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.

22 entries on 1 page. Showing entries 1 - 22.
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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     
-/. - c.5161-10A>C r.(=) p.(=) - - Unknown - benign g.2138218A>C g.2088217A>C PKD1(NM_001009944.3):c.*1510T>G, TSC2(NM_000548.3):c.5161-10A>C, TSC2(NM_000548.5):c.5161-10A>C - TSC2_000336 VKGL data sharing initiative Nederland - - - CLASSIFICATION record - - - - - - - - - - - - - - - - - - - - - - -
-/. - c.5161-10A>C r.(=) p.(=) - - Unknown - benign g.2138218A>C g.2088217A>C PKD1(NM_001009944.3):c.*1510T>G, TSC2(NM_000548.3):c.5161-10A>C, TSC2(NM_000548.5):c.5161-10A>C - TSC2_000336 VKGL data sharing initiative Nederland - - - CLASSIFICATION record - - - - - - - - - - - - - - - - - - - - - - -
-/. - c.5161-10A>C r.(=) p.(=) - - Unknown - benign g.2138218A>C g.2088217A>C PKD1(NM_001009944.3):c.*1510T>G, TSC2(NM_000548.3):c.5161-10A>C, TSC2(NM_000548.5):c.5161-10A>C - TSC2_000336 VKGL data sharing initiative Nederland - - - CLASSIFICATION record - - - - - - - - - - - - - - - - - - - - - - -
-/. 40i c.5161-10A>C r.(?) p.(=) - - Unknown - benign g.2138218A>C g.2088217A>C 5179-10C>A - TSC2_000336 - unpublished - - Germline - - MnlI+ - - DNA DHPLC Blood - TSC - unpublished seen in 58 different patients; all cases are different from those in Jones, 1999 ? - - - - - - - 58 Rosemary Ekong
-/. 40i c.5161-10A>C r.(?) p.(=) - - Unknown - benign g.2138218A>C g.2088217A>C - - TSC2_000336 - PubMed: Rendtorff, 2005 - - Germline - - MnlI+ - - DNA DGGE Blood - TSC - PubMed: Rendtorff, 2005 - ? - - - - - - - 1 Rosemary Ekong
-/. 40i c.5161-10A>C r.(?) p.(=) - - Unknown - benign g.2138218A>C g.2088217A>C - - TSC2_000336 - PubMed: Roberts, 2002 - - Germline - 27% MnlI+ - - DNA DHPLC Blood - TSC - PubMed: Roberts, 2002 - ? - - - - - - - 1 Rosemary Ekong
-/. 40i c.5161-10A>C r.(?) p.(=) - - Unknown - benign g.2138218A>C g.2088217A>C 5161-9A>C - TSC2_000336 frequency reported as calculated from 80 chromosomes in the TSC patient panel PubMed: Beauchamp, 1998 - - Germline - - MnlI+ - - DNA SSCA Blood - TSC - PubMed: Beauchamp, 1998 - ? - - - - - - - 1 Rosemary Ekong
-/. 40i c.5161-10A>C r.(?) p.(=) - - Unknown - benign g.2138218A>C g.2088217A>C 5179-9A>C - TSC2_000336 - PubMed: Jones, 1999 - - Germline - 5%-10% MnlI+ - - DNA HD, SSCA Blood - TSC ? PubMed: Jones, 1999 - ? - - - - - - - 1 Rosemary Ekong
-/. 40i c.5161-10A>C r.(?) p.(=) - - Unknown - benign g.2138218A>C g.2088217A>C - - TSC2_000336 - PubMed: Au, 2007 - - Germline - - MnlI+ - - DNA ? Blood - TSC - PubMed: Au, 2007 - ? - - - - - - - 1 Rosemary Ekong
-/. 40i c.5161-10A>C r.(?) p.(=) - - Unknown - benign g.2138218A>C g.2088217A>C 5179-10A>C - TSC2_000336 - PubMed: Langkau, 2002 - - Germline - 0.074 MnlI+ - - DNA SSCA Blood - TSC - PubMed: Langkau, 2002 variant reported seen in 10/68 cases ? - - - - - - - 10 Rosemary Ekong
-/. 40i c.5161-10A>C r.(?) p.(=) - - Unknown - benign g.2138218A>C g.2088217A>C Intron 39 - TSC2_000336 - PubMed: Tsai, 2011 - - Germline - - MnlI+ - - DNA DHPLC, MCA Blood - Healthy/Control Control group PubMed: Tsai, 2011 variant seen in control group ? - Taiwan - - - - - 1 Rosemary Ekong
-/. 40i c.5161-10A>C r.(?) p.(=) - - Unknown - benign g.2138218A>C g.2088217A>C intron 39 - TSC2_000336 - unpublished - - Germline - - MnlI+ - - DNA SEQ Blood - TSC - unpublished - ? - - - - - - - 1 Rosemary Ekong
-/. 40i c.5161-10A>C r.(?) p.(=) - - Unknown - benign g.2138218A>C g.2088217A>C 5179-10C>A - TSC2_000336 found with TSC2 in-frame deletion c.2369_2371del and 4 other TSC2 variants (c.2546-12C>T, c.2580T>C, c.2639+44C>G and c.3884-56C>G) unpublished - - Germline - - MnlI+ - - DNA DHPLC Blood - TSC - unpublished patient has TSC2 in-frame deletion c.2369_2371del and 5 other TSC2 variants (c.2546-12C>T, c.2580T>C, c.2639+44C>G, c.3884-56C>G and c.5161-10A>C); TSC2 c.2369_2371del is not seen in the unaffected sibling ? - - - - - - - 1 Rosemary Ekong
-/. 40i c.5161-10A>C r.(?) p.(=) - - Unknown - benign g.2138218A>C g.2088217A>C - - TSC2_000336 variant seen in this patient and a normal control unpublished - rs1800718 Germline - - MnlI+ - - DNA SEQ Blood - TSC - unpublished - M - - - - - - - 1 Rosemary Ekong
-/. 40i c.5161-10A>C r.(?) p.(=) - - Unknown - benign g.2138218A>C g.2088217A>C - - TSC2_000336 het freq in submitted dataset = 10-43%; 4 homozygotes (C/C) in submitted dataset unpublished - - Germline - - MnlI+ - - DNA SEQ Blood - TSC - unpublished variant found in probands and an affected family member - some have definite disease-causing variants; 4 other probands are homozygotes (C/C) ? - - - - - - - 20 Rosemary Ekong
-/. 40i c.5161-10A>C r.(?) p.(=) - - Unknown - benign g.2138218A>C g.2088217A>C - - TSC2_000336 found with TSC2 missense c.1939G>A and c.2410T>C, TSC2 polys c.482-3C>T and c.5202T>C unpublished - - Germline - - MnlI+ - - DNA SEQ Blood - TSC - unpublished unaffected parents but not formally examined; one parent tested and TSC2 missense c.1939G>A present but not TSC2 missense c.2410T>C; other parent unavailable M - - - - - - - 1 Rosemary Ekong
-/. 40i c.5161-10A>C r.(?) p.(=) - - Unknown - benign g.2138218A>C g.2088217A>C - - TSC2_000336 found with other TSC2 variants - intronic (c.976-63G>A, c.1600-14C>T, c.2546-12C>T, c.2639+44C>G, c.5260-49C>T, c.5260-25C>G) and silent (c.2580T>C, c.5397G>C) PubMed: Avgeris, 2017 - - Germline - - - - - DNA SEQ Blood - TSC 13 PubMed: Avgeris, 2017 reported that no definite TSC-causing variant found; no other family member tested F - Greece Greek - - - - 1 Rosemary Ekong
-/. 40i c.5161-10A>C r.(?) p.(=) - - Unknown - benign g.2138218A>C g.2088217A>C - - TSC2_000336 common variant found with other common TSC2 variants (c.482-3C>T and c.1600-39C>T) and TSC2 missense c.839T>C PubMed: Dufner Almeida 2019 - - Germline - - MnlI+ - - DNA SEQ Blood - TSC 4.1/4.2/4.3/4.4/4.5 PubMed: Dufner Almeida 2019 5 affected in 3 generations; proband has TSC2 missense c.839T>C and 3 common TSC2 variants (c.482-3C>T, c.1600-39C>T, c.5161-10A>C) (Migone, personal communication); TSC2 c.839T>C segregates with disease; TS features in index found at birth and when < 1yr old; 3/4 individuals tested have the variant and clinical signs; 1/4 with variant does not have signs of TSC on skin and neurological examination; one unaffected relative (skin and neurological examination, and tested) does not have the variant M - - - - - - - 1 Rosemary Ekong
-/. 40i c.5161-10A>C r.(?) p.(=) - - Unknown - benign g.2138218A>C g.2088217A>C - - TSC2_000336 found with other TSC2 variants - intronic (c.1600-14C>T, c.2546-12C>T, c.2639+44C>G) and silent (c.2580T>C, c.5397G>C) PubMed: Avgeris, 2017 - - Germline - - - - - DNA SEQ Blood - TSC 16 PubMed: Avgeris, 2017 reported that no definite TSC-causing variant found; no other family member tested M - Greece Greek - - - - 1 Rosemary Ekong
-/. 40i c.5161-10A>C r.(?) p.(=) - - Unknown - benign g.2138218A>C g.2088217A>C - - TSC2_000336 - unpublished - - Germline ? - - - - DNA MCA, SEQ Fetal blood - - - unpublished TSC2 c.2590C>T not found in mildly affected parent (features not specified) who has been tested repeatedly; sibling also tested negative for TSC2 c.2590C>T ? ? - - - - - - 1 Rosemary Ekong
-/. 40i c.5161-10A>C r.(?) p.(=) - - Unknown - benign g.2138218A>C g.2088217A>C T2 intron 39 - TSC2_000336 variant confirmed by Sanger sequencing unpublished - - Germline ? - - - - DNA SEQ-NG-I, SEQ Blood Illumina TruSight Cancer panel used TSC - unpublished patient with clinical diagnosis of TSC F ? - - - - - - 1 Rosemary Ekong
-/- 40i c.5161-10A>C r.(?) p.(=) - - Unknown - benign g.2138218A>C g.2088217A>C - - TSC2_000336 - - - rs1800718 SUMMARY record - 67207/307904 alleles, 8712 homozygotes MnlI+ - - - - - - - - - - - - - - - - - - - -
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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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