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.

26 entries on 1 page. Showing entries 1 - 26.
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AscendingDNA change (cDNA)     

RNA change     

Protein     

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Predict-BioInf     

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-/. - c.1578C>T r.(?) p.(Ser526=) - - Unknown - benign g.2114407C>T g.2064406C>T TSC2(NM_000548.3):c.1578C>T (p.S526=), TSC2(NM_000548.5):c.1578C>T (p.S526=) - TSC2_000005 VKGL data sharing initiative Nederland - - - CLASSIFICATION record - - - - - - - - - - - - - - - - - - - - - - -
-/. - c.1578C>T r.(?) p.(Ser526=) - - Unknown - benign g.2114407C>T g.2064406C>T TSC2(NM_000548.3):c.1578C>T (p.S526=), TSC2(NM_000548.5):c.1578C>T (p.S526=) - TSC2_000005 VKGL data sharing initiative Nederland - - - CLASSIFICATION record - - - - - - - - - - - - - - - - - - - - - - -
-/. - c.1578C>T r.(?) p.(Ser526=) - - Unknown - benign g.2114407C>T g.2064406C>T TSC2(NM_000548.3):c.1578C>T (p.S526=), TSC2(NM_000548.5):c.1578C>T (p.S526=) - TSC2_000005 VKGL data sharing initiative Nederland - - - CLASSIFICATION record - - - - - - - - - - - - - - - - - - - - - - -
-/. 15 c.1578C>T r.(?) p.(Ser526=) Hamartin binding domain - Unknown - benign g.2114407C>T g.2064406C>T - - TSC2_000005 found with TSC2 variants c.1600-14C>T, c.1716+16G>A; c.5202T>C, c.*61_*62del; and TSC1 c.2829C>T PubMed: Strizheva, 2001 - - Germline - - +HpyCH4III - - 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
-/. 15 c.1578C>T r.(?) p.(Ser526=) Hamartin binding domain - Unknown - benign g.2114407C>T g.2064406C>T - - TSC2_000005 found with TSC1 frameshift c.1664del and TSC2 intronic variant c.1362-32C>G PubMed: Sancak, 2005 - - Germline - - +HpyCH4III - - DNA SEQ Blood - TSC - PubMed: Sancak, 2005 familial case; diagnosed with definite TSC; patient has TSC1 frameshift c.1664del, TSC2 intronic variant c.1362-32C>G and TSC2 silent variant c.1578C>T ? - - - - - - - 2 Rosemary Ekong
-/. 15 c.1578C>T r.(?) p.(Ser526=) Hamartin binding domain - Unknown - benign g.2114407C>T g.2064406C>T - - TSC2_000005 found with TSC2 missense c.1790A>G, TSC2 intronic variant c.1600-14C>T, TSC2 silent variant c.2580T>C and TSC1 silent variant c.2829C>T unpublished - - Germline - - +HpyCH4III - - DNA SEQ Blood - TSC - unpublished patient has TSC2 missense c.1790A>G and 4 polymorphisms (TSC2 c.1578C>T, TSC2 c.1600-14C>T, TSC2 c.2580T>C and TSC1 c.2829C>T); one parent tested for TSC2 missense c.1790A>G and variant not found; other parent unavailable for testing M - - - - - - - 1 Rosemary Ekong
-/. 15 c.1578C>T r.(?) p.(Ser526=) Hamartin binding domain - Unknown - benign g.2114407C>T g.2064406C>T 1596C>T - TSC2_000005 - unpublished - - Germline - 29/414 cases tested have the variant +HpyCH4III - - DNA DHPLC Blood - TSC - unpublished variant seen in 29 cases ? - - - - - - - 29 Rosemary Ekong
-/. 15 c.1578C>T r.(?) p.(Ser526=) Hamartin binding domain - Unknown - benign g.2114407C>T g.2064406C>T - - TSC2_000005 - PubMed: Niida, 1999 - - Germline - 9/124 cases tested have the variant +HpyCH4III - - DNA SSCA Blood - TSC - PubMed: Niida, 1999 seen in 9 cases ? - - - - - - - 9 Rosemary Ekong
-/. 15 c.1578C>T r.(?) p.(Ser526=) Hamartin binding domain - Unknown - benign g.2114407C>T g.2064406C>T - - TSC2_000005 - PubMed: Rendtorff, 2005 - - Germline - - +HpyCH4III - - DNA DGGE Blood - TSC - PubMed: Rendtorff, 2005 - ? - - - - - - - 1 Rosemary Ekong
-/. 15 c.1578C>T r.(?) p.(Ser526=) Hamartin binding domain - Unknown - benign g.2114407C>T g.2064406C>T - - TSC2_000005 found with TSC2 splice variant c.648+1G>A, TSC2 silent variant c.2580T>C and TSC2 c.*61_*62del; also seen in 6 normal controls PubMed: Ali, 2005 - - Germline - 6% +HpyCH4III - - DNA SSCA Blood - TSC TS-01 PubMed: Ali, 2005 patient with TSC2 splice variant c.648+1G>A, two TSC2 silent variants (c.1578C>T and c.2580T>C), and TSC2 c.*61_*62del ? - India - - - - - 1 Rosemary Ekong
-/. 15 c.1578C>T r.(?) p.(Ser526=) Hamartin binding domain - Unknown - benign g.2114407C>T g.2064406C>T - - TSC2_000005 - PubMed: Astrinidis, 2000 - - Germline - - +HpyCH4III - - DNA SSCA Blood - LAM 494 PubMed: Astrinidis, 2000 patient has silent variant TSC2 c.1281C>A and TSC2c.1578C>T ? - - - - - - - 1 Rosemary Ekong
-/. 15 c.1578C>T r.(?) p.(Ser526=) Hamartin binding domain - Unknown - benign g.2114407C>T g.2064406C>T - - TSC2_000005 - PubMed: Au, 2007 - - Germline - - +HpyCH4III - - DNA ? Blood - TSC - PubMed: Au, 2007 - ? - - - - - - - 1 Rosemary Ekong
-/. 15 c.1578C>T r.(?) p.(Ser526=) Hamartin binding domain - Unknown - benign g.2114407C>T g.2064406C>T 1596C>T - TSC2_000005 freq. 5.6% (18/320 alleles) in TSC population and 8.1% (15/186 alleles) in normal controls PubMed: Wang, 1997 - - Germline - - +HpyCH4III - - DNA SSCA, ASO Blood - TSC group PubMed: Wang, 1997 - ? - - - - - - - 1 Rosemary Ekong
-/. 15 c.1578C>T r.(?) p.(Ser526=) Hamartin binding domain - Unknown - benign g.2114407C>T g.2064406C>T - - TSC2_000005 - PubMed: Choy, 1999, PubMed: Roberts, 2002 - - Germline - 6% +HpyCH4III - - DNA DHPLC Blood - TSC - PubMed: Choy, 1999, PubMed: Roberts, 2002 seen 4 times; frequency from Harvard db ? - - - - - - - 1 Rosemary Ekong
-/. 15 c.1578C>T r.(?) p.(Ser526=) Hamartin binding domain - Unknown - benign g.2114407C>T g.2064406C>T 1596C>T - TSC2_000005 - PubMed: Langkau, 2002 - - Germline - 10/68 cases tested have the variant +HpyCH4III - - DNA SSCA Blood - TSC - PubMed: Langkau, 2002 seen in 10/68 cases ? - - - - - - - 10 Rosemary Ekong
-/. 15 c.1578C>T r.1578c>u p.(Ser526=) Hamartin binding domain - Unknown - benign g.2114407C>T g.2064406C>T 1596C>T - TSC2_000005 variant seen in cDNA; normal controls not screened PubMed: Wilson, 1996 - - Germline - 1/60 chromosomes tested +HpyCH4III - - DNA, RNA SSCA Blood - TSC - PubMed: Wilson, 1996 TSC patient with variant ? - - - - - - - 1 Rosemary Ekong
-/. 15 c.1578C>T r.1578c>u p.(Ser526=) Hamartin binding domain - Unknown - benign g.2114407C>T g.2064406C>T AGC>AGT, Ser526Ser - TSC2_000005 - PubMed: van Bakel, 1997 - - Germline - - +HpyCH4III - - DNA, RNA PTT Blood - TSC - PubMed: van Bakel, 1997 - ? - - - - - - - 1 Rosemary Ekong
-/. 15 c.1578C>T r.1578c>u p.(Ser526=) Hamartin binding domain - Unknown - benign g.2114407C>T g.2064406C>T - - TSC2_000005 - PubMed: Jobert, 1997 - - Germline - 24/163 individuals tested have the variant +HpyCH4III - - DNA, RNA DGGE, SSCA Blood - TSC - PubMed: Jobert, 1997 seen in 24 times ? - - - - - - - 24 Rosemary Ekong
-/. 15 c.1578C>T r.(?) p.(Ser526=) Hamartin binding domain - Unknown - benign g.2114407C>T g.2064406C>T - - TSC2_000005 found with TSC2 nonsense variant TSC2 c.2251C>T and TSC2 intronic variant c.5260-15C>T unpublished - rs34012042 Germline - - +HpyCH4III - - DNA MLPA, SEQ Blood - TSC - unpublished both parents tested and TSC2 intronic variant c.5260-15C>T found in one parent and reported as likely a polymorphism; neither parent has TSC2 nonsense variant c.2251C>T; no indication if TSC2 silent variant c.1578C>T tested in parents F - - - - - - - 1 Rosemary Ekong
-/. 15 c.1578C>T r.(?) p.(Ser526=) Hamartin binding domain - Unknown - benign g.2114407C>T g.2064406C>T - - TSC2_000005 found with disease-causing variants in patients unpublished - - Germline - 31/540 individuals tested have the variant +HpyCH4III - - DNA SEQ Blood - TSC - unpublished variant seen in a group of unaffecteds and probands - some probands with definite pathogenic variants (3 frameshift, 4 nonsense, 1 splice) ? - - - - - - - 31 Rosemary Ekong
-/. 15 c.1578C>T r.(?) p.(Ser526=) Hamartin binding domain - Unknown - benign g.2114407C>T g.2064406C>T p.Ser526Ser - TSC2_000005 - PubMed: Papadopoulou, 2018 - - Germline - - - - - DNA SEQ-NG-R, SEQ Blood - TSC - PubMed: Papadopoulou, 2018 - ? - - - - - - - 1 Rosemary Ekong
-/. 15 c.1578C>T r.(?) p.(Ser526=) Hamartin binding domain - Unknown - benign g.2114407C>T g.2064406C>T - - TSC2_000005 found with TSC2 missense c.2150T>C unpublished - - Germline - - - - - DNA SEQ Blood - TSC TS-116 PubMed: Sudarshan 2019 2.6 yr old patient with TSC2 missense c.2150T>C and TSC2 silent c.1578C>T; No clinical findings in parents and TSC2 c.2150T>C absent in both parents; inheritance of TSC2 c.1578C>T not indicated (Chowdhury, personal communication) F - - - - - - - 1 Rosemary Ekong
-/. 15 c.1578C>T r.(?) p.(Ser526=) Hamartin binding domain - Unknown - benign g.2114407C>T g.2064406C>T S526, exon 14 - TSC2_000005 - unpublished - - Germline ? - - - - DNA MCA, SEQ Lung - - - unpublished referral due to poorly differentiated squamous cell carcinoma; parents not tested M ? - - - - - - 1 Rosemary Ekong
-/. 15 c.1578C>T r.(?) p.(Ser526=) Hamartin binding domain - Unknown - benign g.2114407C>T g.2064406C>T S526, exon 14 - TSC2_000005 - 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
-/. 15 c.1578C>T r.(?) p.(Ser526=) Hamartin binding domain - Unknown - benign g.2114407C>T g.2064406C>T p.Ser526Ser T2ex14 - TSC2_000005 - unpublished - - Germline ? - - - - DNA SEQ-NG-I, SEQ Blood Illumina TruSight Cancer panel used TSC - unpublished patient with clinical diagnosis of TSC M ? - - - - - - 1 Rosemary Ekong
-/- 15 c.1578C>T r.(?) p.(Ser526=) Hamartin binding domain - Unknown - benign g.2114407C>T g.2064406C>T - - TSC2_000005 - - - rs34012042 SUMMARY record - 17216/309466 alleles, 558 homozygotes HpyCH4III+ - - - - - - - - - - - - - - - - - - - -
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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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