ClinVar Genomic variation as it relates to human health
NM_000535.7(PMS2):c.1486dup (p.His496fs)
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.1486dup (p.His496fs)
Variation ID: 2674249 Accession: VCV002674249.1
- Type and length
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Duplication, 1 bp
- Location
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Cytogenetic: 7p22.1 7: 5987278-5987279 (GRCh38) [ NCBI UCSC ] 7: 6026909-6026910 (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 Jul 5, 2023 - HGVS
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Nucleotide Protein Molecular
consequenceNM_000535.7:c.1486dup MANE Select Help Transcripts from the Matched Annotation from the NCBI and EMBL-EBI (MANE) collaboration.
NP_000526.2:p.His496fs frameshift NM_001018040.1:c.1081dup NP_001018050.1:p.His361Profs frameshift NM_001322003.2:c.1081dup NP_001308932.1:p.His361fs frameshift NM_001322004.2:c.1081dup NP_001308933.1:p.His361fs frameshift NM_001322005.2:c.1081dup NP_001308934.1:p.His361fs frameshift NM_001322006.2:c.1330dup NP_001308935.1:p.His444fs frameshift NM_001322007.2:c.1168dup NP_001308936.1:p.His390fs frameshift NM_001322008.2:c.1168dup NP_001308937.1:p.His390fs frameshift NM_001322009.2:c.1081dup NP_001308938.1:p.His361fs frameshift NM_001322010.2:c.925dup NP_001308939.1:p.His309fs frameshift NM_001322011.2:c.553dup NP_001308940.1:p.His185fs frameshift NM_001322012.2:c.553dup NP_001308941.1:p.His185fs frameshift NM_001322013.2:c.913dup NP_001308942.1:p.His305fs frameshift NM_001322014.2:c.1486dup NP_001308943.1:p.His496fs frameshift NM_001322015.2:c.1177dup NP_001308944.1:p.His393fs frameshift NM_001406866.1:c.1672dup NP_001393795.1:p.His558fs frameshift NM_001406868.1:c.1510dup NP_001393797.1:p.His504fs frameshift NM_001406869.1:c.1378dup NP_001393798.1:p.His460fs frameshift NM_001406870.1:c.1330dup NP_001393799.1:p.His444fs frameshift NM_001406871.1:c.1486dup NP_001393800.1:p.His496fs frameshift NM_001406872.1:c.1486dup NP_001393801.1:p.His496fs frameshift NM_001406873.1:c.1288dup NP_001393802.1:p.His430fs frameshift NM_001406874.1:c.1318dup NP_001393803.1:p.His440fs frameshift NM_001406875.1:c.1177dup NP_001393804.1:p.His393fs frameshift NM_001406876.1:c.1168dup NP_001393805.1:p.His390fs frameshift NM_001406877.1:c.1177dup NP_001393806.1:p.His393fs frameshift NM_001406878.1:c.1177dup NP_001393807.1:p.His393fs frameshift NM_001406879.1:c.1177dup NP_001393808.1:p.His393fs frameshift NM_001406880.1:c.1177dup NP_001393809.1:p.His393fs frameshift NM_001406881.1:c.1177dup NP_001393810.1:p.His393fs frameshift NM_001406882.1:c.1177dup NP_001393811.1:p.His393fs frameshift NM_001406883.1:c.1168dup NP_001393812.1:p.His390fs frameshift NM_001406884.1:c.1162dup NP_001393813.1:p.His388fs frameshift NM_001406885.1:c.1150dup NP_001393814.1:p.His384fs frameshift NM_001406886.1:c.1120dup NP_001393815.1:p.His374fs frameshift NM_001406887.1:c.1081dup NP_001393816.1:p.His361fs frameshift NM_001406888.1:c.1081dup NP_001393817.1:p.His361fs frameshift NM_001406889.1:c.1081dup NP_001393818.1:p.His361fs frameshift NM_001406890.1:c.1081dup NP_001393819.1:p.His361fs frameshift NM_001406891.1:c.1081dup NP_001393820.1:p.His361fs frameshift NM_001406892.1:c.1081dup NP_001393821.1:p.His361fs frameshift NM_001406893.1:c.1081dup NP_001393822.1:p.His361fs frameshift NM_001406894.1:c.1081dup NP_001393823.1:p.His361fs frameshift NM_001406895.1:c.1081dup NP_001393824.1:p.His361fs frameshift NM_001406896.1:c.1081dup NP_001393825.1:p.His361fs frameshift NM_001406897.1:c.1081dup NP_001393826.1:p.His361fs frameshift NM_001406898.1:c.1081dup NP_001393827.1:p.His361fs frameshift NM_001406899.1:c.1081dup NP_001393828.1:p.His361fs frameshift NM_001406900.1:c.1021dup NP_001393829.1:p.His341fs frameshift NM_001406901.1:c.1012dup NP_001393830.1:p.His338fs frameshift NM_001406902.1:c.1012dup NP_001393831.1:p.His338fs frameshift NM_001406903.1:c.1168dup NP_001393832.1:p.His390fs frameshift NM_001406904.1:c.973dup NP_001393833.1:p.His325fs frameshift NM_001406905.1:c.973dup NP_001393834.1:p.His325fs frameshift NM_001406906.1:c.925dup NP_001393835.1:p.His309fs frameshift NM_001406907.1:c.925dup NP_001393836.1:p.His309fs frameshift NM_001406908.1:c.1081dup NP_001393837.1:p.His361fs frameshift NM_001406909.1:c.913dup NP_001393838.1:p.His305fs frameshift NM_001406910.1:c.1081dup NP_001393839.1:p.His361fs frameshift NM_001406911.1:c.715dup NP_001393840.1:p.His239fs frameshift NM_001406912.1:c.804-4288dup intron variant NR_003085.2:n.1568dup NR_136154.1:n.1573dup non-coding transcript variant NC_000007.14:g.5987279dup NC_000007.13:g.6026910dup NG_008466.1:g.26828dup LRG_161:g.26828dup LRG_161t1:c.1486dup LRG_161p1:p.His496Profs - Protein change
- H185fs, H239fs, H305fs, H309fs, H325fs, H338fs, H341fs, H361fs, H374fs, H384fs, H388fs, H390fs, H393fs, H430fs, H440fs, H444fs, H460fs, H496fs, H504fs, H558fs
- Other names
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- Canonical SPDI
- NC_000007.14:5987278:G:GG
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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 |
5237 | 5339 |
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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Jul 5, 2023 | RCV003452445.1 |
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
(Jul 05, 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: SCV004188664.1
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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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 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.