ClinVar Genomic variation as it relates to human health
NM_000251.3(MSH2):c.1140_1141del (p.Leu380fs)
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_000251.3(MSH2):c.1140_1141del (p.Leu380fs)
Variation ID: 2673392 Accession: VCV002673392.1
- Type and length
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Deletion, 2 bp
- Location
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Cytogenetic: 2p21 2: 47429805-47429806 (GRCh38) [ NCBI UCSC ] 2: 47656944-47656945 (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 Jul 31, 2023 - HGVS
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Nucleotide Protein Molecular
consequenceNM_000251.3:c.1140_1141del MANE Select Help Transcripts from the Matched Annotation from the NCBI and EMBL-EBI (MANE) collaboration.
NP_000242.1:p.Leu380fs frameshift NM_001258281.1:c.942_943del NP_001245210.1:p.Leu314fs frameshift NM_001406631.1:c.1140_1141del NP_001393560.1:p.Leu380fs frameshift NM_001406632.1:c.1140_1141del NP_001393561.1:p.Leu380fs frameshift NM_001406633.1:c.1140_1141del NP_001393562.1:p.Leu380fs frameshift NM_001406634.1:c.1140_1141del NP_001393563.1:p.Leu380fs frameshift NM_001406635.1:c.1140_1141del NP_001393564.1:p.Leu380fs frameshift NM_001406636.1:c.1107_1108del NP_001393565.1:p.Leu369fs frameshift NM_001406637.1:c.1140_1141del NP_001393566.1:p.Leu380fs frameshift NM_001406638.1:c.1140_1141del NP_001393567.1:p.Leu380fs frameshift NM_001406639.1:c.1140_1141del NP_001393568.1:p.Leu380fs frameshift NM_001406640.1:c.1140_1141del NP_001393569.1:p.Leu380fs frameshift NM_001406641.1:c.1140_1141del NP_001393570.1:p.Leu380fs frameshift NM_001406642.1:c.1140_1141del NP_001393571.1:p.Leu380fs frameshift NM_001406643.1:c.1140_1141del NP_001393572.1:p.Leu380fs frameshift NM_001406644.1:c.1140_1141del NP_001393573.1:p.Leu380fs frameshift NM_001406645.1:c.1140_1141del NP_001393574.1:p.Leu380fs frameshift NM_001406646.1:c.1140_1141del NP_001393575.1:p.Leu380fs frameshift NM_001406647.1:c.990_991del NP_001393576.1:p.Leu330fs frameshift NM_001406648.1:c.1140_1141del NP_001393577.1:p.Leu380fs frameshift NM_001406649.1:c.990_991del NP_001393578.1:p.Leu330fs frameshift NM_001406650.1:c.990_991del NP_001393579.1:p.Leu330fs frameshift NM_001406651.1:c.990_991del NP_001393580.1:p.Leu330fs frameshift NM_001406652.1:c.990_991del NP_001393581.1:p.Leu330fs frameshift NM_001406653.1:c.1080_1081del NP_001393582.1:p.Leu360fs frameshift NM_001406654.1:c.720_721del NP_001393583.1:p.Leu240fs frameshift NM_001406655.1:c.1140_1141del NP_001393584.1:p.Leu380fs frameshift NM_001406656.1:c.243_244del NP_001393585.1:p.Leu81fs frameshift NM_001406657.1:c.1140_1141del NP_001393586.1:p.Leu380fs frameshift NM_001406658.1:c.-217_-216del 5 prime UTR NM_001406659.1:c.-217_-216del 5 prime UTR NM_001406660.1:c.-217_-216del 5 prime UTR NM_001406661.1:c.-217_-216del 5 prime UTR NM_001406662.1:c.-217_-216del 5 prime UTR NM_001406666.1:c.1140_1141del NP_001393595.1:p.Leu380fs frameshift NM_001406669.1:c.-217_-216del 5 prime UTR NM_001406672.1:c.990_991del NP_001393601.1:p.Leu330fs frameshift NM_001406674.1:c.1140_1141del NP_001393603.1:p.Leu380fs frameshift NR_176230.1:n.1176_1177del non-coding transcript variant NR_176231.1:n.1176_1177del non-coding transcript variant NR_176232.1:n.1176_1177del non-coding transcript variant NR_176233.1:n.1018_1019del non-coding transcript variant NR_176234.1:n.1176_1177del non-coding transcript variant NR_176235.1:n.1176_1177del non-coding transcript variant NR_176236.1:n.1176_1177del non-coding transcript variant NR_176237.1:n.1176_1177del non-coding transcript variant NR_176238.1:n.1176_1177del non-coding transcript variant NR_176239.1:n.1176_1177del non-coding transcript variant NR_176240.1:n.1176_1177del non-coding transcript variant NR_176241.1:n.1176_1177del non-coding transcript variant NR_176242.1:n.1176_1177del non-coding transcript variant NR_176243.1:n.1026_1027del non-coding transcript variant NR_176244.1:n.1176_1177del non-coding transcript variant NR_176245.1:n.1176_1177del non-coding transcript variant NR_176246.1:n.1176_1177del non-coding transcript variant NR_176247.1:n.1176_1177del non-coding transcript variant NR_176248.1:n.1176_1177del non-coding transcript variant NR_176249.1:n.1176_1177del non-coding transcript variant NR_176250.1:n.1026_1027del non-coding transcript variant NC_000002.12:g.47429805_47429806del NC_000002.11:g.47656944_47656945del NG_007110.2:g.31682_31683del LRG_218:g.31682_31683del LRG_218t1:c.1140_1141del LRG_218p1:p.Leu380Phefs - Protein change
- L240fs, L314fs, L330fs, L360fs, L369fs, L380fs, L81fs
- Other names
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- Canonical SPDI
- NC_000002.12:47429804:AC:
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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
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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
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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
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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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MSH2 | Sufficient evidence for dosage pathogenicity | No evidence available |
GRCh38 GRCh37 |
7401 | 7563 |
Conditions - Germline
Condition
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The condition for this variant-condition (RCV) record in ClinVar. |
Classification
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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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Jul 31, 2023 | RCV003450115.1 |
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
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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
(Jul 31, 2023)
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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: SCV004187857.1
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 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.