This variant is considered pathogenic. This variant creates a frameshift predicted to result in premature protein truncation.
ClinVar Genomic variation as it relates to human health
NM_000251.3(MSH2):c.493_499del (p.Tyr165fs)
Germline
Classification
Help
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.
(1)
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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.
Pathogenic
1
criteria provided, single submitter
Somatic
No data submitted for somatic clinical impact
Somatic
No data submitted for oncogenicity
Variant Details
- Identifiers
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NM_000251.3(MSH2):c.493_499del (p.Tyr165fs)
Variation ID: 2673418 Accession: VCV002673418.1
- Type and length
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Deletion, 7 bp
- Location
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Cytogenetic: 2p21 2: 47410218-47410224 (GRCh38) [ NCBI UCSC ] 2: 47637357-47637363 (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 22, 2023 - HGVS
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... more HGVS ... less HGVSNucleotide Protein Molecular
consequenceNM_000251.3:c.493_499del MANE Select Help Transcripts from the Matched Annotation from the NCBI and EMBL-EBI (MANE) collaboration.
NP_000242.1:p.Tyr165fs frameshift NM_001258281.1:c.295_301del NP_001245210.1:p.Tyr99fs frameshift NM_001406631.1:c.493_499del NP_001393560.1:p.Tyr165fs frameshift NM_001406632.1:c.493_499del NP_001393561.1:p.Tyr165fs frameshift NM_001406633.1:c.493_499del NP_001393562.1:p.Tyr165fs frameshift NM_001406634.1:c.493_499del NP_001393563.1:p.Tyr165fs frameshift NM_001406635.1:c.493_499del NP_001393564.1:p.Tyr165fs frameshift NM_001406636.1:c.493_499del NP_001393565.1:p.Tyr165fs frameshift NM_001406637.1:c.493_499del NP_001393566.1:p.Tyr165fs frameshift NM_001406638.1:c.493_499del NP_001393567.1:p.Tyr165fs frameshift NM_001406639.1:c.493_499del NP_001393568.1:p.Tyr165fs frameshift NM_001406640.1:c.493_499del NP_001393569.1:p.Tyr165fs frameshift NM_001406641.1:c.493_499del NP_001393570.1:p.Tyr165fs frameshift NM_001406642.1:c.493_499del NP_001393571.1:p.Tyr165fs frameshift NM_001406643.1:c.493_499del NP_001393572.1:p.Tyr165fs frameshift NM_001406644.1:c.493_499del NP_001393573.1:p.Tyr165fs frameshift NM_001406645.1:c.493_499del NP_001393574.1:p.Tyr165fs frameshift NM_001406646.1:c.493_499del NP_001393575.1:p.Tyr165fs frameshift NM_001406647.1:c.493_499del NP_001393576.1:p.Tyr165fs frameshift NM_001406648.1:c.493_499del NP_001393577.1:p.Tyr165fs frameshift NM_001406649.1:c.493_499del NP_001393578.1:p.Tyr165fs frameshift NM_001406650.1:c.493_499del NP_001393579.1:p.Tyr165fs frameshift NM_001406651.1:c.493_499del NP_001393580.1:p.Tyr165fs frameshift NM_001406652.1:c.493_499del NP_001393581.1:p.Tyr165fs frameshift NM_001406653.1:c.433_439del NP_001393582.1:p.Tyr145fs frameshift NM_001406654.1:c.73_79del NP_001393583.1:p.Tyr25fs frameshift NM_001406655.1:c.493_499del NP_001393584.1:p.Tyr165fs frameshift NM_001406656.1:c.-503_-497del 5 prime UTR NM_001406657.1:c.493_499del NP_001393586.1:p.Tyr165fs frameshift NM_001406658.1:c.-826_-820del 5 prime UTR NM_001406659.1:c.-976_-970del 5 prime UTR NM_001406660.1:c.-1173_-1167del 5 prime UTR NM_001406661.1:c.-1128_-1122del 5 prime UTR NM_001406662.1:c.-1045_-1039del 5 prime UTR NM_001406666.1:c.493_499del NP_001393595.1:p.Tyr165fs frameshift NM_001406669.1:c.-976_-970del 5 prime UTR NM_001406672.1:c.493_499del NP_001393601.1:p.Tyr165fs frameshift NM_001406674.1:c.493_499del NP_001393603.1:p.Tyr165fs frameshift NR_176230.1:n.529_535del non-coding transcript variant NR_176231.1:n.529_535del non-coding transcript variant NR_176232.1:n.529_535del non-coding transcript variant NR_176233.1:n.521_527del non-coding transcript variant NR_176234.1:n.529_535del non-coding transcript variant NR_176235.1:n.529_535del non-coding transcript variant NR_176236.1:n.529_535del non-coding transcript variant NR_176237.1:n.529_535del non-coding transcript variant NR_176238.1:n.529_535del non-coding transcript variant NR_176239.1:n.529_535del non-coding transcript variant NR_176240.1:n.529_535del non-coding transcript variant NR_176241.1:n.529_535del non-coding transcript variant NR_176242.1:n.529_535del non-coding transcript variant NR_176243.1:n.529_535del non-coding transcript variant NR_176244.1:n.529_535del non-coding transcript variant NR_176245.1:n.529_535del non-coding transcript variant NR_176246.1:n.529_535del non-coding transcript variant NR_176247.1:n.529_535del non-coding transcript variant NR_176248.1:n.529_535del non-coding transcript variant NR_176249.1:n.529_535del non-coding transcript variant NR_176250.1:n.529_535del non-coding transcript variant NC_000002.12:g.47410220_47410226del NC_000002.11:g.47637359_47637365del NG_007110.2:g.12097_12103del LRG_218:g.12097_12103del LRG_218t1:c.493_499del LRG_218p1:p.Tyr165Ilefs - Protein change
- Y145fs, Y165fs, Y25fs, Y99fs
- Other names
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- Canonical SPDI
- NC_000002.12:47410217:GGTATGTGG:GG
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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 | ||
|---|---|---|---|---|---|---|
| HI score
Help
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
Help
The number of variants in ClinVar that are contained within this gene, with a link to view the list of variants. |
All
Help
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 |
7404 | 7566 | |
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
Help
The RCV accession number, with most recent version number, for the variant-condition record, with a link to the RCV web page. |
|---|---|---|---|---|
| Pathogenic (1) |
criteria provided, single submitter
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Aug 22, 2023 | RCV003450141.1 |
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
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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
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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|---|---|---|---|---|---|
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Pathogenic
(Aug 22, 2023)
|
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: SCV004187902.1
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.
|
Comment:
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. |
Comment:
This variant is considered pathogenic. This variant creates a frameshift predicted to result in premature protein truncation.
Citations for germline classification of this variant
Help| There 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.