ClinVar Genomic variation as it relates to human health
NM_000251.3(MSH2):c.2263del (p.Ser755fs)
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.2263del (p.Ser755fs)
Variation ID: 2673472 Accession: VCV002673472.2
- Type and length
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Deletion, 1 bp
- Location
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Cytogenetic: 2p21 2: 47478323 (GRCh38) [ NCBI UCSC ] 2: 47705462 (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 Aug 11, 2024 May 2, 2024 - HGVS
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Nucleotide Protein Molecular
consequenceNM_000251.3:c.2263del MANE Select Help Transcripts from the Matched Annotation from the NCBI and EMBL-EBI (MANE) collaboration.
NP_000242.1:p.Ser755fs frameshift NM_000251.1:c.2263delT NM_001258281.1:c.2065del NP_001245210.1:p.Ser689fs frameshift NM_001406631.1:c.2263del NP_001393560.1:p.Ser755fs frameshift NM_001406632.1:c.2263del NP_001393561.1:p.Ser755fs frameshift NM_001406633.1:c.2263del NP_001393562.1:p.Ser755fs frameshift NM_001406634.1:c.2263del NP_001393563.1:p.Ser755fs frameshift NM_001406635.1:c.2263del NP_001393564.1:p.Ser755fs frameshift NM_001406636.1:c.2230del NP_001393565.1:p.Ser744fs frameshift NM_001406637.1:c.2263del NP_001393566.1:p.Ser755fs frameshift NM_001406638.1:c.2302del NP_001393567.1:p.Ser768fs frameshift NM_001406639.1:c.2263del NP_001393568.1:p.Ser755fs frameshift NM_001406640.1:c.2263del NP_001393569.1:p.Ser755fs frameshift NM_001406641.1:c.2263del NP_001393570.1:p.Ser755fs frameshift NM_001406642.1:c.2263del NP_001393571.1:p.Ser755fs frameshift NM_001406643.1:c.2263del NP_001393572.1:p.Ser755fs frameshift NM_001406644.1:c.2263del NP_001393573.1:p.Ser755fs frameshift NM_001406645.1:c.2263del NP_001393574.1:p.Ser755fs frameshift NM_001406646.1:c.2263del NP_001393575.1:p.Ser755fs frameshift NM_001406647.1:c.2113del NP_001393576.1:p.Ser705fs frameshift NM_001406648.1:c.2263del NP_001393577.1:p.Ser755fs frameshift NM_001406649.1:c.2113del NP_001393578.1:p.Ser705fs frameshift NM_001406650.1:c.2113del NP_001393579.1:p.Ser705fs frameshift NM_001406651.1:c.2113del NP_001393580.1:p.Ser705fs frameshift NM_001406652.1:c.2113del NP_001393581.1:p.Ser705fs frameshift NM_001406653.1:c.2203del NP_001393582.1:p.Ser735fs frameshift NM_001406654.1:c.1843del NP_001393583.1:p.Ser615fs frameshift NM_001406656.1:c.1366del NP_001393585.1:p.Ser456fs frameshift NM_001406658.1:c.907del NP_001393587.1:p.Ser303fs frameshift NM_001406659.1:c.907del NP_001393588.1:p.Ser303fs frameshift NM_001406660.1:c.907del NP_001393589.1:p.Ser303fs frameshift NM_001406661.1:c.907del NP_001393590.1:p.Ser303fs frameshift NM_001406662.1:c.907del NP_001393591.1:p.Ser303fs frameshift NM_001406669.1:c.907del NP_001393598.1:p.Ser303fs frameshift NM_001406674.1:c.2263del NP_001393603.1:p.Ser755fs frameshift NR_176230.1:n.2299del non-coding transcript variant NR_176231.1:n.2267del non-coding transcript variant NR_176232.1:n.2299del non-coding transcript variant NR_176233.1:n.2141del non-coding transcript variant NR_176234.1:n.2299del non-coding transcript variant NR_176235.1:n.2299del non-coding transcript variant NR_176236.1:n.2299del non-coding transcript variant NR_176237.1:n.2299del non-coding transcript variant NR_176238.1:n.2432del non-coding transcript variant NR_176239.1:n.2299del non-coding transcript variant NR_176240.1:n.2094del non-coding transcript variant NR_176241.1:n.2299del non-coding transcript variant NR_176242.1:n.2299del non-coding transcript variant NR_176243.1:n.2149del non-coding transcript variant NR_176244.1:n.2299del non-coding transcript variant NR_176245.1:n.2299del non-coding transcript variant NR_176246.1:n.2299del non-coding transcript variant NR_176247.1:n.2299del non-coding transcript variant NR_176248.1:n.2299del non-coding transcript variant NR_176249.1:n.2529del non-coding transcript variant NR_176250.1:n.2039del non-coding transcript variant NC_000002.12:g.47478324del NC_000002.11:g.47705463del NG_007110.2:g.80201del LRG_218:g.80201del LRG_218t1:c.2263del LRG_218p1:p.Ser755Leufs - Protein change
- S303fs, S456fs, S615fs, S689fs, S705fs, S735fs, S744fs, S755fs, S768fs
- Other names
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- Canonical SPDI
- NC_000002.12:47478322:TT: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
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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 |
7394 | 7556 |
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
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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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Aug 8, 2023 | RCV003450194.1 | |
Pathogenic (1) |
criteria provided, single submitter
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May 2, 2024 | RCV004636739.1 |
Submissions - Germline
Classification
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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
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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
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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
(Aug 08, 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: SCV004188971.1
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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Pathogenic
(May 02, 2024)
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criteria provided, single submitter
Method: clinical testing
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Hereditary cancer-predisposing syndrome
Affected status: unknown
Allele origin:
germline
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Ambry Genetics
Accession: SCV005141921.1
First in ClinVar: Aug 11, 2024 Last updated: Aug 11, 2024 |
Comment:
The c.2263delT pathogenic mutation, located in coding exon 14 of the MSH2 gene, results from a deletion of one nucleotide at nucleotide position 2263, causing … (more)
The c.2263delT pathogenic mutation, located in coding exon 14 of the MSH2 gene, results from a deletion of one nucleotide at nucleotide position 2263, causing a translational frameshift with a predicted alternate stop codon (p.S755Lfs*8). This variant is considered to be rare based on population cohorts in the Genome Aggregation Database (gnomAD). This alteration is expected to result in loss of function by premature protein truncation or nonsense-mediated mRNA decay. As such, this alteration is interpreted as a disease-causing mutation. (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 Aug 11, 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.