ClinVar Genomic variation as it relates to human health
NM_000179.3(MSH6):c.3968_3969del (p.Glu1322_Phe1323insTer)
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_000179.3(MSH6):c.3968_3969del (p.Glu1322_Phe1323insTer)
Variation ID: 1736570 Accession: VCV001736570.2
- Type and length
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Deletion, 2 bp
- Location
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Cytogenetic: 2p16.3 2: 47806617-47806618 (GRCh38) [ NCBI UCSC ] 2: 48033756-48033757 (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 Nov 29, 2022 May 1, 2024 Sep 10, 2019 - HGVS
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Nucleotide Protein Molecular
consequenceNM_000179.3:c.3968_3969del MANE Select Help Transcripts from the Matched Annotation from the NCBI and EMBL-EBI (MANE) collaboration.
NP_000170.1:p.Glu1322_Phe1323insTer nonsense NM_001281492.2:c.3578_3579del NP_001268421.1:p.Glu1192_Phe1193insTer nonsense NM_001281493.2:c.3062_3063del NP_001268422.1:p.Glu1020_Phe1021insTer nonsense NM_001281494.2:c.3062_3063del NP_001268423.1:p.Glu1020_Phe1021insTer nonsense NM_001406795.1:c.4064_4065delTT NP_001393724.1:p.Phe1355Terfs frameshift nonsense NM_001406796.1:c.3968_3969delTT NP_001393725.1:p.Phe1323Terfs frameshift nonsense NM_001406797.1:c.3671_3672delTT NP_001393726.1:p.Phe1224Terfs frameshift nonsense NM_001406798.1:c.3794_3795delTT NP_001393727.1:p.Phe1265Terfs frameshift nonsense NM_001406799.1:c.3443_3444delTT NP_001393728.1:p.Phe1148Terfs frameshift nonsense NM_001406800.1:c.3955_3956delTT NP_001393729.1:p.Leu1319Glufs frameshift NM_001406801.1:c.3671_3672delTT NP_001393730.1:p.Phe1224Terfs frameshift nonsense NM_001406803.1:c.3104_3105delTT NP_001393732.1:p.Phe1035Terfs frameshift nonsense NM_001406804.1:c.3890_3891delTT NP_001393733.1:p.Phe1297Terfs frameshift nonsense NM_001406805.1:c.3671_3672delTT NP_001393734.1:p.Phe1224Terfs frameshift nonsense NM_001406806.1:c.3443_3444delTT NP_001393735.1:p.Phe1148Terfs frameshift nonsense NM_001406807.1:c.3443_3444delTT NP_001393736.1:p.Phe1148Terfs frameshift nonsense NM_001406808.1:c.3968_3969delTT NP_001393737.1:p.Phe1323Terfs frameshift nonsense NM_001406809.1:c.3968_3969delTT NP_001393738.1:p.Phe1323Terfs frameshift nonsense NM_001406811.1:c.3062_3063delTT NP_001393740.1:p.Phe1021Terfs frameshift nonsense NM_001406812.1:c.3062_3063delTT NP_001393741.1:p.Phe1021Terfs frameshift nonsense NM_001406813.1:c.3974_3975delTT NP_001393742.1:p.Phe1325Terfs frameshift nonsense NM_001406814.1:c.3062_3063delTT NP_001393743.1:p.Phe1021Terfs frameshift nonsense NM_001406815.1:c.3062_3063delTT NP_001393744.1:p.Phe1021Terfs frameshift nonsense NM_001406816.1:c.3062_3063delTT NP_001393745.1:p.Phe1021Terfs frameshift nonsense NM_001406817.1:c.2402_2403delTT NP_001393746.1:p.Phe801Terfs frameshift nonsense NM_001406818.1:c.3671_3672delTT NP_001393747.1:p.Phe1224Terfs frameshift nonsense NM_001406819.1:c.3671_3672delTT NP_001393748.1:p.Phe1224Terfs frameshift nonsense NM_001406820.1:c.3671_3672delTT NP_001393749.1:p.Phe1224Terfs frameshift nonsense NM_001406821.1:c.3671_3672delTT NP_001393750.1:p.Phe1224Terfs frameshift nonsense NM_001406822.1:c.3671_3672delTT NP_001393751.1:p.Phe1224Terfs frameshift nonsense NM_001406823.1:c.3062_3063delTT NP_001393752.1:p.Phe1021Terfs frameshift nonsense NM_001406824.1:c.3671_3672delTT NP_001393753.1:p.Phe1224Terfs frameshift nonsense NM_001406825.1:c.3671_3672delTT NP_001393754.1:p.Phe1224Terfs frameshift nonsense NM_001406826.1:c.3800_3801delTT NP_001393755.1:p.Phe1267Terfs frameshift nonsense NM_001406827.1:c.3671_3672delTT NP_001393756.1:p.Phe1224Terfs frameshift nonsense NM_001406828.1:c.3671_3672delTT NP_001393757.1:p.Phe1224Terfs frameshift nonsense NM_001406829.1:c.3062_3063delTT NP_001393758.1:p.Phe1021Terfs frameshift nonsense NM_001406830.1:c.3671_3672delTT NP_001393759.1:p.Phe1224Terfs frameshift nonsense NM_001406831.1:c.749_750delTT NP_001393760.1:p.Phe250Terfs frameshift nonsense NM_001406832.1:c.815_816delTT NP_001393761.1:p.Phe272Terfs frameshift nonsense NM_001407362.1:c.1913_1914delTT NP_001394291.1:p.Phe638Terfs frameshift nonsense NR_176256.1:n.2898_2899delTT NR_176257.1:n.4229_4230delTT NR_176258.1:n.4158_4159delTT NR_176259.1:n.4057_4058delTT NR_176260.1:n.2002_2003delTT NR_176261.1:n.3939_3940delTT NC_000002.12:g.47806618_47806619del NC_000002.11:g.48033757_48033758del NG_007111.1:g.28472_28473del NG_008397.1:g.104058_104059del LRG_219:g.28472_28473del LRG_219t1:c.3968_3969del LRG_219p1:p.Phe1323Terfs - Protein change
- Other names
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- Canonical SPDI
- NC_000002.12:47806616:TTT: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
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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
Help
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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MSH6 | Sufficient evidence for dosage pathogenicity | No evidence available |
GRCh38 GRCh37 |
- | 9377 |
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
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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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Pathogenic (1) |
criteria provided, single submitter
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Sep 10, 2019 | RCV002375469.2 |
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
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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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Pathogenic
(Sep 10, 2019)
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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: SCV002624484.2
First in ClinVar: Nov 29, 2022 Last updated: May 01, 2024 |
Comment:
The c.3968_3969delTT pathogenic mutation, located in coding exon 9 of the MSH6 gene, results from a deletion of two nucleotides at nucleotide positions 3968 to … (more)
The c.3968_3969delTT pathogenic mutation, located in coding exon 9 of the MSH6 gene, results from a deletion of two nucleotides at nucleotide positions 3968 to 3969, causing a translational frameshift with a predicted alternate stop codon (p.F1323*). This alteration is expected to result in loss of function by premature protein truncation or nonsense-mediated mRNA decay. As such, this alteration is interpreted as a disease-causing mutation. (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.