ClinVar Genomic variation as it relates to human health
NM_000179.3(MSH6):c.4004_4006dup (p.Glu1335_Val1336insGlu)
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.4004_4006dup (p.Glu1335_Val1336insGlu)
Variation ID: 3075501 Accession: VCV003075501.1
- Type and length
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Duplication, 3 bp
- Location
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Cytogenetic: 2p16.3 2: 47806779-47806780 (GRCh38) [ NCBI UCSC ] 2: 48033918-48033919 (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 Apr 20, 2024 Apr 20, 2024 Jun 26, 2023 - HGVS
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Nucleotide Protein Molecular
consequenceNM_000179.3:c.4004_4006dup MANE Select Help Transcripts from the Matched Annotation from the NCBI and EMBL-EBI (MANE) collaboration.
NP_000170.1:p.Glu1335_Val1336insGlu inframe insertion NM_001281492.2:c.3614_3616dup NP_001268421.1:p.Glu1205_Val1206insGlu inframe insertion NM_001281493.2:c.3098_3100dup NP_001268422.1:p.Glu1033_Val1034insGlu inframe insertion NM_001281494.2:c.3098_3100dup NP_001268423.1:p.Glu1033_Val1034insGlu inframe insertion NM_001406795.1:c.4100_4102dup NP_001393724.1:p.Glu1367_Val1368insGlu inframe insertion NM_001406796.1:c.4004_4006dup NP_001393725.1:p.Glu1335_Val1336insGlu inframe insertion NM_001406797.1:c.3707_3709dup NP_001393726.1:p.Glu1236_Val1237insGlu inframe insertion NM_001406798.1:c.3830_3832dup NP_001393727.1:p.Glu1277_Val1278insGlu inframe insertion NM_001406799.1:c.3479_3481dup NP_001393728.1:p.Glu1160_Val1161insGlu inframe insertion NM_001406800.1:c.*25_*27dup 3 prime UTR NM_001406801.1:c.3705-3_3705-1dup splice acceptor NM_001406802.1:c.3900_3902dup NP_001393731.1:p.Gly1300_Ser1301insArg inframe insertion NM_001406803.1:c.3140_3142dup NP_001393732.1:p.Glu1047_Val1048insGlu inframe insertion NM_001406804.1:c.3926_3928dup NP_001393733.1:p.Glu1309_Val1310insGlu inframe insertion NM_001406805.1:c.3707_3709dup NP_001393734.1:p.Glu1236_Val1237insGlu inframe insertion NM_001406806.1:c.3479_3481dup NP_001393735.1:p.Glu1160_Val1161insGlu inframe insertion NM_001406807.1:c.3479_3481dup NP_001393736.1:p.Glu1160_Val1161insGlu inframe insertion NM_001406808.1:c.4002-3_4002-1dup splice acceptor NM_001406809.1:c.4004_4006dup NP_001393738.1:p.Glu1335_Val1336insGlu inframe insertion NM_001406811.1:c.3098_3100dup NP_001393740.1:p.Glu1033_Val1034insGlu inframe insertion NM_001406812.1:c.3098_3100dup NP_001393741.1:p.Glu1033_Val1034insGlu inframe insertion NM_001406813.1:c.4010_4012dup NP_001393742.1:p.Glu1337_Val1338insGlu inframe insertion NM_001406814.1:c.3098_3100dup NP_001393743.1:p.Glu1033_Val1034insGlu inframe insertion NM_001406815.1:c.3098_3100dup NP_001393744.1:p.Glu1033_Val1034insGlu inframe insertion NM_001406816.1:c.3098_3100dup NP_001393745.1:p.Glu1033_Val1034insGlu inframe insertion NM_001406817.1:c.2438_2440dup NP_001393746.1:p.Glu813_Val814insGlu inframe insertion NM_001406818.1:c.3707_3709dup NP_001393747.1:p.Glu1236_Val1237insGlu inframe insertion NM_001406819.1:c.3707_3709dup NP_001393748.1:p.Glu1236_Val1237insGlu inframe insertion NM_001406820.1:c.3707_3709dup NP_001393749.1:p.Glu1236_Val1237insGlu inframe insertion NM_001406821.1:c.3707_3709dup NP_001393750.1:p.Glu1236_Val1237insGlu inframe insertion NM_001406822.1:c.3705-3_3705-1dup splice acceptor NM_001406823.1:c.3098_3100dup NP_001393752.1:p.Glu1033_Val1034insGlu inframe insertion NM_001406824.1:c.3707_3709dup NP_001393753.1:p.Glu1236_Val1237insGlu inframe insertion NM_001406825.1:c.3707_3709dup NP_001393754.1:p.Glu1236_Val1237insGlu inframe insertion NM_001406826.1:c.3836_3838dup NP_001393755.1:p.Glu1279_Val1280insGlu inframe insertion NM_001406827.1:c.3707_3709dup NP_001393756.1:p.Glu1236_Val1237insGlu inframe insertion NM_001406828.1:c.3707_3709dup NP_001393757.1:p.Glu1236_Val1237insGlu inframe insertion NM_001406829.1:c.3098_3100dup NP_001393758.1:p.Glu1033_Val1034insGlu inframe insertion NM_001406830.1:c.3707_3709dup NP_001393759.1:p.Glu1236_Val1237insGlu inframe insertion NM_001406831.1:c.785_787dup NP_001393760.1:p.Glu262_Val263insGlu inframe insertion NM_001406832.1:c.851_853dup NP_001393761.1:p.Glu284_Val285insGlu inframe insertion NM_001407362.1:c.1949_1951dup NP_001394291.1:p.Glu650_Val651insGlu inframe insertion NR_176256.1:n.2934_2936dup non-coding transcript variant NR_176257.1:n.4265_4267dup non-coding transcript variant NR_176258.1:n.4194_4196dup non-coding transcript variant NR_176259.1:n.4093_4095dup non-coding transcript variant NR_176260.1:n.2038_2040dup NR_176261.1:n.3975_3977dup non-coding transcript variant NC_000002.12:g.47806781_47806783dup NC_000002.11:g.48033920_48033922dup NG_007111.1:g.28635_28637dup NG_008397.1:g.103894_103896dup LRG_219:g.28635_28637dup LRG_219t1:c.4004_4006dup LRG_219p1:p.Glu1335_Val1336insGlu - Protein change
- Other names
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- Canonical SPDI
- NC_000002.12:47806779:GAAG:GAAGAAG
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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
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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 |
9149 | 9460 |
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
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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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Jun 26, 2023 | RCV004017019.2 |
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
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
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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
(Jun 26, 2023)
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criteria provided, single submitter
Method: clinical testing
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Lynch syndrome
(Autosomal dominant inheritance)
Affected status: unknown
Allele origin:
germline
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All of Us Research Program, National Institutes of Health
Accession: SCV004835195.1
First in ClinVar: Apr 20, 2024 Last updated: Apr 20, 2024
Comment:
This study involves interpretation of variants in research participants for the purpose of population health screening. Participant phenotype was not available at the time of … (more)
This study involves interpretation of variants in research participants for the purpose of population health screening. Participant phenotype was not available at the time of variant classification. Additional details can be found in publication PMID: 35346344, PMCID: PMC8962531 (less)
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Comment:
This variant causes a duplication of a glutamate in the MSH6 gene. To our knowledge, functional studies have not been reported for this variant. This … (more)
This variant causes a duplication of a glutamate in the MSH6 gene. To our knowledge, functional studies have not been reported for this variant. This variant has not been reported in individuals affected with hereditary cancer in the literature. This variant has not been identified in the general population by the Genome Aggregation Database (gnomAD). The available evidence is insufficient to determine the role of this variant in disease conclusively. Therefore, this variant is classified as a Variant of Uncertain Significance. (less)
Number of individuals with the variant: 1
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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 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.