ClinVar Genomic variation as it relates to human health
NM_000548.5(TSC2):c.1089del (p.Asn363fs)
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
-
NM_000548.5(TSC2):c.1089del (p.Asn363fs)
Variation ID: 1878647 Accession: VCV001878647.1
- Type and length
-
Deletion, 1 bp
- Location
-
Cytogenetic: 16p13.3 16: 2060783 (GRCh38) [ NCBI UCSC ] 16: 2110784 (GRCh37) [ NCBI UCSC ]
- Timeline in ClinVar
-
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 Jan 21, 2023 Jan 21, 2023 - HGVS
-
Nucleotide Protein Molecular
consequenceNM_000548.5:c.1089del MANE Select Help Transcripts from the Matched Annotation from the NCBI and EMBL-EBI (MANE) collaboration.
NP_000539.2:p.Asn363fs frameshift NM_001077183.3:c.1089del NP_001070651.1:p.Asn363fs frameshift NM_001114382.3:c.1089del NP_001107854.1:p.Asn363fs frameshift NM_001318827.2:c.978del NP_001305756.1:p.Asn326fs frameshift NM_001318829.2:c.942del NP_001305758.1:p.Asn314fs frameshift NM_001318831.2:c.489del NP_001305760.1:p.Asn163fs frameshift NM_001318832.2:c.1122del NP_001305761.1:p.Asn374fs frameshift NM_001363528.2:c.1089del NP_001350457.1:p.Asn363fs frameshift NM_001370404.1:c.1089del NP_001357333.1:p.Asn363fs frameshift NM_001370405.1:c.1089del NP_001357334.1:p.Asn363fs frameshift NM_001406663.1:c.1089delC NP_001393592.1:p.Asn363Lysfs frameshift NM_001406664.1:c.1089delC NP_001393593.1:p.Asn363Lysfs frameshift NM_001406665.1:c.1089delC NP_001393594.1:p.Asn363Lysfs frameshift NM_001406667.1:c.1179delC NP_001393596.1:p.Asn393Lysfs frameshift NM_001406668.1:c.1179delC NP_001393597.1:p.Asn393Lysfs frameshift NM_001406670.1:c.978delC NP_001393599.1:p.Asn326Lysfs frameshift NM_001406671.1:c.1077delC NP_001393600.1:p.Asn359Lysfs frameshift NM_001406673.1:c.1077delC NP_001393602.1:p.Asn359Lysfs frameshift NM_001406675.1:c.942delC NP_001393604.1:p.Asn314Lysfs frameshift NM_001406676.1:c.942delC NP_001393605.1:p.Asn314Lysfs frameshift NM_001406677.1:c.1032delC NP_001393606.1:p.Asn344Lysfs frameshift NM_001406678.1:c.978delC NP_001393607.1:p.Asn326Lysfs frameshift NM_001406679.1:c.942delC NP_001393608.1:p.Asn314Lysfs frameshift NM_001406680.1:c.489delC NP_001393609.1:p.Asn163Lysfs frameshift NM_001406681.1:c.627delC NP_001393610.1:p.Asn209Lysfs frameshift NM_001406682.1:c.489delC NP_001393611.1:p.Asn163Lysfs frameshift NM_001406683.1:c.489delC NP_001393612.1:p.Asn163Lysfs frameshift NM_001406684.1:c.489delC NP_001393613.1:p.Asn163Lysfs frameshift NM_001406685.1:c.489delC NP_001393614.1:p.Asn163Lysfs frameshift NM_001406686.1:c.489delC NP_001393615.1:p.Asn163Lysfs frameshift NM_001406687.1:c.489delC NP_001393616.1:p.Asn163Lysfs frameshift NM_001406688.1:c.489delC NP_001393617.1:p.Asn163Lysfs frameshift NM_001406689.1:c.-343delC NM_001406690.1:c.-343delC NM_001406691.1:c.-343delC NM_001406692.1:c.-343delC NM_001406693.1:c.-343delC NM_001406694.1:c.-224delC NM_001406695.1:c.-224delC NM_001406696.1:c.-343delC NM_001406697.1:c.-343delC NM_001406698.1:c.-519delC NM_021055.3:c.1089del NP_066399.2:p.Asn363fs frameshift NR_176225.1:n.1199delC NR_176226.1:n.1199delC NR_176227.1:n.1199delC NR_176228.1:n.1199delC NR_176229.1:n.1199delC NC_000016.10:g.2060783del NC_000016.9:g.2110784del NG_005895.1:g.16478del LRG_487:g.16478del LRG_487t1:c.1089del LRG_487p1:p.Asn363Lysfs - Protein change
- N163fs, N314fs, N326fs, N363fs, N374fs
- Other names
- -
- Canonical SPDI
- NC_000016.10:2060782:C:
-
Functional
consequence HelpThe effect of the variant on RNA or protein function, based on experimental evidence from submitters.
-
-
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.
-
-
Allele frequency
Help
The frequency of the allele represented by this VCV record.
-
- 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. |
|||
TSC2 | Sufficient evidence for dosage pathogenicity | No evidence available |
GRCh38 GRCh37 |
10622 | 10797 |
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. |
---|---|---|---|---|
Likely pathogenic (1) |
criteria provided, single submitter
|
- | RCV002510738.2 |
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
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
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
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. |
|
---|---|---|---|---|---|
Likely pathogenic
(-)
|
criteria provided, single submitter
Method: clinical testing
|
Tuberous sclerosis 2
Affected status: yes
Allele origin:
germline
|
Neuberg Centre For Genomic Medicine, NCGM
Accession: SCV002820293.1
First in ClinVar: Jan 21, 2023 Last updated: Jan 21, 2023 |
Comment:
The frameshift deletion p.N363Kfs*26 in TSC2 (NM_000548.5) has not been reported previously as a pathogenic variant nor as a benign variant, to our knowledge. The … (more)
The frameshift deletion p.N363Kfs*26 in TSC2 (NM_000548.5) has not been reported previously as a pathogenic variant nor as a benign variant, to our knowledge. The p.N363Kfs*26 variant is novel (not in any individuals) in gnomAD Exomes and is novel (not in any individuals) in 1000 Genomes.This variant is predicted to cause loss of normal protein function through protein truncation. For these reasons, this variant has been classified as Likely Pathogenic (less)
Clinical Features:
Global developmental delay (present) , Infantile spasms (present) , Hemiparesis (present)
|
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
HelpThere 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 Apr 06, 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.