ClinVar Genomic variation as it relates to human health
NM_000179.3(MSH6):c.2024_2029del (p.Glu675_Ser677delinsGly)
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.2024_2029del (p.Glu675_Ser677delinsGly)
Variation ID: 2701387 Accession: VCV002701387.1
- Type and length
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Deletion, 6 bp
- Location
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Cytogenetic: 2p16.3 2: 47800007-47800012 (GRCh38) [ NCBI UCSC ] 2: 48027146-48027151 (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 Feb 14, 2024 Feb 14, 2024 Jan 2, 2024 - HGVS
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Nucleotide Protein Molecular
consequenceNM_000179.3:c.2024_2029del MANE Select Help Transcripts from the Matched Annotation from the NCBI and EMBL-EBI (MANE) collaboration.
NP_000170.1:p.Glu675_Ser677delinsGly inframe indel NM_001281492.2:c.1634_1639del NP_001268421.1:p.Glu545_Ser547delinsGly inframe indel NM_001281493.2:c.1118_1123del NP_001268422.1:p.Glu373_Ser375delinsGly inframe indel NM_001281494.2:c.1118_1123del NP_001268423.1:p.Glu373_Ser375delinsGly inframe indel NM_001406795.1:c.2120_2125del NP_001393724.1:p.Glu707_Ser709delinsGly inframe indel NM_001406796.1:c.2024_2029del NP_001393725.1:p.Glu675_Ser677delinsGly inframe indel NM_001406797.1:c.1727_1732del NP_001393726.1:p.Glu576_Ser578delinsGly inframe indel NM_001406798.1:c.2024_2029del NP_001393727.1:p.Glu675_Ser677delinsGly inframe indel NM_001406799.1:c.1499_1504del NP_001393728.1:p.Glu500_Ser502delinsGly inframe indel NM_001406800.1:c.2024_2029del NP_001393729.1:p.Glu675_Ser677delinsGly inframe indel NM_001406801.1:c.1727_1732del NP_001393730.1:p.Glu576_Ser578delinsGly inframe indel NM_001406802.1:c.2120_2125del NP_001393731.1:p.Glu707_Ser709delinsGly inframe indel NM_001406803.1:c.2024_2029del NP_001393732.1:p.Glu675_Ser677delinsGly inframe indel NM_001406804.1:c.1946_1951del NP_001393733.1:p.Glu649_Ser651delinsGly inframe indel NM_001406805.1:c.1727_1732del NP_001393734.1:p.Glu576_Ser578delinsGly inframe indel NM_001406806.1:c.1499_1504del NP_001393735.1:p.Glu500_Ser502delinsGly inframe indel NM_001406807.1:c.1499_1504del NP_001393736.1:p.Glu500_Ser502delinsGly inframe indel NM_001406808.1:c.2024_2029del NP_001393737.1:p.Glu675_Ser677delinsGly inframe indel NM_001406809.1:c.2024_2029del NP_001393738.1:p.Glu675_Ser677delinsGly inframe indel NM_001406811.1:c.1118_1123del NP_001393740.1:p.Glu373_Ser375delinsGly inframe indel NM_001406812.1:c.1118_1123del NP_001393741.1:p.Glu373_Ser375delinsGly inframe indel NM_001406813.1:c.2030_2035del NP_001393742.1:p.Glu677_Ser679delinsGly inframe indel NM_001406814.1:c.1118_1123del NP_001393743.1:p.Glu373_Ser375delinsGly inframe indel NM_001406815.1:c.1118_1123del NP_001393744.1:p.Glu373_Ser375delinsGly inframe indel NM_001406816.1:c.1118_1123del NP_001393745.1:p.Glu373_Ser375delinsGly inframe indel NM_001406817.1:c.1606+418_1606+423del intron variant NM_001406818.1:c.1727_1732del NP_001393747.1:p.Glu576_Ser578delinsGly inframe indel NM_001406819.1:c.1727_1732del NP_001393748.1:p.Glu576_Ser578delinsGly inframe indel NM_001406820.1:c.1727_1732del NP_001393749.1:p.Glu576_Ser578delinsGly inframe indel NM_001406821.1:c.1727_1732del NP_001393750.1:p.Glu576_Ser578delinsGly inframe indel NM_001406822.1:c.1727_1732del NP_001393751.1:p.Glu576_Ser578delinsGly inframe indel NM_001406823.1:c.1118_1123del NP_001393752.1:p.Glu373_Ser375delinsGly inframe indel NM_001406824.1:c.1727_1732del NP_001393753.1:p.Glu576_Ser578delinsGly inframe indel NM_001406825.1:c.1727_1732del NP_001393754.1:p.Glu576_Ser578delinsGly inframe indel NM_001406826.1:c.1856_1861del NP_001393755.1:p.Glu619_Ser621delinsGly inframe indel NM_001406827.1:c.1727_1732del NP_001393756.1:p.Glu576_Ser578delinsGly inframe indel NM_001406828.1:c.1727_1732del NP_001393757.1:p.Glu576_Ser578delinsGly inframe indel NM_001406829.1:c.1118_1123del NP_001393758.1:p.Glu373_Ser375delinsGly inframe indel NM_001406830.1:c.1727_1732del NP_001393759.1:p.Glu576_Ser578delinsGly inframe indel NM_001407362.1:c.628-659_628-654del intron variant NR_176256.1:n.886_891del non-coding transcript variant NR_176257.1:n.2113_2118del non-coding transcript variant NR_176258.1:n.2113_2118del non-coding transcript variant NR_176259.1:n.2113_2118del non-coding transcript variant NR_176261.1:n.2113_2118del non-coding transcript variant NC_000002.12:g.47800007_47800012del NC_000002.11:g.48027146_48027151del NG_007111.1:g.21861_21866del LRG_219:g.21861_21866del LRG_219t1:c.2024_2029del LRG_219p1:p.Glu675_Ser677delinsGly - Protein change
- Other names
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- Canonical SPDI
- NC_000002.12:47800006:AGAAAA:
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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 |
9153 | 9466 |
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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Uncertain significance (1) |
criteria provided, single submitter
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Jan 2, 2024 | RCV003594910.2 |
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
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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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Uncertain significance
(Jan 02, 2024)
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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: SCV004254372.1
First in ClinVar: Feb 14, 2024 Last updated: Feb 14, 2024 |
Comment:
This variant, c.2024_2029del, is a complex sequence change that results in the deletion of 3 and insertion of 1 amino acid(s) in the MSH6 protein … (more)
This variant, c.2024_2029del, is a complex sequence change that results in the deletion of 3 and insertion of 1 amino acid(s) in the MSH6 protein (p.Glu675_Ser677delinsGly). This variant is not present in population databases (gnomAD no frequency). This variant has not been reported in the literature in individuals affected with MSH6-related conditions. Experimental studies and prediction algorithms are not available or were not evaluated, and the functional significance of this variant is currently unknown. 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. (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 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.