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.2338_2339del (p.Ala780fs)
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.2338_2339del (p.Ala780fs)
Variation ID: 2673675 Accession: VCV002673675.1
- Type and length
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Deletion, 2 bp
- Location
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Cytogenetic: 2p16.3 2: 47800321-47800322 (GRCh38) [ NCBI UCSC ] 2: 48027460-48027461 (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 17, 2023 - HGVS
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... more HGVS ... less HGVSNucleotide Protein Molecular
consequenceNM_000179.3:c.2338_2339del MANE Select Help Transcripts from the Matched Annotation from the NCBI and EMBL-EBI (MANE) collaboration.
NP_000170.1:p.Ala780fs frameshift NM_001281492.2:c.1948_1949del NP_001268421.1:p.Ala650fs frameshift NM_001281493.2:c.1432_1433del NP_001268422.1:p.Ala478fs frameshift NM_001281494.2:c.1432_1433del NP_001268423.1:p.Ala478fs frameshift NM_001406795.1:c.2434_2435del NP_001393724.1:p.Ala812fs frameshift NM_001406796.1:c.2338_2339del NP_001393725.1:p.Ala780fs frameshift NM_001406797.1:c.2041_2042del NP_001393726.1:p.Ala681fs frameshift NM_001406798.1:c.2338_2339del NP_001393727.1:p.Ala780fs frameshift NM_001406799.1:c.1813_1814del NP_001393728.1:p.Ala605fs frameshift NM_001406800.1:c.2338_2339del NP_001393729.1:p.Ala780fs frameshift NM_001406801.1:c.2041_2042del NP_001393730.1:p.Ala681fs frameshift NM_001406802.1:c.2434_2435del NP_001393731.1:p.Ala812fs frameshift NM_001406803.1:c.2308+30_2308+31del intron variant NM_001406804.1:c.2260_2261del NP_001393733.1:p.Ala754fs frameshift NM_001406805.1:c.2041_2042del NP_001393734.1:p.Ala681fs frameshift NM_001406806.1:c.1813_1814del NP_001393735.1:p.Ala605fs frameshift NM_001406807.1:c.1813_1814del NP_001393736.1:p.Ala605fs frameshift NM_001406808.1:c.2338_2339del NP_001393737.1:p.Ala780fs frameshift NM_001406809.1:c.2338_2339del NP_001393738.1:p.Ala780fs frameshift NM_001406811.1:c.1432_1433del NP_001393740.1:p.Ala478fs frameshift NM_001406812.1:c.1432_1433del NP_001393741.1:p.Ala478fs frameshift NM_001406813.1:c.2344_2345del NP_001393742.1:p.Ala782fs frameshift NM_001406814.1:c.1432_1433del NP_001393743.1:p.Ala478fs frameshift NM_001406815.1:c.1432_1433del NP_001393744.1:p.Ala478fs frameshift NM_001406816.1:c.1432_1433del NP_001393745.1:p.Ala478fs frameshift NM_001406817.1:c.1606+732_1606+733del intron variant NM_001406818.1:c.2041_2042del NP_001393747.1:p.Ala681fs frameshift NM_001406819.1:c.2041_2042del NP_001393748.1:p.Ala681fs frameshift NM_001406820.1:c.2041_2042del NP_001393749.1:p.Ala681fs frameshift NM_001406821.1:c.2041_2042del NP_001393750.1:p.Ala681fs frameshift NM_001406822.1:c.2041_2042del NP_001393751.1:p.Ala681fs frameshift NM_001406823.1:c.1432_1433del NP_001393752.1:p.Ala478fs frameshift NM_001406824.1:c.2041_2042del NP_001393753.1:p.Ala681fs frameshift NM_001406825.1:c.2041_2042del NP_001393754.1:p.Ala681fs frameshift NM_001406826.1:c.2170_2171del NP_001393755.1:p.Ala724fs frameshift NM_001406827.1:c.2041_2042del NP_001393756.1:p.Ala681fs frameshift NM_001406828.1:c.2041_2042del NP_001393757.1:p.Ala681fs frameshift NM_001406829.1:c.1432_1433del NP_001393758.1:p.Ala478fs frameshift NM_001406830.1:c.2041_2042del NP_001393759.1:p.Ala681fs frameshift NM_001407362.1:c.628-345_628-344del intron variant NR_176256.1:n.1200_1201del non-coding transcript variant NR_176257.1:n.2427_2428del non-coding transcript variant NR_176258.1:n.2427_2428del non-coding transcript variant NR_176259.1:n.2427_2428del non-coding transcript variant NR_176261.1:n.2427_2428del non-coding transcript variant NC_000002.12:g.47800321_47800322del NC_000002.11:g.48027460_48027461del NG_007111.1:g.22175_22176del LRG_219:g.22175_22176del LRG_219t1:c.2338_2339del LRG_219p1:p.Ala780Profs - Protein change
- A478fs, A605fs, A650fs, A681fs, A724fs, A754fs, A780fs, A782fs, A812fs
- Other names
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- Canonical SPDI
- NC_000002.12:47800320:GC:
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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 |
9159 | 9475 | |
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 17, 2023 | RCV003450312.1 |
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
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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 17, 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: SCV004187104.1
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.