This variant is considered pathogenic. This variant creates a termination codon and is predicted to result in premature protein truncation.
ClinVar Genomic variation as it relates to human health
NM_000179.3(MSH6):c.2714del (p.Asp904_Leu905insTer)
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.
(2)
Help
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.
Pathogenic
2
criteria provided, multiple submitters, no conflicts
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.2714del (p.Asp904_Leu905insTer)
Variation ID: 1996076 Accession: VCV001996076.3
- Type and length
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Deletion, 1 bp
- Location
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Cytogenetic: 2p16.3 2: 47800695 (GRCh38) [ NCBI UCSC ] 2: 48027834 (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 8, 2023 Feb 20, 2024 Aug 17, 2023 - HGVS
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... more HGVS ... less HGVSNucleotide Protein Molecular
consequenceNM_000179.3:c.2714del MANE Select Help Transcripts from the Matched Annotation from the NCBI and EMBL-EBI (MANE) collaboration.
NP_000170.1:p.Asp904_Leu905insTer nonsense NM_001281492.2:c.2324del NP_001268421.1:p.Asp774_Leu775insTer nonsense NM_001281493.2:c.1808del NP_001268422.1:p.Asp602_Leu603insTer nonsense NM_001281494.2:c.1808del NP_001268423.1:p.Asp602_Leu603insTer nonsense NM_001406795.1:c.2810delT NP_001393724.1:p.Leu937Terfs frameshift nonsense NM_001406796.1:c.2714delT NP_001393725.1:p.Leu905Terfs frameshift nonsense NM_001406797.1:c.2417delT NP_001393726.1:p.Leu806Terfs frameshift nonsense NM_001406798.1:c.2714delT NP_001393727.1:p.Leu905Terfs frameshift nonsense NM_001406799.1:c.2189delT NP_001393728.1:p.Leu730Terfs frameshift nonsense NM_001406800.1:c.2714delT NP_001393729.1:p.Leu905Terfs frameshift nonsense NM_001406801.1:c.2417delT NP_001393730.1:p.Leu806Terfs frameshift nonsense NM_001406802.1:c.2810delT NP_001393731.1:p.Leu937Terfs frameshift nonsense NM_001406804.1:c.2636delT NP_001393733.1:p.Leu879Terfs frameshift nonsense NM_001406805.1:c.2417delT NP_001393734.1:p.Leu806Terfs frameshift nonsense NM_001406806.1:c.2189delT NP_001393735.1:p.Leu730Terfs frameshift nonsense NM_001406807.1:c.2189delT NP_001393736.1:p.Leu730Terfs frameshift nonsense NM_001406808.1:c.2714delT NP_001393737.1:p.Leu905Terfs frameshift nonsense NM_001406809.1:c.2714delT NP_001393738.1:p.Leu905Terfs frameshift nonsense NM_001406811.1:c.1808delT NP_001393740.1:p.Leu603Terfs frameshift nonsense NM_001406812.1:c.1808delT NP_001393741.1:p.Leu603Terfs frameshift nonsense NM_001406813.1:c.2720delT NP_001393742.1:p.Leu907Terfs frameshift nonsense NM_001406814.1:c.1808delT NP_001393743.1:p.Leu603Terfs frameshift nonsense NM_001406815.1:c.1808delT NP_001393744.1:p.Leu603Terfs frameshift nonsense NM_001406816.1:c.1808delT NP_001393745.1:p.Leu603Terfs frameshift nonsense NM_001406818.1:c.2417delT NP_001393747.1:p.Leu806Terfs frameshift nonsense NM_001406819.1:c.2417delT NP_001393748.1:p.Leu806Terfs frameshift nonsense NM_001406820.1:c.2417delT NP_001393749.1:p.Leu806Terfs frameshift nonsense NM_001406821.1:c.2417delT NP_001393750.1:p.Leu806Terfs frameshift nonsense NM_001406822.1:c.2417delT NP_001393751.1:p.Leu806Terfs frameshift nonsense NM_001406823.1:c.1808delT NP_001393752.1:p.Leu603Terfs frameshift nonsense NM_001406824.1:c.2417delT NP_001393753.1:p.Leu806Terfs frameshift nonsense NM_001406825.1:c.2417delT NP_001393754.1:p.Leu806Terfs frameshift nonsense NM_001406826.1:c.2546delT NP_001393755.1:p.Leu849Terfs frameshift nonsense NM_001406827.1:c.2417delT NP_001393756.1:p.Leu806Terfs frameshift nonsense NM_001406828.1:c.2417delT NP_001393757.1:p.Leu806Terfs frameshift nonsense NM_001406829.1:c.1808delT NP_001393758.1:p.Leu603Terfs frameshift nonsense NM_001406830.1:c.2417delT NP_001393759.1:p.Leu806Terfs frameshift nonsense NM_001407362.1:c.659delT NP_001394291.1:p.Leu220Terfs frameshift nonsense NR_176256.1:n.1576delT NR_176257.1:n.2803delT NR_176258.1:n.2803delT NR_176259.1:n.2803delT NR_176260.1:n.748delT NR_176261.1:n.2803delT NC_000002.12:g.47800697del NC_000002.11:g.48027836del NG_007111.1:g.22551del LRG_219:g.22551del LRG_219t1:c.2714del LRG_219p1:p.Leu905Terfs - Protein change
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- Other names
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- Canonical SPDI
- NC_000002.12:47800694:TTT:TT
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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 | ||
|---|---|---|---|---|---|---|
| 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 |
9158 | 9474 | |
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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| Pathogenic (1) |
criteria provided, single submitter
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May 18, 2022 | RCV002801783.3 | |
| Pathogenic (1) |
criteria provided, single submitter
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Aug 17, 2023 | RCV003455578.1 |
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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Pathogenic
(Aug 17, 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: SCV004185752.1
First in ClinVar: Dec 24, 2023 Last updated: Dec 24, 2023 |
Comment:
This variant is considered pathogenic. This variant creates a termination codon and is predicted to result in premature protein truncation.
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Pathogenic
(May 18, 2022)
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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: SCV003198903.2
First in ClinVar: Feb 07, 2023 Last updated: Feb 20, 2024 |
Comment:
This sequence change creates a premature translational stop signal (p.Leu905*) in the MSH6 gene. It is expected to result in an absent or disrupted protein … (more)
This sequence change creates a premature translational stop signal (p.Leu905*) in the MSH6 gene. It is expected to result in an absent or disrupted protein product. Loss-of-function variants in MSH6 are known to be pathogenic (PMID: 18269114, 24362816). 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. For these reasons, this variant has been classified as Pathogenic. (less)
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Comment:
Comment:
This sequence change creates a premature translational stop signal (p.Leu905*) in the MSH6 gene. It is expected to result in an absent or disrupted protein product. Loss-of-function variants in MSH6 are known to be pathogenic (PMID: 18269114, 24362816). 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. For these reasons, this variant has been classified as Pathogenic.
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:
This variant is considered pathogenic. This variant creates a termination codon and is predicted to result in premature protein truncation.
Comment:
This sequence change creates a premature translational stop signal (p.Leu905*) in the MSH6 gene. It is expected to result in an absent or disrupted protein product. Loss-of-function variants in MSH6 are known to be pathogenic (PMID: 18269114, 24362816). 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. For these reasons, this variant has been classified as Pathogenic.
Citations for germline classification of this variant
Help| Title | Author | Journal | Year | Link |
|---|---|---|---|---|
| Application of a 5-tiered scheme for standardized classification of 2,360 unique mismatch repair gene variants in the InSiGHT locus-specific database. | Thompson BA | Nature genetics | 2014 | PMID: 24362816 |
| Germline MSH6 mutations are more prevalent in endometrial cancer patient cohorts than hereditary non polyposis colorectal cancer cohorts. | Devlin LA | The Ulster medical journal | 2008 | PMID: 18269114 |
Text-mined citations for this variant ...
HelpRecord last updated Oct 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.