ClinVar Genomic variation as it relates to human health
NM_000535.7(PMS2):c.1249_1253dup (p.Arg419fs)
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.1249_1253dup (p.Arg419fs)
Variation ID: 2674252 Accession: VCV002674252.1
- Type and length
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Duplication, 5 bp
- Location
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Cytogenetic: 7p22.1 7: 5987511-5987512 (GRCh38) [ NCBI UCSC ] 7: 6027142-6027143 (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 20, 2023 - HGVS
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Nucleotide Protein Molecular
consequenceNM_000535.7:c.1249_1253dup MANE Select Help Transcripts from the Matched Annotation from the NCBI and EMBL-EBI (MANE) collaboration.
NP_000526.2:p.Arg419fs frameshift NM_001018040.1:c.843_847dup NP_001018050.1:p.Arg284Phefs frameshift NM_001322003.2:c.844_848dup NP_001308932.1:p.Arg284fs frameshift NM_001322004.2:c.844_848dup NP_001308933.1:p.Arg284fs frameshift NM_001322005.2:c.844_848dup NP_001308934.1:p.Arg284fs frameshift NM_001322006.2:c.1093_1097dup NP_001308935.1:p.Arg367fs frameshift NM_001322007.2:c.931_935dup NP_001308936.1:p.Arg313fs frameshift NM_001322008.2:c.931_935dup NP_001308937.1:p.Arg313fs frameshift NM_001322009.2:c.844_848dup NP_001308938.1:p.Arg284fs frameshift NM_001322010.2:c.688_692dup NP_001308939.1:p.Arg232fs frameshift NM_001322011.2:c.316_320dup NP_001308940.1:p.Arg108fs frameshift NM_001322012.2:c.316_320dup NP_001308941.1:p.Arg108fs frameshift NM_001322013.2:c.676_680dup NP_001308942.1:p.Arg228fs frameshift NM_001322014.2:c.1249_1253dup NP_001308943.1:p.Arg419fs frameshift NM_001322015.2:c.940_944dup NP_001308944.1:p.Arg316fs frameshift NM_001406866.1:c.1435_1439dup NP_001393795.1:p.Arg481fs frameshift NM_001406868.1:c.1273_1277dup NP_001393797.1:p.Arg427fs frameshift NM_001406869.1:c.1141_1145dup NP_001393798.1:p.Arg383fs frameshift NM_001406870.1:c.1093_1097dup NP_001393799.1:p.Arg367fs frameshift NM_001406871.1:c.1249_1253dup NP_001393800.1:p.Arg419fs frameshift NM_001406872.1:c.1249_1253dup NP_001393801.1:p.Arg419fs frameshift NM_001406873.1:c.1051_1055dup NP_001393802.1:p.Arg353fs frameshift NM_001406874.1:c.1081_1085dup NP_001393803.1:p.Arg363fs frameshift NM_001406875.1:c.940_944dup NP_001393804.1:p.Arg316fs frameshift NM_001406876.1:c.931_935dup NP_001393805.1:p.Arg313fs frameshift NM_001406877.1:c.940_944dup NP_001393806.1:p.Arg316fs frameshift NM_001406878.1:c.940_944dup NP_001393807.1:p.Arg316fs frameshift NM_001406879.1:c.940_944dup NP_001393808.1:p.Arg316fs frameshift NM_001406880.1:c.940_944dup NP_001393809.1:p.Arg316fs frameshift NM_001406881.1:c.940_944dup NP_001393810.1:p.Arg316fs frameshift NM_001406882.1:c.940_944dup NP_001393811.1:p.Arg316fs frameshift NM_001406883.1:c.931_935dup NP_001393812.1:p.Arg313fs frameshift NM_001406884.1:c.925_929dup NP_001393813.1:p.Arg311fs frameshift NM_001406885.1:c.913_917dup NP_001393814.1:p.Arg307fs frameshift NM_001406886.1:c.883_887dup NP_001393815.1:p.Arg297fs frameshift NM_001406887.1:c.844_848dup NP_001393816.1:p.Arg284fs frameshift NM_001406888.1:c.844_848dup NP_001393817.1:p.Arg284fs frameshift NM_001406889.1:c.844_848dup NP_001393818.1:p.Arg284fs frameshift NM_001406890.1:c.844_848dup NP_001393819.1:p.Arg284fs frameshift NM_001406891.1:c.844_848dup NP_001393820.1:p.Arg284fs frameshift NM_001406892.1:c.844_848dup NP_001393821.1:p.Arg284fs frameshift NM_001406893.1:c.844_848dup NP_001393822.1:p.Arg284fs frameshift NM_001406894.1:c.844_848dup NP_001393823.1:p.Arg284fs frameshift NM_001406895.1:c.844_848dup NP_001393824.1:p.Arg284fs frameshift NM_001406896.1:c.844_848dup NP_001393825.1:p.Arg284fs frameshift NM_001406897.1:c.844_848dup NP_001393826.1:p.Arg284fs frameshift NM_001406898.1:c.844_848dup NP_001393827.1:p.Arg284fs frameshift NM_001406899.1:c.844_848dup NP_001393828.1:p.Arg284fs frameshift NM_001406900.1:c.784_788dup NP_001393829.1:p.Arg264fs frameshift NM_001406901.1:c.775_779dup NP_001393830.1:p.Arg261fs frameshift NM_001406902.1:c.775_779dup NP_001393831.1:p.Arg261fs frameshift NM_001406903.1:c.931_935dup NP_001393832.1:p.Arg313fs frameshift NM_001406904.1:c.736_740dup NP_001393833.1:p.Arg248fs frameshift NM_001406905.1:c.736_740dup NP_001393834.1:p.Arg248fs frameshift NM_001406906.1:c.688_692dup NP_001393835.1:p.Arg232fs frameshift NM_001406907.1:c.688_692dup NP_001393836.1:p.Arg232fs frameshift NM_001406908.1:c.844_848dup NP_001393837.1:p.Arg284fs frameshift NM_001406909.1:c.676_680dup NP_001393838.1:p.Arg228fs frameshift NM_001406910.1:c.844_848dup NP_001393839.1:p.Arg284fs frameshift NM_001406911.1:c.478_482dup NP_001393840.1:p.Arg162fs frameshift NM_001406912.1:c.804-4525_804-4521dup intron variant NR_003085.2:n.1330_1334dup NR_136154.1:n.1336_1340dup non-coding transcript variant NC_000007.14:g.5987513_5987517dup NC_000007.13:g.6027144_6027148dup NG_008466.1:g.26591_26595dup LRG_161:g.26591_26595dup LRG_161t1:c.1248_1252dup LRG_161p1:p.Arg419Phefs - Protein change
- R108fs, R162fs, R228fs, R232fs, R248fs, R261fs, R264fs, R284fs, R297fs, R307fs, R311fs, R313fs, R316fs, R353fs, R363fs, R367fs, R383fs, R419fs, R427fs, R481fs
- Other names
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- Canonical SPDI
- NC_000007.14:5987511:GAAATG:GAAATGAAATG
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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 | ||
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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
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 |
5237 | 5339 |
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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Pathogenic (1) |
criteria provided, single submitter
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Sep 20, 2023 | RCV003452448.1 |
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
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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 20, 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: SCV004188668.1
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.