated: Jun 28, 2015 |
Comment:
Variant identified in a genome or exome case(s) and assessed due to predicted null impact of the variant or pathogenic assertions in the literature or … (more)
Variant identified in a genome or exome case(s) and assessed due to predicted null impact of the variant or pathogenic assertions in the literature or databases. Disclaimer: This variant has not undergone full assessment. The following are preliminary notes: No convincing evidence in HGMD, ExAC: 0.8% (541/66472) European chromosomes (less)
Method: Genome/Exome Filtration
|
|
Benign
(Oct 18, 2013)
|
criteria provided, single submitter
Method: clinical testing
|
not specified
Affected status: yes
Allele origin:
germline
|
GeneDx
Accession: SCV000171032.10
First in ClinVar: Jun 23, 2014 Last updated: Feb 19, 2018 |
Comment:
This variant is considered likely benign or benign based on one or more of the following criteria: it is a conservative change, it occurs at … (more)
This variant is considered likely benign or benign based on one or more of the following criteria: it is a conservative change, it occurs at a poorly conserved position in the protein, it is predicted to be benign by multiple in silico algorithms, and/or has population frequency not consistent with disease. (less)
|
|
Benign
(Jan 30, 2017)
|
criteria provided, single submitter
Method: clinical testing
|
not specified
Affected status: unknown
Allele origin:
germline
|
PreventionGenetics, part of Exact Sciences
Accession: SCV000806185.1
First in ClinVar: May 03, 2018 Last updated: May 03, 2018 |
|
|
Benign
(Apr 27, 2017)
|
criteria provided, single submitter
Method: clinical testing
|
Lynch syndrome 4
Affected status: unknown
Allele origin:
germline
|
Illumina Laboratory Services, Illumina
Accession: SCV001320991.1
First in ClinVar: May 31, 2020 Last updated: May 31, 2020 |
Comment:
This variant was observed as part of a predisposition screen in an ostensibly healthy population. A literature search was performed for the gene, cDNA change, … (more)
This variant was observed as part of a predisposition screen in an ostensibly healthy population. A literature search was performed for the gene, cDNA change, and amino acid change (where applicable). Publications were found based on this search. The evidence from the literature, in combination with allele frequency data from public databases where available, was sufficient to rule this variant out of causing disease. Therefore, this variant is classified as benign. (less)
|
|
Likely benign
(Apr 13, 2021)
|
criteria provided, single submitter
Method: clinical testing
|
Breast and/or ovarian cancer
Affected status: unknown
Allele origin:
germline
|
CHEO Genetics Diagnostic Laboratory, Children's Hospital of Eastern Ontario
Accession: SCV002042788.1
First in ClinVar: Jan 01, 2022 Last updated: Jan 01, 2022 |
|
|
Likely benign
(Jun 01, 2016)
|
criteria provided, single submitter
Method: clinical testing
|
Lynch syndrome 4
Affected status: unknown
Allele origin:
unknown
|
Counsyl
Accession: SCV000488713.2
First in ClinVar: Jan 09, 2017 Last updated: Dec 24, 2022 |
|
|
Benign
(Sep 12, 2022)
|
criteria provided, single submitter
Method: clinical testing
|
Lynch syndrome 4
Mismatch repair cancer syndrome 4
Affected status: unknown
Allele origin:
germline
|
Center for Genomics, Ann and Robert H. Lurie Children's Hospital of Chicago
Accession: SCV003920333.1
First in ClinVar: Apr 30, 2023 Last updated: Apr 30, 2023 |
Comment:
This variant has been reported in association with cancer (Clendenning 2006 PMID: 16619239). This variant is present in the Genome Aggregation Database (Highest reported MAF: … (more)
This variant has been reported in association with cancer (Clendenning 2006 PMID: 16619239). This variant is present in the Genome Aggregation Database (Highest reported MAF: 1.0% [157/15246], and in 3 homozygotes; https://gnomad.broadinstitute.org/variant/7-5987077-C-A?dataset=gnomad_r3). This variant is also present in ClinVar, with numerous laboratories classifying it as benign or likely benign, including as likely benign by the InSiGHT expert panel (Variation ID: 41705). Evolutionary conservation and computational predictive tools suggest that this variant may not impact the protein. In summary, this variant is classified as benign. (less)
|
|
Likely benign
(Nov 03, 2021)
|
criteria provided, single submitter
Method: clinical testing
|
not provided
Affected status: not provided
Allele origin:
germline
|
Institute for Clinical Genetics, University Hospital TU Dresden, University Hospital TU Dresden
Accession: SCV002009110.3
First in ClinVar: Nov 06, 2021 Last updated: Jul 16, 2023 |
|
|
Likely benign
(Aug 15, 2023)
|
criteria provided, single submitter
Method: clinical testing
|
not specified
Affected status: unknown
Allele origin:
germline
|
Center for Genomic Medicine, Rigshospitalet, Copenhagen University Hospital
Accession: SCV002550705.4
First in ClinVar: Jul 30, 2022 Last updated: Aug 18, 2023 |
|
|
Benign
(Feb 01, 2024)
|
criteria provided, single submitter
Method: clinical testing
|
Hereditary nonpolyposis colorectal neoplasms
Affected status: unknown
Allele origin:
germline
|
Invitae
Accession: SCV000153923.14
First in ClinVar: Jun 03, 2014 Last updated: Feb 20, 2024 |
|
|
Likely benign
(Jul 01, 2024)
|
criteria provided, single submitter
Method: clinical testing
|
not provided
Affected status: yes
Allele origin:
germline
|
CeGaT Center for Human Genetics Tuebingen
Accession: SCV001155029.24
First in ClinVar: Feb 03, 2020 Last updated: Jul 15, 2024 |
Comment:
PMS2: BP4, BS2
Number of individuals with the variant: 66
|
|
no known pathogenicity
(Jul 13, 2012)
|
no assertion criteria provided
Method: research
|
not provided
Affected status: no
Allele origin:
germline
|
Biesecker Lab/Clinical Genomics Section, National Institutes of Health
Study: ClinSeq
Accession: SCV000043424.1 First in ClinVar: Apr 12, 2013 Last updated: Apr 12, 2013 |
Comment:
Converted during submission to Benign.
Number of individuals with the variant: 14
Comment on evidence:
The study set was not selected for affection status in relation to any cancer. Pathogenicity categories were based on literature curation. See Pubmed ID:22703879 for … (more)
The study set was not selected for affection status in relation to any cancer. Pathogenicity categories were based on literature curation. See Pubmed ID:22703879 for details. (less)
|
|
Likely benign
(Jul 24, 2014)
|
no assertion criteria provided
Method: clinical testing
|
Lynch syndrome I
Affected status: unknown
Allele origin:
germline
|
Pathway Genomics
Accession: SCV000189978.1
First in ClinVar: Oct 19, 2014 Last updated: Oct 19, 2014 |
|
|
Likely benign
(-)
|
no assertion criteria provided
Method: clinical testing
|
not specified
Affected status: unknown
Allele origin:
unknown
|
Mayo Clinic Laboratories, Mayo Clinic
Accession: SCV000691967.1
First in ClinVar: Feb 19, 2018 Last updated: Feb 19, 2018 |
|
|
Benign
(May 04, 2015)
|
no assertion criteria provided
Method: clinical testing
|
Lynch syndrome 4
Affected status: yes
Allele origin:
germline
|
Genome Diagnostics Laboratory, Amsterdam University Medical Center
Study: VKGL Data-share Consensus
Accession: SCV000745839.1 First in ClinVar: Apr 09, 2018 Last updated: Apr 09, 2018 |
|
|
Benign
(-)
|
no assertion criteria provided
Method: clinical testing
|
Endometrial carcinoma
Affected status: yes
Allele origin:
unknown
|
Department of Pathology and Laboratory Medicine, Sinai Health System
Additional submitter:
Franklin by Genoox
Study: The Canadian Open Genetics Repository (COGR)
Accession: SCV000592939.2 First in ClinVar: Jun 28, 2015 Last updated: Apr 13, 2021 |
Comment:
PMS2, EXON 11, c.1688G>T, p. Arg563Leu, Benign (ACMG 5) The PMS2 p.Arg563Leu variant was identified in 5 of 416 proband chromosomes (frequency: 0.012) from individuals … (more)
PMS2, EXON 11, c.1688G>T, p. Arg563Leu, Benign (ACMG 5) The PMS2 p.Arg563Leu variant was identified in 5 of 416 proband chromosomes (frequency: 0.012) from individuals or families with Lynch Syndrome (16472587_Hendriks_2006, 16619239_Clendenning_2006, 24027009_Drost_2014, 24689082_Hansen_2014). The variant was also identified in dbSNP (ID: rs63750668) “With likely benign, uncertain significance allele”, with a minor allele frequency of 0.003 (1000 Genomes Project), HGMD, COSMIC, “Mismatch Repair Genes Variant Database”, and “InSiGHT Colon Cancer Database”. The variant was classified as a benign/likely benign variant by the Sharing Clinical Reports Project (SCRP) (submitted within the ClinVar database and derived from Myriad reports). The variant was classified as “unclassified” by a clinical laboratory within the Canadian Open Genetics Repository (http://opengenetics.ca/). This variant was identified in the 1000 Genomes Project in 17 of 2178 chromosomes (frequency: 0.0014), and Exome Variant Server project in 86 of 8600 European American (frequency: 0.01) and 18 of 4406 African American alleles (frequency: 0.004), increasing the likelihood that this is/may be a low frequency benign variant in certain populations of origin. The p.Arg563 residue is not conserved in mammals and the variant amino acid Leucine (Leu) is present in Ciona intestinalis, increasing the likelihood that this variant does not have clinical significance. The p.Arg563 residue is not conserved in mammals and computational analyses (PolyPhen-2, SIFT, AlignGVGD, BLOSUM, MutationTaster) do not suggest a high likelihood of impact to the protein. However, this information is not predictive enough to rule out pathogenicity. Computational analyses (PolyPhen-2, SIFT, AlignGVGD, BLOSUM, MutationTaster) do not suggest a high likelihood of impact to the protein. The DNA NOMENCLATURE variant occurs outside of the splicing consensus sequence and in silico or computational prediction software (SpliceSiteFinder, MaxEntScan, NNSPLICE, GeneSplicer, HumanSpliceFinder) does not predict a difference in splicing in 5 of 5 different programs. (However, this information is not predictive enough to rule out pathogenicity.) In summary, based on the above information, this variant meets our laboratory's criteria to be classified as benign. (less)
|
|
Likely benign
(-)
|
no assertion criteria provided
Method: clinical testing
|
not provided
Affected status: yes
Allele origin:
germline
|
Laboratory of Diagnostic Genome Analysis, Leiden University Medical Center (LUMC)
Study: VKGL Data-share Consensus
Accession: SCV001798367.1 First in ClinVar: Aug 21, 2021 Last updated: Aug 21, 2021 |
|
|
Likely benign
(-)
|
no assertion criteria provided
Method: clinical testing
|
not provided
Affected status: yes
Allele origin:
germline
|
Joint Genome Diagnostic Labs from Nijmegen and Maastricht, Radboudumc and MUMC+
Additional submitter:
Diagnostic Laboratory, Department of Genetics, University Medical Center Groningen
Study: VKGL Data-share Consensus
Accession: SCV001953076.1 First in ClinVar: Oct 02, 2021 Last updated: Oct 02, 2021 |
|
|
Likely benign
(-)
|
no assertion criteria provided
Method: clinical testing
|
not provided
Affected status: yes
Allele origin:
germline
|
Clinical Genetics Laboratory, Department of Pathology, Netherlands Cancer Institute
Additional submitter:
Diagnostic Laboratory, Department of Genetics, University Medical Center Groningen
Study: VKGL Data-share Consensus
Accession: SCV001977631.1 First in ClinVar: Oct 16, 2021 Last updated: Oct 16, 2021 |
|
|
Likely benign
(-)
|
no assertion criteria provided
Method: clinical testing
|
Lynch syndrome 4
Affected status: yes
Allele origin:
germline
|
Diagnostic Laboratory, Department of Genetics, University Medical Center Groningen
Study: VKGL Data-share Consensus
Accession: SCV000734563.1 First in ClinVar: Apr 09, 2018 Last updated: Apr 09, 2018 |
|
|
Likely benign
(Dec 08, 2017)
|
no assertion criteria provided
Method: clinical testing
|
Hereditary cancer-predisposing syndrome
Affected status: unknown
Allele origin:
germline
|
True Health Diagnostics
Accession: SCV000788107.1
First in ClinVar: Mar 24, 2015 Last updated: Mar 24, 2015 |
|
|
Likely benign
(-)
|
no assertion criteria provided
Method: clinical testing
|
not provided
Affected status: yes
Allele origin:
germline
|
Clinical Genetics, Academic Medical Center
Additional submitter:
Diagnostic Laboratory, Department of Genetics, University Medical Center Groningen
Study: VKGL Data-share Consensus
Accession: SCV001920777.1 First in ClinVar: Sep 26, 2021 Last updated: Sep 26, 2021 |
|
|
not provided
(Sep 19, 2013)
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no classification provided
Method: reference population
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AllHighlyPenetrant
Affected status: unknown
Allele origin:
germline
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ITMI
Accession: SCV000086050.1
First in ClinVar: Jun 09, 2014 Last updated: Jun 09, 2014
Comment:
Please see associated publication for description of ethnicities
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Observation 1:
Ethnicity/Population group: Whole_cohort
Observation 2:
Ethnicity/Population group: African
Observation 3:
Ethnicity/Population group: African_European
Observation 4:
Ethnicity/Population group: Central_Asian
Observation 5:
Ethnicity/Population group: East_Asian
Observation 6:
Ethnicity/Population group: European
Observation 7:
Ethnicity/Population group: Hispanic
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Germline Functional Evidence
There is no functional evidence in ClinVar for this variation. If you have generated functional data for this variation, please consider submitting that data to ClinVar. |
Citations for germline classification of this variant
HelpTitle | Author | Journal | Year | Link |
---|---|---|---|---|
Prevalence of Pathogenic Mutations in Cancer Predisposition Genes among Pancreatic Cancer Patients. | Hu C | Cancer epidemiology, biomarkers & prevention : a publication of the American Association for Cancer Research, cosponsored by the American Society of Preventive Oncology | 2016 | PMID: 26483394 |
Germline variation in cancer-susceptibility genes in a healthy, ancestrally diverse cohort: implications for individual genome sequencing. | Bodian DL | PloS one | 2014 | PMID: 24728327 |
A massive parallel sequencing workflow for diagnostic genetic testing of mismatch repair genes. | Hansen MF | Molecular genetics & genomic medicine | 2014 | PMID: 24689082 |
Inactivation of DNA mismatch repair by variants of uncertain significance in the PMS2 gene. | Drost M | Human mutation | 2013 | PMID: 24027009 |
Refining the role of PMS2 in Lynch syndrome: germline mutational analysis improved by comprehensive assessment of variants. | Borràs E | Journal of medical genetics | 2013 | PMID: 23709753 |
Secondary variants in individuals undergoing exome sequencing: screening of 572 individuals identifies high-penetrance mutations in cancer-susceptibility genes. | Johnston JJ | American journal of human genetics | 2012 | PMID: 22703879 |
PMS2 involvement in patients suspected of Lynch syndrome. | Niessen RC | Genes, chromosomes & cancer | 2009 | PMID: 19132747 |
Long-range PCR facilitates the identification of PMS2-specific mutations. | Clendenning M | Human mutation | 2006 | PMID: 16619239 |
Heterozygous mutations in PMS2 cause hereditary nonpolyposis colorectal carcinoma (Lynch syndrome). | Hendriks YM | Gastroenterology | 2006 | PMID: 16472587 |
Genetic polymorphisms of bilirubin uridine diphosphate-glucuronosyltransferase gene in Japanese patients with Crigler-Najjar syndrome or Gilbert's syndrome as well as in healthy Japanese subjects. | Takeuchi K | Journal of gastroenterology and hepatology | 2004 | PMID: 15304120 |
Structure of human succinic semialdehyde dehydrogenase gene: identification of promoter region and alternatively processed isoforms. | Blasi P | Molecular genetics and metabolism | 2002 | PMID: 12208142 |
http://chromium.liacs.nl/LOVD2/colon_cancer/variants.php?select_db=PMS2&action=search_all&search_Variant%2FDNA=c.1688G%3ET | - | - | - | - |
http://www.egl-eurofins.com/emvclass/emvclass.php?approved_symbol=PMS2 | - | - | - | - |
http://www.insight-database.org/classifications/index.html?gene=PMS2&variant=c.1688G%3ET | - | - | - | - |
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Text-mined citations for rs63750668 ...
HelpRecord last updated Jul 15, 2024
This date represents the last time this VCV record was updated. The update may be due to an update to one of the included submitted records (SCVs), or due to an update that ClinVar made to the variant such as adding HGVS expressions or a rs number. So this date may be different from the date of the “most recent submission” reported at the top of this page.