ClinVar Genomic variation as it relates to human health
NM_000179.3(MSH6):c.2067del (p.Tyr690fs)
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.2067del (p.Tyr690fs)
Variation ID: 2431266 Accession: VCV002431266.1
- Type and length
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Deletion, 1 bp
- Location
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Cytogenetic: 2p16.3 2: 47800050 (GRCh38) [ NCBI UCSC ] 2: 48027189 (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 Mar 5, 2023 Mar 4, 2023 Jan 12, 2023 - HGVS
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Nucleotide Protein Molecular
consequenceNM_000179.3:c.2067del MANE Select Help Transcripts from the Matched Annotation from the NCBI and EMBL-EBI (MANE) collaboration.
NP_000170.1:p.Tyr690fs frameshift NM_001281492.2:c.1677del NP_001268421.1:p.Tyr560fs frameshift NM_001281493.2:c.1161del NP_001268422.1:p.Tyr388fs frameshift NM_001281494.2:c.1161del NP_001268423.1:p.Tyr388fs frameshift NM_001406795.1:c.2163delC NP_001393724.1:p.Tyr722Thrfs frameshift NM_001406796.1:c.2067delC NP_001393725.1:p.Tyr690Thrfs frameshift NM_001406797.1:c.1770delC NP_001393726.1:p.Tyr591Thrfs frameshift NM_001406798.1:c.2067delC NP_001393727.1:p.Tyr690Thrfs frameshift NM_001406799.1:c.1542delC NP_001393728.1:p.Tyr515Thrfs frameshift NM_001406800.1:c.2067delC NP_001393729.1:p.Tyr690Thrfs frameshift NM_001406801.1:c.1770delC NP_001393730.1:p.Tyr591Thrfs frameshift NM_001406802.1:c.2163delC NP_001393731.1:p.Tyr722Thrfs frameshift NM_001406803.1:c.2067delC NP_001393732.1:p.Tyr690Thrfs frameshift NM_001406804.1:c.1989delC NP_001393733.1:p.Tyr664Thrfs frameshift NM_001406805.1:c.1770delC NP_001393734.1:p.Tyr591Thrfs frameshift NM_001406806.1:c.1542delC NP_001393735.1:p.Tyr515Thrfs frameshift NM_001406807.1:c.1542delC NP_001393736.1:p.Tyr515Thrfs frameshift NM_001406808.1:c.2067delC NP_001393737.1:p.Tyr690Thrfs frameshift NM_001406809.1:c.2067delC NP_001393738.1:p.Tyr690Thrfs frameshift NM_001406811.1:c.1161delC NP_001393740.1:p.Tyr388Thrfs frameshift NM_001406812.1:c.1161delC NP_001393741.1:p.Tyr388Thrfs frameshift NM_001406813.1:c.2073delC NP_001393742.1:p.Tyr692Thrfs frameshift NM_001406814.1:c.1161delC NP_001393743.1:p.Tyr388Thrfs frameshift NM_001406815.1:c.1161delC NP_001393744.1:p.Tyr388Thrfs frameshift NM_001406816.1:c.1161delC NP_001393745.1:p.Tyr388Thrfs frameshift NM_001406818.1:c.1770delC NP_001393747.1:p.Tyr591Thrfs frameshift NM_001406819.1:c.1770delC NP_001393748.1:p.Tyr591Thrfs frameshift NM_001406820.1:c.1770delC NP_001393749.1:p.Tyr591Thrfs frameshift NM_001406821.1:c.1770delC NP_001393750.1:p.Tyr591Thrfs frameshift NM_001406822.1:c.1770delC NP_001393751.1:p.Tyr591Thrfs frameshift NM_001406823.1:c.1161delC NP_001393752.1:p.Tyr388Thrfs frameshift NM_001406824.1:c.1770delC NP_001393753.1:p.Tyr591Thrfs frameshift NM_001406825.1:c.1770delC NP_001393754.1:p.Tyr591Thrfs frameshift NM_001406826.1:c.1899delC NP_001393755.1:p.Tyr634Thrfs frameshift NM_001406827.1:c.1770delC NP_001393756.1:p.Tyr591Thrfs frameshift NM_001406828.1:c.1770delC NP_001393757.1:p.Tyr591Thrfs frameshift NM_001406829.1:c.1161delC NP_001393758.1:p.Tyr388Thrfs frameshift NM_001406830.1:c.1770delC NP_001393759.1:p.Tyr591Thrfs frameshift NR_176256.1:n.929delC NR_176257.1:n.2156delC NR_176258.1:n.2156delC NR_176259.1:n.2156delC NR_176261.1:n.2156delC NC_000002.12:g.47800050del NC_000002.11:g.48027189del NG_007111.1:g.21904del LRG_219:g.21904del LRG_219t1:c.2067del LRG_219p1:p.Tyr690Thrfs - Protein change
- Y388fs, Y560fs, Y690fs
- Other names
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- Canonical SPDI
- NC_000002.12:47800049:C:
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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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MSH6 | Sufficient evidence for dosage pathogenicity | No evidence available |
GRCh38 GRCh37 |
9148 | 9458 |
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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Pathogenic (1) |
criteria provided, single submitter
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Jan 12, 2023 | RCV003140326.1 |
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
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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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Pathogenic
(Jan 12, 2023)
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criteria provided, single submitter
Method: clinical testing
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Lynch syndrome 5
Affected status: unknown
Allele origin:
unknown
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Myriad Genetics, Inc.
Accession: SCV003806535.1
First in ClinVar: Mar 04, 2023 Last updated: Mar 04, 2023 |
Comment:
This variant is considered pathogenic. This variant creates a frameshift predicted to result in premature protein truncation.
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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 Aug 06, 2023
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.