This variant is considered pathogenic. This variant creates a termination codon and is predicted to result in premature protein truncation.
ClinVar Genomic variation as it relates to human health
NM_000535.7(PMS2):c.1417G>T (p.Glu473Ter)
Germline
Classification
Help
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.
(1)
Help
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.
Pathogenic
1
criteria provided, single submitter
Somatic
No data submitted for somatic clinical impact
Somatic
No data submitted for oncogenicity
Variant Details
- Identifiers
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NM_000535.7(PMS2):c.1417G>T (p.Glu473Ter)
Variation ID: 2674236 Accession: VCV002674236.1
- Type and length
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single nucleotide variant, 1 bp
- Location
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Cytogenetic: 7p22.1 7: 5987348 (GRCh38) [ NCBI UCSC ] 7: 6026979 (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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... more HGVS ... less HGVSNucleotide Protein Molecular
consequenceNM_000535.7:c.1417G>T MANE Select Help Transcripts from the Matched Annotation from the NCBI and EMBL-EBI (MANE) collaboration.
NP_000526.2:p.Glu473Ter nonsense NM_001018040.1:c.1012G>T NP_001018050.1:p.Glu338Ter nonsense NM_001322003.2:c.1012G>T NP_001308932.1:p.Glu338Ter nonsense NM_001322004.2:c.1012G>T NP_001308933.1:p.Glu338Ter nonsense NM_001322005.2:c.1012G>T NP_001308934.1:p.Glu338Ter nonsense NM_001322006.2:c.1261G>T NP_001308935.1:p.Glu421Ter nonsense NM_001322007.2:c.1099G>T NP_001308936.1:p.Glu367Ter nonsense NM_001322008.2:c.1099G>T NP_001308937.1:p.Glu367Ter nonsense NM_001322009.2:c.1012G>T NP_001308938.1:p.Glu338Ter nonsense NM_001322010.2:c.856G>T NP_001308939.1:p.Glu286Ter nonsense NM_001322011.2:c.484G>T NP_001308940.1:p.Glu162Ter nonsense NM_001322012.2:c.484G>T NP_001308941.1:p.Glu162Ter nonsense NM_001322013.2:c.844G>T NP_001308942.1:p.Glu282Ter nonsense NM_001322014.2:c.1417G>T NP_001308943.1:p.Glu473Ter nonsense NM_001322015.2:c.1108G>T NP_001308944.1:p.Glu370Ter nonsense NM_001406866.1:c.1603G>T NP_001393795.1:p.Glu535Ter nonsense NM_001406868.1:c.1441G>T NP_001393797.1:p.Glu481Ter nonsense NM_001406869.1:c.1309G>T NP_001393798.1:p.Glu437Ter nonsense NM_001406870.1:c.1261G>T NP_001393799.1:p.Glu421Ter nonsense NM_001406871.1:c.1417G>T NP_001393800.1:p.Glu473Ter nonsense NM_001406872.1:c.1417G>T NP_001393801.1:p.Glu473Ter nonsense NM_001406873.1:c.1219G>T NP_001393802.1:p.Glu407Ter nonsense NM_001406874.1:c.1249G>T NP_001393803.1:p.Glu417Ter nonsense NM_001406875.1:c.1108G>T NP_001393804.1:p.Glu370Ter nonsense NM_001406876.1:c.1099G>T NP_001393805.1:p.Glu367Ter nonsense NM_001406877.1:c.1108G>T NP_001393806.1:p.Glu370Ter nonsense NM_001406878.1:c.1108G>T NP_001393807.1:p.Glu370Ter nonsense NM_001406879.1:c.1108G>T NP_001393808.1:p.Glu370Ter nonsense NM_001406880.1:c.1108G>T NP_001393809.1:p.Glu370Ter nonsense NM_001406881.1:c.1108G>T NP_001393810.1:p.Glu370Ter nonsense NM_001406882.1:c.1108G>T NP_001393811.1:p.Glu370Ter nonsense NM_001406883.1:c.1099G>T NP_001393812.1:p.Glu367Ter nonsense NM_001406884.1:c.1093G>T NP_001393813.1:p.Glu365Ter nonsense NM_001406885.1:c.1081G>T NP_001393814.1:p.Glu361Ter nonsense NM_001406886.1:c.1051G>T NP_001393815.1:p.Glu351Ter nonsense NM_001406887.1:c.1012G>T NP_001393816.1:p.Glu338Ter nonsense NM_001406888.1:c.1012G>T NP_001393817.1:p.Glu338Ter nonsense NM_001406889.1:c.1012G>T NP_001393818.1:p.Glu338Ter nonsense NM_001406890.1:c.1012G>T NP_001393819.1:p.Glu338Ter nonsense NM_001406891.1:c.1012G>T NP_001393820.1:p.Glu338Ter nonsense NM_001406892.1:c.1012G>T NP_001393821.1:p.Glu338Ter nonsense NM_001406893.1:c.1012G>T NP_001393822.1:p.Glu338Ter nonsense NM_001406894.1:c.1012G>T NP_001393823.1:p.Glu338Ter nonsense NM_001406895.1:c.1012G>T NP_001393824.1:p.Glu338Ter nonsense NM_001406896.1:c.1012G>T NP_001393825.1:p.Glu338Ter nonsense NM_001406897.1:c.1012G>T NP_001393826.1:p.Glu338Ter nonsense NM_001406898.1:c.1012G>T NP_001393827.1:p.Glu338Ter nonsense NM_001406899.1:c.1012G>T NP_001393828.1:p.Glu338Ter nonsense NM_001406900.1:c.952G>T NP_001393829.1:p.Glu318Ter nonsense NM_001406901.1:c.943G>T NP_001393830.1:p.Glu315Ter nonsense NM_001406902.1:c.943G>T NP_001393831.1:p.Glu315Ter nonsense NM_001406903.1:c.1099G>T NP_001393832.1:p.Glu367Ter nonsense NM_001406904.1:c.904G>T NP_001393833.1:p.Glu302Ter nonsense NM_001406905.1:c.904G>T NP_001393834.1:p.Glu302Ter nonsense NM_001406906.1:c.856G>T NP_001393835.1:p.Glu286Ter nonsense NM_001406907.1:c.856G>T NP_001393836.1:p.Glu286Ter nonsense NM_001406908.1:c.1012G>T NP_001393837.1:p.Glu338Ter nonsense NM_001406909.1:c.844G>T NP_001393838.1:p.Glu282Ter nonsense NM_001406910.1:c.1012G>T NP_001393839.1:p.Glu338Ter nonsense NM_001406911.1:c.646G>T NP_001393840.1:p.Glu216Ter nonsense NM_001406912.1:c.804-4357G>T intron variant NR_003085.2:n.1499G>T NR_136154.1:n.1504G>T non-coding transcript variant NC_000007.14:g.5987348C>A NC_000007.13:g.6026979C>A NG_008466.1:g.26759G>T LRG_161:g.26759G>T LRG_161t1:c.1417G>T LRG_161p1:p.Glu473Ter - Protein change
- E162*, E216*, E282*, E286*, E302*, E315*, E318*, E338*, E351*, E361*, E365*, E367*, E370*, E407*, E417*, E421*, E437*, E473*, E481*, E535*
- Other names
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- Canonical SPDI
- NC_000007.14:5987347:C:A
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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 | ||
|---|---|---|---|---|---|---|
| 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 |
5241 | 5343 | |
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
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Sep 20, 2023 | RCV003452432.1 |
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: SCV004188610.1
First in ClinVar: Dec 24, 2023 Last updated: Dec 24, 2023 |
Comment:
This variant is considered pathogenic. This variant creates a termination codon and is predicted to result in premature protein truncation.
|
Comment:
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. |
Comment:
This variant is considered pathogenic. This variant creates a termination codon and is predicted to result in premature protein truncation.
Citations for germline classification of this variant
Help| There 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.