Advanced modeling of protein sequence and biophysical properties (such as structural, functional, and spatial information, amino acid conservation, physicochemical variation, residue mobility, and thermodynamic stability) performed at Invitae indicates that this missense variant is not expected to disrupt TSC2 protein function. In summary, the available evidence is currently insufficient to determine the role of this variant in disease. Therefore, it has been classified as a Variant of Uncertain Significance. This variant has not been reported in the literature in individuals affected with TSC2-related conditions. This sequence change replaces tyrosine, which is neutral and polar, with phenylalanine, which is neutral and non-polar, at codon 643 of the TSC2 protein (p.Tyr643Phe). This variant is not present in population databases (gnomAD no frequency).
ClinVar Genomic variation as it relates to human health
NM_000548.5(TSC2):c.1928A>T (p.Tyr643Phe)
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.
Uncertain significance
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.1928A>T (p.Tyr643Phe)
Variation ID: 2842027 Accession: VCV002842027.1
- Type and length
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single nucleotide variant, 1 bp
- Location
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Cytogenetic: 16p13.3 16: 2071598 (GRCh38) [ NCBI UCSC ] 16: 2121599 (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 Mar 2, 2023 - HGVS
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... more HGVS ... less HGVSNucleotide Protein Molecular
consequenceNM_000548.5:c.1928A>T MANE Select Help Transcripts from the Matched Annotation from the NCBI and EMBL-EBI (MANE) collaboration.
NP_000539.2:p.Tyr643Phe missense NM_001077183.3:c.1928A>T NP_001070651.1:p.Tyr643Phe missense NM_001114382.3:c.1928A>T NP_001107854.1:p.Tyr643Phe missense NM_001318827.2:c.1817A>T NP_001305756.1:p.Tyr606Phe missense NM_001318829.2:c.1781A>T NP_001305758.1:p.Tyr594Phe missense NM_001318831.2:c.1328A>T NP_001305760.1:p.Tyr443Phe missense NM_001318832.2:c.1961A>T NP_001305761.1:p.Tyr654Phe missense NM_001363528.2:c.1928A>T NP_001350457.1:p.Tyr643Phe missense NM_001370404.1:c.1928A>T NP_001357333.1:p.Tyr643Phe missense NM_001370405.1:c.1928A>T NP_001357334.1:p.Tyr643Phe missense NM_001406663.1:c.1928A>T NP_001393592.1:p.Tyr643Phe missense NM_001406664.1:c.1928A>T NP_001393593.1:p.Tyr643Phe missense NM_001406665.1:c.1928A>T NP_001393594.1:p.Tyr643Phe missense NM_001406667.1:c.2018A>T NP_001393596.1:p.Tyr673Phe missense NM_001406668.1:c.2018A>T NP_001393597.1:p.Tyr673Phe missense NM_001406670.1:c.1817A>T NP_001393599.1:p.Tyr606Phe missense NM_001406671.1:c.1916A>T NP_001393600.1:p.Tyr639Phe missense NM_001406673.1:c.1916A>T NP_001393602.1:p.Tyr639Phe missense NM_001406675.1:c.1781A>T NP_001393604.1:p.Tyr594Phe missense NM_001406676.1:c.1781A>T NP_001393605.1:p.Tyr594Phe missense NM_001406677.1:c.1871A>T NP_001393606.1:p.Tyr624Phe missense NM_001406678.1:c.1817A>T NP_001393607.1:p.Tyr606Phe missense NM_001406679.1:c.1781A>T NP_001393608.1:p.Tyr594Phe missense NM_001406680.1:c.1328A>T NP_001393609.1:p.Tyr443Phe missense NM_001406681.1:c.1466A>T NP_001393610.1:p.Tyr489Phe missense NM_001406682.1:c.1328A>T NP_001393611.1:p.Tyr443Phe missense NM_001406683.1:c.1328A>T NP_001393612.1:p.Tyr443Phe missense NM_001406684.1:c.1328A>T NP_001393613.1:p.Tyr443Phe missense NM_001406685.1:c.1328A>T NP_001393614.1:p.Tyr443Phe missense NM_001406686.1:c.1328A>T NP_001393615.1:p.Tyr443Phe missense NM_001406687.1:c.1328A>T NP_001393616.1:p.Tyr443Phe missense NM_001406688.1:c.1328A>T NP_001393617.1:p.Tyr443Phe missense NM_001406689.1:c.584A>T NP_001393618.1:p.Tyr195Phe missense NM_001406690.1:c.584A>T NP_001393619.1:p.Tyr195Phe missense NM_001406691.1:c.584A>T NP_001393620.1:p.Tyr195Phe missense NM_001406692.1:c.584A>T NP_001393621.1:p.Tyr195Phe missense NM_001406693.1:c.584A>T NP_001393622.1:p.Tyr195Phe missense NM_001406694.1:c.584A>T NP_001393623.1:p.Tyr195Phe missense NM_001406695.1:c.584A>T NP_001393624.1:p.Tyr195Phe missense NM_001406696.1:c.584A>T NP_001393625.1:p.Tyr195Phe missense NM_001406697.1:c.584A>T NP_001393626.1:p.Tyr195Phe missense NM_001406698.1:c.326A>T NP_001393627.1:p.Tyr109Phe missense NM_021055.3:c.1928A>T NP_066399.2:p.Tyr643Phe missense NR_176225.1:n.2038A>T non-coding transcript variant NR_176226.1:n.2257A>T non-coding transcript variant NR_176227.1:n.2257A>T non-coding transcript variant NR_176228.1:n.2038A>T non-coding transcript variant NR_176229.1:n.2038A>T non-coding transcript variant NC_000016.10:g.2071598A>T NC_000016.9:g.2121599A>T NG_005895.1:g.27293A>T LRG_487:g.27293A>T LRG_487t1:c.1928A>T LRG_487p1:p.Tyr643Phe - Protein change
- Y443F, Y624F, Y643F, Y109F, Y639F, Y195F, Y489F, Y594F, Y606F, Y654F, Y673F
- Other names
- -
- Canonical SPDI
- NC_000016.10:2071597:A:T
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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 |
10752 | 10951 | |
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. |
|---|---|---|---|---|
| Uncertain significance (1) |
criteria provided, single submitter
|
Mar 2, 2023 | RCV003628391.2 |
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. |
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|---|---|---|---|---|---|
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Uncertain significance
(Mar 02, 2023)
|
criteria provided, single submitter
Method: clinical testing
|
Tuberous sclerosis 2
Affected status: unknown
Allele origin:
germline
|
Labcorp Genetics (formerly Invitae), Labcorp
Accession: SCV004503958.1
First in ClinVar: Feb 20, 2024 Last updated: Feb 20, 2024 |
Comment:
Advanced modeling of protein sequence and biophysical properties (such as structural, functional, and spatial information, amino acid conservation, physicochemical variation, residue mobility, and thermodynamic stability) … (more)
Advanced modeling of protein sequence and biophysical properties (such as structural, functional, and spatial information, amino acid conservation, physicochemical variation, residue mobility, and thermodynamic stability) performed at Invitae indicates that this missense variant is not expected to disrupt TSC2 protein function. In summary, the available evidence is currently insufficient to determine the role of this variant in disease. Therefore, it has been classified as a Variant of Uncertain Significance. This variant has not been reported in the literature in individuals affected with TSC2-related conditions. This sequence change replaces tyrosine, which is neutral and polar, with phenylalanine, which is neutral and non-polar, at codon 643 of the TSC2 protein (p.Tyr643Phe). This variant is not present in population databases (gnomAD no frequency). (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:
Advanced modeling of protein sequence and biophysical properties (such as structural, functional, and spatial information, amino acid conservation, physicochemical variation, residue mobility, and thermodynamic stability) performed at Invitae indicates that this missense variant is not expected to disrupt TSC2 protein function. In summary, the available evidence is currently insufficient to determine the role of this variant in disease. Therefore, it has been classified as a Variant of Uncertain Significance. This variant has not been reported in the literature in individuals affected with TSC2-related conditions. This sequence change replaces tyrosine, which is neutral and polar, with phenylalanine, which is neutral and non-polar, at codon 643 of the TSC2 protein (p.Tyr643Phe). This variant is not present in population databases (gnomAD no frequency).
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 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.