ClinVar Genomic variation as it relates to human health
NM_000548.5(TSC2):c.5399_5401del (p.Val1800del)
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.5399_5401del (p.Val1800del)
Variation ID: 2705985 Accession: VCV002705985.1
- Type and length
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Deletion, 3 bp
- Location
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Cytogenetic: 16p13.3 16: 2088583-2088585 (GRCh38) [ NCBI UCSC ] 16: 2138584-2138586 (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 14, 2024 Feb 14, 2024 Jan 1, 2024 - HGVS
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Nucleotide Protein Molecular
consequenceNM_000548.5:c.5399_5401del MANE Select Help Transcripts from the Matched Annotation from the NCBI and EMBL-EBI (MANE) collaboration.
NP_000539.2:p.Val1800del inframe deletion NM_001077183.3:c.5198_5200del NP_001070651.1:p.Val1733del inframe deletion NM_001114382.3:c.5330_5332del NP_001107854.1:p.Val1777del inframe deletion NM_001318827.2:c.5090_5092del NP_001305756.1:p.Val1697del inframe deletion NM_001318829.2:c.5054_5056del NP_001305758.1:p.Val1685del inframe deletion NM_001318831.2:c.4667_4669del NP_001305760.1:p.Val1556del inframe deletion NM_001318832.2:c.5231_5233del NP_001305761.1:p.Val1744del inframe deletion NM_001363528.2:c.5201_5203del NP_001350457.1:p.Val1734del inframe deletion NM_001370404.1:c.5267_5269del NP_001357333.1:p.Val1756del inframe deletion NM_001370405.1:c.5258_5260del NP_001357334.1:p.Val1753del inframe deletion NM_001406663.1:c.5396_5398del NP_001393592.1:p.Val1799del inframe deletion NM_001406664.1:c.5327_5329del NP_001393593.1:p.Val1776del inframe deletion NM_001406665.1:c.5321_5323del NP_001393594.1:p.Val1774del inframe deletion NM_001406667.1:c.5291_5293del NP_001393596.1:p.Val1764del inframe deletion NM_001406668.1:c.5288_5290del NP_001393597.1:p.Val1763del inframe deletion NM_001406670.1:c.5219_5221del NP_001393599.1:p.Val1740del inframe deletion NM_001406671.1:c.5189_5191del NP_001393600.1:p.Val1730del inframe deletion NM_001406673.1:c.5186_5188del NP_001393602.1:p.Val1729del inframe deletion NM_001406675.1:c.5183_5185del NP_001393604.1:p.Val1728del inframe deletion NM_001406676.1:c.5180_5182del NP_001393605.1:p.Val1727del inframe deletion NM_001406677.1:c.5141_5143del NP_001393606.1:p.Val1714del inframe deletion NM_001406678.1:c.5087_5089del NP_001393607.1:p.Val1696del inframe deletion NM_001406679.1:c.5051_5053del NP_001393608.1:p.Val1684del inframe deletion NM_001406680.1:c.4799_4801del NP_001393609.1:p.Val1600del inframe deletion NM_001406681.1:c.4739_4741del NP_001393610.1:p.Val1580del inframe deletion NM_001406682.1:c.4730_4732del NP_001393611.1:p.Val1577del inframe deletion NM_001406683.1:c.4730_4732del NP_001393612.1:p.Val1577del inframe deletion NM_001406684.1:c.4727_4729del NP_001393613.1:p.Val1576del inframe deletion NM_001406685.1:c.4601_4603del NP_001393614.1:p.Val1534del inframe deletion NM_001406686.1:c.4601_4603del NP_001393615.1:p.Val1534del inframe deletion NM_001406687.1:c.4598_4600del NP_001393616.1:p.Val1533del inframe deletion NM_001406688.1:c.4598_4600del NP_001393617.1:p.Val1533del inframe deletion NM_001406689.1:c.3986_3988del NP_001393618.1:p.Val1329del inframe deletion NM_001406690.1:c.3926_3928del NP_001393619.1:p.Val1309del inframe deletion NM_001406691.1:c.3923_3925del NP_001393620.1:p.Val1308del inframe deletion NM_001406692.1:c.3857_3859del NP_001393621.1:p.Val1286del inframe deletion NM_001406693.1:c.3857_3859del NP_001393622.1:p.Val1286del inframe deletion NM_001406694.1:c.3857_3859del NP_001393623.1:p.Val1286del inframe deletion NM_001406695.1:c.3854_3856del NP_001393624.1:p.Val1285del inframe deletion NM_001406696.1:c.3854_3856del NP_001393625.1:p.Val1285del inframe deletion NM_001406697.1:c.3854_3856del NP_001393626.1:p.Val1285del inframe deletion NM_001406698.1:c.3596_3598del NP_001393627.1:p.Val1199del inframe deletion NM_021055.3:c.5270_5272del NP_066399.2:p.Val1757del inframe deletion NR_176225.1:n.5351_5353del non-coding transcript variant NR_176226.1:n.5599_5601del non-coding transcript variant NR_176227.1:n.5527_5529del non-coding transcript variant NR_176228.1:n.5348_5350del non-coding transcript variant NR_176229.1:n.5273_5275del non-coding transcript variant NC_000016.10:g.2088585_2088587del NC_000016.9:g.2138586_2138588del NG_005895.1:g.44280_44282del NG_008617.1:g.54636_54638del LRG_487:g.44280_44282del LRG_487t1:c.5399_5401del LRG_487p1:p.Val1800del - Protein change
- V1286del, V1534del, V1697del, V1729del, V1763del, V1799del, V1308del, V1309del, V1329del, V1533del, V1556del, V1600del, V1684del, V1727del, V1728del, V1730del, V1756del, V1757del, V1764del, V1777del, V1199del, V1580del, V1740del, V1776del, V1285del, V1576del, V1577del, V1685del, V1696del, V1714del, V1733del, V1734del, V1744del, V1753del, V1774del, V1800del
- Other names
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- Canonical SPDI
- NC_000016.10:2088582:GGTGG:GG
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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
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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 |
10664 | 10858 |
Conditions - Germline
Condition
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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
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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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Uncertain significance (1) |
criteria provided, single submitter
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Jan 1, 2024 | RCV003512935.1 |
Submissions - Germline
Classification
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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
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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
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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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Uncertain significance
(Jan 01, 2024)
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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: SCV004367106.1
First in ClinVar: Feb 14, 2024 Last updated: Feb 14, 2024 |
Comment:
This variant, c.5399_5401del, results in the deletion of 1 amino acid(s) of the TSC2 protein (p.Val1800del), but otherwise preserves the integrity of the reading frame. … (more)
This variant, c.5399_5401del, results in the deletion of 1 amino acid(s) of the TSC2 protein (p.Val1800del), but otherwise preserves the integrity of the reading frame. This variant is not present in population databases (gnomAD no frequency). This variant has not been reported in the literature in individuals affected with TSC2-related conditions. Experimental studies and prediction algorithms are not available or were not evaluated, and the functional significance of this variant is currently unknown. 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. (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
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 Feb 20, 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.