ClinVar Genomic variation as it relates to human health
NM_000535.7(PMS2):c.512del (p.Lys171fs)
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.512del (p.Lys171fs)
Variation ID: 1745534 Accession: VCV001745534.3
- Type and length
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Deletion, 1 bp
- Location
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Cytogenetic: 7p22.1 7: 6002478 (GRCh38) [ NCBI UCSC ] 7: 6042109 (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 Sep 19, 2023 - HGVS
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Nucleotide Protein Molecular
consequenceNM_000535.7:c.512del MANE Select Help Transcripts from the Matched Annotation from the NCBI and EMBL-EBI (MANE) collaboration.
NP_000526.2:p.Lys171fs frameshift NM_000535.5:c.512delA frameshift NM_001018040.1:c.106delA NP_001018050.1:p.Lys36Argfs frameshift NM_001322003.2:c.107del NP_001308932.1:p.Lys36fs frameshift NM_001322004.2:c.107del NP_001308933.1:p.Lys36fs frameshift NM_001322005.2:c.107del NP_001308934.1:p.Lys36fs frameshift NM_001322006.2:c.512del NP_001308935.1:p.Lys171fs frameshift NM_001322007.2:c.194del NP_001308936.1:p.Lys65fs frameshift NM_001322008.2:c.194del NP_001308937.1:p.Lys65fs frameshift NM_001322009.2:c.107del NP_001308938.1:p.Lys36fs frameshift NM_001322010.2:c.107del NP_001308939.1:p.Lys36fs frameshift NM_001322011.2:c.-373del 5 prime UTR NM_001322012.2:c.-373del 5 prime UTR NM_001322013.2:c.107del NP_001308942.1:p.Lys36fs frameshift NM_001322014.2:c.512del NP_001308943.1:p.Lys171fs frameshift NM_001322015.2:c.203del NP_001308944.1:p.Lys68fs frameshift NM_001406866.1:c.697delA NP_001393795.1:p.Lys233Argfs frameshift NM_001406868.1:c.535delA NP_001393797.1:p.Lys179Argfs frameshift NM_001406869.1:c.511delA NP_001393798.1:p.Lys171Argfs frameshift NM_001406870.1:c.511delA NP_001393799.1:p.Lys171Argfs frameshift NM_001406871.1:c.511delA NP_001393800.1:p.Lys171Argfs frameshift NM_001406872.1:c.511delA NP_001393801.1:p.Lys171Argfs frameshift NM_001406873.1:c.511delA NP_001393802.1:p.Lys171Argfs frameshift NM_001406874.1:c.511delA NP_001393803.1:p.Lys171Argfs frameshift NM_001406875.1:c.202delA NP_001393804.1:p.Lys68Argfs frameshift NM_001406876.1:c.193delA NP_001393805.1:p.Lys65Argfs frameshift NM_001406877.1:c.202delA NP_001393806.1:p.Lys68Argfs frameshift NM_001406878.1:c.202delA NP_001393807.1:p.Lys68Argfs frameshift NM_001406879.1:c.202delA NP_001393808.1:p.Lys68Argfs frameshift NM_001406880.1:c.202delA NP_001393809.1:p.Lys68Argfs frameshift NM_001406881.1:c.202delA NP_001393810.1:p.Lys68Argfs frameshift NM_001406882.1:c.202delA NP_001393811.1:p.Lys68Argfs frameshift NM_001406883.1:c.193delA NP_001393812.1:p.Lys65Argfs frameshift NM_001406884.1:c.511delA NP_001393813.1:p.Lys171Argfs frameshift NM_001406886.1:c.511delA NP_001393815.1:p.Lys171Argfs frameshift NM_001406887.1:c.106delA NP_001393816.1:p.Lys36Argfs frameshift NM_001406888.1:c.106delA NP_001393817.1:p.Lys36Argfs frameshift NM_001406889.1:c.106delA NP_001393818.1:p.Lys36Argfs frameshift NM_001406890.1:c.106delA NP_001393819.1:p.Lys36Argfs frameshift NM_001406891.1:c.106delA NP_001393820.1:p.Lys36Argfs frameshift NM_001406892.1:c.106delA NP_001393821.1:p.Lys36Argfs frameshift NM_001406893.1:c.106delA NP_001393822.1:p.Lys36Argfs frameshift NM_001406894.1:c.106delA NP_001393823.1:p.Lys36Argfs frameshift NM_001406895.1:c.106delA NP_001393824.1:p.Lys36Argfs frameshift NM_001406896.1:c.106delA NP_001393825.1:p.Lys36Argfs frameshift NM_001406897.1:c.106delA NP_001393826.1:p.Lys36Argfs frameshift NM_001406898.1:c.106delA NP_001393827.1:p.Lys36Argfs frameshift NM_001406899.1:c.106delA NP_001393828.1:p.Lys36Argfs frameshift NM_001406900.1:c.202delA NP_001393829.1:p.Lys68Argfs frameshift NM_001406901.1:c.193delA NP_001393830.1:p.Lys65Argfs frameshift NM_001406902.1:c.193delA NP_001393831.1:p.Lys65Argfs frameshift NM_001406903.1:c.193delA NP_001393832.1:p.Lys65Argfs frameshift NM_001406904.1:c.106delA NP_001393833.1:p.Lys36Argfs frameshift NM_001406905.1:c.106delA NP_001393834.1:p.Lys36Argfs frameshift NM_001406906.1:c.106delA NP_001393835.1:p.Lys36Argfs frameshift NM_001406907.1:c.106delA NP_001393836.1:p.Lys36Argfs frameshift NM_001406908.1:c.106delA NP_001393837.1:p.Lys36Argfs frameshift NM_001406909.1:c.106delA NP_001393838.1:p.Lys36Argfs frameshift NM_001406910.1:c.106delA NP_001393839.1:p.Lys36Argfs frameshift NM_001406911.1:c.106delA NP_001393840.1:p.Lys36Argfs frameshift NM_001406912.1:c.511delA NP_001393841.1:p.Lys171Argfs frameshift NR_003085.2:n.593delA NR_136154.1:n.599del non-coding transcript variant NC_000007.14:g.6002479del NC_000007.13:g.6042110del NG_008466.1:g.11629del LRG_161:g.11629del LRG_161t1:c.511del LRG_161p1:p.Lys171Argfs - Protein change
- K36fs, K68fs, K171fs, K65fs
- Other names
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- Canonical SPDI
- NC_000007.14:6002477:TT:T
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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 |
5163 | 5257 |
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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Pathogenic (1) |
criteria provided, single submitter
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Sep 4, 2015 | RCV002338167.2 | |
Pathogenic (1) |
criteria provided, single submitter
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Sep 19, 2023 | RCV003454164.1 |
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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Pathogenic
(Sep 19, 2023)
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criteria provided, single submitter
Method: clinical testing
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Lynch syndrome 4
Affected status: unknown
Allele origin:
unknown
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Myriad Genetics, Inc.
Accession: SCV004187699.1
First in ClinVar: Dec 24, 2023 Last updated: Dec 24, 2023 |
Comment:
This variant is considered pathogenic. This variant creates a frameshift predicted to result in premature protein truncation.
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Pathogenic
(Sep 04, 2015)
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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: SCV002644717.2
First in ClinVar: Nov 29, 2022 Last updated: May 01, 2024 |
Comment:
The c.512delA pathogenic mutation, located in coding exon 5 of the PMS2 gene, results from a deletion of one nucleotide at position 512, causing a … (more)
The c.512delA pathogenic mutation, located in coding exon 5 of the PMS2 gene, results from a deletion of one nucleotide at position 512, causing a translational frameshift with a predicted alternate stop codon. Since frameshifts are typically deleterious in nature, this alteration is interpreted as a disease-causing mutation (ACMG Recommendations for Standards for Interpretation and Reporting of Sequence Variations. Revision 2007. Genet Med. 2008;10:294). (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.