ClinVar Genomic variation as it relates to human health
NM_000251.3(MSH2):c.2222_2225del (p.Lys741fs)
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.2222_2225del (p.Lys741fs)
Variation ID: 2673461 Accession: VCV002673461.1
- Type and length
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Deletion, 4 bp
- Location
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Cytogenetic: 2p21 2: 47478282-47478285 (GRCh38) [ NCBI UCSC ] 2: 47705421-47705424 (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 8, 2023 - HGVS
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Nucleotide Protein Molecular
consequenceNM_000251.3:c.2222_2225del MANE Select Help Transcripts from the Matched Annotation from the NCBI and EMBL-EBI (MANE) collaboration.
NP_000242.1:p.Lys741fs frameshift NM_001258281.1:c.2024_2027del NP_001245210.1:p.Lys675fs frameshift NM_001406631.1:c.2222_2225del NP_001393560.1:p.Lys741fs frameshift NM_001406632.1:c.2222_2225del NP_001393561.1:p.Lys741fs frameshift NM_001406633.1:c.2222_2225del NP_001393562.1:p.Lys741fs frameshift NM_001406634.1:c.2222_2225del NP_001393563.1:p.Lys741fs frameshift NM_001406635.1:c.2222_2225del NP_001393564.1:p.Lys741fs frameshift NM_001406636.1:c.2189_2192del NP_001393565.1:p.Lys730fs frameshift NM_001406637.1:c.2222_2225del NP_001393566.1:p.Lys741fs frameshift NM_001406638.1:c.2261_2264del NP_001393567.1:p.Lys754fs frameshift NM_001406639.1:c.2222_2225del NP_001393568.1:p.Lys741fs frameshift NM_001406640.1:c.2222_2225del NP_001393569.1:p.Lys741fs frameshift NM_001406641.1:c.2222_2225del NP_001393570.1:p.Lys741fs frameshift NM_001406642.1:c.2222_2225del NP_001393571.1:p.Lys741fs frameshift NM_001406643.1:c.2222_2225del NP_001393572.1:p.Lys741fs frameshift NM_001406644.1:c.2222_2225del NP_001393573.1:p.Lys741fs frameshift NM_001406645.1:c.2222_2225del NP_001393574.1:p.Lys741fs frameshift NM_001406646.1:c.2222_2225del NP_001393575.1:p.Lys741fs frameshift NM_001406647.1:c.2072_2075del NP_001393576.1:p.Lys691fs frameshift NM_001406648.1:c.2222_2225del NP_001393577.1:p.Lys741fs frameshift NM_001406649.1:c.2072_2075del NP_001393578.1:p.Lys691fs frameshift NM_001406650.1:c.2072_2075del NP_001393579.1:p.Lys691fs frameshift NM_001406651.1:c.2072_2075del NP_001393580.1:p.Lys691fs frameshift NM_001406652.1:c.2072_2075del NP_001393581.1:p.Lys691fs frameshift NM_001406653.1:c.2162_2165del NP_001393582.1:p.Lys721fs frameshift NM_001406654.1:c.1802_1805del NP_001393583.1:p.Lys601fs frameshift NM_001406656.1:c.1325_1328del NP_001393585.1:p.Lys442fs frameshift NM_001406658.1:c.866_869del NP_001393587.1:p.Lys289fs frameshift NM_001406659.1:c.866_869del NP_001393588.1:p.Lys289fs frameshift NM_001406660.1:c.866_869del NP_001393589.1:p.Lys289fs frameshift NM_001406661.1:c.866_869del NP_001393590.1:p.Lys289fs frameshift NM_001406662.1:c.866_869del NP_001393591.1:p.Lys289fs frameshift NM_001406669.1:c.866_869del NP_001393598.1:p.Lys289fs frameshift NM_001406674.1:c.2222_2225del NP_001393603.1:p.Lys741fs frameshift NR_176230.1:n.2258_2261del non-coding transcript variant NR_176232.1:n.2258_2261del non-coding transcript variant NR_176233.1:n.2100_2103del non-coding transcript variant NR_176234.1:n.2258_2261del non-coding transcript variant NR_176235.1:n.2258_2261del non-coding transcript variant NR_176236.1:n.2258_2261del non-coding transcript variant NR_176237.1:n.2258_2261del non-coding transcript variant NR_176238.1:n.2391_2394del non-coding transcript variant NR_176239.1:n.2258_2261del non-coding transcript variant NR_176240.1:n.2053_2056del non-coding transcript variant NR_176241.1:n.2258_2261del non-coding transcript variant NR_176242.1:n.2258_2261del non-coding transcript variant NR_176243.1:n.2108_2111del non-coding transcript variant NR_176244.1:n.2258_2261del non-coding transcript variant NR_176245.1:n.2258_2261del non-coding transcript variant NR_176246.1:n.2258_2261del non-coding transcript variant NR_176247.1:n.2258_2261del non-coding transcript variant NR_176248.1:n.2258_2261del non-coding transcript variant NR_176249.1:n.2488_2491del non-coding transcript variant NR_176250.1:n.1998_2001del non-coding transcript variant NC_000002.12:g.47478283_47478286del NC_000002.11:g.47705422_47705425del NG_007110.2:g.80160_80163del LRG_218:g.80160_80163del LRG_218t1:c.2222_2225del LRG_218p1:p.Lys741Ilefs - Protein change
- K289fs, K442fs, K601fs, K675fs, K691fs, K721fs, K730fs, K741fs, K754fs
- Other names
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- Canonical SPDI
- NC_000002.12:47478281:AAAGA:A
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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 |
7313 | 7466 |
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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Aug 8, 2023 | RCV003450183.1 |
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
(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: SCV004188181.1
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 Dec 30, 2023
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.