ClinVar Genomic variation as it relates to human health
NM_000251.3(MSH2):c.871_872dup (p.Leu291_Thr292insTer)
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.871_872dup (p.Leu291_Thr292insTer)
Variation ID: 2673365 Accession: VCV002673365.2
- Type and length
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Duplication, 2 bp
- Location
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Cytogenetic: 2p21 2: 47414346-47414347 (GRCh38) [ NCBI UCSC ] 2: 47641485-47641486 (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 Jan 6, 2024 Jul 28, 2023 - HGVS
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Nucleotide Protein Molecular
consequenceNM_000251.3:c.871_872dup MANE Select Help Transcripts from the Matched Annotation from the NCBI and EMBL-EBI (MANE) collaboration.
NP_000242.1:p.Leu291_Thr292insTer frameshift NM_001258281.1:c.673_674dup NP_001245210.1:p.Leu225_Thr226insTer frameshift NM_001406631.1:c.871_872dup NP_001393560.1:p.Leu291_Thr292insTer frameshift NM_001406632.1:c.871_872dup NP_001393561.1:p.Leu291_Thr292insTer frameshift NM_001406633.1:c.871_872dup NP_001393562.1:p.Leu291_Thr292insTer frameshift NM_001406634.1:c.871_872dup NP_001393563.1:p.Leu291_Thr292insTer frameshift NM_001406635.1:c.871_872dup NP_001393564.1:p.Leu291_Thr292insTer frameshift NM_001406636.1:c.838_839dup NP_001393565.1:p.Leu280_Thr281insTer frameshift NM_001406637.1:c.871_872dup NP_001393566.1:p.Leu291_Thr292insTer frameshift NM_001406638.1:c.871_872dup NP_001393567.1:p.Leu291_Thr292insTer frameshift NM_001406639.1:c.871_872dup NP_001393568.1:p.Leu291_Thr292insTer frameshift NM_001406640.1:c.871_872dup NP_001393569.1:p.Leu291_Thr292insTer frameshift NM_001406641.1:c.871_872dup NP_001393570.1:p.Leu291_Thr292insTer frameshift NM_001406642.1:c.871_872dup NP_001393571.1:p.Leu291_Thr292insTer frameshift NM_001406643.1:c.871_872dup NP_001393572.1:p.Leu291_Thr292insTer frameshift NM_001406644.1:c.871_872dup NP_001393573.1:p.Leu291_Thr292insTer frameshift NM_001406645.1:c.871_872dup NP_001393574.1:p.Leu291_Thr292insTer frameshift NM_001406646.1:c.871_872dup NP_001393575.1:p.Leu291_Thr292insTer frameshift NM_001406647.1:c.792+1787_792+1788dup intron variant NM_001406648.1:c.871_872dup NP_001393577.1:p.Leu291_Thr292insTer frameshift NM_001406649.1:c.792+1787_792+1788dup intron variant NM_001406650.1:c.792+1787_792+1788dup intron variant NM_001406651.1:c.792+1787_792+1788dup intron variant NM_001406652.1:c.792+1787_792+1788dup intron variant NM_001406653.1:c.811_812dup NP_001393582.1:p.Leu271_Thr272insTer frameshift NM_001406654.1:c.451_452dup NP_001393583.1:p.Leu151_Thr152insTer frameshift NM_001406655.1:c.871_872dup NP_001393584.1:p.Leu291_Thr292insTer frameshift NM_001406656.1:c.-27_-26dup 5 prime UTR NM_001406657.1:c.871_872dup NP_001393586.1:p.Leu291_Thr292insTer frameshift NM_001406658.1:c.-527+1787_-527+1788dup intron variant NM_001406659.1:c.-598_-597dup 5 prime UTR NM_001406660.1:c.-795_-794dup 5 prime UTR NM_001406661.1:c.-750_-749dup 5 prime UTR NM_001406662.1:c.-667_-666dup 5 prime UTR NM_001406666.1:c.871_872dup NP_001393595.1:p.Leu291_Thr292insTer frameshift NM_001406669.1:c.-598_-597dup 5 prime UTR NM_001406672.1:c.792+1787_792+1788dup intron variant NM_001406674.1:c.871_872dup NP_001393603.1:p.Leu291_Thr292insTer frameshift NR_176230.1:n.907_908dup non-coding transcript variant NR_176231.1:n.907_908dup non-coding transcript variant NR_176232.1:n.907_908dup non-coding transcript variant NR_176234.1:n.907_908dup non-coding transcript variant NR_176235.1:n.907_908dup non-coding transcript variant NR_176236.1:n.907_908dup non-coding transcript variant NR_176237.1:n.907_908dup non-coding transcript variant NR_176238.1:n.907_908dup non-coding transcript variant NR_176239.1:n.907_908dup non-coding transcript variant NR_176240.1:n.907_908dup non-coding transcript variant NR_176241.1:n.907_908dup non-coding transcript variant NR_176242.1:n.907_908dup non-coding transcript variant NR_176244.1:n.907_908dup non-coding transcript variant NR_176245.1:n.907_908dup non-coding transcript variant NR_176246.1:n.907_908dup non-coding transcript variant NR_176247.1:n.907_908dup non-coding transcript variant NR_176248.1:n.907_908dup non-coding transcript variant NR_176249.1:n.907_908dup non-coding transcript variant NC_000002.12:g.47414347_47414348dup NC_000002.11:g.47641486_47641487dup NG_007110.2:g.16224_16225dup LRG_218:g.16224_16225dup LRG_218t1:c.871_872dup LRG_218p1:p.Thr292Terfs - Protein change
- Other names
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- Canonical SPDI
- NC_000002.12:47414346:CT:CTCT
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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 | ||
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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
Help
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 |
7325 | 7478 |
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
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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 28, 2023 | RCV003450088.1 | |
Likely pathogenic (1) |
criteria provided, single submitter
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Jun 7, 2023 | RCV003477090.1 |
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
(Jul 28, 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: SCV004187030.1
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.
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Likely pathogenic
(Jun 07, 2023)
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criteria provided, single submitter
Method: clinical testing
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not provided
Affected status: unknown
Allele origin:
unknown
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Quest Diagnostics Nichols Institute San Juan Capistrano
Accession: SCV004221023.1
First in ClinVar: Jan 06, 2024 Last updated: Jan 06, 2024 |
Comment:
The MSH2 c.871_872dup (p.Thr292*) variant alters the translational reading frame of the MSH2 mRNA and is predicted to cause the premature termination of MSH2 protein … (more)
The MSH2 c.871_872dup (p.Thr292*) variant alters the translational reading frame of the MSH2 mRNA and is predicted to cause the premature termination of MSH2 protein synthesis. This variant has not been reported in individuals with MSH2-related conditions in the published literature. This variant has not been reported in large, multi-ethnic general populations (Genome Aggregation Database, http://gnomad.broadinstitute.org). Based on the available information, this variant is classified as likely pathogenic. (less)
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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.