This variant is considered pathogenic. This variant creates a frameshift predicted to result in premature protein truncation.
ClinVar Genomic variation as it relates to human health
NM_000179.3(MSH6):c.3403_3407del (p.Pro1135fs)
Germline
Classification
Help
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.
(1)
Help
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.
Pathogenic
1
criteria provided, single submitter
Somatic
No data submitted for somatic clinical impact
Somatic
No data submitted for oncogenicity
Variant Details
- Identifiers
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NM_000179.3(MSH6):c.3403_3407del (p.Pro1135fs)
Variation ID: 2673731 Accession: VCV002673731.1
- Type and length
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Deletion, 5 bp
- Location
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Cytogenetic: 2p16.3 2: 47803649-47803653 (GRCh38) [ NCBI UCSC ] 2: 48030788-48030792 (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 Dec 25, 2023 Dec 24, 2023 Aug 23, 2023 - HGVS
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... more HGVS ... less HGVSNucleotide Protein Molecular
consequenceNM_000179.3:c.3403_3407del MANE Select Help Transcripts from the Matched Annotation from the NCBI and EMBL-EBI (MANE) collaboration.
NP_000170.1:p.Pro1135fs frameshift NM_001281492.2:c.3013_3017del NP_001268421.1:p.Pro1005fs frameshift NM_001281493.2:c.2497_2501del NP_001268422.1:p.Pro833fs frameshift NM_001281494.2:c.2497_2501del NP_001268423.1:p.Pro833fs frameshift NM_001406795.1:c.3499_3503del NP_001393724.1:p.Pro1167fs frameshift NM_001406796.1:c.3403_3407del NP_001393725.1:p.Pro1135fs frameshift NM_001406797.1:c.3106_3110del NP_001393726.1:p.Pro1036fs frameshift NM_001406798.1:c.3229_3233del NP_001393727.1:p.Pro1077fs frameshift NM_001406799.1:c.2878_2882del NP_001393728.1:p.Pro960fs frameshift NM_001406800.1:c.3403_3407del NP_001393729.1:p.Pro1135fs frameshift NM_001406801.1:c.3106_3110del NP_001393730.1:p.Pro1036fs frameshift NM_001406802.1:c.3499_3503del NP_001393731.1:p.Pro1167fs frameshift NM_001406803.1:c.2539_2543del NP_001393732.1:p.Pro847fs frameshift NM_001406804.1:c.3325_3329del NP_001393733.1:p.Pro1109fs frameshift NM_001406805.1:c.3106_3110del NP_001393734.1:p.Pro1036fs frameshift NM_001406806.1:c.2878_2882del NP_001393735.1:p.Pro960fs frameshift NM_001406807.1:c.2878_2882del NP_001393736.1:p.Pro960fs frameshift NM_001406808.1:c.3403_3407del NP_001393737.1:p.Pro1135fs frameshift NM_001406809.1:c.3403_3407del NP_001393738.1:p.Pro1135fs frameshift NM_001406811.1:c.2497_2501del NP_001393740.1:p.Pro833fs frameshift NM_001406812.1:c.2497_2501del NP_001393741.1:p.Pro833fs frameshift NM_001406813.1:c.3409_3413del NP_001393742.1:p.Pro1137fs frameshift NM_001406814.1:c.2497_2501del NP_001393743.1:p.Pro833fs frameshift NM_001406815.1:c.2497_2501del NP_001393744.1:p.Pro833fs frameshift NM_001406816.1:c.2497_2501del NP_001393745.1:p.Pro833fs frameshift NM_001406817.1:c.1837_1841del NP_001393746.1:p.Pro613fs frameshift NM_001406818.1:c.3106_3110del NP_001393747.1:p.Pro1036fs frameshift NM_001406819.1:c.3106_3110del NP_001393748.1:p.Pro1036fs frameshift NM_001406820.1:c.3106_3110del NP_001393749.1:p.Pro1036fs frameshift NM_001406821.1:c.3106_3110del NP_001393750.1:p.Pro1036fs frameshift NM_001406822.1:c.3106_3110del NP_001393751.1:p.Pro1036fs frameshift NM_001406823.1:c.2497_2501del NP_001393752.1:p.Pro833fs frameshift NM_001406824.1:c.3106_3110del NP_001393753.1:p.Pro1036fs frameshift NM_001406825.1:c.3106_3110del NP_001393754.1:p.Pro1036fs frameshift NM_001406826.1:c.3235_3239del NP_001393755.1:p.Pro1079fs frameshift NM_001406827.1:c.3106_3110del NP_001393756.1:p.Pro1036fs frameshift NM_001406828.1:c.3106_3110del NP_001393757.1:p.Pro1036fs frameshift NM_001406829.1:c.2497_2501del NP_001393758.1:p.Pro833fs frameshift NM_001406830.1:c.3106_3110del NP_001393759.1:p.Pro1036fs frameshift NM_001406831.1:c.184_188del NP_001393760.1:p.Pro62fs frameshift NM_001406832.1:c.250_254del NP_001393761.1:p.Pro84fs frameshift NM_001407362.1:c.1348_1352del NP_001394291.1:p.Pro450fs frameshift NR_176256.1:n.2333_2337del non-coding transcript variant NR_176257.1:n.3664_3668del non-coding transcript variant NR_176258.1:n.3593_3597del non-coding transcript variant NR_176259.1:n.3492_3496del non-coding transcript variant NR_176260.1:n.1437_1441delCCAAA NR_176261.1:n.3492_3496del non-coding transcript variant NC_000002.12:g.47803650_47803654del NC_000002.11:g.48030789_48030793del NG_007111.1:g.25504_25508del LRG_219:g.25504_25508del LRG_219t1:c.3403_3407del LRG_219p1:p.Pro1135Tyrfs - Protein change
- P1005fs, P1036fs, P1077fs, P1079fs, P1109fs, P1135fs, P1137fs, P1167fs, P450fs, P613fs, P62fs, P833fs, P847fs, P84fs, P960fs
- Other names
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- Canonical SPDI
- NC_000002.12:47803648:ACCAAA: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
Help
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
Help
Links to Variation Viewer, a genome browser to view variation data from NCBI databases. |
Related variants | ||
|---|---|---|---|---|---|---|
| HI score
Help
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
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
Help
The most recent date that a submitter evaluated this variant for the condition. |
Variation/condition record
Help
The RCV accession number, with most recent version number, for the variant-condition record, with a link to the RCV web page. |
|---|---|---|---|---|
| Pathogenic (1) |
criteria provided, single submitter
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Aug 23, 2023 | RCV003450368.1 |
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
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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
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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Pathogenic
(Aug 23, 2023)
|
criteria provided, single submitter
Method: clinical testing
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Lynch syndrome 5
Affected status: unknown
Allele origin:
unknown
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Myriad Genetics, Inc.
Accession: SCV004187256.1
First in ClinVar: Dec 24, 2023 Last updated: Dec 24, 2023 |
Comment:
This variant is considered pathogenic. This variant creates a frameshift predicted to result in premature protein truncation.
|
Comment:
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. |
Comment:
This variant is considered pathogenic. This variant creates a frameshift predicted to result in premature protein truncation.
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.