ClinVar Genomic variation as it relates to human health
NM_000179.3(MSH6):c.4069_4070dup (p.Lys1358fs)
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.4069_4070dup (p.Lys1358fs)
Variation ID: 1801575 Accession: VCV001801575.1
- Type and length
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Duplication, 2 bp
- Location
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Cytogenetic: 2p16.3 2: 47806845-47806846 (GRCh38) [ NCBI UCSC ] 2: 48033984-48033985 (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 15, 2023 Apr 15, 2023 Jul 1, 2021 - HGVS
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... more HGVS ... less HGVSNucleotide Protein Molecular
consequenceNM_000179.3:c.4069_4070dup MANE Select Help Transcripts from the Matched Annotation from the NCBI and EMBL-EBI (MANE) collaboration.
NP_000170.1:p.Lys1358fs frameshift NM_001281492.2:c.3679_3680dup NP_001268421.1:p.Lys1228fs frameshift NM_001281493.2:c.3163_3164dup NP_001268422.1:p.Lys1056fs frameshift NM_001281494.2:c.3163_3164dup NP_001268423.1:p.Lys1056fs frameshift NM_001406795.1:c.4165_4166dup NP_001393724.1:p.Lys1390Leufs frameshift NM_001406796.1:c.4069_4070dup NP_001393725.1:p.Lys1358Leufs frameshift NM_001406797.1:c.3772_3773dup NP_001393726.1:p.Lys1259Leufs frameshift NM_001406798.1:c.3895_3896dup NP_001393727.1:p.Lys1300Leufs frameshift NM_001406799.1:c.3544_3545dup NP_001393728.1:p.Lys1183Leufs frameshift NM_001406800.1:c.*90_*91dup NM_001406801.1:c.*50_*51dup NM_001406802.1:c.*50_*51dup NM_001406803.1:c.3205_3206dup NP_001393732.1:p.Lys1070Leufs frameshift NM_001406804.1:c.3991_3992dup NP_001393733.1:p.Lys1332Leufs frameshift NM_001406805.1:c.3772_3773dup NP_001393734.1:p.Lys1259Leufs frameshift NM_001406806.1:c.3544_3545dup NP_001393735.1:p.Lys1183Leufs frameshift NM_001406807.1:c.3544_3545dup NP_001393736.1:p.Lys1183Leufs frameshift NM_001406808.1:c.*50_*51dup NM_001406809.1:c.4069_4070dup NP_001393738.1:p.Lys1358Leufs frameshift NM_001406811.1:c.3163_3164dup NP_001393740.1:p.Lys1056Leufs frameshift NM_001406812.1:c.3163_3164dup NP_001393741.1:p.Lys1056Leufs frameshift NM_001406813.1:c.4075_4076dup NP_001393742.1:p.Lys1360Leufs frameshift NM_001406814.1:c.3163_3164dup NP_001393743.1:p.Lys1056Leufs frameshift NM_001406815.1:c.3163_3164dup NP_001393744.1:p.Lys1056Leufs frameshift NM_001406816.1:c.3163_3164dup NP_001393745.1:p.Lys1056Leufs frameshift NM_001406817.1:c.2503_2504dup NP_001393746.1:p.Lys836Leufs frameshift NM_001406818.1:c.3772_3773dup NP_001393747.1:p.Lys1259Leufs frameshift NM_001406819.1:c.3772_3773dup NP_001393748.1:p.Lys1259Leufs frameshift NM_001406820.1:c.3772_3773dup NP_001393749.1:p.Lys1259Leufs frameshift NM_001406821.1:c.3772_3773dup NP_001393750.1:p.Lys1259Leufs frameshift NM_001406822.1:c.*50_*51dup NM_001406823.1:c.3163_3164dup NP_001393752.1:p.Lys1056Leufs frameshift NM_001406824.1:c.3772_3773dup NP_001393753.1:p.Lys1259Leufs frameshift NM_001406825.1:c.3772_3773dup NP_001393754.1:p.Lys1259Leufs frameshift NM_001406826.1:c.3901_3902dup NP_001393755.1:p.Lys1302Leufs frameshift NM_001406827.1:c.3772_3773dup NP_001393756.1:p.Lys1259Leufs frameshift NM_001406828.1:c.3772_3773dup NP_001393757.1:p.Lys1259Leufs frameshift NM_001406829.1:c.3163_3164dup NP_001393758.1:p.Lys1056Leufs frameshift NM_001406830.1:c.3772_3773dup NP_001393759.1:p.Lys1259Leufs frameshift NM_001406831.1:c.850_851dup NP_001393760.1:p.Lys285Leufs frameshift NM_001406832.1:c.916_917dup NP_001393761.1:p.Lys307Leufs frameshift NM_001407362.1:c.2014_2015dup NP_001394291.1:p.Lys673Leufs frameshift NR_176256.1:n.2999_3000dup NR_176257.1:n.4330_4331dup NR_176258.1:n.4259_4260dup NR_176259.1:n.4158_4159dup NR_176260.1:n.2103_2104dup NR_176261.1:n.4040_4041dup NC_000002.12:g.47806846_47806847dup NC_000002.11:g.48033985_48033986dup NG_007111.1:g.28700_28701dup NG_008397.1:g.103829_103830dup LRG_219:g.28700_28701dup LRG_219t1:c.4069_4070dup LRG_219p1:p.Lys1358Leufs - Protein change
- K1056fs, K1228fs, K1358fs
- Other names
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- Canonical SPDI
- NC_000002.12:47806845:AT:ATAT
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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 | ||
|---|---|---|---|---|---|---|
| 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
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 | - | |
Conditions - Germline
| Condition
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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
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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. |
|---|---|---|---|---|
| Pathogenic (1) |
no assertion criteria provided
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Jul 1, 2021 | RCV003164610.2 |
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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Pathogenic
(Jul 01, 2021)
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no assertion criteria provided
Method: research
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Gastric cancer
Affected status: unknown
Allele origin:
germline
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Laboratory for Genotyping Development, RIKEN
Accession: SCV002758274.1
First in ClinVar: Apr 15, 2023 Last updated: Apr 15, 2023 |
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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
Help| Title | Author | Journal | Year | Link |
|---|---|---|---|---|
| Helicobacter pylori, Homologous-Recombination Genes, and Gastric Cancer. | Usui Y | The New England journal of medicine | 2023 | PMID: 36988593 |
Text-mined citations for this variant ...
HelpRecord last updated Sep 17, 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.