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     

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Frequency     

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Methylation     

Template     

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Disease     

ID_report     

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Consanguinity     

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Owner     
-/. - c.5202T>C r.(?) p.(Asp1734=) - - Unknown - benign g.2138269T>C g.2088268T>C PKD1(NM_001009944.3):c.*1459A>G, TSC2(NM_000548.3):c.5202T>C (p.D1734=), TSC2(NM_000548.5):c.5202T>C (p.D1734=) - TSC2_000001 VKGL data sharing initiative Nederland - - - CLASSIFICATION record - - - - - - - - - - - - - - - - - - - - - - -
-/. - c.5202T>C r.(?) p.(Asp1734=) - - Unknown - benign g.2138269T>C g.2088268T>C PKD1(NM_001009944.3):c.*1459A>G, TSC2(NM_000548.3):c.5202T>C (p.D1734=), TSC2(NM_000548.5):c.5202T>C (p.D1734=) - TSC2_000001 VKGL data sharing initiative Nederland - - - CLASSIFICATION record - - - - - - - - - - - - - - - - - - - - - - -
-/. - c.5202T>C r.(?) p.(Asp1734=) - - Unknown - benign g.2138269T>C g.2088268T>C PKD1(NM_001009944.3):c.*1459A>G, TSC2(NM_000548.3):c.5202T>C (p.D1734=), TSC2(NM_000548.5):c.5202T>C (p.D1734=) - TSC2_000001 VKGL data sharing initiative Nederland - - - CLASSIFICATION record - - - - - - - - - - - - - - - - - - - - - - -
-/. 41 c.5202T>C r.(?) p.(Asp1734=) GAP domain - Unknown - benign g.2138269T>C g.2088268T>C - - TSC2_000001 - PubMed: Strizheva, 2001 - - Germline - - -EcoRV - - DNA SSCA Blood - ? - PubMed: Strizheva, 2001 TSC patient with symptomatic LAM who has TSC2 variants c.1600-14C>T, c.1578C>T, c.1716+16G>A; c.5202T>C, c.*61_*62del and TSC1 variant c.2829C>T ? - - - - - - - 1 Rosemary Ekong
-/. 41 c.5202T>C r.(?) p.(Asp1734=) GAP domain - Unknown - benign g.2138269T>C g.2088268T>C - - TSC2_000001 - PubMed: Cai, 2017, PubMed: Li, 2017 - - Germline - - -EcoRV - - DNA SEQ-NG-I Blood - TSC - {PMID:Cai, 2017; PMID29344138:Li, 2017:28065512} 2 generations with affecteds; proband (9yrs) and father (43yrs) have definite TSC - age at TSC diagnosis indicated; only proband has renal AML; proband has TSC1 c.733C>T (inherited from father), TSC1 c.2626-5_2626-4dup, TSC2 c.5161‑9C>T and TSC2 c.5202T>C (inheritance not indicated) M - China - - - - - 2 Rosemary Ekong
-/. 41 c.5202T>C r.(?) p.(Asp1734=) GAP domain - Unknown - benign g.2138269T>C g.2088268T>C 5220T>C - TSC2_000001 - unpublished - - Germline - - -EcoRV - - DNA DHPLC Blood - TSC - unpublished seen in 104 TSC cases ? - - - - - - - 104 Rosemary Ekong
-/. 41 c.5202T>C r.(?) p.(Asp1734=) GAP domain - Unknown - benign g.2138269T>C g.2088268T>C - - TSC2_000001 - - - rs1748 Germline - see remarks -EcoRV - - RNA, DNA MS, RT-PCR, SEQ Blood Mass Array (Sequenom) Healthy/Control - - SEQUENOM: 92 CEPH Multi-National individuals f(A)=0.910; APPLERA_GI: 39 individuals North-American females (Caucasian and African-American) f(A)=0.603; rs1748 ? - - - - - - - 1 Rosemary Ekong
-/. 41 c.5202T>C r.(?) p.(Asp1734=) GAP domain - Unknown - benign g.2138269T>C g.2088268T>C - - TSC2_000001 - PubMed: Feng, 2004 - - Germline - - -EcoRV - - DNA SSCA Blood - TSC - PubMed: Feng, 2004 variant found in Japanese control panel and patients ? - - - - - - - 1 Rosemary Ekong
-/. 41 c.5202T>C r.(?) p.(Asp1734=) GAP domain - Unknown - benign g.2138269T>C g.2088268T>C - - TSC2_000001 - PubMed: Roberts, 2002 - - Germline - 19% -EcoRV - - DNA DHPLC Blood - TSC - PubMed: Roberts, 2002 - ? - - - - - - - 1 Rosemary Ekong
-/. 41 c.5202T>C r.(?) p.(Asp1734=) GAP domain - Unknown - benign g.2138269T>C g.2088268T>C - - TSC2_000001 - PubMed: Rendtorff, 2005 - - Germline - - -EcoRV - - DNA DGGE Blood - TSC - PubMed: Rendtorff, 2005 - ? - - - - - - - 1 Rosemary Ekong
-/. 41 c.5202T>C r.(?) p.(Asp1734=) GAP domain - Unknown - benign g.2138269T>C g.2088268T>C - - TSC2_000001 frequency reported as calculated from 80 chromosomes in the TSC patient panel PubMed: Beauchamp, 1998 - - Germline - 0.163 -EcoRV - - DNA SSCA Blood - TSC - PubMed: Beauchamp, 1998 - ? - - - - - - - 1 Rosemary Ekong
-/. 41 c.5202T>C r.(?) p.(Asp1734=) GAP domain - Unknown - benign g.2138269T>C g.2088268T>C - - TSC2_000001 - PubMed: Au, 2007 - - Germline - - -EcoRV - - DNA ? Blood - TSC - PubMed: Au, 2007 - ? - - - - - - - 1 Rosemary Ekong
-/. 41 c.5202T>C r.(?) p.(Asp1734=) GAP domain - Unknown - benign g.2138269T>C g.2088268T>C 5220T>C - TSC2_000001 - PubMed: Langkau, 2002 - - Germline - 0.15 -EcoRV - - DNA SSCA Blood - TSC - PubMed: Langkau, 2002 variant seen in 20/68 cases ? - - - - - - - 20 Rosemary Ekong
-/. 41 c.5202T>C r.(?) p.(Asp1734=) GAP domain - Unknown - benign g.2138269T>C g.2088268T>C T5151C, Asp1711Asp - TSC2_000001 published without exon 32 PubMed: van Bakel, 1997 - - Germline - - -EcoRV - - DNA, RNA RFLP Blood - TSC - PubMed: van Bakel, 1997 23/71 people heterozygous, 46/71 people homozygous for T; 2/71 people homozygous for C; freq. of T = 0.81; freq. of C = 0.19 ? - - - - - - - 1 Rosemary Ekong
-/. 41 c.5202T>C r.(?) p.(Asp1734=) GAP domain - Unknown - benign g.2138269T>C g.2088268T>C - - TSC2_000001 - unpublished - - Germline - - -EcoRV - - DNA SEQ Blood - TSC - unpublished - ? - - - - - - - 1 Rosemary Ekong
-/. 41 c.5202T>C r.(?) p.(Asp1734=) GAP domain - Unknown - benign g.2138269T>C g.2088268T>C - - TSC2_000001 found with intronic TSC2 c.5260-49C>T unpublished - rs1748 Germline - - -EcoRV - - DNA SEQ Blood - TSC - unpublished both parents tested and variant present in one parent; TS status of parents not indicated F - - - - - - - 1 Rosemary Ekong
-/. 41 c.5202T>C r.(?) p.(Asp1734=) GAP domain - Unknown - benign g.2138269T>C g.2088268T>C 5220T>C, 1734D - TSC2_000001 germline variant in tumour; controls (a) 100 Caucasians without FH of epilepsy or other known CNS disease; (b) 7 normal brain cortex without histopath. alteration; tumours had neuronal and glial cells PubMed: Becker, 2001 - - Somatic - - -EcoRV - - DNA SSCA, SEQ Brain tumour - ? - PubMed: Becker, 2001 patient has ganglioglioma and chronic epilepsy ? - - - - - - - 4 Rosemary Ekong
-/. 41 c.5202T>C r.(?) p.(Asp1734=) GAP domain - Unknown - benign g.2138269T>C g.2088268T>C - - TSC2_000001 het freq in submitted dataset = 16-30%; 3 homozygotes (C/C) in submitted dataset unpublished - - Germline - - -EcoRV - - DNA SEQ Blood - TSC - unpublished variant seen in both affected and healthy individuals; homozygotes (C/C) seen 3 times ? - - - - - - - 37 Rosemary Ekong
-/. 41 c.5202T>C r.(?) p.(Asp1734=) GAP domain - Unknown - benign g.2138269T>C g.2088268T>C - - TSC2_000001 found with TSC2 missense c.1939G>A and c.2410T>C, TSC2 variants c.482-3C>T and c.5161-10A>C unpublished - - Germline - - -EcoRV - - 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
-/. 41 c.5202T>C r.(?) p.(Asp1734=) GAP domain - Unknown - benign g.2138269T>C g.2088268T>C - - TSC2_000001 found with TSC2 c.1600-39C>T, TSC2 c.5068+27_5069-47dup and TSC2 c.2392C>T unpublished - - Germline - - -EcoRV - - DNA SEQ Blood - TSC - unpublished no evidence of clinical TS in proband and no definite disease-causing variant identified; proband has 3 common TSC2 polymorhisms (c.1600-39C>T, c.5068+27_5069-47dup and c.5202T>C) and TSC2 missense c.2392C>T; TSC2 c.2392C>T is inherited from one parent; inheritance of other variants not indicated ? - - - - - - - 1 Rosemary Ekong
-/. 41 c.5202T>C r.(?) p.(Asp1734=) GAP domain - Unknown - benign g.2138269T>C g.2088268T>C - - TSC2_000001 found with TSC frameshift c.826del PubMed: Avgeris, 2017 - - Germline - - - - - DNA SEQ Blood - TSC 1 PubMed: Avgeris, 2017 parents tested and TSC2 frameshift c.826del absent; reported that paternity testing not performed F - Greece Greek - - - - 1 Rosemary Ekong
-/. 41 c.5202T>C r.(?) p.(Asp1734=) GAP domain - Maternal (confirmed) - benign g.2138269T>C g.2088268T>C - - TSC2_000001 - PubMed: Avgeris, 2017 - - Germline - - - - - DNA SEQ Blood - TSC 11 PubMed: Avgeris, 2017 patient has TSC2 splice variant c.5160+5G>T and TSC2 silent variant c.5202T>C - both inherited from affected mother; father and sibling tested negative F - Greece Greek - - - - 2 Rosemary Ekong
-/. 41 c.5202T>C r.(?) p.(Asp1734=) GAP domain - Unknown - benign g.2138269T>C g.2088268T>C D1734, exon 40 - TSC2_000001 - 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
-/. 41 c.5202T>C r.(?) p.(Asp1734=) GAP domain - Unknown - benign g.2138269T>C g.2088268T>C D1734, exon 40 (homozygous) - TSC2_000001 homozygous variant unpublished - - Germline ? - - - - DNA MCA, SEQ Blood - - - unpublished patient reported as a somatic mosaic for TSC2 c.4802del; a relative is reported to have seizures; patient is homozygous for TSC2 c.5202T>C; parents not tested F ? - - - - - - 1 Rosemary Ekong
-/. 41 c.5202T>C r.(?) p.(Asp1734=) GAP domain - Unknown - benign g.2138269T>C g.2088268T>C D1734, exon 40 - TSC2_000001 - unpublished - - Germline ? - - - - DNA MCA, SEQ Lung - - - unpublished referral due to poorly differentiated squamous cell carcinoma; parents not tested M ? - - - - - - 1 Rosemary Ekong
-/. 41 c.5202T>C r.(?) p.(Asp1734=) GAP domain - Unknown - benign g.2138269T>C g.2088268T>C D1734, exon 40 - TSC2_000001 - unpublished - - Germline ? - - - - DNA MCA, SEQ Blood - - - unpublished TS affected; 2 children with TSC confirmed on MRI - not tested; TSC features in the children not specifed; parents not tested M ? - - - - - - 1 Rosemary Ekong
-/. 41 c.5202T>C r.(?) p.(Asp1734=) GAP domain - Unknown - benign g.2138269T>C g.2088268T>C c.5202 C>T P.Asp1734Asp T2ex40 - TSC2_000001 nucleotides transposed; 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
-/. 41 c.5202T>C r.(?) p.(Asp1734=) GAP domain - Unknown - benign g.2138269T>C g.2088268T>C 5220T>C (D1734) exon 40 - TSC2_000001 no variant seen in previous DHPLC testing; No large deletion or duplication found in MLPA unpublished - - Germline ? - - - - DNA DHPLC, MLPA Blood - TSC - unpublished - F ? - - - - - - 1 Rosemary Ekong
-/- 41 c.5202T>C r.(?) p.(Asp1734=) GAP domain - Unknown - benign g.2138269T>C g.2088268T>C - - TSC2_000001 - - - rs1748 SUMMARY record - 46454/132714 alleles, 10307 homozygotes EcoRV- - - - - - - - - - - - - - - - - - - - -
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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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