ClinVar Genomic variation as it relates to human health
NM_000548.5(TSC2):c.1912_1920del (p.Val638_Phe640del)
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.1912_1920del (p.Val638_Phe640del)
Variation ID: 3252035 Accession: VCV003252035.1
- Type and length
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Deletion, 9 bp
- Location
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Cytogenetic: 16p13.3 16: 2071580-2071588 (GRCh38) [ NCBI UCSC ] 16: 2121581-2121589 (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 Jul 15, 2024 Jul 15, 2024 May 6, 2024 - HGVS
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Nucleotide Protein Molecular
consequenceNM_000548.5:c.1912_1920del MANE Select Help Transcripts from the Matched Annotation from the NCBI and EMBL-EBI (MANE) collaboration.
NP_000539.2:p.Val638_Phe640del inframe deletion NM_001077183.3:c.1912_1920del NP_001070651.1:p.Val638_Phe640del inframe deletion NM_001114382.3:c.1912_1920del NP_001107854.1:p.Val638_Phe640del inframe deletion NM_001318827.2:c.1801_1809del NP_001305756.1:p.Val601_Phe603del inframe deletion NM_001318829.2:c.1765_1773del NP_001305758.1:p.Val589_Phe591del inframe deletion NM_001318831.2:c.1312_1320del NP_001305760.1:p.Val438_Phe440del inframe deletion NM_001318832.2:c.1945_1953del NP_001305761.1:p.Val649_Phe651del inframe deletion NM_001363528.2:c.1912_1920del NP_001350457.1:p.Val638_Phe640del inframe deletion NM_001370404.1:c.1912_1920del NP_001357333.1:p.Val638_Phe640del inframe deletion NM_001370405.1:c.1912_1920del NP_001357334.1:p.Val638_Phe640del inframe deletion NM_001406663.1:c.1912_1920del NP_001393592.1:p.Val638_Phe640del inframe deletion NM_001406664.1:c.1912_1920del NP_001393593.1:p.Val638_Phe640del inframe deletion NM_001406665.1:c.1912_1920del NP_001393594.1:p.Val638_Phe640del inframe deletion NM_001406667.1:c.2002_2010del NP_001393596.1:p.Val668_Phe670del inframe deletion NM_001406668.1:c.2002_2010del NP_001393597.1:p.Val668_Phe670del inframe deletion NM_001406670.1:c.1801_1809del NP_001393599.1:p.Val601_Phe603del inframe deletion NM_001406671.1:c.1900_1908del NP_001393600.1:p.Val634_Phe636del inframe deletion NM_001406673.1:c.1900_1908del NP_001393602.1:p.Val634_Phe636del inframe deletion NM_001406675.1:c.1765_1773del NP_001393604.1:p.Val589_Phe591del inframe deletion NM_001406676.1:c.1765_1773del NP_001393605.1:p.Val589_Phe591del inframe deletion NM_001406677.1:c.1855_1863del NP_001393606.1:p.Val619_Phe621del inframe deletion NM_001406678.1:c.1801_1809del NP_001393607.1:p.Val601_Phe603del inframe deletion NM_001406679.1:c.1765_1773del NP_001393608.1:p.Val589_Phe591del inframe deletion NM_001406680.1:c.1312_1320del NP_001393609.1:p.Val438_Phe440del inframe deletion NM_001406681.1:c.1450_1458del NP_001393610.1:p.Val484_Phe486del inframe deletion NM_001406682.1:c.1312_1320del NP_001393611.1:p.Val438_Phe440del inframe deletion NM_001406683.1:c.1312_1320del NP_001393612.1:p.Val438_Phe440del inframe deletion NM_001406684.1:c.1312_1320del NP_001393613.1:p.Val438_Phe440del inframe deletion NM_001406685.1:c.1312_1320del NP_001393614.1:p.Val438_Phe440del inframe deletion NM_001406686.1:c.1312_1320del NP_001393615.1:p.Val438_Phe440del inframe deletion NM_001406687.1:c.1312_1320del NP_001393616.1:p.Val438_Phe440del inframe deletion NM_001406688.1:c.1312_1320del NP_001393617.1:p.Val438_Phe440del inframe deletion NM_001406689.1:c.568_576del NP_001393618.1:p.Val190_Phe192del inframe deletion NM_001406690.1:c.568_576del NP_001393619.1:p.Val190_Phe192del inframe deletion NM_001406691.1:c.568_576del NP_001393620.1:p.Val190_Phe192del inframe deletion NM_001406692.1:c.568_576del NP_001393621.1:p.Val190_Phe192del inframe deletion NM_001406693.1:c.568_576del NP_001393622.1:p.Val190_Phe192del inframe deletion NM_001406694.1:c.568_576del NP_001393623.1:p.Val190_Phe192del inframe deletion NM_001406695.1:c.568_576del NP_001393624.1:p.Val190_Phe192del inframe deletion NM_001406696.1:c.568_576del NP_001393625.1:p.Val190_Phe192del inframe deletion NM_001406697.1:c.568_576del NP_001393626.1:p.Val190_Phe192del inframe deletion NM_001406698.1:c.310_318del NP_001393627.1:p.Val104_Phe106del inframe deletion NM_021055.3:c.1912_1920del NP_066399.2:p.Val638_Phe640del inframe deletion NR_176225.1:n.2022_2030del non-coding transcript variant NR_176226.1:n.2241_2249del non-coding transcript variant NR_176227.1:n.2241_2249del non-coding transcript variant NR_176228.1:n.2022_2030del non-coding transcript variant NR_176229.1:n.2022_2030del non-coding transcript variant NC_000016.10:g.2071582_2071590del NC_000016.9:g.2121583_2121591del NG_005895.1:g.27277_27285del LRG_487:g.27277_27285del LRG_487t1:c.1912_1920del LRG_487p1:p.Val638_Phe640del - Protein change
- Other names
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- Canonical SPDI
- NC_000016.10:2071579:TCGTGCGGTTC:TC
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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
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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
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 |
10735 | 10932 |
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
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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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May 6, 2024 | RCV004586476.1 |
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
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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
(May 06, 2024)
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criteria provided, single submitter
Method: clinical testing
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Tuberous sclerosis 2
Affected status: yes
Allele origin:
germline
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Institute of Human Genetics, Cologne University
Accession: SCV005077849.1
First in ClinVar: Jul 15, 2024 Last updated: Jul 15, 2024 |
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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 Jul 23, 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.