The c.66_68delCTT variant (also known as p.F23del) is located in coding exon 1 of the MSH2 gene. This variant results from an in-frame CTT deletion at nucleotide positions 66 to 68. This results in the in-frame deletion of a phenylalanine at codon 23. This amino acid position is not well 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.
ClinVar Genomic variation as it relates to human health
NM_000251.3(MSH2):c.63CTT[1] (p.Phe23del)
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)
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.
Uncertain significance
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.63CTT[1] (p.Phe23del)
Variation ID: 3230851 Accession: VCV003230851.1
- Type and length
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Microsatellite, 3 bp
- Location
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Cytogenetic: 2p21 2: 47403254-47403256 (GRCh38) [ NCBI UCSC ] 2: 47630393-47630395 (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 May 1, 2024 May 1, 2024 Nov 13, 2023 - HGVS
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... more HGVS ... less HGVSNucleotide Protein Molecular
consequenceNM_000251.3:c.63CTT[1] MANE Select Help Transcripts from the Matched Annotation from the NCBI and EMBL-EBI (MANE) collaboration.
NP_000242.1:p.Phe23del inframe deletion NM_001258281.1:c.-31+82_-31+84del intron variant NM_001406631.1:c.63CTT[1] NP_001393560.1:p.Phe23del inframe deletion NM_001406632.1:c.63CTT[1] NP_001393561.1:p.Phe23del inframe deletion NM_001406633.1:c.63CTT[1] NP_001393562.1:p.Phe23del inframe deletion NM_001406634.1:c.63CTT[1] NP_001393563.1:p.Phe23del inframe deletion NM_001406635.1:c.63CTT[1] NP_001393564.1:p.Phe23del inframe deletion NM_001406636.1:c.63CTT[1] NP_001393565.1:p.Phe23del inframe deletion NM_001406637.1:c.63CTT[1] NP_001393566.1:p.Phe23del inframe deletion NM_001406638.1:c.63CTT[1] NP_001393567.1:p.Phe23del inframe deletion NM_001406639.1:c.63CTT[1] NP_001393568.1:p.Phe23del inframe deletion NM_001406640.1:c.63CTT[1] NP_001393569.1:p.Phe23del inframe deletion NM_001406641.1:c.63CTT[1] NP_001393570.1:p.Phe23del inframe deletion NM_001406642.1:c.63CTT[1] NP_001393571.1:p.Phe23del inframe deletion NM_001406643.1:c.63CTT[1] NP_001393572.1:p.Phe23del inframe deletion NM_001406644.1:c.63CTT[1] NP_001393573.1:p.Phe23del inframe deletion NM_001406645.1:c.63CTT[1] NP_001393574.1:p.Phe23del inframe deletion NM_001406646.1:c.63CTT[1] NP_001393575.1:p.Phe23del inframe deletion NM_001406647.1:c.63CTT[1] NP_001393576.1:p.Phe23del inframe deletion NM_001406648.1:c.63CTT[1] NP_001393577.1:p.Phe23del inframe deletion NM_001406649.1:c.63CTT[1] NP_001393578.1:p.Phe23del inframe deletion NM_001406650.1:c.63CTT[1] NP_001393579.1:p.Phe23del inframe deletion NM_001406651.1:c.63CTT[1] NP_001393580.1:p.Phe23del inframe deletion NM_001406652.1:c.63CTT[1] NP_001393581.1:p.Phe23del inframe deletion NM_001406653.1:c.63CTT[1] NP_001393582.1:p.Phe23del inframe deletion NM_001406654.1:c.-278CTT[1] 5 prime UTR NM_001406655.1:c.63CTT[1] NP_001393584.1:p.Phe23del inframe deletion NM_001406656.1:c.-933CTT[1] 5 prime UTR NM_001406657.1:c.63CTT[1] NP_001393586.1:p.Phe23del inframe deletion NM_001406658.1:c.-1256CTT[1] 5 prime UTR NM_001406659.1:c.-1406CTT[1] 5 prime UTR NM_001406660.1:c.-1603CTT[1] 5 prime UTR NM_001406661.1:c.-1558CTT[1] 5 prime UTR NM_001406662.1:c.-1475CTT[1] 5 prime UTR NM_001406666.1:c.63CTT[1] NP_001393595.1:p.Phe23del inframe deletion NM_001406669.1:c.-1406CTT[1] 5 prime UTR NM_001406672.1:c.63CTT[1] NP_001393601.1:p.Phe23del inframe deletion NM_001406674.1:c.63CTT[1] NP_001393603.1:p.Phe23del inframe deletion NR_176230.1:n.99CTT[1] non-coding transcript variant NR_176231.1:n.99CTT[1] non-coding transcript variant NR_176232.1:n.99CTT[1] non-coding transcript variant NR_176233.1:n.99CTT[1] non-coding transcript variant NR_176234.1:n.99CTT[1] non-coding transcript variant NR_176235.1:n.99CTT[1] non-coding transcript variant NR_176236.1:n.99CTT[1] non-coding transcript variant NR_176237.1:n.99CTT[1] non-coding transcript variant NR_176238.1:n.99CTT[1] non-coding transcript variant NR_176239.1:n.99CTT[1] non-coding transcript variant NR_176240.1:n.99CTT[1] non-coding transcript variant NR_176241.1:n.99CTT[1] non-coding transcript variant NR_176242.1:n.99CTT[1] non-coding transcript variant NR_176243.1:n.99CTT[1] non-coding transcript variant NR_176244.1:n.99CTT[1] non-coding transcript variant NR_176245.1:n.99CTT[1] non-coding transcript variant NR_176246.1:n.99CTT[1] non-coding transcript variant NR_176247.1:n.99CTT[1] non-coding transcript variant NR_176248.1:n.99CTT[1] non-coding transcript variant NR_176249.1:n.99CTT[1] non-coding transcript variant NR_176250.1:n.99CTT[1] non-coding transcript variant NC_000002.12:g.47403254CTT[1] NC_000002.11:g.47630393CTT[1] NG_007110.2:g.5131CTT[1] NG_095167.1:g.458CTT[1] LRG_218:g.5131CTT[1] LRG_218t1:c.63_65CTT[1] LRG_218p1:p.Phe23del - Protein change
- F23del
- Other names
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- Canonical SPDI
- NC_000002.12:47403253:CTTCTT:CTT
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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. |
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| Uncertain significance (1) |
criteria provided, single submitter
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Nov 13, 2023 | RCV004522965.1 |
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
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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Uncertain significance
(Nov 13, 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: SCV005033693.1
First in ClinVar: May 01, 2024 Last updated: May 01, 2024 |
Comment:
The c.66_68delCTT variant (also known as p.F23del) is located in coding exon 1 of the MSH2 gene. This variant results from an in-frame CTT deletion … (more)
The c.66_68delCTT variant (also known as p.F23del) is located in coding exon 1 of the MSH2 gene. This variant results from an in-frame CTT deletion at nucleotide positions 66 to 68. This results in the in-frame deletion of a phenylalanine at codon 23. This amino acid position is not well 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)
|
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:
The c.66_68delCTT variant (also known as p.F23del) is located in coding exon 1 of the MSH2 gene. This variant results from an in-frame CTT deletion at nucleotide positions 66 to 68. This results in the in-frame deletion of a phenylalanine at codon 23. This amino acid position is not well 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.
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 May 08, 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.