ClinVar Genomic variation as it relates to human health
NM_000179.3(MSH6):c.4072_4074del (p.Lys1358del)
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.4072_4074del (p.Lys1358del)
Variation ID: 2116903 Accession: VCV002116903.2
- Type and length
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Deletion, 3 bp
- Location
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Cytogenetic: 2p16.3 2: 47806849-47806851 (GRCh38) [ NCBI UCSC ] 2: 48033988-48033990 (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 Nov 5, 2023 - HGVS
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Nucleotide Protein Molecular
consequenceNM_000179.3:c.4072_4074del MANE Select Help Transcripts from the Matched Annotation from the NCBI and EMBL-EBI (MANE) collaboration.
NP_000170.1:p.Lys1358del inframe deletion NM_001281492.2:c.3682_3684del NP_001268421.1:p.Lys1228del inframe deletion NM_001281493.2:c.3166_3168del NP_001268422.1:p.Lys1056del inframe deletion NM_001281494.2:c.3166_3168del NP_001268423.1:p.Lys1056del inframe deletion NM_001406795.1:c.4168_4170delAAG NP_001393724.1:p.Lys1390del inframe indel NM_001406796.1:c.4072_4074delAAG NP_001393725.1:p.Lys1358del inframe indel NM_001406797.1:c.3775_3777delAAG NP_001393726.1:p.Lys1259del inframe indel NM_001406798.1:c.3898_3900delAAG NP_001393727.1:p.Lys1300del inframe indel NM_001406799.1:c.3547_3549delAAG NP_001393728.1:p.Lys1183del inframe indel NM_001406800.1:c.*93_*95delAAG NM_001406801.1:c.*53_*55delAAG NM_001406802.1:c.*53_*55delAAG NM_001406803.1:c.3208_3210delAAG NP_001393732.1:p.Lys1070del inframe indel NM_001406804.1:c.3994_3996delAAG NP_001393733.1:p.Lys1332del inframe indel NM_001406805.1:c.3775_3777delAAG NP_001393734.1:p.Lys1259del inframe indel NM_001406806.1:c.3547_3549delAAG NP_001393735.1:p.Lys1183del inframe indel NM_001406807.1:c.3547_3549delAAG NP_001393736.1:p.Lys1183del inframe indel NM_001406808.1:c.*53_*55delAAG NM_001406809.1:c.4072_4074delAAG NP_001393738.1:p.Lys1358del inframe indel NM_001406811.1:c.3166_3168delAAG NP_001393740.1:p.Lys1056del inframe indel NM_001406812.1:c.3166_3168delAAG NP_001393741.1:p.Lys1056del inframe indel NM_001406813.1:c.4078_4080delAAG NP_001393742.1:p.Lys1360del inframe indel NM_001406814.1:c.3166_3168delAAG NP_001393743.1:p.Lys1056del inframe indel NM_001406815.1:c.3166_3168delAAG NP_001393744.1:p.Lys1056del inframe indel NM_001406816.1:c.3166_3168delAAG NP_001393745.1:p.Lys1056del inframe indel NM_001406817.1:c.2506_2508delAAG NP_001393746.1:p.Lys836del inframe indel NM_001406818.1:c.3775_3777delAAG NP_001393747.1:p.Lys1259del inframe indel NM_001406819.1:c.3775_3777delAAG NP_001393748.1:p.Lys1259del inframe indel NM_001406820.1:c.3775_3777delAAG NP_001393749.1:p.Lys1259del inframe indel NM_001406821.1:c.3775_3777delAAG NP_001393750.1:p.Lys1259del inframe indel NM_001406822.1:c.*53_*55delAAG NM_001406823.1:c.3166_3168delAAG NP_001393752.1:p.Lys1056del inframe indel NM_001406824.1:c.3775_3777delAAG NP_001393753.1:p.Lys1259del inframe indel NM_001406825.1:c.3775_3777delAAG NP_001393754.1:p.Lys1259del inframe indel NM_001406826.1:c.3904_3906delAAG NP_001393755.1:p.Lys1302del inframe indel NM_001406827.1:c.3775_3777delAAG NP_001393756.1:p.Lys1259del inframe indel NM_001406828.1:c.3775_3777delAAG NP_001393757.1:p.Lys1259del inframe indel NM_001406829.1:c.3166_3168delAAG NP_001393758.1:p.Lys1056del inframe indel NM_001406830.1:c.3775_3777delAAG NP_001393759.1:p.Lys1259del inframe indel NM_001406831.1:c.853_855delAAG NP_001393760.1:p.Lys285del inframe indel NM_001406832.1:c.919_921delAAG NP_001393761.1:p.Lys307del inframe indel NM_001407362.1:c.2017_2019delAAG NP_001394291.1:p.Lys673del inframe indel NR_176256.1:n.3002_3004delAAG NR_176257.1:n.4333_4335delAAG NR_176258.1:n.4262_4264delAAG NR_176259.1:n.4161_4163delAAG NR_176260.1:n.2106_2108delAAG NR_176261.1:n.4043_4045delAAG NC_000002.12:g.47806849_47806851del NC_000002.11:g.48033988_48033990del NG_007111.1:g.28703_28705del NG_008397.1:g.103825_103827del LRG_219:g.28703_28705del LRG_219t1:c.4072_4074del LRG_219p1:p.Lys1358del - Protein change
- K1056del, K1300del, K1302del, K1358del, K1360del, K285del, K1070del, K1183del, K1332del, K836del, K1259del, K1390del, K673del, K1228del, K307del
- Other names
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- Canonical SPDI
- NC_000002.12:47806848:AAG:
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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
Help
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 |
9149 | 9460 |
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
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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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Uncertain significance (1) |
criteria provided, single submitter
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Nov 5, 2023 | RCV003027469.2 |
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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Uncertain significance
(Nov 05, 2023)
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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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Invitae
Accession: SCV003337989.2
First in ClinVar: Feb 07, 2023 Last updated: Feb 20, 2024 |
Comment:
This variant, c.4072_4074del, results in the deletion of 1 amino acid(s) of the MSH6 protein (p.Lys1358del), but otherwise preserves the integrity of the reading frame. … (more)
This variant, c.4072_4074del, results in the deletion of 1 amino acid(s) of the MSH6 protein (p.Lys1358del), but otherwise preserves the integrity of the reading frame. 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. ClinVar contains an entry for this variant (Variation ID: 2116903). Experimental studies and prediction algorithms are not available or were not evaluated, and the functional significance of this variant is currently unknown. In summary, the available evidence is currently insufficient to determine the role of this variant in disease. Therefore, it has been classified as a Variant of Uncertain Significance. (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 Feb 29, 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.