The c.3866_3880del15 variant (also known as p.F1289_A1293del) is located in coding exon 9 of the MSH6 gene. This variant results from an in-frame TCATTAAGGGAGCTT deletion at nucleotide positions 3866 to 3880. This results in the in-frame deletion of FIKGA residues at codons 1289 to 1293. This amino acid region is 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). Based on the available evidence, the clinical significance of this alteration remains unclear.
ClinVar Genomic variation as it relates to human health
NM_000179.3(MSH6):c.3866_3880del (p.Phe1289_Ala1293del)
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.
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_000179.3(MSH6):c.3866_3880del (p.Phe1289_Ala1293del)
Variation ID: 3230567 Accession: VCV003230567.1
- Type and length
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Deletion, 15 bp
- Location
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Cytogenetic: 2p16.3 2: 47806515-47806529 (GRCh38) [ NCBI UCSC ] 2: 48033654-48033668 (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 Mar 12, 2024 - HGVS
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... more HGVS ... less HGVSNucleotide Protein Molecular
consequenceNM_000179.3:c.3866_3880del MANE Select Help Transcripts from the Matched Annotation from the NCBI and EMBL-EBI (MANE) collaboration.
NP_000170.1:p.Phe1289_Ala1293del inframe deletion NM_000179.2:c.3866_3880del15 inframe indel NM_001281492.2:c.3476_3490del NP_001268421.1:p.Phe1159_Ala1163del inframe deletion NM_001281493.2:c.2960_2974del NP_001268422.1:p.Phe987_Ala991del inframe deletion NM_001281494.2:c.2960_2974del NP_001268423.1:p.Phe987_Ala991del inframe deletion NM_001406795.1:c.3962_3976del NP_001393724.1:p.Phe1321_Ala1325del inframe deletion NM_001406796.1:c.3866_3880del NP_001393725.1:p.Phe1289_Ala1293del inframe deletion NM_001406797.1:c.3569_3583del NP_001393726.1:p.Phe1190_Ala1194del inframe deletion NM_001406798.1:c.3692_3706del NP_001393727.1:p.Phe1231_Ala1235del inframe deletion NM_001406799.1:c.3341_3355del NP_001393728.1:p.Phe1114_Ala1118del inframe deletion NM_001406800.1:c.3853_3867del NP_001393729.1:p.Ser1285_Leu1289del inframe deletion NM_001406801.1:c.3569_3583del NP_001393730.1:p.Phe1190_Ala1194del inframe deletion NM_001406802.1:c.3897+158_3897+172del intron variant NM_001406803.1:c.3002_3016del NP_001393732.1:p.Phe1001_Ala1005del inframe deletion NM_001406804.1:c.3788_3802del NP_001393733.1:p.Phe1263_Ala1267del inframe deletion NM_001406805.1:c.3569_3583del NP_001393734.1:p.Phe1190_Ala1194del inframe deletion NM_001406806.1:c.3341_3355del NP_001393735.1:p.Phe1114_Ala1118del inframe deletion NM_001406807.1:c.3341_3355del NP_001393736.1:p.Phe1114_Ala1118del inframe deletion NM_001406808.1:c.3866_3880del NP_001393737.1:p.Phe1289_Ala1293del inframe deletion NM_001406809.1:c.3866_3880del NP_001393738.1:p.Phe1289_Ala1293del inframe deletion NM_001406811.1:c.2960_2974del NP_001393740.1:p.Phe987_Ala991del inframe deletion NM_001406812.1:c.2960_2974del NP_001393741.1:p.Phe987_Ala991del inframe deletion NM_001406813.1:c.3872_3886del NP_001393742.1:p.Phe1291_Ala1295del inframe deletion NM_001406814.1:c.2960_2974del NP_001393743.1:p.Phe987_Ala991del inframe deletion NM_001406815.1:c.2960_2974del NP_001393744.1:p.Phe987_Ala991del inframe deletion NM_001406816.1:c.2960_2974del NP_001393745.1:p.Phe987_Ala991del inframe deletion NM_001406817.1:c.2300_2314del NP_001393746.1:p.Phe767_Ala771del inframe deletion NM_001406818.1:c.3569_3583del NP_001393747.1:p.Phe1190_Ala1194del inframe deletion NM_001406819.1:c.3569_3583del NP_001393748.1:p.Phe1190_Ala1194del inframe deletion NM_001406820.1:c.3569_3583del NP_001393749.1:p.Phe1190_Ala1194del inframe deletion NM_001406821.1:c.3569_3583del NP_001393750.1:p.Phe1190_Ala1194del inframe deletion NM_001406822.1:c.3569_3583del NP_001393751.1:p.Phe1190_Ala1194del inframe deletion NM_001406823.1:c.2960_2974del NP_001393752.1:p.Phe987_Ala991del inframe deletion NM_001406824.1:c.3569_3583del NP_001393753.1:p.Phe1190_Ala1194del inframe deletion NM_001406825.1:c.3569_3583del NP_001393754.1:p.Phe1190_Ala1194del inframe deletion NM_001406826.1:c.3698_3712del NP_001393755.1:p.Phe1233_Ala1237del inframe deletion NM_001406827.1:c.3569_3583del NP_001393756.1:p.Phe1190_Ala1194del inframe deletion NM_001406828.1:c.3569_3583del NP_001393757.1:p.Phe1190_Ala1194del inframe deletion NM_001406829.1:c.2960_2974del NP_001393758.1:p.Phe987_Ala991del inframe deletion NM_001406830.1:c.3569_3583del NP_001393759.1:p.Phe1190_Ala1194del inframe deletion NM_001406831.1:c.647_661del NP_001393760.1:p.Phe216_Ala220del inframe deletion NM_001406832.1:c.713_727del NP_001393761.1:p.Phe238_Ala242del inframe deletion NM_001407362.1:c.1811_1825del NP_001394291.1:p.Phe604_Ala608del inframe deletion NR_176256.1:n.2796_2810del non-coding transcript variant NR_176257.1:n.4127_4141del non-coding transcript variant NR_176258.1:n.4056_4070del non-coding transcript variant NR_176259.1:n.3955_3969del non-coding transcript variant NR_176260.1:n.1900_1914delTCATTAAGGGAGCTT NR_176261.1:n.3837_3851del non-coding transcript variant NC_000002.12:g.47806516_47806530del NC_000002.11:g.48033655_48033669del NG_007111.1:g.28370_28384del NG_008397.1:g.104147_104161del LRG_219:g.28370_28384del LRG_219t1:c.3866_3880del LRG_219p1:p.Phe1289_Ala1293del - Protein change
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- Other names
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- Canonical SPDI
- NC_000002.12:47806514:TTCATTAAGGGAGCTT:T
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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 | ||
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| 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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| MSH6 | Sufficient evidence for dosage pathogenicity | No evidence available |
GRCh38 GRCh37 |
9161 | 9479 | |
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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Mar 12, 2024 | RCV004520718.1 |
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
(Mar 12, 2024)
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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: SCV005033375.1
First in ClinVar: May 01, 2024 Last updated: May 01, 2024 |
Comment:
The c.3866_3880del15 variant (also known as p.F1289_A1293del) is located in coding exon 9 of the MSH6 gene. This variant results from an in-frame TCATTAAGGGAGCTT deletion … (more)
The c.3866_3880del15 variant (also known as p.F1289_A1293del) is located in coding exon 9 of the MSH6 gene. This variant results from an in-frame TCATTAAGGGAGCTT deletion at nucleotide positions 3866 to 3880. This results in the in-frame deletion of FIKGA residues at codons 1289 to 1293. This amino acid region is 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). Based on the available evidence, 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.3866_3880del15 variant (also known as p.F1289_A1293del) is located in coding exon 9 of the MSH6 gene. This variant results from an in-frame TCATTAAGGGAGCTT deletion at nucleotide positions 3866 to 3880. This results in the in-frame deletion of FIKGA residues at codons 1289 to 1293. This amino acid region is 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). Based on the available evidence, 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.