ClinVar Genomic variation as it relates to human health
NM_000535.7(PMS2):c.1415_1418del (p.Lys472fs)
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.1415_1418del (p.Lys472fs)
Variation ID: 2673976 Accession: VCV002673976.1
- Type and length
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Deletion, 4 bp
- Location
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Cytogenetic: 7p22.1 7: 5987347-5987350 (GRCh38) [ NCBI UCSC ] 7: 6026978-6026981 (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 Oct 9, 2023 - HGVS
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Nucleotide Protein Molecular
consequenceNM_000535.7:c.1415_1418del MANE Select Help Transcripts from the Matched Annotation from the NCBI and EMBL-EBI (MANE) collaboration.
NP_000526.2:p.Lys472fs frameshift NM_001018040.1:c.1007_1010delAGAA NP_001018050.1:p.Lys337Argfs frameshift NM_001322003.2:c.1010_1013del NP_001308932.1:p.Lys337fs frameshift NM_001322004.2:c.1010_1013del NP_001308933.1:p.Lys337fs frameshift NM_001322005.2:c.1010_1013del NP_001308934.1:p.Lys337fs frameshift NM_001322006.2:c.1259_1262del NP_001308935.1:p.Lys420fs frameshift NM_001322007.2:c.1097_1100del NP_001308936.1:p.Lys366fs frameshift NM_001322008.2:c.1097_1100del NP_001308937.1:p.Lys366fs frameshift NM_001322009.2:c.1010_1013del NP_001308938.1:p.Lys337fs frameshift NM_001322010.2:c.854_857del NP_001308939.1:p.Lys285fs frameshift NM_001322011.2:c.482_485del NP_001308940.1:p.Lys161fs frameshift NM_001322012.2:c.482_485del NP_001308941.1:p.Lys161fs frameshift NM_001322013.2:c.842_845del NP_001308942.1:p.Lys281fs frameshift NM_001322014.2:c.1415_1418del NP_001308943.1:p.Lys472fs frameshift NM_001322015.2:c.1106_1109del NP_001308944.1:p.Lys369fs frameshift NM_001406866.1:c.1601_1604del NP_001393795.1:p.Lys534fs frameshift NM_001406868.1:c.1439_1442del NP_001393797.1:p.Lys480fs frameshift NM_001406869.1:c.1307_1310del NP_001393798.1:p.Lys436fs frameshift NM_001406870.1:c.1259_1262del NP_001393799.1:p.Lys420fs frameshift NM_001406871.1:c.1415_1418del NP_001393800.1:p.Lys472fs frameshift NM_001406872.1:c.1415_1418del NP_001393801.1:p.Lys472fs frameshift NM_001406873.1:c.1217_1220del NP_001393802.1:p.Lys406fs frameshift NM_001406874.1:c.1247_1250del NP_001393803.1:p.Lys416fs frameshift NM_001406875.1:c.1106_1109del NP_001393804.1:p.Lys369fs frameshift NM_001406876.1:c.1097_1100del NP_001393805.1:p.Lys366fs frameshift NM_001406877.1:c.1106_1109del NP_001393806.1:p.Lys369fs frameshift NM_001406878.1:c.1106_1109del NP_001393807.1:p.Lys369fs frameshift NM_001406879.1:c.1106_1109del NP_001393808.1:p.Lys369fs frameshift NM_001406880.1:c.1106_1109del NP_001393809.1:p.Lys369fs frameshift NM_001406881.1:c.1106_1109del NP_001393810.1:p.Lys369fs frameshift NM_001406882.1:c.1106_1109del NP_001393811.1:p.Lys369fs frameshift NM_001406883.1:c.1097_1100del NP_001393812.1:p.Lys366fs frameshift NM_001406884.1:c.1091_1094del NP_001393813.1:p.Lys364fs frameshift NM_001406885.1:c.1079_1082del NP_001393814.1:p.Lys360fs frameshift NM_001406886.1:c.1049_1052del NP_001393815.1:p.Lys350fs frameshift NM_001406887.1:c.1010_1013del NP_001393816.1:p.Lys337fs frameshift NM_001406888.1:c.1010_1013del NP_001393817.1:p.Lys337fs frameshift NM_001406889.1:c.1010_1013del NP_001393818.1:p.Lys337fs frameshift NM_001406890.1:c.1010_1013del NP_001393819.1:p.Lys337fs frameshift NM_001406891.1:c.1010_1013del NP_001393820.1:p.Lys337fs frameshift NM_001406892.1:c.1010_1013del NP_001393821.1:p.Lys337fs frameshift NM_001406893.1:c.1010_1013del NP_001393822.1:p.Lys337fs frameshift NM_001406894.1:c.1010_1013del NP_001393823.1:p.Lys337fs frameshift NM_001406895.1:c.1010_1013del NP_001393824.1:p.Lys337fs frameshift NM_001406896.1:c.1010_1013del NP_001393825.1:p.Lys337fs frameshift NM_001406897.1:c.1010_1013del NP_001393826.1:p.Lys337fs frameshift NM_001406898.1:c.1010_1013del NP_001393827.1:p.Lys337fs frameshift NM_001406899.1:c.1010_1013del NP_001393828.1:p.Lys337fs frameshift NM_001406900.1:c.950_953del NP_001393829.1:p.Lys317fs frameshift NM_001406901.1:c.941_944del NP_001393830.1:p.Lys314fs frameshift NM_001406902.1:c.941_944del NP_001393831.1:p.Lys314fs frameshift NM_001406903.1:c.1097_1100del NP_001393832.1:p.Lys366fs frameshift NM_001406904.1:c.902_905del NP_001393833.1:p.Lys301fs frameshift NM_001406905.1:c.902_905del NP_001393834.1:p.Lys301fs frameshift NM_001406906.1:c.854_857del NP_001393835.1:p.Lys285fs frameshift NM_001406907.1:c.854_857del NP_001393836.1:p.Lys285fs frameshift NM_001406908.1:c.1010_1013del NP_001393837.1:p.Lys337fs frameshift NM_001406909.1:c.842_845del NP_001393838.1:p.Lys281fs frameshift NM_001406910.1:c.1010_1013del NP_001393839.1:p.Lys337fs frameshift NM_001406911.1:c.644_647del NP_001393840.1:p.Lys215fs frameshift NM_001406912.1:c.804-4359_804-4356del intron variant NR_003085.2:n.1494_1497delAGAA NR_136154.1:n.1502_1505del non-coding transcript variant NC_000007.14:g.5987350_5987353del NC_000007.13:g.6026981_6026984del NG_008466.1:g.26757_26760del LRG_161:g.26757_26760del LRG_161t1:c.1412_1415del LRG_161p1:p.Lys472Argfs - Protein change
- K337fs, K350fs, K360fs, K364fs, K366fs, K369fs, K406fs, K416fs, K420fs, K436fs, K472fs, K480fs, K534fs, K161fs, K215fs, K281fs, K285fs, K301fs, K314fs, K317fs
- Other names
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- Canonical SPDI
- NC_000007.14:5987346:TCTTTCT:TCT
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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
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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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Oct 9, 2023 | RCV003450581.1 |
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
(Oct 09, 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: SCV004185944.1
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.