ClinVar Genomic variation as it relates to human health
NM_000179.3(MSH6):c.3658G>T (p.Ala1220Ser)
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.3658G>T (p.Ala1220Ser)
Variation ID: 3071304 Accession: VCV003071304.1
- Type and length
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single nucleotide variant, 1 bp
- Location
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Cytogenetic: 2p16.3 2: 47806215 (GRCh38) [ NCBI UCSC ] 2: 48033354 (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 20, 2024 Apr 20, 2024 May 31, 2023 - HGVS
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... more HGVS ... less HGVSNucleotide Protein Molecular
consequenceNM_000179.3:c.3658G>T MANE Select Help Transcripts from the Matched Annotation from the NCBI and EMBL-EBI (MANE) collaboration.
NP_000170.1:p.Ala1220Ser missense NM_001281492.2:c.3268G>T NP_001268421.1:p.Ala1090Ser missense NM_001281493.2:c.2752G>T NP_001268422.1:p.Ala918Ser missense NM_001281494.2:c.2752G>T NP_001268423.1:p.Ala918Ser missense NM_001406795.1:c.3754G>T NP_001393724.1:p.Ala1252Ser missense NM_001406796.1:c.3658G>T NP_001393725.1:p.Ala1220Ser missense NM_001406797.1:c.3361G>T NP_001393726.1:p.Ala1121Ser missense NM_001406798.1:c.3484G>T NP_001393727.1:p.Ala1162Ser missense NM_001406799.1:c.3133G>T NP_001393728.1:p.Ala1045Ser missense NM_001406800.1:c.3658G>T NP_001393729.1:p.Ala1220Ser missense NM_001406801.1:c.3361G>T NP_001393730.1:p.Ala1121Ser missense NM_001406802.1:c.3754G>T NP_001393731.1:p.Ala1252Ser missense NM_001406803.1:c.2794G>T NP_001393732.1:p.Ala932Ser missense NM_001406804.1:c.3580G>T NP_001393733.1:p.Ala1194Ser missense NM_001406805.1:c.3361G>T NP_001393734.1:p.Ala1121Ser missense NM_001406806.1:c.3133G>T NP_001393735.1:p.Ala1045Ser missense NM_001406807.1:c.3133G>T NP_001393736.1:p.Ala1045Ser missense NM_001406808.1:c.3658G>T NP_001393737.1:p.Ala1220Ser missense NM_001406809.1:c.3658G>T NP_001393738.1:p.Ala1220Ser missense NM_001406811.1:c.2752G>T NP_001393740.1:p.Ala918Ser missense NM_001406812.1:c.2752G>T NP_001393741.1:p.Ala918Ser missense NM_001406813.1:c.3664G>T NP_001393742.1:p.Ala1222Ser missense NM_001406814.1:c.2752G>T NP_001393743.1:p.Ala918Ser missense NM_001406815.1:c.2752G>T NP_001393744.1:p.Ala918Ser missense NM_001406816.1:c.2752G>T NP_001393745.1:p.Ala918Ser missense NM_001406817.1:c.2092G>T NP_001393746.1:p.Ala698Ser missense NM_001406818.1:c.3361G>T NP_001393747.1:p.Ala1121Ser missense NM_001406819.1:c.3361G>T NP_001393748.1:p.Ala1121Ser missense NM_001406820.1:c.3361G>T NP_001393749.1:p.Ala1121Ser missense NM_001406821.1:c.3361G>T NP_001393750.1:p.Ala1121Ser missense NM_001406822.1:c.3361G>T NP_001393751.1:p.Ala1121Ser missense NM_001406823.1:c.2752G>T NP_001393752.1:p.Ala918Ser missense NM_001406824.1:c.3361G>T NP_001393753.1:p.Ala1121Ser missense NM_001406825.1:c.3361G>T NP_001393754.1:p.Ala1121Ser missense NM_001406826.1:c.3490G>T NP_001393755.1:p.Ala1164Ser missense NM_001406827.1:c.3361G>T NP_001393756.1:p.Ala1121Ser missense NM_001406828.1:c.3361G>T NP_001393757.1:p.Ala1121Ser missense NM_001406829.1:c.2752G>T NP_001393758.1:p.Ala918Ser missense NM_001406830.1:c.3361G>T NP_001393759.1:p.Ala1121Ser missense NM_001406831.1:c.439G>T NP_001393760.1:p.Ala147Ser missense NM_001406832.1:c.505G>T NP_001393761.1:p.Ala169Ser missense NM_001407362.1:c.1603G>T NP_001394291.1:p.Ala535Ser missense NR_176256.1:n.2588G>T non-coding transcript variant NR_176257.1:n.3919G>T non-coding transcript variant NR_176258.1:n.3848G>T non-coding transcript variant NR_176259.1:n.3747G>T non-coding transcript variant NR_176260.1:n.1692G>T NR_176261.1:n.3629G>T non-coding transcript variant NC_000002.12:g.47806215G>T NC_000002.11:g.48033354G>T NG_007111.1:g.28069G>T NG_008397.1:g.104461C>A LRG_219:g.28069G>T LRG_219t1:c.3658G>T LRG_219p1:p.Ala1220Ser - Protein change
- A1045S, A1090S, A1121S, A1162S, A1164S, A1194S, A1220S, A1222S, A1252S, A147S, A169S, A535S, A698S, A918S, A932S
- Other names
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- Canonical SPDI
- NC_000002.12:47806214:G:T
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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
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
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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. |
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| Uncertain significance (1) |
criteria provided, single submitter
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May 31, 2023 | RCV004014806.2 |
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
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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Uncertain Significance
(May 31, 2023)
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criteria provided, single submitter
Method: clinical testing
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Lynch syndrome
(Autosomal dominant inheritance)
Affected status: unknown
Allele origin:
germline
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All of Us Research Program, National Institutes of Health
Accession: SCV004828169.1
First in ClinVar: Apr 20, 2024 Last updated: Apr 20, 2024
Comment:
This study involves interpretation of variants in research participants for the purpose of population health screening. Participant phenotype was not available at the time of … (more)
This study involves interpretation of variants in research participants for the purpose of population health screening. Participant phenotype was not available at the time of variant classification. Additional details can be found in publication PMID: 35346344, PMCID: PMC8962531 (less)
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Number of individuals with the variant: 1
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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| 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 May 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.