ClinVar Genomic variation as it relates to human health
NM_000251.3(MSH2):c.1869del (p.Ile624fs)
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.1869del (p.Ile624fs)
Variation ID: 1781619 Accession: VCV001781619.3
- Type and length
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Deletion, 1 bp
- Location
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Cytogenetic: 2p21 2: 47475133 (GRCh38) [ NCBI UCSC ] 2: 47702272 (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 Nov 29, 2022 May 1, 2024 Aug 4, 2023 - HGVS
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Nucleotide Protein Molecular
consequenceNM_000251.3:c.1869del MANE Select Help Transcripts from the Matched Annotation from the NCBI and EMBL-EBI (MANE) collaboration.
NP_000242.1:p.Ile624fs frameshift NM_001258281.1:c.1671del NP_001245210.1:p.Ile558fs frameshift NM_001406631.1:c.1869delC NP_001393560.1:p.Ile624Phefs frameshift NM_001406632.1:c.1869delC NP_001393561.1:p.Ile624Phefs frameshift NM_001406633.1:c.1869delC NP_001393562.1:p.Ile624Phefs frameshift NM_001406634.1:c.1869delC NP_001393563.1:p.Ile624Phefs frameshift NM_001406635.1:c.1869delC NP_001393564.1:p.Ile624Phefs frameshift NM_001406636.1:c.1836delC NP_001393565.1:p.Ile613Phefs frameshift NM_001406637.1:c.1869delC NP_001393566.1:p.Ile624Phefs frameshift NM_001406638.1:c.1908delC NP_001393567.1:p.Ile637Phefs frameshift NM_001406639.1:c.1869delC NP_001393568.1:p.Ile624Phefs frameshift NM_001406640.1:c.1869delC NP_001393569.1:p.Ile624Phefs frameshift NM_001406641.1:c.1869delC NP_001393570.1:p.Ile624Phefs frameshift NM_001406642.1:c.1869delC NP_001393571.1:p.Ile624Phefs frameshift NM_001406643.1:c.1869delC NP_001393572.1:p.Ile624Phefs frameshift NM_001406644.1:c.1869delC NP_001393573.1:p.Ile624Phefs frameshift NM_001406645.1:c.1869delC NP_001393574.1:p.Ile624Phefs frameshift NM_001406646.1:c.1869delC NP_001393575.1:p.Ile624Phefs frameshift NM_001406647.1:c.1719delC NP_001393576.1:p.Ile574Phefs frameshift NM_001406648.1:c.1869delC NP_001393577.1:p.Ile624Phefs frameshift NM_001406649.1:c.1719delC NP_001393578.1:p.Ile574Phefs frameshift NM_001406650.1:c.1719delC NP_001393579.1:p.Ile574Phefs frameshift NM_001406651.1:c.1719delC NP_001393580.1:p.Ile574Phefs frameshift NM_001406652.1:c.1719delC NP_001393581.1:p.Ile574Phefs frameshift NM_001406653.1:c.1809delC NP_001393582.1:p.Ile604Phefs frameshift NM_001406654.1:c.1449delC NP_001393583.1:p.Ile484Phefs frameshift NM_001406655.1:c.1869delC NP_001393584.1:p.Ile624Phefs frameshift NM_001406656.1:c.972delC NP_001393585.1:p.Ile325Phefs frameshift NM_001406657.1:c.*79delC NM_001406658.1:c.513delC NP_001393587.1:p.Ile172Phefs frameshift NM_001406659.1:c.513delC NP_001393588.1:p.Ile172Phefs frameshift NM_001406660.1:c.513delC NP_001393589.1:p.Ile172Phefs frameshift NM_001406661.1:c.513delC NP_001393590.1:p.Ile172Phefs frameshift NM_001406662.1:c.513delC NP_001393591.1:p.Ile172Phefs frameshift NM_001406669.1:c.513delC NP_001393598.1:p.Ile172Phefs frameshift NM_001406674.1:c.1869delC NP_001393603.1:p.Ile624Phefs frameshift NR_176230.1:n.1905delC NR_176231.1:n.1905delC NR_176232.1:n.1905delC NR_176233.1:n.1747delC NR_176234.1:n.1905delC NR_176235.1:n.1905delC NR_176236.1:n.1905delC NR_176237.1:n.1905delC NR_176238.1:n.2038delC NR_176239.1:n.1905delC NR_176240.1:n.1905delC NR_176241.1:n.1905delC NR_176242.1:n.1905delC NR_176243.1:n.1755delC NR_176244.1:n.1905delC NR_176245.1:n.1905delC NR_176246.1:n.1905delC NR_176247.1:n.1905delC NR_176248.1:n.1905delC NR_176249.1:n.2135delC NR_176250.1:n.1645delC NC_000002.12:g.47475134del NC_000002.11:g.47702273del NG_007110.2:g.77011del LRG_218:g.77011del LRG_218t1:c.1869del LRG_218p1:p.Ile624Phefs - Protein change
- I624fs, I558fs
- Other names
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- Canonical SPDI
- NC_000002.12:47475132:CC:C
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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
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
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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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Dec 19, 2019 | RCV002415036.2 | |
Pathogenic (1) |
criteria provided, single submitter
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Aug 4, 2023 | RCV003454294.1 |
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
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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 04, 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: SCV004186910.1
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
(Dec 19, 2019)
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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: SCV002723170.2
First in ClinVar: Nov 29, 2022 Last updated: May 01, 2024 |
Comment:
The c.1869delC pathogenic mutation, located in coding exon 12 of the MSH2 gene, results from a deletion of one nucleotide at nucleotide position 1869, causing … (more)
The c.1869delC pathogenic mutation, located in coding exon 12 of the MSH2 gene, results from a deletion of one nucleotide at nucleotide position 1869, causing a translational frameshift with a predicted alternate stop codon (p.I624Ffs*11). 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 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.