ClinVar Genomic variation as it relates to human health
NM_000179.3(MSH6):c.904del (p.Arg302fs)
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.904del (p.Arg302fs)
Variation ID: 1765598 Accession: VCV001765598.2
- Type and length
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Deletion, 1 bp
- Location
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Cytogenetic: 2p16.3 2: 47798887 (GRCh38) [ NCBI UCSC ] 2: 48026026 (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 Nov 29, 2022 May 1, 2024 Oct 11, 2017 - HGVS
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Nucleotide Protein Molecular
consequenceNM_000179.3:c.904del MANE Select Help Transcripts from the Matched Annotation from the NCBI and EMBL-EBI (MANE) collaboration.
NP_000170.1:p.Arg302fs frameshift NM_001281492.2:c.514del NP_001268421.1:p.Arg172fs frameshift NM_001281493.2:c.-3del 5 prime UTR NM_001281494.2:c.-3del 5 prime UTR NM_001406795.1:c.1000delA NP_001393724.1:p.Arg334Glufs frameshift NM_001406796.1:c.904delA NP_001393725.1:p.Arg302Glufs frameshift NM_001406797.1:c.607delA NP_001393726.1:p.Arg203Glufs frameshift NM_001406798.1:c.904delA NP_001393727.1:p.Arg302Glufs frameshift NM_001406799.1:c.379delA NP_001393728.1:p.Arg127Glufs frameshift NM_001406800.1:c.904delA NP_001393729.1:p.Arg302Glufs frameshift NM_001406801.1:c.607delA NP_001393730.1:p.Arg203Glufs frameshift NM_001406802.1:c.1000delA NP_001393731.1:p.Arg334Glufs frameshift NM_001406803.1:c.904delA NP_001393732.1:p.Arg302Glufs frameshift NM_001406804.1:c.826delA NP_001393733.1:p.Arg276Glufs frameshift NM_001406805.1:c.607delA NP_001393734.1:p.Arg203Glufs frameshift NM_001406806.1:c.379delA NP_001393735.1:p.Arg127Glufs frameshift NM_001406807.1:c.379delA NP_001393736.1:p.Arg127Glufs frameshift NM_001406808.1:c.904delA NP_001393737.1:p.Arg302Glufs frameshift NM_001406809.1:c.904delA NP_001393738.1:p.Arg302Glufs frameshift NM_001406811.1:c.-3delA NM_001406812.1:c.-3delA NM_001406813.1:c.910delA NP_001393742.1:p.Arg304Glufs frameshift NM_001406814.1:c.-3delA NM_001406815.1:c.-3delA NM_001406816.1:c.-3delA NM_001406817.1:c.904delA NP_001393746.1:p.Arg302Glufs frameshift NM_001406818.1:c.607delA NP_001393747.1:p.Arg203Glufs frameshift NM_001406819.1:c.607delA NP_001393748.1:p.Arg203Glufs frameshift NM_001406820.1:c.607delA NP_001393749.1:p.Arg203Glufs frameshift NM_001406821.1:c.607delA NP_001393750.1:p.Arg203Glufs frameshift NM_001406822.1:c.607delA NP_001393751.1:p.Arg203Glufs frameshift NM_001406823.1:c.-3delA NM_001406824.1:c.607delA NP_001393753.1:p.Arg203Glufs frameshift NM_001406825.1:c.607delA NP_001393754.1:p.Arg203Glufs frameshift NM_001406826.1:c.736delA NP_001393755.1:p.Arg246Glufs frameshift NM_001406827.1:c.607delA NP_001393756.1:p.Arg203Glufs frameshift NM_001406828.1:c.607delA NP_001393757.1:p.Arg203Glufs frameshift NM_001406829.1:c.-3delA NM_001406830.1:c.607delA NP_001393759.1:p.Arg203Glufs frameshift NR_176257.1:n.993delA NR_176258.1:n.993delA NR_176259.1:n.993delA NR_176261.1:n.993delA NC_000002.12:g.47798887del NC_000002.11:g.48026026del NG_007111.1:g.20741del LRG_219:g.20741del LRG_219t1:c.904del LRG_219p1:p.Arg302Glufs - Protein change
- R172fs, R302fs
- Other names
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- Canonical SPDI
- NC_000002.12:47798886:A:
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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 |
9157 | 9471 |
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
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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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Pathogenic (1) |
criteria provided, single submitter
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Oct 11, 2017 | RCV002378498.2 |
Submissions - Germline
Classification
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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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Pathogenic
(Oct 11, 2017)
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criteria provided, single submitter
Method: clinical testing
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Hereditary cancer-predisposing syndrome
Affected status: unknown
Allele origin:
germline
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Ambry Genetics
Accession: SCV002688067.2
First in ClinVar: Nov 29, 2022 Last updated: May 01, 2024 |
Comment:
The c.904delA pathogenic mutation, located in coding exon 4 of the MSH6 gene, results from a deletion of one nucleotide at nucleotide position 904, causing … (more)
The c.904delA pathogenic mutation, located in coding exon 4 of the MSH6 gene, results from a deletion of one nucleotide at nucleotide position 904, causing a translational frameshift with a predicted alternate stop codon (p.R302Efs*3). This alteration is expected to result in loss of function by premature protein truncation or nonsense-mediated mRNA decay. As such, this alteration is interpreted as a disease-causing mutation. (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 May 01, 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.