ClinVar Genomic variation as it relates to human health
NM_000535.7(PMS2):c.2587T>C (p.Ter863Arg)
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.2587T>C (p.Ter863Arg)
Variation ID: 1793444 Accession: VCV001793444.2
- Type and length
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single nucleotide variant, 1 bp
- Location
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Cytogenetic: 7p22.1 7: 5973401 (GRCh38) [ NCBI UCSC ] 7: 6013032 (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 Nov 29, 2022 May 1, 2024 Dec 1, 2020 - HGVS
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Nucleotide Protein Molecular
consequenceNM_000535.7:c.2587T>C MANE Select Help Transcripts from the Matched Annotation from the NCBI and EMBL-EBI (MANE) collaboration.
NP_000526.2:p.Ter863Arg stop lost NM_001018040.1:c.2182T>C NP_001018050.1:p.Ter728Arg stop lost NM_001322003.2:c.2182T>C NP_001308932.1:p.Ter728Arg stop lost NM_001322004.2:c.2182T>C NP_001308933.1:p.Ter728Arg stop lost NM_001322005.2:c.2182T>C NP_001308934.1:p.Ter728Arg stop lost NM_001322006.2:c.2431T>C NP_001308935.1:p.Ter811Arg stop lost NM_001322007.2:c.2269T>C NP_001308936.1:p.Ter757Arg stop lost NM_001322008.2:c.2269T>C NP_001308937.1:p.Ter757Arg stop lost NM_001322009.2:c.2215T>C NP_001308938.1:p.Ter739Arg stop lost NM_001322010.2:c.2026T>C NP_001308939.1:p.Ter676Arg stop lost NM_001322011.2:c.1654T>C NP_001308940.1:p.Ter552Arg stop lost NM_001322012.2:c.1654T>C NP_001308941.1:p.Ter552Arg stop lost NM_001322013.2:c.2014T>C NP_001308942.1:p.Ter672Arg stop lost NM_001322014.2:c.2620T>C NP_001308943.1:p.Ter874Arg stop lost NM_001322015.2:c.2278T>C NP_001308944.1:p.Ter760Arg stop lost NM_001406866.1:c.2773T>C NP_001393795.1:p.Ter925Arg stop lost NM_001406868.1:c.2611T>C NP_001393797.1:p.Ter871Arg stop lost NM_001406869.1:c.2479T>C NP_001393798.1:p.Ter827Arg stop lost NM_001406870.1:c.2464T>C NP_001393799.1:p.Ter822Arg stop lost NM_001406871.1:c.2443T>C NP_001393800.1:p.Ter815Arg stop lost NM_001406872.1:c.2419T>C NP_001393801.1:p.Ter807Arg stop lost NM_001406873.1:c.2389T>C NP_001393802.1:p.Ter797Arg stop lost NM_001406874.1:c.2419T>C NP_001393803.1:p.Ter807Arg stop lost NM_001406875.1:c.2311T>C NP_001393804.1:p.Ter771Arg stop lost NM_001406876.1:c.2302T>C NP_001393805.1:p.Ter768Arg stop lost NM_001406877.1:c.2278T>C NP_001393806.1:p.Ter760Arg stop lost NM_001406878.1:c.2278T>C NP_001393807.1:p.Ter760Arg stop lost NM_001406879.1:c.2278T>C NP_001393808.1:p.Ter760Arg stop lost NM_001406880.1:c.2278T>C NP_001393809.1:p.Ter760Arg stop lost NM_001406881.1:c.2278T>C NP_001393810.1:p.Ter760Arg stop lost NM_001406882.1:c.2278T>C NP_001393811.1:p.Ter760Arg stop lost NM_001406883.1:c.2269T>C NP_001393812.1:p.Ter757Arg stop lost NM_001406884.1:c.2263T>C NP_001393813.1:p.Ter755Arg stop lost NM_001406885.1:c.2251T>C NP_001393814.1:p.Ter751Arg stop lost NM_001406886.1:c.2221T>C NP_001393815.1:p.Ter741Arg stop lost NM_001406887.1:c.2215T>C NP_001393816.1:p.Ter739Arg stop lost NM_001406888.1:c.2215T>C NP_001393817.1:p.Ter739Arg stop lost NM_001406889.1:c.2182T>C NP_001393818.1:p.Ter728Arg stop lost NM_001406890.1:c.2182T>C NP_001393819.1:p.Ter728Arg stop lost NM_001406891.1:c.2182T>C NP_001393820.1:p.Ter728Arg stop lost NM_001406892.1:c.2182T>C NP_001393821.1:p.Ter728Arg stop lost NM_001406893.1:c.2182T>C NP_001393822.1:p.Ter728Arg stop lost NM_001406894.1:c.2182T>C NP_001393823.1:p.Ter728Arg stop lost NM_001406895.1:c.2182T>C NP_001393824.1:p.Ter728Arg stop lost NM_001406896.1:c.2182T>C NP_001393825.1:p.Ter728Arg stop lost NM_001406897.1:c.2182T>C NP_001393826.1:p.Ter728Arg stop lost NM_001406898.1:c.2182T>C NP_001393827.1:p.Ter728Arg stop lost NM_001406899.1:c.2182T>C NP_001393828.1:p.Ter728Arg stop lost NM_001406900.1:c.2122T>C NP_001393829.1:p.Ter708Arg stop lost NM_001406901.1:c.2113T>C NP_001393830.1:p.Ter705Arg stop lost NM_001406902.1:c.2113T>C NP_001393831.1:p.Ter705Arg stop lost NM_001406903.1:c.2101T>C NP_001393832.1:p.Ter701Arg stop lost NM_001406904.1:c.2074T>C NP_001393833.1:p.Ter692Arg stop lost NM_001406905.1:c.2074T>C NP_001393834.1:p.Ter692Arg stop lost NM_001406906.1:c.2026T>C NP_001393835.1:p.Ter676Arg stop lost NM_001406907.1:c.2026T>C NP_001393836.1:p.Ter676Arg stop lost NM_001406908.1:c.2014T>C NP_001393837.1:p.Ter672Arg stop lost NM_001406909.1:c.2014T>C NP_001393838.1:p.Ter672Arg stop lost NM_001406910.1:c.1870T>C NP_001393839.1:p.Ter624Arg stop lost NM_001406911.1:c.1816T>C NP_001393840.1:p.Ter606Arg stop lost NM_001406912.1:c.1384T>C NP_001393841.1:p.Ter462Arg stop lost NR_003085.2:n.2669T>C NR_136154.1:n.2631T>C non-coding transcript variant NC_000007.14:g.5973401A>G NC_000007.13:g.6013032A>G NG_008466.1:g.40706T>C LRG_161:g.40706T>C LRG_161t1:c.2587T>C LRG_161p1:p.Ter863Arg - Protein change
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- Other names
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- Canonical SPDI
- NC_000007.14:5973400:A: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
Help
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 |
5241 | 5343 |
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
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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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Dec 1, 2020 | RCV002452872.2 |
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
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
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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
(Dec 01, 2020)
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criteria provided, single submitter
Method: clinical testing
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Hereditary cancer-predisposing syndrome
Affected status: unknown
Allele origin:
germline
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Ambry Genetics
Accession: SCV002739189.2
First in ClinVar: Nov 29, 2022 Last updated: May 01, 2024 |
Comment:
The c.2587T>C variant (also known as p.*863Rext*2), located in coding exon 15 of the PMS2 gene, results from a T to C substitution at nucleotide … (more)
The c.2587T>C variant (also known as p.*863Rext*2), located in coding exon 15 of the PMS2 gene, results from a T to C substitution at nucleotide position 2587. This alteration disrupts the stop codon of the PMS2 gene and is predicted to preserve the native sequence while resulting in the elongation of the protein by two amino acids. The exact functional effect of the additional amino acids is unknown. Since supporting evidence is limited at this time, the clinical significance of this alteration remains unclear. (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 May 01, 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.