This variant is considered pathogenic. This variant creates a frameshift predicted to result in premature protein truncation.
ClinVar Genomic variation as it relates to human health
NM_000179.3(MSH6):c.3834dup (p.Ser1279fs)
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.
(1)
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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
1
criteria provided, single submitter
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.3834dup (p.Ser1279fs)
Variation ID: 2673638 Accession: VCV002673638.1
- Type and length
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Duplication, 1 bp
- Location
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Cytogenetic: 2p16.3 2: 47806480-47806481 (GRCh38) [ NCBI UCSC ] 2: 48033619-48033620 (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 Dec 25, 2023 Dec 24, 2023 Aug 25, 2023 - HGVS
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... more HGVS ... less HGVSNucleotide Protein Molecular
consequenceNM_000179.3:c.3834dup MANE Select Help Transcripts from the Matched Annotation from the NCBI and EMBL-EBI (MANE) collaboration.
NP_000170.1:p.Ser1279fs frameshift NM_001281492.2:c.3444dup NP_001268421.1:p.Ser1149fs frameshift NM_001281493.2:c.2928dup NP_001268422.1:p.Ser977fs frameshift NM_001281494.2:c.2928dup NP_001268423.1:p.Ser977fs frameshift NM_001406795.1:c.3930dup NP_001393724.1:p.Ser1311fs frameshift NM_001406796.1:c.3834dup NP_001393725.1:p.Ser1279fs frameshift NM_001406797.1:c.3537dup NP_001393726.1:p.Ser1180fs frameshift NM_001406798.1:c.3660dup NP_001393727.1:p.Ser1221fs frameshift NM_001406799.1:c.3309dup NP_001393728.1:p.Ser1104fs frameshift NM_001406800.1:c.3821dup NP_001393729.1:p.Ala1275fs frameshift NM_001406801.1:c.3537dup NP_001393730.1:p.Ser1180fs frameshift NM_001406802.1:c.3897+126dup intron variant NM_001406803.1:c.2970dup NP_001393732.1:p.Ser991fs frameshift NM_001406804.1:c.3756dup NP_001393733.1:p.Ser1253fs frameshift NM_001406805.1:c.3537dup NP_001393734.1:p.Ser1180fs frameshift NM_001406806.1:c.3309dup NP_001393735.1:p.Ser1104fs frameshift NM_001406807.1:c.3309dup NP_001393736.1:p.Ser1104fs frameshift NM_001406808.1:c.3834dup NP_001393737.1:p.Ser1279fs frameshift NM_001406809.1:c.3834dup NP_001393738.1:p.Ser1279fs frameshift NM_001406811.1:c.2928dup NP_001393740.1:p.Ser977fs frameshift NM_001406812.1:c.2928dup NP_001393741.1:p.Ser977fs frameshift NM_001406813.1:c.3840dup NP_001393742.1:p.Ser1281fs frameshift NM_001406814.1:c.2928dup NP_001393743.1:p.Ser977fs frameshift NM_001406815.1:c.2928dup NP_001393744.1:p.Ser977fs frameshift NM_001406816.1:c.2928dup NP_001393745.1:p.Ser977fs frameshift NM_001406817.1:c.2268dup NP_001393746.1:p.Ser757fs frameshift NM_001406818.1:c.3537dup NP_001393747.1:p.Ser1180fs frameshift NM_001406819.1:c.3537dup NP_001393748.1:p.Ser1180fs frameshift NM_001406820.1:c.3537dup NP_001393749.1:p.Ser1180fs frameshift NM_001406821.1:c.3537dup NP_001393750.1:p.Ser1180fs frameshift NM_001406822.1:c.3537dup NP_001393751.1:p.Ser1180fs frameshift NM_001406823.1:c.2928dup NP_001393752.1:p.Ser977fs frameshift NM_001406824.1:c.3537dup NP_001393753.1:p.Ser1180fs frameshift NM_001406825.1:c.3537dup NP_001393754.1:p.Ser1180fs frameshift NM_001406826.1:c.3666dup NP_001393755.1:p.Ser1223fs frameshift NM_001406827.1:c.3537dup NP_001393756.1:p.Ser1180fs frameshift NM_001406828.1:c.3537dup NP_001393757.1:p.Ser1180fs frameshift NM_001406829.1:c.2928dup NP_001393758.1:p.Ser977fs frameshift NM_001406830.1:c.3537dup NP_001393759.1:p.Ser1180fs frameshift NM_001406831.1:c.615dup NP_001393760.1:p.Ser206fs frameshift NM_001406832.1:c.681dup NP_001393761.1:p.Ser228fs frameshift NM_001407362.1:c.1779dup NP_001394291.1:p.Ser594fs frameshift NR_176256.1:n.2764dup non-coding transcript variant NR_176257.1:n.4095dup non-coding transcript variant NR_176258.1:n.4024dup non-coding transcript variant NR_176259.1:n.3923dup non-coding transcript variant NR_176260.1:n.1868dup NR_176261.1:n.3805dup non-coding transcript variant NC_000002.12:g.47806484dup NC_000002.11:g.48033623dup NG_007111.1:g.28338dup NG_008397.1:g.104195dup LRG_219:g.28338dup LRG_219t1:c.3834dup LRG_219p1:p.Ser1279Glnfs - Protein change
- A1275fs, S1104fs, S1149fs, S1180fs, S1221fs, S1223fs, S1253fs, S1279fs, S1281fs, S1311fs, S206fs, S228fs, S594fs, S757fs, S977fs, S991fs
- Other names
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- Canonical SPDI
- NC_000002.12:47806480:CCCC:CCCCC
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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 |
9161 | 9479 | |
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
Help
The RCV accession number, with most recent version number, for the variant-condition record, with a link to the RCV web page. |
|---|---|---|---|---|
| Pathogenic (1) |
criteria provided, single submitter
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Aug 25, 2023 | RCV003450275.1 |
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
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 25, 2023)
|
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: SCV004185812.1
First in ClinVar: Dec 24, 2023 Last updated: Dec 24, 2023 |
Comment:
This variant is considered pathogenic. This variant creates a frameshift predicted to result in premature protein truncation.
|
Comment:
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 frameshift predicted to result in premature protein truncation.
Citations for germline classification of this variant
Help| There 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 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.