Frameshift variant predicted to result in protein truncation or nonsense mediated decay in a gene for which loss of function is a known mechanism of disease; Not observed at significant frequency in large population cohorts (gnomAD); This variant is associated with the following publications: (PMID: 32461669)
ClinVar Genomic variation as it relates to human health
NM_000548.5(TSC2):c.4536_4543del (p.Asp1512fs)
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_000548.5(TSC2):c.4536_4543del (p.Asp1512fs)
Variation ID: 2577654 Accession: VCV002577654.1
- Type and length
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Deletion, 8 bp
- Location
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Cytogenetic: 16p13.3 16: 2084992-2084999 (GRCh38) [ NCBI UCSC ] 16: 2134993-2135000 (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 Sep 3, 2023 Sep 3, 2023 Mar 1, 2023 - HGVS
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... more HGVS ... less HGVSNucleotide Protein Molecular
consequenceNM_000548.5:c.4536_4543del MANE Select Help Transcripts from the Matched Annotation from the NCBI and EMBL-EBI (MANE) collaboration.
NP_000539.2:p.Asp1512fs frameshift NM_000548.3:c.4536_4543delCGAGTCAA NP_000539.2:p.Asp1512Glufs frameshift NM_001077183.3:c.4335_4342del NP_001070651.1:p.Asp1445fs frameshift NM_001114382.3:c.4467_4474del NP_001107854.1:p.Asp1489fs frameshift NM_001318827.2:c.4227_4234del NP_001305756.1:p.Asp1409fs frameshift NM_001318829.2:c.4191_4198del NP_001305758.1:p.Asp1397fs frameshift NM_001318831.2:c.3804_3811del NP_001305760.1:p.Asp1268fs frameshift NM_001318832.2:c.4368_4375del NP_001305761.1:p.Asp1456fs frameshift NM_001363528.2:c.4338_4345del NP_001350457.1:p.Asp1446fs frameshift NM_001370404.1:c.4404_4411del NP_001357333.1:p.Asp1468fs frameshift NM_001370405.1:c.4407_4414del NP_001357334.1:p.Asp1469fs frameshift NM_001406663.1:c.4533_4540del NP_001393592.1:p.Asp1511fs frameshift NM_001406664.1:c.4464_4471del NP_001393593.1:p.Asp1488fs frameshift NM_001406665.1:c.4458_4465del NP_001393594.1:p.Asp1486fs frameshift NM_001406667.1:c.4428_4435del NP_001393596.1:p.Asp1476fs frameshift NM_001406668.1:c.4425_4432del NP_001393597.1:p.Asp1475fs frameshift NM_001406670.1:c.4356_4363del NP_001393599.1:p.Asp1452fs frameshift NM_001406671.1:c.4326_4333del NP_001393600.1:p.Asp1442fs frameshift NM_001406673.1:c.4323_4330del NP_001393602.1:p.Asp1441fs frameshift NM_001406675.1:c.4320_4327del NP_001393604.1:p.Asp1440fs frameshift NM_001406676.1:c.4317_4324del NP_001393605.1:p.Asp1439fs frameshift NM_001406677.1:c.4278_4285del NP_001393606.1:p.Asp1426fs frameshift NM_001406678.1:c.4224_4231del NP_001393607.1:p.Asp1408fs frameshift NM_001406679.1:c.4188_4195del NP_001393608.1:p.Asp1396fs frameshift NM_001406680.1:c.3936_3943del NP_001393609.1:p.Asp1312fs frameshift NM_001406681.1:c.3876_3883del NP_001393610.1:p.Asp1292fs frameshift NM_001406682.1:c.3867_3874del NP_001393611.1:p.Asp1289fs frameshift NM_001406683.1:c.3867_3874del NP_001393612.1:p.Asp1289fs frameshift NM_001406684.1:c.3864_3871del NP_001393613.1:p.Asp1288fs frameshift NM_001406685.1:c.3738_3745del NP_001393614.1:p.Asp1246fs frameshift NM_001406686.1:c.3738_3745del NP_001393615.1:p.Asp1246fs frameshift NM_001406687.1:c.3735_3742del NP_001393616.1:p.Asp1245fs frameshift NM_001406688.1:c.3735_3742del NP_001393617.1:p.Asp1245fs frameshift NM_001406689.1:c.3123_3130del NP_001393618.1:p.Asp1041fs frameshift NM_001406690.1:c.3063_3070del NP_001393619.1:p.Asp1021fs frameshift NM_001406691.1:c.3060_3067del NP_001393620.1:p.Asp1020fs frameshift NM_001406692.1:c.2994_3001del NP_001393621.1:p.Asp998fs frameshift NM_001406693.1:c.2994_3001del NP_001393622.1:p.Asp998fs frameshift NM_001406694.1:c.2994_3001del NP_001393623.1:p.Asp998fs frameshift NM_001406695.1:c.2991_2998del NP_001393624.1:p.Asp997fs frameshift NM_001406696.1:c.2991_2998del NP_001393625.1:p.Asp997fs frameshift NM_001406697.1:c.2991_2998del NP_001393626.1:p.Asp997fs frameshift NM_001406698.1:c.2733_2740del NP_001393627.1:p.Asp911fs frameshift NM_021055.3:c.4407_4414del NP_066399.2:p.Asp1469fs frameshift NR_176225.1:n.4488_4495del non-coding transcript variant NR_176226.1:n.4736_4743del non-coding transcript variant NR_176227.1:n.4664_4671del non-coding transcript variant NR_176228.1:n.4485_4492del non-coding transcript variant NR_176229.1:n.4445_4452del non-coding transcript variant NC_000016.10:g.2084993_2085000del NC_000016.9:g.2134994_2135001del NG_005895.1:g.40688_40695del LRG_487:g.40688_40695del LRG_487t1:c.4536_4543del - Protein change
- D1020fs, D1021fs, D1041fs, D1245fs, D1246fs, D1268fs, D1288fs, D1289fs, D1292fs, D1312fs, D1396fs, D1397fs, D1408fs, D1409fs, D1426fs, D1439fs, D1440fs, D1441fs, D1442fs, D1445fs, D1446fs, D1452fs, D1456fs, D1468fs, D1469fs, D1475fs, D1476fs, D1486fs, D1488fs, D1489fs, D1511fs, D1512fs, D911fs, D997fs, D998fs
- Other names
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- Canonical SPDI
- NC_000016.10:2084991:ACGAGTCAA: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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| TSC2 | Sufficient evidence for dosage pathogenicity | No evidence available |
GRCh38 GRCh37 |
10754 | 10953 | |
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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Mar 1, 2023 | RCV003324991.1 |
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
(Mar 01, 2023)
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criteria provided, single submitter
Method: clinical testing
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Not Provided
Affected status: yes
Allele origin:
germline
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GeneDx
Accession: SCV004030746.1
First in ClinVar: Sep 03, 2023 Last updated: Sep 03, 2023 |
Comment:
Frameshift variant predicted to result in protein truncation or nonsense mediated decay in a gene for which loss of function is a known mechanism of … (more)
Frameshift variant predicted to result in protein truncation or nonsense mediated decay in a gene for which loss of function is a known mechanism of disease; Not observed at significant frequency in large population cohorts (gnomAD); This variant is associated with the following publications: (PMID: 32461669) (less)
|
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:
Frameshift variant predicted to result in protein truncation or nonsense mediated decay in a gene for which loss of function is a known mechanism of disease; Not observed at significant frequency in large population cohorts (gnomAD); This variant is associated with the following publications: (PMID: 32461669)
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 Sep 03, 2023
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.