This sequence change replaces phenylalanine, which is neutral and non-polar, with valine, which is neutral and non-polar, at codon 366 of the MSH2 protein (p.Phe366Val). This variant is not present in population databases (gnomAD no frequency). In summary, the available evidence is currently insufficient to determine the role of this variant in disease. Therefore, it has been classified as a Variant of Uncertain Significance. Advanced modeling performed at Invitae incorporating data from internal and/or published experimental studies (PMID: 333574060) indicates that this missense variant is not expected to disrupt MSH2 function. This variant has not been reported in the literature in individuals affected with MSH2-related conditions.
ClinVar Genomic variation as it relates to human health
NM_000251.3(MSH2):c.1096T>G (p.Phe366Val)
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.
(2)
Help
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.
Conflicting classifications of pathogenicity
Uncertain significance(1); Likely benign(1)
Uncertain significance(1); Likely benign(1)
2
criteria provided, conflicting classifications
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.1096T>G (p.Phe366Val)
Variation ID: 2567750 Accession: VCV002567750.3
- Type and length
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single nucleotide variant, 1 bp
- Location
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Cytogenetic: 2p21 2: 47429761 (GRCh38) [ NCBI UCSC ] 2: 47656900 (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 Jul 8, 2023 May 1, 2024 Apr 19, 2023 - HGVS
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... more HGVS ... less HGVSNucleotide Protein Molecular
consequenceNM_000251.3:c.1096T>G MANE Select Help Transcripts from the Matched Annotation from the NCBI and EMBL-EBI (MANE) collaboration.
NP_000242.1:p.Phe366Val missense NM_001258281.1:c.898T>G NP_001245210.1:p.Phe300Val missense NM_001406631.1:c.1096T>G NP_001393560.1:p.Phe366Val missense NM_001406632.1:c.1096T>G NP_001393561.1:p.Phe366Val missense NM_001406633.1:c.1096T>G NP_001393562.1:p.Phe366Val missense NM_001406634.1:c.1096T>G NP_001393563.1:p.Phe366Val missense NM_001406635.1:c.1096T>G NP_001393564.1:p.Phe366Val missense NM_001406636.1:c.1063T>G NP_001393565.1:p.Phe355Val missense NM_001406637.1:c.1096T>G NP_001393566.1:p.Phe366Val missense NM_001406638.1:c.1096T>G NP_001393567.1:p.Phe366Val missense NM_001406639.1:c.1096T>G NP_001393568.1:p.Phe366Val missense NM_001406640.1:c.1096T>G NP_001393569.1:p.Phe366Val missense NM_001406641.1:c.1096T>G NP_001393570.1:p.Phe366Val missense NM_001406642.1:c.1096T>G NP_001393571.1:p.Phe366Val missense NM_001406643.1:c.1096T>G NP_001393572.1:p.Phe366Val missense NM_001406644.1:c.1096T>G NP_001393573.1:p.Phe366Val missense NM_001406645.1:c.1096T>G NP_001393574.1:p.Phe366Val missense NM_001406646.1:c.1096T>G NP_001393575.1:p.Phe366Val missense NM_001406647.1:c.946T>G NP_001393576.1:p.Phe316Val missense NM_001406648.1:c.1096T>G NP_001393577.1:p.Phe366Val missense NM_001406649.1:c.946T>G NP_001393578.1:p.Phe316Val missense NM_001406650.1:c.946T>G NP_001393579.1:p.Phe316Val missense NM_001406651.1:c.946T>G NP_001393580.1:p.Phe316Val missense NM_001406652.1:c.946T>G NP_001393581.1:p.Phe316Val missense NM_001406653.1:c.1036T>G NP_001393582.1:p.Phe346Val missense NM_001406654.1:c.676T>G NP_001393583.1:p.Phe226Val missense NM_001406655.1:c.1096T>G NP_001393584.1:p.Phe366Val missense NM_001406656.1:c.199T>G NP_001393585.1:p.Phe67Val missense NM_001406657.1:c.1096T>G NP_001393586.1:p.Phe366Val missense NM_001406658.1:c.-261T>G 5 prime UTR NM_001406659.1:c.-261T>G 5 prime UTR NM_001406660.1:c.-261T>G 5 prime UTR NM_001406661.1:c.-261T>G 5 prime UTR NM_001406662.1:c.-261T>G 5 prime UTR NM_001406666.1:c.1096T>G NP_001393595.1:p.Phe366Val missense NM_001406669.1:c.-261T>G 5 prime UTR NM_001406672.1:c.946T>G NP_001393601.1:p.Phe316Val missense NM_001406674.1:c.1096T>G NP_001393603.1:p.Phe366Val missense NR_176230.1:n.1132T>G non-coding transcript variant NR_176231.1:n.1132T>G non-coding transcript variant NR_176232.1:n.1132T>G non-coding transcript variant NR_176233.1:n.974T>G non-coding transcript variant NR_176234.1:n.1132T>G non-coding transcript variant NR_176235.1:n.1132T>G non-coding transcript variant NR_176236.1:n.1132T>G non-coding transcript variant NR_176237.1:n.1132T>G non-coding transcript variant NR_176238.1:n.1132T>G non-coding transcript variant NR_176239.1:n.1132T>G non-coding transcript variant NR_176240.1:n.1132T>G non-coding transcript variant NR_176241.1:n.1132T>G non-coding transcript variant NR_176242.1:n.1132T>G non-coding transcript variant NR_176243.1:n.982T>G non-coding transcript variant NR_176244.1:n.1132T>G non-coding transcript variant NR_176245.1:n.1132T>G non-coding transcript variant NR_176246.1:n.1132T>G non-coding transcript variant NR_176247.1:n.1132T>G non-coding transcript variant NR_176248.1:n.1132T>G non-coding transcript variant NR_176249.1:n.1132T>G non-coding transcript variant NR_176250.1:n.982T>G non-coding transcript variant NC_000002.12:g.47429761T>G NC_000002.11:g.47656900T>G NG_007110.2:g.31638T>G LRG_218:g.31638T>G LRG_218t1:c.1096T>G LRG_218p1:p.Phe366Val - Protein change
- F346V, F355V, F67V, F226V, F300V, F316V, F366V
- Other names
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- Canonical SPDI
- NC_000002.12:47429760:T:G
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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. |
|---|---|---|---|---|
| Likely benign (1) |
criteria provided, single submitter
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Apr 19, 2023 | RCV003311401.2 | |
| Uncertain significance (1) |
criteria provided, single submitter
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Mar 8, 2023 | RCV003759812.2 |
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
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
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
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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Uncertain significance
(Mar 08, 2023)
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criteria provided, single submitter
Method: clinical testing
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Hereditary nonpolyposis colorectal neoplasms
Affected status: unknown
Allele origin:
germline
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Labcorp Genetics (formerly Invitae), Labcorp
Accession: SCV004503516.1
First in ClinVar: Feb 20, 2024 Last updated: Feb 20, 2024 |
Comment:
This sequence change replaces phenylalanine, which is neutral and non-polar, with valine, which is neutral and non-polar, at codon 366 of the MSH2 protein (p.Phe366Val). … (more)
This sequence change replaces phenylalanine, which is neutral and non-polar, with valine, which is neutral and non-polar, at codon 366 of the MSH2 protein (p.Phe366Val). This variant is not present in population databases (gnomAD no frequency). In summary, the available evidence is currently insufficient to determine the role of this variant in disease. Therefore, it has been classified as a Variant of Uncertain Significance. Advanced modeling performed at Invitae incorporating data from internal and/or published experimental studies (PMID: 333574060) indicates that this missense variant is not expected to disrupt MSH2 function. This variant has not been reported in the literature in individuals affected with MSH2-related conditions. (less)
|
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Likely benign
(Apr 19, 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: SCV004002452.2
First in ClinVar: Jul 08, 2023 Last updated: May 01, 2024 |
Comment:
This alteration is classified as likely benign based on a combination of the following: seen in unaffected individuals, population frequency, intact protein function, lack of … (more)
This alteration is classified as likely benign based on a combination of the following: seen in unaffected individuals, population frequency, intact protein function, lack of segregation with disease, co-occurrence, RNA analysis, in silico models, amino acid conservation, lack of disease association in case-control studies, and/or the mechanism of disease or impacted region is inconsistent with a known cause of pathogenicity. (less)
|
Comment:
Comment:
This alteration is classified as likely benign based on a combination of the following: seen in unaffected individuals, population frequency, intact protein function, lack of segregation with disease, co-occurrence, RNA analysis, in silico models, amino acid conservation, lack of disease association in case-control studies, and/or the mechanism of disease or impacted region is inconsistent with a known cause of pathogenicity.
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 sequence change replaces phenylalanine, which is neutral and non-polar, with valine, which is neutral and non-polar, at codon 366 of the MSH2 protein (p.Phe366Val). This variant is not present in population databases (gnomAD no frequency). In summary, the available evidence is currently insufficient to determine the role of this variant in disease. Therefore, it has been classified as a Variant of Uncertain Significance. Advanced modeling performed at Invitae incorporating data from internal and/or published experimental studies (PMID: 333574060) indicates that this missense variant is not expected to disrupt MSH2 function. This variant has not been reported in the literature in individuals affected with MSH2-related conditions.
Comment:
This alteration is classified as likely benign based on a combination of the following: seen in unaffected individuals, population frequency, intact protein function, lack of segregation with disease, co-occurrence, RNA analysis, in silico models, amino acid conservation, lack of disease association in case-control studies, and/or the mechanism of disease or impacted region is inconsistent with a known cause of pathogenicity.
Citations for germline classification of this variant
Help| Title | Author | Journal | Year | Link |
|---|---|---|---|---|
| - | - | - | - | PMID: 333574060 |
Text-mined citations for this variant ...
HelpRecord last updated Sep 30, 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.