This variant is considered pathogenic. This variant creates a frameshift predicted to result in premature protein truncation.
ClinVar Genomic variation as it relates to human health
NM_000535.7(PMS2):c.2050del (p.Leu684fs)
Germline
Classification
Help
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.
(1)
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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.
Pathogenic
1
criteria provided, single submitter
Somatic
No data submitted for somatic clinical impact
Somatic
No data submitted for oncogenicity
Variant Details
- Identifiers
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NM_000535.7(PMS2):c.2050del (p.Leu684fs)
Variation ID: 2674243 Accession: VCV002674243.1
- Type and length
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Deletion, 1 bp
- Location
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Cytogenetic: 7p22.1 7: 5982948 (GRCh38) [ NCBI UCSC ] 7: 6022579 (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 Dec 25, 2023 Dec 24, 2023 Sep 21, 2023 - HGVS
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... more HGVS ... less HGVSNucleotide Protein Molecular
consequenceNM_000535.7:c.2050del MANE Select Help Transcripts from the Matched Annotation from the NCBI and EMBL-EBI (MANE) collaboration.
NP_000526.2:p.Leu684fs frameshift NM_001018040.1:c.1644delC NP_001018050.1:p.Leu549Trpfs frameshift NM_001322003.2:c.1645del NP_001308932.1:p.Leu549fs frameshift NM_001322004.2:c.1645del NP_001308933.1:p.Leu549fs frameshift NM_001322005.2:c.1645del NP_001308934.1:p.Leu549fs frameshift NM_001322006.2:c.1894del NP_001308935.1:p.Leu632fs frameshift NM_001322007.2:c.1732del NP_001308936.1:p.Leu578fs frameshift NM_001322008.2:c.1732del NP_001308937.1:p.Leu578fs frameshift NM_001322009.2:c.1645del NP_001308938.1:p.Leu549fs frameshift NM_001322010.2:c.1489del NP_001308939.1:p.Leu497fs frameshift NM_001322011.2:c.1117del NP_001308940.1:p.Leu373fs frameshift NM_001322012.2:c.1117del NP_001308941.1:p.Leu373fs frameshift NM_001322013.2:c.1477del NP_001308942.1:p.Leu493fs frameshift NM_001322014.2:c.2050del NP_001308943.1:p.Leu684fs frameshift NM_001322015.2:c.1741del NP_001308944.1:p.Leu581fs frameshift NM_001406866.1:c.2236del NP_001393795.1:p.Leu746fs frameshift NM_001406868.1:c.2074del NP_001393797.1:p.Leu692fs frameshift NM_001406869.1:c.1942del NP_001393798.1:p.Leu648fs frameshift NM_001406870.1:c.1894del NP_001393799.1:p.Leu632fs frameshift NM_001406871.1:c.2050del NP_001393800.1:p.Leu684fs frameshift NM_001406872.1:c.2006+3811del intron variant NM_001406873.1:c.1852del NP_001393802.1:p.Leu618fs frameshift NM_001406874.1:c.1882del NP_001393803.1:p.Leu628fs frameshift NM_001406875.1:c.1741del NP_001393804.1:p.Leu581fs frameshift NM_001406876.1:c.1732del NP_001393805.1:p.Leu578fs frameshift NM_001406877.1:c.1741del NP_001393806.1:p.Leu581fs frameshift NM_001406878.1:c.1741del NP_001393807.1:p.Leu581fs frameshift NM_001406879.1:c.1741del NP_001393808.1:p.Leu581fs frameshift NM_001406880.1:c.1741del NP_001393809.1:p.Leu581fs frameshift NM_001406881.1:c.1741del NP_001393810.1:p.Leu581fs frameshift NM_001406882.1:c.1741del NP_001393811.1:p.Leu581fs frameshift NM_001406883.1:c.1732del NP_001393812.1:p.Leu578fs frameshift NM_001406884.1:c.1726del NP_001393813.1:p.Leu576fs frameshift NM_001406885.1:c.1714del NP_001393814.1:p.Leu572fs frameshift NM_001406886.1:c.1684del NP_001393815.1:p.Leu562fs frameshift NM_001406887.1:c.1645del NP_001393816.1:p.Leu549fs frameshift NM_001406888.1:c.1645del NP_001393817.1:p.Leu549fs frameshift NM_001406889.1:c.1645del NP_001393818.1:p.Leu549fs frameshift NM_001406890.1:c.1645del NP_001393819.1:p.Leu549fs frameshift NM_001406891.1:c.1645del NP_001393820.1:p.Leu549fs frameshift NM_001406892.1:c.1645del NP_001393821.1:p.Leu549fs frameshift NM_001406893.1:c.1645del NP_001393822.1:p.Leu549fs frameshift NM_001406894.1:c.1645del NP_001393823.1:p.Leu549fs frameshift NM_001406895.1:c.1645del NP_001393824.1:p.Leu549fs frameshift NM_001406896.1:c.1645del NP_001393825.1:p.Leu549fs frameshift NM_001406897.1:c.1645del NP_001393826.1:p.Leu549fs frameshift NM_001406898.1:c.1645del NP_001393827.1:p.Leu549fs frameshift NM_001406899.1:c.1645del NP_001393828.1:p.Leu549fs frameshift NM_001406900.1:c.1585del NP_001393829.1:p.Leu529fs frameshift NM_001406901.1:c.1576del NP_001393830.1:p.Leu526fs frameshift NM_001406902.1:c.1576del NP_001393831.1:p.Leu526fs frameshift NM_001406903.1:c.1688+3811del intron variant NM_001406904.1:c.1537del NP_001393833.1:p.Leu513fs frameshift NM_001406905.1:c.1537del NP_001393834.1:p.Leu513fs frameshift NM_001406906.1:c.1489del NP_001393835.1:p.Leu497fs frameshift NM_001406907.1:c.1489del NP_001393836.1:p.Leu497fs frameshift NM_001406908.1:c.1601+3811del intron variant NM_001406909.1:c.1477del NP_001393838.1:p.Leu493fs frameshift NM_001406910.1:c.1601+3811del intron variant NM_001406911.1:c.1279del NP_001393840.1:p.Leu427fs frameshift NM_001406912.1:c.847del NP_001393841.1:p.Leu283fs frameshift NR_003085.2:n.2131delC NR_136154.1:n.2137del non-coding transcript variant NC_000007.14:g.5982949del NC_000007.13:g.6022580del NG_008466.1:g.31159del LRG_161:g.31159del LRG_161t1:c.2049del LRG_161p1:p.Leu684Trpfs - Protein change
- L283fs, L373fs, L427fs, L493fs, L497fs, L513fs, L526fs, L529fs, L549fs, L562fs, L572fs, L576fs, L578fs, L581fs, L618fs, L628fs, L632fs, L648fs, L684fs, L692fs, L746fs
- Other names
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- Canonical SPDI
- NC_000007.14:5982947:GG: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
Help
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 | ||
|---|---|---|---|---|---|---|
| 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 |
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
Help
The RCV accession number, with most recent version number, for the variant-condition record, with a link to the RCV web page. |
|---|---|---|---|---|
| Pathogenic (1) |
criteria provided, single submitter
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Sep 21, 2023 | RCV003452439.1 |
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
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. |
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Pathogenic
(Sep 21, 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: SCV004188642.1
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.
|
Comment:
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. |
Comment:
This variant is considered pathogenic. This variant creates a frameshift predicted to result in premature protein truncation.
Citations for germline classification of this variant
Help| There 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 Dec 30, 2023
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.