ClinVar Genomic variation as it relates to human health
NM_000251.3(MSH2):c.2135_2137del (p.Val712del)
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.2135_2137del (p.Val712del)
Variation ID: 2453502 Accession: VCV002453502.2
- Type and length
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Deletion, 3 bp
- Location
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Cytogenetic: 2p21 2: 47476494-47476496 (GRCh38) [ NCBI UCSC ] 2: 47703633-47703635 (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 Apr 15, 2023 May 1, 2024 Feb 28, 2023 - HGVS
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Nucleotide Protein Molecular
consequenceNM_000251.3:c.2135_2137del MANE Select Help Transcripts from the Matched Annotation from the NCBI and EMBL-EBI (MANE) collaboration.
NP_000242.1:p.Val712del inframe deletion NM_001258281.1:c.1937_1939del NP_001245210.1:p.Val646del inframe deletion NM_001406631.1:c.2135_2137del NP_001393560.1:p.Val712del inframe deletion NM_001406632.1:c.2135_2137del NP_001393561.1:p.Val712del inframe deletion NM_001406633.1:c.2135_2137del NP_001393562.1:p.Val712del inframe deletion NM_001406634.1:c.2135_2137del NP_001393563.1:p.Val712del inframe deletion NM_001406635.1:c.2135_2137del NP_001393564.1:p.Val712del inframe deletion NM_001406636.1:c.2102_2104del NP_001393565.1:p.Val701del inframe deletion NM_001406637.1:c.2135_2137del NP_001393566.1:p.Val712del inframe deletion NM_001406638.1:c.2174_2176del NP_001393567.1:p.Val725del inframe deletion NM_001406639.1:c.2135_2137del NP_001393568.1:p.Val712del inframe deletion NM_001406640.1:c.2135_2137del NP_001393569.1:p.Val712del inframe deletion NM_001406641.1:c.2135_2137del NP_001393570.1:p.Val712del inframe deletion NM_001406642.1:c.2135_2137del NP_001393571.1:p.Val712del inframe deletion NM_001406643.1:c.2135_2137del NP_001393572.1:p.Val712del inframe deletion NM_001406644.1:c.2135_2137del NP_001393573.1:p.Val712del inframe deletion NM_001406645.1:c.2135_2137del NP_001393574.1:p.Val712del inframe deletion NM_001406646.1:c.2135_2137del NP_001393575.1:p.Val712del inframe deletion NM_001406647.1:c.1985_1987del NP_001393576.1:p.Val662del inframe deletion NM_001406648.1:c.2135_2137del NP_001393577.1:p.Val712del inframe deletion NM_001406649.1:c.1985_1987del NP_001393578.1:p.Val662del inframe deletion NM_001406650.1:c.1985_1987del NP_001393579.1:p.Val662del inframe deletion NM_001406651.1:c.1985_1987del NP_001393580.1:p.Val662del inframe deletion NM_001406652.1:c.1985_1987del NP_001393581.1:p.Val662del inframe deletion NM_001406653.1:c.2075_2077del NP_001393582.1:p.Val692del inframe deletion NM_001406654.1:c.1715_1717del NP_001393583.1:p.Val572del inframe deletion NM_001406656.1:c.1238_1240del NP_001393585.1:p.Val413del inframe deletion NM_001406658.1:c.779_781del NP_001393587.1:p.Val260del inframe deletion NM_001406659.1:c.779_781del NP_001393588.1:p.Val260del inframe deletion NM_001406660.1:c.779_781del NP_001393589.1:p.Val260del inframe deletion NM_001406661.1:c.779_781del NP_001393590.1:p.Val260del inframe deletion NM_001406662.1:c.779_781del NP_001393591.1:p.Val260del inframe deletion NM_001406669.1:c.779_781del NP_001393598.1:p.Val260del inframe deletion NM_001406674.1:c.2135_2137del NP_001393603.1:p.Val712del inframe deletion NR_176230.1:n.2171_2173del non-coding transcript variant NR_176231.1:n.2171_2173del non-coding transcript variant NR_176232.1:n.2171_2173del non-coding transcript variant NR_176233.1:n.2013_2015del non-coding transcript variant NR_176234.1:n.2171_2173del non-coding transcript variant NR_176235.1:n.2171_2173del non-coding transcript variant NR_176236.1:n.2171_2173del non-coding transcript variant NR_176237.1:n.2171_2173del non-coding transcript variant NR_176238.1:n.2304_2306del non-coding transcript variant NR_176239.1:n.2171_2173del non-coding transcript variant NR_176241.1:n.2171_2173del non-coding transcript variant NR_176242.1:n.2171_2173del non-coding transcript variant NR_176243.1:n.2021_2023del non-coding transcript variant NR_176244.1:n.2171_2173del non-coding transcript variant NR_176245.1:n.2171_2173del non-coding transcript variant NR_176246.1:n.2171_2173del non-coding transcript variant NR_176247.1:n.2171_2173del non-coding transcript variant NR_176248.1:n.2171_2173del non-coding transcript variant NR_176249.1:n.2401_2403del non-coding transcript variant NR_176250.1:n.1911_1913del non-coding transcript variant NC_000002.12:g.47476496_47476498del NC_000002.11:g.47703635_47703637del NG_007110.2:g.78373_78375del LRG_218:g.78373_78375del LRG_218t1:c.2135_2137del LRG_218p1:p.Val712del - Protein change
- V646del, V725del, V413del, V662del, V692del, V572del, V701del, V712del, V260del
- Other names
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- Canonical SPDI
- NC_000002.12:47476493:AGTAG:AG
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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
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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Uncertain significance (1) |
criteria provided, single submitter
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Feb 28, 2023 | RCV003182957.2 |
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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Uncertain significance
(Feb 28, 2023)
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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: SCV003870565.2
First in ClinVar: Apr 15, 2023 Last updated: May 01, 2024 |
Comment:
The c.2135_2137delTAG variant (also known as p.V712del) is located in coding exon 13 of the MSH2 gene. This variant results from an in-frame TAG deletion … (more)
The c.2135_2137delTAG variant (also known as p.V712del) is located in coding exon 13 of the MSH2 gene. This variant results from an in-frame TAG deletion at nucleotide positions 2135 to 2137. This results in the in-frame deletion of a valine at codon 712. This amino acid position is highly conserved in available vertebrate species. In addition, this alteration is predicted to be deleterious by in silico analysis (Choi Y et al. PLoS ONE. 2012; 7(10):e46688). Since supporting evidence is limited at this time, the clinical significance of this alteration remains unclear. (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 May 01, 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.