ClinVar Genomic variation as it relates to human health
NM_000535.7(PMS2):c.1266_1281del (p.Glu422fs)
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.1266_1281del (p.Glu422fs)
Variation ID: 2674271 Accession: VCV002674271.1
- Type and length
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Deletion, 16 bp
- Location
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Cytogenetic: 7p22.1 7: 5987484-5987499 (GRCh38) [ NCBI UCSC ] 7: 6027115-6027130 (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.1266_1281del MANE Select Help Transcripts from the Matched Annotation from the NCBI and EMBL-EBI (MANE) collaboration.
NP_000526.2:p.Glu422fs frameshift NM_001018040.1:c.861_876del16 NP_001018050.1:p.Glu287Aspfs frameshift NM_001322003.2:c.861_876del NP_001308932.1:p.Glu287fs frameshift NM_001322004.2:c.861_876del NP_001308933.1:p.Glu287fs frameshift NM_001322005.2:c.861_876del NP_001308934.1:p.Glu287fs frameshift NM_001322006.2:c.1110_1125del NP_001308935.1:p.Glu370fs frameshift NM_001322007.2:c.948_963del NP_001308936.1:p.Glu316fs frameshift NM_001322008.2:c.948_963del NP_001308937.1:p.Glu316fs frameshift NM_001322009.2:c.861_876del NP_001308938.1:p.Glu287fs frameshift NM_001322010.2:c.705_720del NP_001308939.1:p.Glu235fs frameshift NM_001322011.2:c.333_348del NP_001308940.1:p.Glu111fs frameshift NM_001322012.2:c.333_348del NP_001308941.1:p.Glu111fs frameshift NM_001322013.2:c.693_708del NP_001308942.1:p.Glu231fs frameshift NM_001322014.2:c.1266_1281del NP_001308943.1:p.Glu422fs frameshift NM_001322015.2:c.957_972del NP_001308944.1:p.Glu319fs frameshift NM_001406866.1:c.1452_1467del NP_001393795.1:p.Glu484fs frameshift NM_001406868.1:c.1290_1305del NP_001393797.1:p.Glu430fs frameshift NM_001406869.1:c.1158_1173del NP_001393798.1:p.Glu386fs frameshift NM_001406870.1:c.1110_1125del NP_001393799.1:p.Glu370fs frameshift NM_001406871.1:c.1266_1281del NP_001393800.1:p.Glu422fs frameshift NM_001406872.1:c.1266_1281del NP_001393801.1:p.Glu422fs frameshift NM_001406873.1:c.1068_1083del NP_001393802.1:p.Glu356fs frameshift NM_001406874.1:c.1098_1113del NP_001393803.1:p.Glu366fs frameshift NM_001406875.1:c.957_972del NP_001393804.1:p.Glu319fs frameshift NM_001406876.1:c.948_963del NP_001393805.1:p.Glu316fs frameshift NM_001406877.1:c.957_972del NP_001393806.1:p.Glu319fs frameshift NM_001406878.1:c.957_972del NP_001393807.1:p.Glu319fs frameshift NM_001406879.1:c.957_972del NP_001393808.1:p.Glu319fs frameshift NM_001406880.1:c.957_972del NP_001393809.1:p.Glu319fs frameshift NM_001406881.1:c.957_972del NP_001393810.1:p.Glu319fs frameshift NM_001406882.1:c.957_972del NP_001393811.1:p.Glu319fs frameshift NM_001406883.1:c.948_963del NP_001393812.1:p.Glu316fs frameshift NM_001406884.1:c.942_957del NP_001393813.1:p.Glu314fs frameshift NM_001406885.1:c.930_945del NP_001393814.1:p.Glu310fs frameshift NM_001406886.1:c.900_915del NP_001393815.1:p.Glu300fs frameshift NM_001406887.1:c.861_876del NP_001393816.1:p.Glu287fs frameshift NM_001406888.1:c.861_876del NP_001393817.1:p.Glu287fs frameshift NM_001406889.1:c.861_876del NP_001393818.1:p.Glu287fs frameshift NM_001406890.1:c.861_876del NP_001393819.1:p.Glu287fs frameshift NM_001406891.1:c.861_876del NP_001393820.1:p.Glu287fs frameshift NM_001406892.1:c.861_876del NP_001393821.1:p.Glu287fs frameshift NM_001406893.1:c.861_876del NP_001393822.1:p.Glu287fs frameshift NM_001406894.1:c.861_876del NP_001393823.1:p.Glu287fs frameshift NM_001406895.1:c.861_876del NP_001393824.1:p.Glu287fs frameshift NM_001406896.1:c.861_876del NP_001393825.1:p.Glu287fs frameshift NM_001406897.1:c.861_876del NP_001393826.1:p.Glu287fs frameshift NM_001406898.1:c.861_876del NP_001393827.1:p.Glu287fs frameshift NM_001406899.1:c.861_876del NP_001393828.1:p.Glu287fs frameshift NM_001406900.1:c.801_816del NP_001393829.1:p.Glu267fs frameshift NM_001406901.1:c.792_807del NP_001393830.1:p.Glu264fs frameshift NM_001406902.1:c.792_807del NP_001393831.1:p.Glu264fs frameshift NM_001406903.1:c.948_963del NP_001393832.1:p.Glu316fs frameshift NM_001406904.1:c.753_768del NP_001393833.1:p.Glu251fs frameshift NM_001406905.1:c.753_768del NP_001393834.1:p.Glu251fs frameshift NM_001406906.1:c.705_720del NP_001393835.1:p.Glu235fs frameshift NM_001406907.1:c.705_720del NP_001393836.1:p.Glu235fs frameshift NM_001406908.1:c.861_876del NP_001393837.1:p.Glu287fs frameshift NM_001406909.1:c.693_708del NP_001393838.1:p.Glu231fs frameshift NM_001406910.1:c.861_876del NP_001393839.1:p.Glu287fs frameshift NM_001406911.1:c.495_510del NP_001393840.1:p.Glu165fs frameshift NM_001406912.1:c.804-4508_804-4493del intron variant NR_003085.2:n.1348_1363del16 NR_136154.1:n.1353_1368del non-coding transcript variant NC_000007.14:g.5987484_5987499del NC_000007.13:g.6027115_6027130del NG_008466.1:g.26608_26623del LRG_161:g.26608_26623del LRG_161t1:c.1266_1281del16 LRG_161p1:p.Glu422Aspfs - Protein change
- E111fs, E165fs, E231fs, E235fs, E251fs, E264fs, E267fs, E287fs, E300fs, E310fs, E314fs, E316fs, E319fs, E356fs, E366fs, E370fs, E386fs, E422fs, E430fs, E484fs
- Other names
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- Canonical SPDI
- NC_000007.14:5987483:ACGAAGAGAAAAGGCC:
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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
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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 |
5154 | 5248 |
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 | RCV003452467.1 |
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: SCV004188706.1
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.