This variant is considered pathogenic. This variant creates a frameshift predicted to result in premature protein truncation.
ClinVar Genomic variation as it relates to human health
NM_000251.3(MSH2):c.1433del (p.Leu478fs)
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_000251.3(MSH2):c.1433del (p.Leu478fs)
Variation ID: 2673382 Accession: VCV002673382.1
- Type and length
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Deletion, 1 bp
- Location
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Cytogenetic: 2p21 2: 47463077 (GRCh38) [ NCBI UCSC ] 2: 47690216 (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 Aug 2, 2023 - HGVS
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... more HGVS ... less HGVSNucleotide Protein Molecular
consequenceNM_000251.3:c.1433del MANE Select Help Transcripts from the Matched Annotation from the NCBI and EMBL-EBI (MANE) collaboration.
NP_000242.1:p.Leu478fs frameshift NM_001258281.1:c.1235del NP_001245210.1:p.Leu412fs frameshift NM_001406631.1:c.1433del NP_001393560.1:p.Leu478fs frameshift NM_001406632.1:c.1433del NP_001393561.1:p.Leu478fs frameshift NM_001406633.1:c.1433del NP_001393562.1:p.Leu478fs frameshift NM_001406634.1:c.1433del NP_001393563.1:p.Leu478fs frameshift NM_001406635.1:c.1433del NP_001393564.1:p.Leu478fs frameshift NM_001406636.1:c.1400del NP_001393565.1:p.Leu467fs frameshift NM_001406637.1:c.1433del NP_001393566.1:p.Leu478fs frameshift NM_001406638.1:c.1472del NP_001393567.1:p.Leu491fs frameshift NM_001406639.1:c.1433del NP_001393568.1:p.Leu478fs frameshift NM_001406640.1:c.1433del NP_001393569.1:p.Leu478fs frameshift NM_001406641.1:c.1433del NP_001393570.1:p.Leu478fs frameshift NM_001406642.1:c.1433del NP_001393571.1:p.Leu478fs frameshift NM_001406643.1:c.1433del NP_001393572.1:p.Leu478fs frameshift NM_001406644.1:c.1433del NP_001393573.1:p.Leu478fs frameshift NM_001406645.1:c.1433del NP_001393574.1:p.Leu478fs frameshift NM_001406646.1:c.1433del NP_001393575.1:p.Leu478fs frameshift NM_001406647.1:c.1283del NP_001393576.1:p.Leu428fs frameshift NM_001406648.1:c.1433del NP_001393577.1:p.Leu478fs frameshift NM_001406649.1:c.1283del NP_001393578.1:p.Leu428fs frameshift NM_001406650.1:c.1283del NP_001393579.1:p.Leu428fs frameshift NM_001406651.1:c.1283del NP_001393580.1:p.Leu428fs frameshift NM_001406652.1:c.1283del NP_001393581.1:p.Leu428fs frameshift NM_001406653.1:c.1373del NP_001393582.1:p.Leu458fs frameshift NM_001406654.1:c.1013del NP_001393583.1:p.Leu338fs frameshift NM_001406655.1:c.1433del NP_001393584.1:p.Leu478fs frameshift NM_001406656.1:c.536del NP_001393585.1:p.Leu179fs frameshift NM_001406657.1:c.1433del NP_001393586.1:p.Leu478fs frameshift NM_001406658.1:c.77del NP_001393587.1:p.Leu26fs frameshift NM_001406659.1:c.77del NP_001393588.1:p.Leu26fs frameshift NM_001406660.1:c.77del NP_001393589.1:p.Leu26fs frameshift NM_001406661.1:c.77del NP_001393590.1:p.Leu26fs frameshift NM_001406662.1:c.77del NP_001393591.1:p.Leu26fs frameshift NM_001406669.1:c.77del NP_001393598.1:p.Leu26fs frameshift NM_001406674.1:c.1433del NP_001393603.1:p.Leu478fs frameshift NR_176230.1:n.1469del non-coding transcript variant NR_176231.1:n.1469del non-coding transcript variant NR_176232.1:n.1469del non-coding transcript variant NR_176233.1:n.1311del non-coding transcript variant NR_176234.1:n.1469del non-coding transcript variant NR_176235.1:n.1469del non-coding transcript variant NR_176236.1:n.1469del non-coding transcript variant NR_176237.1:n.1469del non-coding transcript variant NR_176238.1:n.1469del non-coding transcript variant NR_176239.1:n.1469del non-coding transcript variant NR_176240.1:n.1469del non-coding transcript variant NR_176241.1:n.1469del non-coding transcript variant NR_176242.1:n.1469del non-coding transcript variant NR_176243.1:n.1319del non-coding transcript variant NR_176244.1:n.1469del non-coding transcript variant NR_176245.1:n.1469del non-coding transcript variant NR_176246.1:n.1469del non-coding transcript variant NR_176247.1:n.1469del non-coding transcript variant NR_176248.1:n.1469del non-coding transcript variant NR_176249.1:n.1699del non-coding transcript variant NR_176250.1:n.1209del non-coding transcript variant NC_000002.12:g.47463077del NC_000002.11:g.47690216del NG_007110.2:g.64954del LRG_218:g.64954del LRG_218t1:c.1433del LRG_218p1:p.Leu478Profs - Protein change
- L179fs, L26fs, L338fs, L412fs, L428fs, L458fs, L467fs, L478fs, L491fs
- Other names
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- Canonical SPDI
- NC_000002.12:47463076:T:
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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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| MSH2 | Sufficient evidence for dosage pathogenicity | No evidence available |
GRCh38 GRCh37 |
7404 | 7566 | |
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
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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Aug 2, 2023 | RCV003450105.1 |
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
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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
(Aug 02, 2023)
|
criteria provided, single submitter
Method: clinical testing
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Lynch syndrome 1
Affected status: unknown
Allele origin:
unknown
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Myriad Genetics, Inc.
Accession: SCV004187829.1
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.
|
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 frameshift 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 Jun 10, 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.