ClinVar Genomic variation as it relates to human health
NM_000179.3(MSH6):c.1846T>C (p.Ser616Pro)
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.1846T>C (p.Ser616Pro)
Variation ID: 3065147 Accession: VCV003065147.1
- Type and length
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single nucleotide variant, 1 bp
- Location
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Cytogenetic: 2p16.3 2: 47799829 (GRCh38) [ NCBI UCSC ] 2: 48026968 (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 6, 2024 Apr 6, 2024 Mar 26, 2024 - HGVS
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... more HGVS ... less HGVSNucleotide Protein Molecular
consequenceNM_000179.3:c.1846T>C MANE Select Help Transcripts from the Matched Annotation from the NCBI and EMBL-EBI (MANE) collaboration.
NP_000170.1:p.Ser616Pro missense NM_001281492.2:c.1456T>C NP_001268421.1:p.Ser486Pro missense NM_001281493.2:c.940T>C NP_001268422.1:p.Ser314Pro missense NM_001281494.2:c.940T>C NP_001268423.1:p.Ser314Pro missense NM_001406795.1:c.1942T>C NP_001393724.1:p.Ser648Pro missense NM_001406796.1:c.1846T>C NP_001393725.1:p.Ser616Pro missense NM_001406797.1:c.1549T>C NP_001393726.1:p.Ser517Pro missense NM_001406798.1:c.1846T>C NP_001393727.1:p.Ser616Pro missense NM_001406799.1:c.1321T>C NP_001393728.1:p.Ser441Pro missense NM_001406800.1:c.1846T>C NP_001393729.1:p.Ser616Pro missense NM_001406801.1:c.1549T>C NP_001393730.1:p.Ser517Pro missense NM_001406802.1:c.1942T>C NP_001393731.1:p.Ser648Pro missense NM_001406803.1:c.1846T>C NP_001393732.1:p.Ser616Pro missense NM_001406804.1:c.1768T>C NP_001393733.1:p.Ser590Pro missense NM_001406805.1:c.1549T>C NP_001393734.1:p.Ser517Pro missense NM_001406806.1:c.1321T>C NP_001393735.1:p.Ser441Pro missense NM_001406807.1:c.1321T>C NP_001393736.1:p.Ser441Pro missense NM_001406808.1:c.1846T>C NP_001393737.1:p.Ser616Pro missense NM_001406809.1:c.1846T>C NP_001393738.1:p.Ser616Pro missense NM_001406811.1:c.940T>C NP_001393740.1:p.Ser314Pro missense NM_001406812.1:c.940T>C NP_001393741.1:p.Ser314Pro missense NM_001406813.1:c.1852T>C NP_001393742.1:p.Ser618Pro missense NM_001406814.1:c.940T>C NP_001393743.1:p.Ser314Pro missense NM_001406815.1:c.940T>C NP_001393744.1:p.Ser314Pro missense NM_001406816.1:c.940T>C NP_001393745.1:p.Ser314Pro missense NM_001406817.1:c.1606+240T>C intron variant NM_001406818.1:c.1549T>C NP_001393747.1:p.Ser517Pro missense NM_001406819.1:c.1549T>C NP_001393748.1:p.Ser517Pro missense NM_001406820.1:c.1549T>C NP_001393749.1:p.Ser517Pro missense NM_001406821.1:c.1549T>C NP_001393750.1:p.Ser517Pro missense NM_001406822.1:c.1549T>C NP_001393751.1:p.Ser517Pro missense NM_001406823.1:c.940T>C NP_001393752.1:p.Ser314Pro missense NM_001406824.1:c.1549T>C NP_001393753.1:p.Ser517Pro missense NM_001406825.1:c.1549T>C NP_001393754.1:p.Ser517Pro missense NM_001406826.1:c.1678T>C NP_001393755.1:p.Ser560Pro missense NM_001406827.1:c.1549T>C NP_001393756.1:p.Ser517Pro missense NM_001406828.1:c.1549T>C NP_001393757.1:p.Ser517Pro missense NM_001406829.1:c.940T>C NP_001393758.1:p.Ser314Pro missense NM_001406830.1:c.1549T>C NP_001393759.1:p.Ser517Pro missense NM_001407362.1:c.628-837T>C intron variant NR_176257.1:n.1935T>C non-coding transcript variant NR_176258.1:n.1935T>C non-coding transcript variant NR_176259.1:n.1935T>C non-coding transcript variant NR_176261.1:n.1935T>C non-coding transcript variant NC_000002.12:g.47799829T>C NC_000002.11:g.48026968T>C NG_007111.1:g.21683T>C LRG_219:g.21683T>C LRG_219t1:c.1846T>C LRG_219p1:p.Ser616Pro - Protein change
- S314P, S441P, S486P, S517P, S560P, S590P, S616P, S618P, S648P
- Other names
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- Canonical SPDI
- NC_000002.12:47799828:T:C
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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 |
9166 | 9485 | |
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
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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| Likely benign (1) |
criteria provided, single submitter
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Mar 26, 2024 | RCV003990224.2 |
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
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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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Likely benign
(Mar 26, 2024)
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criteria provided, single submitter
Method: clinical testing
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Lynch syndrome 5
Affected status: unknown
Allele origin:
germline
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Center for Genomic Medicine, King Faisal Specialist Hospital and Research Center
Accession: SCV004806647.1
First in ClinVar: Apr 06, 2024 Last updated: Apr 06, 2024 |
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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 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.