ClinVar Genomic variation as it relates to human health
NM_000535.7(PMS2):c.2326_2327del (p.Trp776fs)
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
-
NM_000535.7(PMS2):c.2326_2327del (p.Trp776fs)
Variation ID: 3254261 Accession: VCV003254261.1
- Type and length
-
Deletion, 2 bp
- Location
-
Cytogenetic: 7p22.1 7: 5977706-5977707 (GRCh38) [ NCBI UCSC ] 7: 6017337-6017338 (GRCh37) [ NCBI UCSC ]
- Timeline in ClinVar
-
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 Jul 23, 2024 Jul 23, 2024 Jun 12, 2024 - HGVS
-
Nucleotide Protein Molecular
consequenceNM_000535.7:c.2326_2327del MANE Select Help Transcripts from the Matched Annotation from the NCBI and EMBL-EBI (MANE) collaboration.
NP_000526.2:p.Trp776fs frameshift NM_001322003.2:c.1921_1922del NP_001308932.1:p.Trp641fs frameshift NM_001322004.2:c.1921_1922del NP_001308933.1:p.Trp641fs frameshift NM_001322005.2:c.1921_1922del NP_001308934.1:p.Trp641fs frameshift NM_001322006.2:c.2170_2171del NP_001308935.1:p.Trp724fs frameshift NM_001322007.2:c.2008_2009del NP_001308936.1:p.Trp670fs frameshift NM_001322008.2:c.2008_2009del NP_001308937.1:p.Trp670fs frameshift NM_001322009.2:c.1954_1955del NP_001308938.1:p.Trp652fs frameshift NM_001322010.2:c.1765_1766del NP_001308939.1:p.Trp589fs frameshift NM_001322011.2:c.1393_1394del NP_001308940.1:p.Trp465fs frameshift NM_001322012.2:c.1393_1394del NP_001308941.1:p.Trp465fs frameshift NM_001322013.2:c.1753_1754del NP_001308942.1:p.Trp585fs frameshift NM_001322014.2:c.2359_2360del NP_001308943.1:p.Trp787fs frameshift NM_001322015.2:c.2017_2018del NP_001308944.1:p.Trp673fs frameshift NM_001406866.1:c.2512_2513del NP_001393795.1:p.Trp838fs frameshift NM_001406868.1:c.2350_2351del NP_001393797.1:p.Trp784fs frameshift NM_001406869.1:c.2218_2219del NP_001393798.1:p.Trp740fs frameshift NM_001406870.1:c.2203_2204del NP_001393799.1:p.Trp735fs frameshift NM_001406871.1:c.2182_2183del NP_001393800.1:p.Trp728fs frameshift NM_001406872.1:c.2158_2159del NP_001393801.1:p.Trp720fs frameshift NM_001406873.1:c.2128_2129del NP_001393802.1:p.Trp710fs frameshift NM_001406874.1:c.2158_2159del NP_001393803.1:p.Trp720fs frameshift NM_001406875.1:c.2050_2051del NP_001393804.1:p.Trp684fs frameshift NM_001406876.1:c.2041_2042del NP_001393805.1:p.Trp681fs frameshift NM_001406877.1:c.2017_2018del NP_001393806.1:p.Trp673fs frameshift NM_001406878.1:c.2017_2018del NP_001393807.1:p.Trp673fs frameshift NM_001406879.1:c.2017_2018del NP_001393808.1:p.Trp673fs frameshift NM_001406880.1:c.2017_2018del NP_001393809.1:p.Trp673fs frameshift NM_001406881.1:c.2017_2018del NP_001393810.1:p.Trp673fs frameshift NM_001406882.1:c.2017_2018del NP_001393811.1:p.Trp673fs frameshift NM_001406883.1:c.2008_2009del NP_001393812.1:p.Trp670fs frameshift NM_001406884.1:c.2002_2003del NP_001393813.1:p.Trp668fs frameshift NM_001406885.1:c.1990_1991del NP_001393814.1:p.Trp664fs frameshift NM_001406886.1:c.1960_1961del NP_001393815.1:p.Trp654fs frameshift NM_001406887.1:c.1954_1955del NP_001393816.1:p.Trp652fs frameshift NM_001406888.1:c.1954_1955del NP_001393817.1:p.Trp652fs frameshift NM_001406889.1:c.1921_1922del NP_001393818.1:p.Trp641fs frameshift NM_001406890.1:c.1921_1922del NP_001393819.1:p.Trp641fs frameshift NM_001406891.1:c.1921_1922del NP_001393820.1:p.Trp641fs frameshift NM_001406892.1:c.1921_1922del NP_001393821.1:p.Trp641fs frameshift NM_001406893.1:c.1921_1922del NP_001393822.1:p.Trp641fs frameshift NM_001406894.1:c.1921_1922del NP_001393823.1:p.Trp641fs frameshift NM_001406895.1:c.1921_1922del NP_001393824.1:p.Trp641fs frameshift NM_001406896.1:c.1921_1922del NP_001393825.1:p.Trp641fs frameshift NM_001406897.1:c.1921_1922del NP_001393826.1:p.Trp641fs frameshift NM_001406898.1:c.1921_1922del NP_001393827.1:p.Trp641fs frameshift NM_001406899.1:c.1921_1922del NP_001393828.1:p.Trp641fs frameshift NM_001406900.1:c.1861_1862del NP_001393829.1:p.Trp621fs frameshift NM_001406901.1:c.1852_1853del NP_001393830.1:p.Trp618fs frameshift NM_001406902.1:c.1852_1853del NP_001393831.1:p.Trp618fs frameshift NM_001406903.1:c.1840_1841del NP_001393832.1:p.Trp614fs frameshift NM_001406904.1:c.1813_1814del NP_001393833.1:p.Trp605fs frameshift NM_001406905.1:c.1813_1814del NP_001393834.1:p.Trp605fs frameshift NM_001406906.1:c.1765_1766del NP_001393835.1:p.Trp589fs frameshift NM_001406907.1:c.1765_1766del NP_001393836.1:p.Trp589fs frameshift NM_001406908.1:c.1753_1754del NP_001393837.1:p.Trp585fs frameshift NM_001406909.1:c.1753_1754del NP_001393838.1:p.Trp585fs frameshift NM_001406910.1:c.1609_1610del NP_001393839.1:p.Trp537fs frameshift NM_001406911.1:c.1555_1556del NP_001393840.1:p.Trp519fs frameshift NM_001406912.1:c.1123_1124del NP_001393841.1:p.Trp375fs frameshift NR_136154.1:n.2370_2371del non-coding transcript variant NC_000007.14:g.5977706_5977707del NC_000007.13:g.6017337_6017338del NG_008466.1:g.36400_36401del LRG_161:g.36400_36401del LRG_161t1:c.2326_2327del LRG_161p1:p.Trp776Aspfs - Protein change
- W375fs, W465fs, W519fs, W537fs, W585fs, W589fs, W605fs, W614fs, W618fs, W621fs, W641fs, W652fs, W654fs, W664fs, W668fs, W670fs, W673fs, W681fs, W684fs, W710fs, W720fs, W724fs, W728fs, W735fs, W740fs, W776fs, W784fs, W787fs, W838fs
- Other names
- -
- Canonical SPDI
- NC_000007.14:5977705:CA:
-
Functional
consequence HelpThe effect of the variant on RNA or protein function, based on experimental evidence from submitters.
-
-
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.
-
-
Allele frequency
Help
The frequency of the allele represented by this VCV record.
-
- 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 | ||
---|---|---|---|---|---|---|
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. |
|||
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
Help
The RCV accession number, with most recent version number, for the variant-condition record, with a link to the RCV web page. |
---|---|---|---|---|
Pathogenic (1) |
criteria provided, single submitter
|
Jun 12, 2024 | RCV004589216.1 |
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. |
|
---|---|---|---|---|---|
Pathogenic
(Jun 12, 2024)
|
criteria provided, single submitter
Method: clinical testing
|
Lynch syndrome 4
Affected status: unknown
Allele origin:
unknown
|
Myriad Genetics, Inc.
Accession: SCV005082482.1
First in ClinVar: Jul 23, 2024 Last updated: Jul 23, 2024 |
Comment:
This variant is considered pathogenic. This variant creates a frameshift predicted to result in premature protein truncation.
|
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 Jul 29, 2024
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.