This variant has been identified by standard clinical testing. Selected ACMG criteria: Likely pathogenic (I):PM2;PVS1
ClinVar Genomic variation as it relates to human health
NM_000548.5(TSC2):c.3161dup (p.Gly1055fs)
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.
Likely pathogenic
1
criteria provided, single submitter
Somatic
No data submitted for somatic clinical impact
Somatic
No data submitted for oncogenicity
Variant Details
- Identifiers
-
NM_000548.5(TSC2):c.3161dup (p.Gly1055fs)
Variation ID: 3376539 Accession: VCV003376539.1
- Type and length
-
Duplication, 1 bp
- Location
-
Cytogenetic: 16p13.3 16: 2079302-2079303 (GRCh38) [ NCBI UCSC ] 16: 2129303-2129304 (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 Nov 25, 2024 Nov 24, 2024 Nov 17, 2024 - HGVS
-
... more HGVS ... less HGVSNucleotide Protein Molecular
consequenceNM_000548.5:c.3161dup MANE Select Help Transcripts from the Matched Annotation from the NCBI and EMBL-EBI (MANE) collaboration.
NP_000539.2:p.Gly1055fs frameshift NM_001077183.3:c.3029dup NP_001070651.1:p.Gly1011fs frameshift NM_001114382.3:c.3161dup NP_001107854.1:p.Gly1055fs frameshift NM_001318827.2:c.2921dup NP_001305756.1:p.Gly975fs frameshift NM_001318829.2:c.2885dup NP_001305758.1:p.Gly963fs frameshift NM_001318831.2:c.2429dup NP_001305760.1:p.Gly811fs frameshift NM_001318832.2:c.3062dup NP_001305761.1:p.Gly1022fs frameshift NM_001363528.2:c.3032dup NP_001350457.1:p.Gly1012fs frameshift NM_001370404.1:c.3029dup NP_001357333.1:p.Gly1011fs frameshift NM_001370405.1:c.3032dup NP_001357334.1:p.Gly1012fs frameshift NM_001406663.1:c.3158dup NP_001393592.1:p.Gly1054fs frameshift NM_001406664.1:c.3158dup NP_001393593.1:p.Gly1054fs frameshift NM_001406665.1:c.3029dup NP_001393594.1:p.Gly1011fs frameshift NM_001406667.1:c.3122dup NP_001393596.1:p.Gly1042fs frameshift NM_001406668.1:c.3119dup NP_001393597.1:p.Gly1041fs frameshift NM_001406670.1:c.3050dup NP_001393599.1:p.Gly1018fs frameshift NM_001406671.1:c.3020dup NP_001393600.1:p.Gly1008fs frameshift NM_001406673.1:c.3017dup NP_001393602.1:p.Gly1007fs frameshift NM_001406675.1:c.3014dup NP_001393604.1:p.Gly1006fs frameshift NM_001406676.1:c.3011dup NP_001393605.1:p.Gly1005fs frameshift NM_001406677.1:c.2972dup NP_001393606.1:p.Gly992fs frameshift NM_001406678.1:c.2918dup NP_001393607.1:p.Gly974fs frameshift NM_001406679.1:c.2882dup NP_001393608.1:p.Gly962fs frameshift NM_001406680.1:c.2561dup NP_001393609.1:p.Gly855fs frameshift NM_001406681.1:c.2570dup NP_001393610.1:p.Gly858fs frameshift NM_001406682.1:c.2561dup NP_001393611.1:p.Gly855fs frameshift NM_001406683.1:c.2561dup NP_001393612.1:p.Gly855fs frameshift NM_001406684.1:c.2558dup NP_001393613.1:p.Gly854fs frameshift NM_001406685.1:c.2432dup NP_001393614.1:p.Gly812fs frameshift NM_001406686.1:c.2432dup NP_001393615.1:p.Gly812fs frameshift NM_001406687.1:c.2429dup NP_001393616.1:p.Gly811fs frameshift NM_001406688.1:c.2429dup NP_001393617.1:p.Gly811fs frameshift NM_001406689.1:c.1817dup NP_001393618.1:p.Gly607fs frameshift NM_001406690.1:c.1688dup NP_001393619.1:p.Gly564fs frameshift NM_001406691.1:c.1685dup NP_001393620.1:p.Gly563fs frameshift NM_001406692.1:c.1688dup NP_001393621.1:p.Gly564fs frameshift NM_001406693.1:c.1688dup NP_001393622.1:p.Gly564fs frameshift NM_001406694.1:c.1688dup NP_001393623.1:p.Gly564fs frameshift NM_001406695.1:c.1685dup NP_001393624.1:p.Gly563fs frameshift NM_001406696.1:c.1685dup NP_001393625.1:p.Gly563fs frameshift NM_001406697.1:c.1685dup NP_001393626.1:p.Gly563fs frameshift NM_001406698.1:c.1427dup NP_001393627.1:p.Gly477fs frameshift NM_021055.3:c.3032dup NP_066399.2:p.Gly1012fs frameshift NR_176225.1:n.3182dup non-coding transcript variant NR_176226.1:n.3361dup non-coding transcript variant NR_176227.1:n.3358dup non-coding transcript variant NR_176228.1:n.3179dup non-coding transcript variant NR_176229.1:n.3139dup non-coding transcript variant NC_000016.10:g.2079305dup NC_000016.9:g.2129306dup NG_005895.1:g.35000dup LRG_487:g.35000dup LRG_487t1:c.3161dup LRG_487p1:p.Gly1055Trpfs - Protein change
- G1005fs, G1006fs, G1007fs, G1008fs, G1011fs, G1012fs, G1018fs, G1022fs, G1041fs, G1042fs, G1054fs, G1055fs, G477fs, G563fs, G564fs, G607fs, G811fs, G812fs, G854fs, G855fs, G858fs, G962fs, G963fs, G974fs, G975fs, G992fs
- Other names
- -
- Canonical SPDI
- NC_000016.10:2079302:GGG:GGGG
-
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 |
10758 | 10957 | |
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
|
Nov 17, 2024 | RCV004787173.1 |
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
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
(Nov 17, 2024)
|
criteria provided, single submitter
Method: clinical testing
|
Tuberous sclerosis 2
(Unknown mechanism)
Affected status: yes
Allele origin:
germline
|
Institute of Human Genetics, FAU Erlangen, Friedrich-Alexander-Universität Erlangen-Nürnberg
Accession: SCV005397937.1
First in ClinVar: Nov 24, 2024 Last updated: Nov 24, 2024 |
Comment:
This variant has been identified by standard clinical testing. Selected ACMG criteria: Likely pathogenic (I):PM2;PVS1
Number of individuals with the variant: 1
|
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 has been identified by standard clinical testing. Selected ACMG criteria: Likely pathogenic (I):PM2;PVS1
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 Nov 30, 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.