ClinVar Genomic variation as it relates to human health
NM_000535.7(PMS2):c.1289_1292del (p.Thr430fs)
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.1289_1292del (p.Thr430fs)
Variation ID: 2674277 Accession: VCV002674277.1
- Type and length
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Deletion, 4 bp
- Location
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Cytogenetic: 7p22.1 7: 5987473-5987476 (GRCh38) [ NCBI UCSC ] 7: 6027104-6027107 (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.1289_1292del MANE Select Help Transcripts from the Matched Annotation from the NCBI and EMBL-EBI (MANE) collaboration.
NP_000526.2:p.Thr430fs frameshift NM_001018040.1:c.883_886delACAG NP_001018050.1:p.Thr295Argfs frameshift NM_001322003.2:c.884_887del NP_001308932.1:p.Thr295fs frameshift NM_001322004.2:c.884_887del NP_001308933.1:p.Thr295fs frameshift NM_001322005.2:c.884_887del NP_001308934.1:p.Thr295fs frameshift NM_001322006.2:c.1133_1136del NP_001308935.1:p.Thr378fs frameshift NM_001322007.2:c.971_974del NP_001308936.1:p.Thr324fs frameshift NM_001322008.2:c.971_974del NP_001308937.1:p.Thr324fs frameshift NM_001322009.2:c.884_887del NP_001308938.1:p.Thr295fs frameshift NM_001322010.2:c.728_731del NP_001308939.1:p.Thr243fs frameshift NM_001322011.2:c.356_359del NP_001308940.1:p.Thr119fs frameshift NM_001322012.2:c.356_359del NP_001308941.1:p.Thr119fs frameshift NM_001322013.2:c.716_719del NP_001308942.1:p.Thr239fs frameshift NM_001322014.2:c.1289_1292del NP_001308943.1:p.Thr430fs frameshift NM_001322015.2:c.980_983del NP_001308944.1:p.Thr327fs frameshift NM_001406866.1:c.1475_1478del NP_001393795.1:p.Thr492fs frameshift NM_001406868.1:c.1313_1316del NP_001393797.1:p.Thr438fs frameshift NM_001406869.1:c.1181_1184del NP_001393798.1:p.Thr394fs frameshift NM_001406870.1:c.1133_1136del NP_001393799.1:p.Thr378fs frameshift NM_001406871.1:c.1289_1292del NP_001393800.1:p.Thr430fs frameshift NM_001406872.1:c.1289_1292del NP_001393801.1:p.Thr430fs frameshift NM_001406873.1:c.1091_1094del NP_001393802.1:p.Thr364fs frameshift NM_001406874.1:c.1121_1124del NP_001393803.1:p.Thr374fs frameshift NM_001406875.1:c.980_983del NP_001393804.1:p.Thr327fs frameshift NM_001406876.1:c.971_974del NP_001393805.1:p.Thr324fs frameshift NM_001406877.1:c.980_983del NP_001393806.1:p.Thr327fs frameshift NM_001406878.1:c.980_983del NP_001393807.1:p.Thr327fs frameshift NM_001406879.1:c.980_983del NP_001393808.1:p.Thr327fs frameshift NM_001406880.1:c.980_983del NP_001393809.1:p.Thr327fs frameshift NM_001406881.1:c.980_983del NP_001393810.1:p.Thr327fs frameshift NM_001406882.1:c.980_983del NP_001393811.1:p.Thr327fs frameshift NM_001406883.1:c.971_974del NP_001393812.1:p.Thr324fs frameshift NM_001406884.1:c.965_968del NP_001393813.1:p.Thr322fs frameshift NM_001406885.1:c.953_956del NP_001393814.1:p.Thr318fs frameshift NM_001406886.1:c.923_926del NP_001393815.1:p.Thr308fs frameshift NM_001406887.1:c.884_887del NP_001393816.1:p.Thr295fs frameshift NM_001406888.1:c.884_887del NP_001393817.1:p.Thr295fs frameshift NM_001406889.1:c.884_887del NP_001393818.1:p.Thr295fs frameshift NM_001406890.1:c.884_887del NP_001393819.1:p.Thr295fs frameshift NM_001406891.1:c.884_887del NP_001393820.1:p.Thr295fs frameshift NM_001406892.1:c.884_887del NP_001393821.1:p.Thr295fs frameshift NM_001406893.1:c.884_887del NP_001393822.1:p.Thr295fs frameshift NM_001406894.1:c.884_887del NP_001393823.1:p.Thr295fs frameshift NM_001406895.1:c.884_887del NP_001393824.1:p.Thr295fs frameshift NM_001406896.1:c.884_887del NP_001393825.1:p.Thr295fs frameshift NM_001406897.1:c.884_887del NP_001393826.1:p.Thr295fs frameshift NM_001406898.1:c.884_887del NP_001393827.1:p.Thr295fs frameshift NM_001406899.1:c.884_887del NP_001393828.1:p.Thr295fs frameshift NM_001406900.1:c.824_827del NP_001393829.1:p.Thr275fs frameshift NM_001406901.1:c.815_818del NP_001393830.1:p.Thr272fs frameshift NM_001406902.1:c.815_818del NP_001393831.1:p.Thr272fs frameshift NM_001406903.1:c.971_974del NP_001393832.1:p.Thr324fs frameshift NM_001406904.1:c.776_779del NP_001393833.1:p.Thr259fs frameshift NM_001406905.1:c.776_779del NP_001393834.1:p.Thr259fs frameshift NM_001406906.1:c.728_731del NP_001393835.1:p.Thr243fs frameshift NM_001406907.1:c.728_731del NP_001393836.1:p.Thr243fs frameshift NM_001406908.1:c.884_887del NP_001393837.1:p.Thr295fs frameshift NM_001406909.1:c.716_719del NP_001393838.1:p.Thr239fs frameshift NM_001406910.1:c.884_887del NP_001393839.1:p.Thr295fs frameshift NM_001406911.1:c.518_521del NP_001393840.1:p.Thr173fs frameshift NM_001406912.1:c.804-4485_804-4482del intron variant NR_003085.2:n.1370_1373delACAG NR_136154.1:n.1376_1379del non-coding transcript variant NC_000007.14:g.5987474_5987477del NC_000007.13:g.6027105_6027108del NG_008466.1:g.26631_26634del LRG_161:g.26631_26634del LRG_161t1:c.1288_1291del LRG_161p1:p.Thr430Argfs - Protein change
- T322fs, T324fs, T327fs, T364fs, T374fs, T378fs, T394fs, T430fs, T438fs, T492fs, T119fs, T173fs, T239fs, T243fs, T259fs, T272fs, T275fs, T295fs, T308fs, T318fs
- Other names
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- Canonical SPDI
- NC_000007.14:5987472:TCTGT: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
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
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 |
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
Help
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 | RCV003452473.1 |
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 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: SCV004188720.1
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.