ClinVar Genomic variation as it relates to human health
NM_000535.7(PMS2):c.2331dup (p.Phe778fs)
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.2331dup (p.Phe778fs)
Variation ID: 2674214 Accession: VCV002674214.1
- Type and length
-
Duplication, 1 bp
- Location
-
Cytogenetic: 7p22.1 7: 5977701-5977702 (GRCh38) [ NCBI UCSC ] 7: 6017332-6017333 (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 Dec 25, 2023 Dec 24, 2023 Sep 22, 2023 - HGVS
-
Nucleotide Protein Molecular
consequenceNM_000535.7:c.2331dup MANE Select Help Transcripts from the Matched Annotation from the NCBI and EMBL-EBI (MANE) collaboration.
NP_000526.2:p.Phe778fs frameshift NM_001018040.1:c.1925dup NP_001018050.1:p.Phe643Leufs frameshift NM_001322003.2:c.1926dup NP_001308932.1:p.Phe643fs frameshift NM_001322004.2:c.1926dup NP_001308933.1:p.Phe643fs frameshift NM_001322005.2:c.1926dup NP_001308934.1:p.Phe643fs frameshift NM_001322006.2:c.2175dup NP_001308935.1:p.Phe726fs frameshift NM_001322007.2:c.2013dup NP_001308936.1:p.Phe672fs frameshift NM_001322008.2:c.2013dup NP_001308937.1:p.Phe672fs frameshift NM_001322009.2:c.1959dup NP_001308938.1:p.Phe654fs frameshift NM_001322010.2:c.1770dup NP_001308939.1:p.Phe591fs frameshift NM_001322011.2:c.1398dup NP_001308940.1:p.Phe467fs frameshift NM_001322012.2:c.1398dup NP_001308941.1:p.Phe467fs frameshift NM_001322013.2:c.1758dup NP_001308942.1:p.Phe587fs frameshift NM_001322014.2:c.2364dup NP_001308943.1:p.Phe789fs frameshift NM_001322015.2:c.2022dup NP_001308944.1:p.Phe675fs frameshift NM_001406866.1:c.2517dup NP_001393795.1:p.Phe840fs frameshift NM_001406868.1:c.2355dup NP_001393797.1:p.Phe786fs frameshift NM_001406869.1:c.2223dup NP_001393798.1:p.Phe742fs frameshift NM_001406870.1:c.2208dup NP_001393799.1:p.Phe737fs frameshift NM_001406871.1:c.2187dup NP_001393800.1:p.Phe730fs frameshift NM_001406872.1:c.2163dup NP_001393801.1:p.Phe722fs frameshift NM_001406873.1:c.2133dup NP_001393802.1:p.Phe712fs frameshift NM_001406874.1:c.2163dup NP_001393803.1:p.Phe722fs frameshift NM_001406875.1:c.2055dup NP_001393804.1:p.Phe686fs frameshift NM_001406876.1:c.2046dup NP_001393805.1:p.Phe683fs frameshift NM_001406877.1:c.2022dup NP_001393806.1:p.Phe675fs frameshift NM_001406878.1:c.2022dup NP_001393807.1:p.Phe675fs frameshift NM_001406879.1:c.2022dup NP_001393808.1:p.Phe675fs frameshift NM_001406880.1:c.2022dup NP_001393809.1:p.Phe675fs frameshift NM_001406881.1:c.2022dup NP_001393810.1:p.Phe675fs frameshift NM_001406882.1:c.2022dup NP_001393811.1:p.Phe675fs frameshift NM_001406883.1:c.2013dup NP_001393812.1:p.Phe672fs frameshift NM_001406884.1:c.2007dup NP_001393813.1:p.Phe670fs frameshift NM_001406885.1:c.1995dup NP_001393814.1:p.Phe666fs frameshift NM_001406886.1:c.1965dup NP_001393815.1:p.Phe656fs frameshift NM_001406887.1:c.1959dup NP_001393816.1:p.Phe654fs frameshift NM_001406888.1:c.1959dup NP_001393817.1:p.Phe654fs frameshift NM_001406889.1:c.1926dup NP_001393818.1:p.Phe643fs frameshift NM_001406890.1:c.1926dup NP_001393819.1:p.Phe643fs frameshift NM_001406891.1:c.1926dup NP_001393820.1:p.Phe643fs frameshift NM_001406892.1:c.1926dup NP_001393821.1:p.Phe643fs frameshift NM_001406893.1:c.1926dup NP_001393822.1:p.Phe643fs frameshift NM_001406894.1:c.1926dup NP_001393823.1:p.Phe643fs frameshift NM_001406895.1:c.1926dup NP_001393824.1:p.Phe643fs frameshift NM_001406896.1:c.1926dup NP_001393825.1:p.Phe643fs frameshift NM_001406897.1:c.1926dup NP_001393826.1:p.Phe643fs frameshift NM_001406898.1:c.1926dup NP_001393827.1:p.Phe643fs frameshift NM_001406899.1:c.1926dup NP_001393828.1:p.Phe643fs frameshift NM_001406900.1:c.1866dup NP_001393829.1:p.Phe623fs frameshift NM_001406901.1:c.1857dup NP_001393830.1:p.Phe620fs frameshift NM_001406902.1:c.1857dup NP_001393831.1:p.Phe620fs frameshift NM_001406903.1:c.1845dup NP_001393832.1:p.Phe616fs frameshift NM_001406904.1:c.1818dup NP_001393833.1:p.Phe607fs frameshift NM_001406905.1:c.1818dup NP_001393834.1:p.Phe607fs frameshift NM_001406906.1:c.1770dup NP_001393835.1:p.Phe591fs frameshift NM_001406907.1:c.1770dup NP_001393836.1:p.Phe591fs frameshift NM_001406908.1:c.1758dup NP_001393837.1:p.Phe587fs frameshift NM_001406909.1:c.1758dup NP_001393838.1:p.Phe587fs frameshift NM_001406910.1:c.1614dup NP_001393839.1:p.Phe539fs frameshift NM_001406911.1:c.1560dup NP_001393840.1:p.Phe521fs frameshift NM_001406912.1:c.1128dup NP_001393841.1:p.Phe377fs frameshift NR_003085.2:n.2412dup NR_136154.1:n.2375dup non-coding transcript variant NC_000007.14:g.5977703dup NC_000007.13:g.6017334dup NG_008466.1:g.36405dup LRG_161:g.36405dup LRG_161t1:c.2330dup LRG_161p1:p.Phe778Leufs - Protein change
- F377fs, F467fs, F521fs, F539fs, F587fs, F591fs, F607fs, F616fs, F620fs, F623fs, F643fs, F654fs, F656fs, F666fs, F670fs, F672fs, F675fs, F683fs, F686fs, F712fs, F722fs, F726fs, F730fs, F737fs, F742fs, F778fs, F786fs, F789fs, F840fs
- Other names
- -
- Canonical SPDI
- NC_000007.14:5977701:GG:GGG
-
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
|
Sep 22, 2023 | RCV003452410.1 |
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
(Sep 22, 2023)
|
criteria provided, single submitter
Method: clinical testing
|
Lynch syndrome 4
Affected status: unknown
Allele origin:
unknown
|
Myriad Genetics, Inc.
Accession: SCV004187757.1
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.
|
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.