ClinVar Genomic variation as it relates to human health
NM_000535.7(PMS2):c.632G>C (p.Arg211Pro)
The aggregate germline classification for this variant, typically for a monogenic or Mendelian disorder as in the ACMG/AMP guidelines, or for response to a drug. This value is calculated by NCBI based on data from submitters. Read our rules for calculating the aggregate classification.
Stars represent the aggregate review status, or the level of review supporting the aggregate germline classification for this VCV record. This value is calculated by NCBI based on data from submitters. Read our rules for calculating the review status. The number of submissions which contribute to this review status is shown in parentheses.
No data submitted for somatic clinical impact
No data submitted for oncogenicity
Variant Details
- Identifiers
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NM_000535.7(PMS2):c.632G>C (p.Arg211Pro)
Variation ID: 2898126 Accession: VCV002898126.1
- Type and length
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single nucleotide variant, 1 bp
- Location
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Cytogenetic: 7p22.1 7: 5999181 (GRCh38) [ NCBI UCSC ] 7: 6038812 (GRCh37) [ NCBI UCSC ]
- Timeline in ClinVar
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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 Feb 20, 2024 Feb 20, 2024 Apr 15, 2023 - HGVS
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Nucleotide Protein Molecular
consequenceNM_000535.7:c.632G>C MANE Select Help Transcripts from the Matched Annotation from the NCBI and EMBL-EBI (MANE) collaboration.
NP_000526.2:p.Arg211Pro missense NM_001018040.1:c.227G>C NP_001018050.1:p.Arg76Pro missense NM_001322003.2:c.227G>C NP_001308932.1:p.Arg76Pro missense NM_001322004.2:c.227G>C NP_001308933.1:p.Arg76Pro missense NM_001322005.2:c.227G>C NP_001308934.1:p.Arg76Pro missense NM_001322006.2:c.632G>C NP_001308935.1:p.Arg211Pro missense NM_001322007.2:c.314G>C NP_001308936.1:p.Arg105Pro missense NM_001322008.2:c.314G>C NP_001308937.1:p.Arg105Pro missense NM_001322009.2:c.227G>C NP_001308938.1:p.Arg76Pro missense NM_001322010.2:c.227G>C NP_001308939.1:p.Arg76Pro missense NM_001322011.2:c.-302G>C 5 prime UTR NM_001322012.2:c.-302G>C 5 prime UTR NM_001322013.2:c.133-1758G>C intron variant NM_001322014.2:c.632G>C NP_001308943.1:p.Arg211Pro missense NM_001322015.2:c.323G>C NP_001308944.1:p.Arg108Pro missense NM_001406866.1:c.818G>C NP_001393795.1:p.Arg273Pro missense NM_001406868.1:c.656G>C NP_001393797.1:p.Arg219Pro missense NM_001406869.1:c.597+35G>C intron variant NM_001406870.1:c.632G>C NP_001393799.1:p.Arg211Pro missense NM_001406871.1:c.632G>C NP_001393800.1:p.Arg211Pro missense NM_001406872.1:c.632G>C NP_001393801.1:p.Arg211Pro missense NM_001406873.1:c.632G>C NP_001393802.1:p.Arg211Pro missense NM_001406874.1:c.538-1758G>C intron variant NM_001406875.1:c.323G>C NP_001393804.1:p.Arg108Pro missense NM_001406876.1:c.314G>C NP_001393805.1:p.Arg105Pro missense NM_001406877.1:c.323G>C NP_001393806.1:p.Arg108Pro missense NM_001406878.1:c.323G>C NP_001393807.1:p.Arg108Pro missense NM_001406879.1:c.323G>C NP_001393808.1:p.Arg108Pro missense NM_001406880.1:c.323G>C NP_001393809.1:p.Arg108Pro missense NM_001406881.1:c.323G>C NP_001393810.1:p.Arg108Pro missense NM_001406882.1:c.323G>C NP_001393811.1:p.Arg108Pro missense NM_001406883.1:c.314G>C NP_001393812.1:p.Arg105Pro missense NM_001406884.1:c.538-1758G>C intron variant NM_001406885.1:c.296G>C NP_001393814.1:p.Arg99Pro missense NM_001406886.1:c.537+3272G>C intron variant NM_001406887.1:c.227G>C NP_001393816.1:p.Arg76Pro missense NM_001406888.1:c.227G>C NP_001393817.1:p.Arg76Pro missense NM_001406889.1:c.227G>C NP_001393818.1:p.Arg76Pro missense NM_001406890.1:c.227G>C NP_001393819.1:p.Arg76Pro missense NM_001406891.1:c.227G>C NP_001393820.1:p.Arg76Pro missense NM_001406892.1:c.227G>C NP_001393821.1:p.Arg76Pro missense NM_001406893.1:c.227G>C NP_001393822.1:p.Arg76Pro missense NM_001406894.1:c.227G>C NP_001393823.1:p.Arg76Pro missense NM_001406895.1:c.227G>C NP_001393824.1:p.Arg76Pro missense NM_001406896.1:c.227G>C NP_001393825.1:p.Arg76Pro missense NM_001406897.1:c.227G>C NP_001393826.1:p.Arg76Pro missense NM_001406898.1:c.227G>C NP_001393827.1:p.Arg76Pro missense NM_001406899.1:c.227G>C NP_001393828.1:p.Arg76Pro missense NM_001406900.1:c.323G>C NP_001393829.1:p.Arg108Pro missense NM_001406901.1:c.314G>C NP_001393830.1:p.Arg105Pro missense NM_001406902.1:c.314G>C NP_001393831.1:p.Arg105Pro missense NM_001406903.1:c.314G>C NP_001393832.1:p.Arg105Pro missense NM_001406904.1:c.192+35G>C intron variant NM_001406905.1:c.192+35G>C intron variant NM_001406906.1:c.227G>C NP_001393835.1:p.Arg76Pro missense NM_001406907.1:c.227G>C NP_001393836.1:p.Arg76Pro missense NM_001406908.1:c.227G>C NP_001393837.1:p.Arg76Pro missense NM_001406909.1:c.133-1758G>C intron variant NM_001406910.1:c.227G>C NP_001393839.1:p.Arg76Pro missense NM_001406911.1:c.132+3272G>C intron variant NM_001406912.1:c.632G>C NP_001393841.1:p.Arg211Pro missense NR_003085.2:n.714G>C NR_136154.1:n.719G>C non-coding transcript variant NC_000007.14:g.5999181C>G NC_000007.13:g.6038812C>G NG_008466.1:g.14926G>C LRG_161:g.14926G>C LRG_161t1:c.632G>C LRG_161p1:p.Arg211Pro - Protein change
- R211P, R76P, R219P, R99P, R108P, R273P, R105P
- Other names
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- Canonical SPDI
- NC_000007.14:5999180:C:G
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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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Allele frequency
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The frequency of the allele represented by this VCV record.
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- Links
Genes
Gene | OMIM | ClinGen Gene Dosage Sensitivity Curation |
Variation Viewer
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Links to Variation Viewer, a genome browser to view variation data from NCBI databases. |
Related variants | ||
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HI score
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The haploinsufficiency score for the gene, curated by ClinGen’s Dosage Sensitivity Curation task team. |
TS score
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The triplosensitivity score for the gene, curated by ClinGen’s Dosage Sensitivity Curation task team. |
Within gene
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The number of variants in ClinVar that are contained within this gene, with a link to view the list of variants. |
All
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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 |
5240 | 5342 |
Conditions - Germline
Condition
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The condition for this variant-condition (RCV) record in ClinVar. |
Classification
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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
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The most recent date that a submitter evaluated this variant for the condition. |
Variation/condition record
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The RCV accession number, with most recent version number, for the variant-condition record, with a link to the RCV web page. |
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Uncertain significance (1) |
criteria provided, single submitter
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Apr 15, 2023 | RCV003760292.2 |
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
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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
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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
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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. |
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Uncertain significance
(Apr 15, 2023)
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criteria provided, single submitter
Method: clinical testing
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Hereditary nonpolyposis colorectal neoplasms
Affected status: unknown
Allele origin:
germline
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Labcorp Genetics (formerly Invitae), Labcorp
Accession: SCV004525214.1
First in ClinVar: Feb 20, 2024 Last updated: Feb 20, 2024 |
Comment:
In summary, the available evidence is currently insufficient to determine the role of this variant in disease. Therefore, it has been classified as a Variant … (more)
In summary, the available evidence is currently insufficient to determine the role of this variant in disease. Therefore, it has been classified as a Variant of Uncertain Significance. Advanced modeling of protein sequence and biophysical properties (such as structural, functional, and spatial information, amino acid conservation, physicochemical variation, residue mobility, and thermodynamic stability) performed at Invitae indicates that this missense variant is expected to disrupt PMS2 protein function. This variant has not been reported in the literature in individuals affected with PMS2-related conditions. This variant is not present in population databases (gnomAD no frequency). This sequence change replaces arginine, which is basic and polar, with proline, which is neutral and non-polar, at codon 211 of the PMS2 protein (p.Arg211Pro). (less)
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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
HelpThere are no citations for germline classification of this variant in ClinVar. If you know of citations for this variation, please consider submitting that information to ClinVar. |
Text-mined citations for this variant ...
HelpRecord last updated Sep 30, 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.