Full data view for gene TSC2

The curator’s expert opinion on the classification of a variant, can be found in the
SUMMARY record. Regarding the classification, please note that where there are several
records of the same variant, the classification of that variant may differ depending on the
submitter’s conclusion.
Information The variants shown are described using the NM_000548.3 transcript reference sequence.

29 entries on 1 page. Showing entries 1 - 29.
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Effect     

Exon     

AscendingDNA change (cDNA)     

RNA change     

Protein     

P-domain     

Predict-BioInf     

Allele     

Classification method     

Clinical classification     

DNA change (genomic) (hg19)     

DNA change (hg38)     

Published as     

ISCN     

DB-ID     

Variant remarks     

Reference     

ClinVar ID     

dbSNP ID     

Origin     

Segregation     

Frequency     

Re-site     

VIP     

Methylation     

Template     

Technique     

Tissue     

Remarks     

Disease     

ID_report     

Reference     

Remarks     

Gender     

Consanguinity     

Country     

Population     

Age at death     

VIP     

Data_av     

Treatment     

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Owner     
+/. 1i_42_ c.(-30+1_-29-1)_(*102_?)del r.0? p.0? - - Unknown - pathogenic g.(2098067_2098587)_(2138713_?)del g.(2048066_2048586)_(2088712_?)del - - TSC2_001440 entire TSC2 gene deleted PubMed: Rendtorff 2005 - - Germline ? - - - - DNA MLPA, PCRq Blood - TSC - PubMed: Rendtorff 2005 - ? ? - - - - - - 1 Rosemary Ekong
+/. 1i_42_ c.(-30+1_-29-1)_(*102_?)del r.0? p.0? - - Unknown - pathogenic g.(2098067_2098587)_(2138713_?)del g.(2048066_2048586)_(2088712_?)del - - TSC2_001440 entire TSC2 gene deleted PubMed: Rendtorff 2005 - - Germline ? - - - - DNA MLPA, PCRq Blood - TSC - PubMed: Rendtorff 2005 different patient reported in this paper ? ? - - - - - - 1 Rosemary Ekong
+/. 1i_42_ c.(-30+1_-29-1)_(*102_?)del r.0? p.0? - - Unknown - pathogenic g.(2098067_2098587)_(2138713_?)del g.(2048066_2048586)_(2088712_?)del - - TSC2_001440 TSC2 exons 2-42 deleted; deletion not found in both parents; both TSC1 and TSC2 genes tested unpubished - - De novo no 1/6 chromosomes - - - DNA MLPA, SEQ Blood - TSC - unpublished - M ? - - - - - - 1 Rosemary Ekong
+/. 1i_42_ c.(-30+1_-29-1)_(*102_?)del r.0? p.0? - - Unknown - pathogenic g.(2098067_2098587)_(2138713_?)del g.(2048066_2048586)_(2088712_?)del - - TSC2_001440 variant not found in the one parent tested; both TSC1 and TSC2 genes tested unpubished - - Germline ? 1/4 chromosomes - - - DNA MLPA, SEQ Blood - TSC - unpublished - M ? - - - - - - 1 Rosemary Ekong
+/. 1i_42_ c.(-30+1_-29-1)_(*102_?)del r.0? p.0? - - Unknown - pathogenic g.(2098067_2098587)_(2138713_?)del g.(2048066_2048586)_(2088712_?)del - - TSC2_001440 both TSC1 and TSC2 genes tested unpubished - - Germline ? - - - - DNA MLPA, SEQ Blood - TSC - unpublished - F ? - - - - - - 1 Rosemary Ekong
+/. 1i_42_ c.(-30+1_-29-1)_(*102_?)del r.0? p.0? - - Unknown - pathogenic g.(2098067_2098587)_(2138713_?)del g.(2048066_2048586)_(2088712_?)del ex1-41del - TSC2_001440 entire gene deleted; found with known TSC2 variants c.5202T>C and c.5397G>C unpublished - - Germline ? - - - - DNA MLPA Blood - TSC - unpublished - M ? - - - - - - 1 Rosemary Ekong
+/. 1i_42_ c.(-30+1_-29-1)_(*102_?)del r.0? p.0? - - Unknown - pathogenic g.(2098067_2098587)_(2138713_?)del g.(2048066_2048586)_(2088712_?)del Ex1-Ex41del, also PKD1 Ex35 to Ex46 deleted - TSC2_001440 entire gene deleted (exons 2-42) including PKD1 exons 35-46 unpublished - - Germline ? - - - - DNA MLPA Blood - TSC - unpublished TS affected F ? - - - - - - 1 Rosemary Ekong
+/. 1i_42_ c.(-30+1_-29-1)_(*102_?)del r.0? p.0? - - Unknown - pathogenic g.(2098067_2098587)_(2138713_?)del g.(2048066_2048586)_(2088712_?)del c.(?_1)_(*_?)del - TSC2_001440 exons 2-42 deleted; variant in more than one affected PubMed: Sancak 2005 - - Germline yes - - - - DNA MLPA Blood - TSC - PubMed: Sancak 2005 diagnosed with definite TSC ? ? - - - - - - 2 Rosemary Ekong
+/. 1i_42_ c.(-30+1_-29-1)_(*102_?)del r.0? p.0? - - Unknown - pathogenic g.(2098067_2098587)_(2138713_?)del g.(2048066_2048586)_(2088712_?)del c.(?_1)_(*_?)del - TSC2_001440 exons 2-42 deleted; variant in 2/2 unrelated affecteds tested unpublished - - Germline ? - - - - DNA MLPA Blood - TSC - unpublished entry represents 2 different cases ? ? - - - - - - 2 Rosemary Ekong
+/. 1i_42_ c.(-30+1_-29-1)_(*102_?)del r.0? p.0? - - Unknown - pathogenic g.(2098067_2098587)_(2138713_?)del g.(2048066_2048586)_(2088712_?)del del ex. 1–41 - TSC2_001440 Germline variant also seen in periungual fibroma; entire TS2 gene deleted; confirmed by Sanger SEQ; MAF in normal skin tissue = 0.5; MAF in tumor = 0.5; blood or saliva also tested; NGS median read-depth of >5000x PubMed: Tyburczy 2014 - - Germline ? - - - - DNA, RNA MLPA, SEQ, SEQ-NG-I Tumour, Normal Skin - TSC - PubMed: Tyburczy 2014 childhood onset and adult diagnosis of TSC F ? - - - - - - 1 Rosemary Ekong
+/. 1i_42_ c.(-30+1_-29-1)_(*102_?)del r.0? p.0? - - Unknown - pathogenic g.(2098067_2098587)_(2138713_?)del g.(2048066_2048586)_(2088712_?)del exons 1-41 del + PKD1 exons 40 & 46 - TSC2_001440 contiguous TSC2/PKD1 gene deletion involving entire TSC2 gene + PDK1 ex 40 and 46; no small mutation detected but consistently reduced amplification of TSC2 exons 2-42 and PKD1 exons 40 & 46; both parents tested and reduced amplification not found unpublished - - De novo no 1/6 chromosomes - - - DNA MLPA, SEQ Blood - TSC - unpublished patient referred for diagnostic TS testing M ? - - - - - - 1 Rosemary Ekong
+/. 1i_42_ c.(-30+1_-29-1)_(*102_?)del r.0? p.0? - - Unknown - pathogenic g.(2098067_2098587)_(2138713_?)del g.(2048066_2048586)_(2088712_?)del exons 1-41 + PKD1 ex 31-46 del - TSC2_001440 contiguous TSC2/PKD1 gene deletion involving entire TSC2 gene + PDK1 exons 31-46; both parents tested and variant not found; complete screen; MLPA kits P124 (TSC1), P046 (TSC2), P351 & P352 (PKD1) unpublished - - De novo no 1/6 chromosomes - - - DNA MLPA, SEQ Blood - TSC - unpublished index has suspected TS on CT scan and a large head M ? - - - - - - 1 Rosemary Ekong
+/. 1i_42_ c.(-30+1_-29-1)_(*102_?)del r.0? p.0? - - Unknown - pathogenic g.(2098067_2098587)_(2138713_?)del g.(2048066_2048586)_(2088712_?)del exons 1-41del - TSC2_001440 contiguous TSC2/PKD1 gene deletion involving entire TSC2 + PKD1 ex 46; one parent with <3HMs does not have the variant; no variant found by sequencing; complete screen; MLPA kits P124 (TSC1), P046 (TSC2) unpublished - - Germline ? 1/4 chromosomes - - - DNA MLPA, SEQ Blood - TSC - unpublished index reported as possibly a somatic mosaic; one parent tested and the other parent not tested M ? - - - - - - 1 Rosemary Ekong
+/. 1i_42_ c.(-30+1_-29-1)_(*102_?)del r.0? p.0? - - Unknown - pathogenic g.(2098067_2098587)_(2138713_?)del g.(2048066_2048586)_(2088712_?)del exon 1-41 del - TSC2_001440 contiguous TSC2/PKD1 gene deletion involving entire TSC2 gene + PKD1 ex 46; complete screen; MLPA kits P124 (TSC1), P046 (TSC2) unpublished - - Germline ? - - - - DNA MLPA, SEQ Blood - TSC - unpublished patient reported as possibly a somatic mosaic; no clinical features indicated; parents not tested M ? - - - - - - 1 Rosemary Ekong
+/. 1i_42_ c.(-30+1_-29-1)_(*102_?)del r.0? p.0? - - Unknown - pathogenic g.(2098067_2098587)_(2138713_?)del g.(2048066_2048586)_(2088712_?)del exons 1-41del - TSC2_001440 entire TSC2 gene deleted + PDK1 ex 46; both parents tested and TSC2 deletion not found; complete screen; MLPA kits P124 (TSC1), P046 (TSC2) used unpublished - - De novo no 1/6 chromosomes - - - DNA MLPA, SEQ Blood - TSC - unpublished patient also has NF1 inherited from one parent M ? - - - - - - 1 Rosemary Ekong
+/. 1i_42_ c.(-30+1_-29-1)_(*102_?)del r.0? p.0? - - Unknown - pathogenic g.(2098067_2098587)_(2138713_?)del g.(2048066_2048586)_(2088712_?)del exons 1-41 deleted - TSC2_001440 entire TSC2 gene deleted + PDK1 ex 46; no variants found by sequencing; complete screen; MLPA kits P124 (TSC1), P046 (TSC2) used unpublished - - Germline ? - - - - DNA MLPA, SEQ Blood - TSC - unpublished patient diagnosed with definite TS; both parents reported as phenotypically unaffected but not examined; parents not tested M ? - - - - - - 1 Rosemary Ekong
+/. 1i_42_ c.(-30+1_-29-1)_(*102_?)del r.0? p.0? - - Unknown - pathogenic g.(2098067_2098587)_(2138713_?)del g.(2048066_2048586)_(2088712_?)del exon 1-41 deleted - TSC2_001440 contiguous TSC2/PKD1 gene deletion involving entire TSC2 + PKD1 exon 46; both parents tested and variant not found; complete screen; MLPA kits P124 (TSC1), P046 (TSC2) used unpublished - - De novo no 1/6 chromosomes - - - DNA MLPA, SEQ Blood - TSC - unpublished - M ? - - - - - - 1 Rosemary Ekong
+/. 1i_42_ c.(-30+1_-29-1)_(*102_?)del r.0? p.0? - - Unknown - pathogenic g.(2098067_2098587)_(2138713_?)del g.(2048066_2048586)_(2088712_?)del exons 1-41 del + PKD1 ex 1-46 - TSC2_001440 contiguous TSC2/PKD1 gene deletion involving entire TSC2 + PKD1 ex 1-46 + upstream of PKD1 (extend unknown); complete screen; MLPA kits P124 (TSC1), P046 (TSC2), P351 & P352 (PKD1) used unpublished - - Germline ? - - - - DNA MLPA, SEQ Blood - TSC - unpublished both parents reported as unaffected but not tested M ? - - - - - - 1 Rosemary Ekong
+/. 1i_42_ c.(-30+1_-29-1)_(*102_?)del r.0? p.0? - - Unknown - pathogenic g.(2098067_2098587)_(2138713_?)del g.(2048066_2048586)_(2088712_?)del exons 1-41 deleted - TSC2_001440 entire TSC2 gene (exons 2-42) deleted; reported disease-associated mutation; only TSC2 MLPA done unpublished - - Germline ? - - - - DNA MLPA Blood - TSC - unpublished TS affected F ? - - - - - - 1 Rosemary Ekong
+/. 1i_42_ c.(-30+1_-29-1)_(*102_?)del r.0? p.0? - - Unknown - pathogenic g.(2098067_2098587)_(2138713_?)del g.(2048066_2048586)_(2088712_?)del TSC2 exons 1-41 deleted; PKD1 exons 1-46 deleted - TSC2_001440 entire TSC2 gene (ex 2-42) deleted; found with entire PKD1 gene deletion; one unaffected parent tested and TSC2 deletion not found but PKD1 variant reported as 10254G>A found; PKD1 variant described as VUS; TSC2 MLPA and complete PKDx screenings done unpublished - - Germline ? - - - - DNA MLPA Blood - TSC - unpublished TS affected F ? - - - - - - 1 Rosemary Ekong
+/. 1i_42_ c.(-30+1_-29-1)_(*102_?)del r.0? p.0? - - Unknown - pathogenic g.(2098067_2098587)_(2138713_?)del g.(2048066_2048586)_(2088712_?)del exons 1-41 deleted - TSC2_001440 entire TSC2 gene (exons 2-42) deleted; reported as predicted disease-associated mutation; both parents tested and variant not found; complete TSC1 and TSC2 genes tested; TSC MLPA done unpublished - - De novo no 1/6 chromosomes - - - DNA MLPA Blood - TSC - unpublished TS affected; both parents reported as unaffected F ? - - - - - - 1 Rosemary Ekong
+/. 1i_42_ c.(-30+1_-29-1)_(*102_?)del r.0? p.0? - - Unknown - pathogenic g.(2098067_2098587)_(2138713_?)del g.(2048066_2048586)_(2088712_?)del exons 1-41 deleted - TSC2_001440 entire TSC2 gene (exons 2-42) deleted; reported as disease-associated mutation; variant not found in the one parent tested (reported as unaffected); complete TSC1 and TSC2 genes tested; TSC MLPA done unpublished - - Germline ? 1/4 chromosomes - - - DNA MLPA Blood - TSC - unpublished TS affected; the one parent tested is reported as unaffected F ? - - - - - - 1 Rosemary Ekong
+/. 1i_42_ c.(-30+1_-29-1)_(*102_?)del r.0? p.0? - - Unknown - pathogenic g.(2098067_2098587)_(2138713_?)del g.(2048066_2048586)_(2088712_?)del deletion exons 1-41, c.(?_-29)_(*102+?)del - TSC2_001440 exons 2-42 deleted PubMed: Kwiatkowski 2015 - - Germline ? - - - - DNA MLPA Blood - TSC - PubMed: Kwiatkowski 2015 TSC affected patient with SEGA ? ? - - - - - - 1 Rosemary Ekong
+/. 1i_42_ c.(-30+1_-29-1)_(*102_?)del r.0? p.0? - - Unknown - pathogenic g.(2098067_2098587)_(2138713_?)del g.(2048066_2048586)_(2088712_?)del c.(?_-29)_(*102+?)del - TSC2_001440 exons 2-42 deleted PubMed: Kwiatkowski 2015 - - Germline ? - - - - DNA MLPA Blood - TSC - PubMed: Kwiatkowski 2015 patient has TSC with AML ? ? - - - - - - 1 Rosemary Ekong
+/. 1i_42_ c.(-30+1_-29-1)_(*102_?)del r.0? p.0? - - Unknown - pathogenic g.(2098067_2098587)_(2138713_?)del g.(2048066_2048586)_(2088712_?)del whole gene deletion - TSC2_001440 entire deletion of TSC2 gene (exons 2-42) PubMed: Lee 2014 - - Germline ? - - - - DNA MLPA Blood - TSC - PubMed: Lee 2014 - ? ? Korea - - - - - 1 Rosemary Ekong
+/. 1i_42_ c.(-30+1_-29-1)_(*102_?)del r.0? p.0? - - Unknown - pathogenic g.(2098067_2098587)_(2138713_?)del g.(2048066_2048586)_(2088712_?)del whole gene/PKD1 gene deletion - TSC2_001440 deletion involving entire TSC2 gene (exons 2-42) and the PKD1 gene PubMed: Lee 2014 - - Germline ? - - - - DNA MLPA Blood - TSC - PubMed: Lee 2014 - ? ? Korea - - - - - 1 Rosemary Ekong
+/. 1i_42_ c.(-30+1_-29-1)_(*102_?)del r.0? p.0? - - Unknown - pathogenic (dominant) g.(2098067_2098587)_(2138713_?)del g.(2048066_2048586)_(2088712_?)del - - TSC2_001440 entire TSC2 gene deleted; found with known TSC1 c.2209-9C>T Au, personal communication - - Germline - - - - - DNA SEQ Blood - TSC - PubMed: Au, 2007 - ? - - - - - - - 1 Rosemary Ekong
+/. 1i_42_ c.(-30+1_-29-1)_(*102_?)del r.0? p.0? - - Unknown - pathogenic (dominant) g.(2098067_2098587)_(2138713_?)del g.(2048066_2048586)_(2088712_?)del TSC2 loss exons 41 of 41 - TSC2_001440 exons 2-42 deleted; changes in TP53 gene not specified PubMed: Akumalla, 2020 - - Somatic - - - - - DNA SEQ-NG Tumour coding exons of 405 cancer-related genes sequenced ? 12 PubMed: Akumalla, 2020 patient with clinically advanced metastatic Perivascular Epithelioid Cell tumour (PEComa) M ? (United States) - - - - - 1 Rosemary Ekong
+/+ 1i_42_ c.(-30+1_-29-1)_(*102_?)del r.0? p.0? - - Unknown - pathogenic (dominant) g.(2098067_2098587)_(2138713_?)del g.(2048066_2048586)_(2088712_?)del - - TSC2_001440 TSC2 exons 2-42 deleted - - - SUMMARY record - - - - - - - - - - - - - - - - - - - - - - -
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Assessment of functional consequences - Our conclusions on the functional consequences of variants are based on the type of variant, results of in vitro functional tests (doi: 10.1002/humu.21451; doi: 10.1002/humu.22202; doi: 10.1002/humu.23963), population frequencies, output from in silico splice site prediction algorithms, and any clinical/family data available to us. We also have output from protein prediction programs in this database for comparison purposes and they are not considered in our assessment of pathogenicity. PolyPhen Predictions - Note that these results are from PolyPhen-2 and only the HumDiv classification is shown.


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