ClinVar Genomic variation as it relates to human health
NM_000548.5(TSC2):c.3255_3262del (p.Gly1086fs)
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.3255_3262del (p.Gly1086fs)
Variation ID: 2855992 Accession: VCV002855992.1
- Type and length
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Deletion, 8 bp
- Location
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Cytogenetic: 16p13.3 16: 2079398-2079405 (GRCh38) [ NCBI UCSC ] 16: 2129399-2129406 (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 Apr 14, 2023 - HGVS
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Nucleotide Protein Molecular
consequenceNM_000548.5:c.3255_3262del MANE Select Help Transcripts from the Matched Annotation from the NCBI and EMBL-EBI (MANE) collaboration.
NP_000539.2:p.Gly1086fs frameshift NM_001077183.3:c.3123_3130del NP_001070651.1:p.Gly1042fs frameshift NM_001114382.3:c.3255_3262del NP_001107854.1:p.Gly1086fs frameshift NM_001318827.2:c.3015_3022del NP_001305756.1:p.Gly1006fs frameshift NM_001318829.2:c.2979_2986del NP_001305758.1:p.Gly994fs frameshift NM_001318831.2:c.2523_2530del NP_001305760.1:p.Gly842fs frameshift NM_001318832.2:c.3156_3163del NP_001305761.1:p.Gly1053fs frameshift NM_001363528.2:c.3126_3133del NP_001350457.1:p.Gly1043fs frameshift NM_001370404.1:c.3123_3130del NP_001357333.1:p.Gly1042fs frameshift NM_001370405.1:c.3126_3133del NP_001357334.1:p.Gly1043fs frameshift NM_001406663.1:c.3252_3259del NP_001393592.1:p.Gly1085fs frameshift NM_001406664.1:c.3252_3259del NP_001393593.1:p.Gly1085fs frameshift NM_001406665.1:c.3123_3130del NP_001393594.1:p.Gly1042fs frameshift NM_001406667.1:c.3216_3223del NP_001393596.1:p.Gly1073fs frameshift NM_001406668.1:c.3213_3220del NP_001393597.1:p.Gly1072fs frameshift NM_001406670.1:c.3144_3151del NP_001393599.1:p.Gly1049fs frameshift NM_001406671.1:c.3114_3121del NP_001393600.1:p.Gly1039fs frameshift NM_001406673.1:c.3111_3118del NP_001393602.1:p.Gly1038fs frameshift NM_001406675.1:c.3108_3115del NP_001393604.1:p.Gly1037fs frameshift NM_001406676.1:c.3105_3112del NP_001393605.1:p.Gly1036fs frameshift NM_001406677.1:c.3066_3073del NP_001393606.1:p.Gly1023fs frameshift NM_001406678.1:c.3012_3019del NP_001393607.1:p.Gly1005fs frameshift NM_001406679.1:c.2976_2983del NP_001393608.1:p.Gly993fs frameshift NM_001406680.1:c.2655_2662del NP_001393609.1:p.Gly886fs frameshift NM_001406681.1:c.2664_2671del NP_001393610.1:p.Gly889fs frameshift NM_001406682.1:c.2655_2662del NP_001393611.1:p.Gly886fs frameshift NM_001406683.1:c.2655_2662del NP_001393612.1:p.Gly886fs frameshift NM_001406684.1:c.2652_2659del NP_001393613.1:p.Gly885fs frameshift NM_001406685.1:c.2526_2533del NP_001393614.1:p.Gly843fs frameshift NM_001406686.1:c.2526_2533del NP_001393615.1:p.Gly843fs frameshift NM_001406687.1:c.2523_2530del NP_001393616.1:p.Gly842fs frameshift NM_001406688.1:c.2523_2530del NP_001393617.1:p.Gly842fs frameshift NM_001406689.1:c.1911_1918del NP_001393618.1:p.Gly638fs frameshift NM_001406690.1:c.1782_1789del NP_001393619.1:p.Gly595fs frameshift NM_001406691.1:c.1779_1786del NP_001393620.1:p.Gly594fs frameshift NM_001406692.1:c.1782_1789del NP_001393621.1:p.Gly595fs frameshift NM_001406693.1:c.1782_1789del NP_001393622.1:p.Gly595fs frameshift NM_001406694.1:c.1782_1789del NP_001393623.1:p.Gly595fs frameshift NM_001406695.1:c.1779_1786del NP_001393624.1:p.Gly594fs frameshift NM_001406696.1:c.1779_1786del NP_001393625.1:p.Gly594fs frameshift NM_001406697.1:c.1779_1786del NP_001393626.1:p.Gly594fs frameshift NM_001406698.1:c.1521_1528del NP_001393627.1:p.Gly508fs frameshift NM_021055.3:c.3126_3133del NP_066399.2:p.Gly1043fs frameshift NR_176225.1:n.3276_3283del non-coding transcript variant NR_176226.1:n.3455_3462del non-coding transcript variant NR_176227.1:n.3452_3459del non-coding transcript variant NR_176228.1:n.3273_3280del non-coding transcript variant NR_176229.1:n.3233_3240del non-coding transcript variant NC_000016.10:g.2079399_2079406del NC_000016.9:g.2129400_2129407del NG_005895.1:g.35094_35101del LRG_487:g.35094_35101del LRG_487t1:c.3255_3262del LRG_487p1:p.Gly1086Alafs - Protein change
- G1005fs, G1037fs, G1042fs, G1086fs, G842fs, G885fs, G993fs, G994fs, G1023fs, G1036fs, G1049fs, G1072fs, G508fs, G638fs, G1006fs, G1038fs, G1039fs, G1073fs, G1085fs, G594fs, G843fs, G889fs, G1043fs, G1053fs, G595fs, G886fs
- Other names
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- Canonical SPDI
- NC_000016.10:2079397:CGGGGGAGC: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
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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TSC2 | Sufficient evidence for dosage pathogenicity | No evidence available |
GRCh38 GRCh37 |
10625 | 10800 |
Conditions - Germline
Condition
Help
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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Apr 14, 2023 | RCV003626115.1 |
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
(Apr 14, 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: SCV004454773.1
First in ClinVar: Feb 20, 2024 Last updated: Feb 20, 2024 |
Comment:
For these reasons, this variant has been classified as Pathogenic. This variant has not been reported in the literature in individuals affected with TSC2-related conditions. … (more)
For these reasons, this variant has been classified as Pathogenic. This variant has not been reported in the literature in individuals affected with TSC2-related conditions. This variant is not present in population databases (gnomAD no frequency). This sequence change creates a premature translational stop signal (p.Gly1086Alafs*79) 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). (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.