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.

18 entries on 1 page. Showing entries 1 - 18.
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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     

Panel size     

Owner     
+?/. _1i_16i c.(?_-29-1)_(1716+1_1717-1)del r.? p.? - - Unknown - likely pathogenic g.(?_2098587)_(2115637_2120456)del g.(?_2048586)_(2065636_2070455)del TSC2 c.(?_1)_138+? - TSC2_001076 deletion involves exons 2-16; exon 17 (probe has 5' position c.1754) to exon 42 not deleted unpublished - - De novo - - - - - DNA MLPA Blood - TSC - unpublished - M - - - - - - - 1 Rosemary Ekong
+?/. _1i_16i c.(?_-29-1)_(1716+1_1717-1)del r.? p.? - - Unknown - likely pathogenic g.(?_2098587)_(2115637_2120456)del g.(?_2048586)_(2065636_2070455)del c.1-?_1716+?del - TSC2_001076 Deletion of TSC2 exons 2 through 16. Breakpoints not determined. MLPA probe sites: TSC2 exon 2 at c.20_c.35, TSC2 exon 16 at c.1675_c.1690 unpublished - - De novo - - - - - DNA MLPA Blood - TSC - unpublished - M - - - - - - - 1 Rosemary Ekong
+/. _1i_16i c.(?_-29-1)_(1716+1_1717-1)del r.? p.? - - Unknown - pathogenic g.(?_2098587)_(2115637_2120456)del g.(?_2048586)_(2065636_2070455)del del ex1-15 - TSC2_001076 exons 2-16 deleted unpublished - - Germline - - - - - DNA MLPA Blood - TSC - unpublished affected TS case M - - - - - - - 1 Rosemary Ekong
+/. _1i_16i c.(?_-29-1)_(1716+1_1717-1)del r.? p.? - - Unknown - pathogenic g.(?_2098587)_(2115637_2120456)del g.(?_2048586)_(2065636_2070455)del del exon 1-15 - TSC2_001076 exons 2-16 deleted unpublished - - Germline - - - - - DNA MLPA Blood - TSC - unpublished different case M - - - - - - - 1 Rosemary Ekong
+/. _1i_16i c.(?_-29-1)_(1716+1_1717-1)del r.? p.? - - Unknown - pathogenic g.(?_2098587)_(2115637_2120456)del g.(?_2048586)_(2065636_2070455)del exon 1-15 deleted - TSC2_001076 exons 2-16 deleted; TSC1 and TSC2 analysed by sequencing and deletion/duplication assay PubMed: Priya, 2012 - - De novo - - - - - DNA MLPA Blood - TSC - PubMed: Priya, 2012 3yr old patient; both parents clinically assessed and phenotypically normal; both parents tested and variant not found; variant also absent in fetus M no - - - - - - 1 Rosemary Ekong
+/. _1i_16i c.(?_-29-1)_(1716+1_1717-1)del r.? p.? - - Unknown - pathogenic g.(?_2098587)_(2115637_2120456)del g.(?_2048586)_(2065636_2070455)del exons 1-15 deleted - TSC2_001076 16971bp del of ex2-16 detected with TSC2 MLPA P046-B3 kit; breakpoints not determined; ex2 probes at c.16_39; ex16 probes at c.1671_1694 PubMed: Jang, 2012 - - Germline - - - - - DNA MLPA Blood - TSC - PubMed: Jang, 2012 5yr old patient M - Korea, South (Republic) Seoul - - - - 1 Rosemary Ekong
+/. _1i_16i c.(?_-29-1)_(1716+1_1717-1)del r.? p.? - - Unknown - pathogenic g.(?_2098587)_(2115637_2120456)del g.(?_2048586)_(2065636_2070455)del exons 1-15 deleted - TSC2_001076 exons 2-16 deleted; MLPA kits P124 (TSC1), P046B2 (TSC2) used unpublished - - Germline - - - - - DNA MLPA Blood - TSC - unpublished no FH of TS in the last 3 generations; sibling tested and variant not found; parents not tested F - - - - - - - 1 Rosemary Ekong
+/. _1i_16i c.(?_-29-1)_(1716+1_1717-1)del r.? p.? - - Unknown - pathogenic g.(?_2098587)_(2115637_2120456)del g.(?_2048586)_(2065636_2070455)del c.(?_-29)_1716+?del - TSC2_001076 exons 2-16 deleted PubMed: Kwiatkowski, 2015 - - Germline - - - - - DNA MLPA Blood - TSC - PubMed: Kwiatkowski, 2015 patient has TSC with AML ? - - - - - - - 1 Rosemary Ekong
+/. _1i_16i c.(?_-29-1)_(1716+1_1717-1)del r.? p.? - - Unknown - pathogenic g.(?_2098587)_(2115637_2120456)del g.(?_2048586)_(2065636_2070455)del intragenic large deletion - TSC2_001076 intragenic large deletion of TSC2 exons 2-16 PubMed: Lee, 2014 - - Germline - - - - - DNA MLPA Blood - TSC - PubMed: Lee, 2014 korean patient ? - Korea - - - - - 1 Rosemary Ekong
+/. _1i_16i c.(?_-29-1)_(1716+1_1717-1)del r.? p.? - - Unknown - pathogenic g.(?_2098587)_(2115637_2120456)del g.(?_2048586)_(2065636_2070455)del deletion exon 1 to 15 - TSC2_001076 exons 2-16 deleted unpublished - - Germline - - - - - DNA MLPA Blood - TSC - unpublished No other family member tested F - - - - - - - 1 Rosemary Ekong
+/. _1i_16i c.(?_-29-1)_(1716+1_1717-1)del r.? p.? - - Unknown - pathogenic g.(?_2098587)_(2115637_2120456)del g.(?_2048586)_(2065636_2070455)del deletion exon 1 to 15 - TSC2_001076 exons 2-16 deleted unpublished - - De novo - - - - - DNA MLPA Blood - TSC - unpublished both parents tested negative for variant F - - - - - - - 1 Rosemary Ekong
+/. _1i_16i c.(?_-29-1)_(1716+1_1717-1)del r.? p.? - - Unknown - pathogenic g.(?_2098587)_(2115637_2120456)del g.(?_2048586)_(2065636_2070455)del g.del ex1-ex15; c.1_1716del1716 - TSC2_001076 exons 2-16 deleted; TSC2 MLPA P046-C1 used PubMed: Ismail, 2017 - - Germline - - - - - DNA MLPA Blood - TSC 009-002-001 PubMed: Ismail, 2017 no clinical information F - Malaysia - - - - - 1 Rosemary Ekong
+/. _1i_16i c.(?_-29-1)_(1716+1_1717-1)del r.? p.? - - Unknown - pathogenic g.(?_2098587)_(2115637_2120456)del g.(?_2048586)_(2065636_2070455)del EX2_16 DEL - TSC2_001076 exons 2-16 deleted PubMed: Cai, 2017 - - Germline - - - - - DNA PCRq Blood - TSC 1 PubMed: Cai, 2017 patient diagnosed with definite TSC accompanied by renal lesions (either renal AML or renal cysts) ? - China - - - - - 1 Rosemary Ekong
+/. _1i_16i c.(?_-29-1)_(1716+1_1717-1)del r.? p.? - - Unknown - pathogenic g.(?_2098587)_(2115637_2120456)del g.(?_2048586)_(2065636_2070455)del c.(?_1)_1716+?del - TSC2_001076 exons 2-16 deleted unpublished - - De novo - - - - - DNA SEQ Blood - TSC - unpublished both parents tested and variant absent ? - - - - - - - 1 Rosemary Ekong
+/. _1i_16i c.(?_-29-1)_(1716+1_1717-1)del r.? p.? - - Unknown - pathogenic g.(?_2098587)_(2115637_2120456)del g.(?_2048586)_(2065636_2070455)del c.(?_1)_1716+?del - TSC2_001076 exons 2-16 deleted unpublished - - Germline - - - - - DNA SEQ Blood - TSC - unpublished - ? - - - - - - - 1 Rosemary Ekong
+/. _1i_16i c.(?_-29-1)_(1716+1_1717-1)del r.? p.? - - Unknown - pathogenic (dominant) g.(?_2098587)_(2115637_2120456)del g.(?_2048586)_(2065636_2070455)del deletion exons 1 to 15 - TSC2_001076 exons 2-16 deleted unpublished - - Germline ? - - - - DNA MLPA Blood Diagnostic testing, All exons for TSC1 and TSC2, exon 40 and 46 only for PKD1 tested TSC - unpublished No other family member tested F ? - - - - - - 1 Rosemary Ekong
+/+ _1i_16i c.(?_-29-1)_(1716+1_1717-1)del r.? p.? - - Unknown - pathogenic (dominant) g.(?_2098587)_(2115637_2120456)del g.(?_2048586)_(2065636_2070455)del - - TSC2_001076 deletion involves exons 2-16; exon 17 to exon 42 not deleted - - - SUMMARY record - - - - - - - - - - - - - - - - - - - - - - -
+/. _1i_16i c.(?_-29-1)_(1716+1_1717-1)del r.? p.? - - Unknown - pathogenic (dominant) g.(?_2098587)_(2115637_2120456)del g.(?_2048586)_(2065636_2070455)del - - TSC2_001076 exon 2–16 deleted; reported that deletion includes the initiation codon; 5′ end of deletion undetermined; no variants in colorectal cancer/colorectal polyposis genes were identified PubMed: Reis, 2020 - - Germline - - - - - DNA SEQ-NG Blood 80 cancer predisposition genes screened TSC - PubMed: Reis, 2020 patient with TSC and polyposis of the digestive tract; family history of cancer (central nervous system tumours in father and brother) but no family history of TSC. M - (Brazil) - - - - - 1 Rosemary Ekong
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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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