ClinVar Genomic variation as it relates to human health
NM_000548.5(TSC2):c.2678_2679del (p.Ile893fs)
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_000548.5(TSC2):c.2678_2679del (p.Ile893fs)
Variation ID: 2835590 Accession: VCV002835590.1
- Type and length
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Deletion, 2 bp
- Location
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Cytogenetic: 16p13.3 16: 2076105-2076106 (GRCh38) [ NCBI UCSC ] 16: 2126106-2126107 (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 20, 2024 Feb 20, 2024 Feb 8, 2023 - HGVS
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Nucleotide Protein Molecular
consequenceNM_000548.5:c.2678_2679del MANE Select Help Transcripts from the Matched Annotation from the NCBI and EMBL-EBI (MANE) collaboration.
NP_000539.2:p.Ile893fs frameshift NM_001077183.3:c.2678_2679del NP_001070651.1:p.Ile893fs frameshift NM_001114382.3:c.2678_2679del NP_001107854.1:p.Ile893fs frameshift NM_001318827.2:c.2567_2568del NP_001305756.1:p.Ile856fs frameshift NM_001318829.2:c.2531_2532del NP_001305758.1:p.Ile844fs frameshift NM_001318831.2:c.2078_2079del NP_001305760.1:p.Ile693fs frameshift NM_001318832.2:c.2711_2712del NP_001305761.1:p.Ile904fs frameshift NM_001363528.2:c.2678_2679del NP_001350457.1:p.Ile893fs frameshift NM_001370404.1:c.2678_2679del NP_001357333.1:p.Ile893fs frameshift NM_001370405.1:c.2678_2679del NP_001357334.1:p.Ile893fs frameshift NM_001406663.1:c.2678_2679del NP_001393592.1:p.Ile893fs frameshift NM_001406664.1:c.2678_2679del NP_001393593.1:p.Ile893fs frameshift NM_001406665.1:c.2678_2679del NP_001393594.1:p.Ile893fs frameshift NM_001406667.1:c.2768_2769del NP_001393596.1:p.Ile923fs frameshift NM_001406668.1:c.2768_2769del NP_001393597.1:p.Ile923fs frameshift NM_001406670.1:c.2567_2568del NP_001393599.1:p.Ile856fs frameshift NM_001406671.1:c.2666_2667del NP_001393600.1:p.Ile889fs frameshift NM_001406673.1:c.2666_2667del NP_001393602.1:p.Ile889fs frameshift NM_001406675.1:c.2531_2532del NP_001393604.1:p.Ile844fs frameshift NM_001406676.1:c.2531_2532del NP_001393605.1:p.Ile844fs frameshift NM_001406677.1:c.2621_2622del NP_001393606.1:p.Ile874fs frameshift NM_001406678.1:c.2567_2568del NP_001393607.1:p.Ile856fs frameshift NM_001406679.1:c.2531_2532del NP_001393608.1:p.Ile844fs frameshift NM_001406680.1:c.2078_2079del NP_001393609.1:p.Ile693fs frameshift NM_001406681.1:c.2216_2217del NP_001393610.1:p.Ile739fs frameshift NM_001406682.1:c.2078_2079del NP_001393611.1:p.Ile693fs frameshift NM_001406683.1:c.2078_2079del NP_001393612.1:p.Ile693fs frameshift NM_001406684.1:c.2078_2079del NP_001393613.1:p.Ile693fs frameshift NM_001406685.1:c.2078_2079del NP_001393614.1:p.Ile693fs frameshift NM_001406686.1:c.2078_2079del NP_001393615.1:p.Ile693fs frameshift NM_001406687.1:c.2078_2079del NP_001393616.1:p.Ile693fs frameshift NM_001406688.1:c.2078_2079del NP_001393617.1:p.Ile693fs frameshift NM_001406689.1:c.1334_1335del NP_001393618.1:p.Ile445fs frameshift NM_001406690.1:c.1334_1335del NP_001393619.1:p.Ile445fs frameshift NM_001406691.1:c.1334_1335del NP_001393620.1:p.Ile445fs frameshift NM_001406692.1:c.1334_1335del NP_001393621.1:p.Ile445fs frameshift NM_001406693.1:c.1334_1335del NP_001393622.1:p.Ile445fs frameshift NM_001406694.1:c.1334_1335del NP_001393623.1:p.Ile445fs frameshift NM_001406695.1:c.1334_1335del NP_001393624.1:p.Ile445fs frameshift NM_001406696.1:c.1334_1335del NP_001393625.1:p.Ile445fs frameshift NM_001406697.1:c.1334_1335del NP_001393626.1:p.Ile445fs frameshift NM_001406698.1:c.1076_1077del NP_001393627.1:p.Ile359fs frameshift NM_021055.3:c.2678_2679del NP_066399.2:p.Ile893fs frameshift NR_176225.1:n.2828_2829del non-coding transcript variant NR_176226.1:n.3007_3008del non-coding transcript variant NR_176227.1:n.3007_3008del non-coding transcript variant NR_176228.1:n.2828_2829del non-coding transcript variant NR_176229.1:n.2788_2789del non-coding transcript variant NC_000016.10:g.2076106_2076107del NC_000016.9:g.2126107_2126108del NG_005895.1:g.31801_31802del LRG_487:g.31801_31802del LRG_487t1:c.2678_2679del LRG_487p1:p.Ile893Serfs - Protein change
- I856fs, I893fs, I904fs, I923fs, I359fs, I445fs, I739fs, I844fs, I889fs, I693fs, I874fs
- Other names
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- Canonical SPDI
- NC_000016.10:2076104:ATA: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
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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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TSC2 | Sufficient evidence for dosage pathogenicity | No evidence available |
GRCh38 GRCh37 |
10625 | 10800 |
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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Pathogenic (1) |
criteria provided, single submitter
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Feb 8, 2023 | RCV003628285.1 |
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
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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
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
(Feb 08, 2023)
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criteria provided, single submitter
Method: clinical testing
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Tuberous sclerosis 2
Affected status: unknown
Allele origin:
germline
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Invitae
Accession: SCV004430746.1
First in ClinVar: Feb 20, 2024 Last updated: Feb 20, 2024 |
Comment:
This sequence change creates a premature translational stop signal (p.Ile893Serfs*21) in the TSC2 gene. It is expected to result in an absent or disrupted protein … (more)
This sequence change creates a premature translational stop signal (p.Ile893Serfs*21) in the TSC2 gene. It is expected to result in an absent or disrupted protein product. Loss-of-function variants in TSC2 are known to be pathogenic (PMID: 10205261, 17304050). This variant is not present in population databases (gnomAD no frequency). This variant has not been reported in the literature in individuals affected with TSC2-related conditions. For these reasons, this variant has been classified as Pathogenic. (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
HelpTitle | Author | Journal | Year | Link |
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Genotype/phenotype correlation in 325 individuals referred for a diagnosis of tuberous sclerosis complex in the United States. | Au KS | Genetics in medicine : official journal of the American College of Medical Genetics | 2007 | PMID: 17304050 |
Comprehensive mutation analysis of TSC1 and TSC2-and phenotypic correlations in 150 families with tuberous sclerosis. | Jones AC | American journal of human genetics | 1999 | PMID: 10205261 |
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.