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.

21 entries on 1 page. Showing entries 1 - 21.
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Effect     

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AscendingDNA change (cDNA)     

RNA change     

Protein     

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Predict-BioInf     

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DNA change (hg38)     

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Variant remarks     

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-/. - c.2580T>C r.(?) p.(Phe860=) - - Unknown - benign g.2125834T>C g.2075833T>C TSC2(NM_000548.3):c.2580T>C (p.F860=), TSC2(NM_000548.5):c.2580T>C (p.F860=) - TSC2_000054 VKGL data sharing initiative Nederland - - - CLASSIFICATION record - - - - - - - - - - - - - - - - - - - - - - -
-/. - c.2580T>C r.(?) p.(Phe860=) - - Unknown - benign g.2125834T>C g.2075833T>C TSC2(NM_000548.3):c.2580T>C (p.F860=), TSC2(NM_000548.5):c.2580T>C (p.F860=) - TSC2_000054 VKGL data sharing initiative Nederland - - - CLASSIFICATION record - - - - - - - - - - - - - - - - - - - - - - -
-/. 23 c.2580T>C r.(?) p.(Phe860=) Hamartin binding domain - Unknown - benign g.2125834T>C g.2075833T>C - - TSC2_000054 found with TSC2 missense c.1790A>G, TSC2 intronic variant c.1600-14C>T, TSC2 silent variant c.1578C>T and TSC1 silent variant c.2829C>T unpublished - - Germline - - - - - DNA SEQ Blood - TSC - unpublished patient has TSC2 missense c.1790A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
-/. 23 c.2580T>C r.(?) p.(Phe860=) Hamartin binding domain - Unknown - benign g.2125834T>C g.2075833T>C 2598T>C - TSC2_000054 - unpublished - - Germline - - - - - DNA DHPLC Blood - TSC - unpublished variant seen in different patients ? - United Kingdom (Great Britain) - - - - - 12 Rosemary Ekong
-/. 23 c.2580T>C r.(?) p.(Phe860=) Hamartin binding domain - Unknown - benign g.2125834T>C g.2075833T>C - - TSC2_000054 variant seen in 1 normal control; found with TSC1 variants (c.663+35T>C, c.965T>C & c.2829C>T) and TSC2 variants (c.3131+1G>A and c.*61_*62del) PubMed: Ali, 2005 - - Germline - 1% - - - DNA SSCA Blood - TSC TS-09 PubMed: Ali, 2005 patient with TSC2 splice variant c.3131+1G>A, TSC2 silent c.2580T>C, TSC2 c.*61_*62del and other well-known variants in TSC1 (c.663+35T>C, c.965T>C, c.2829C>T) and in TSC2 (c.2580T>C, c.*61_*62del) ? - India - - - - - 1 Rosemary Ekong
-/. 23 c.2580T>C r.(?) p.(Phe860=) Hamartin binding domain - Unknown - benign g.2125834T>C g.2075833T>C - - TSC2_000054 - PubMed: Rendtorff, 2005 - - Germline - - - - - DNA DGGE Blood - TSC - PubMed: Rendtorff, 2005 - ? - - - - - - - 1 Rosemary Ekong
-/. 23 c.2580T>C r.(?) p.(Phe860=) Hamartin binding domain - Unknown - benign g.2125834T>C g.2075833T>C - - TSC2_000054 found with TSC2 splice variant c.648+1G>A, TSC2 silent variant c.1578C>T and TSC2 c.*61_*62del; variant seen in a normal control PubMed: Ali, 2005 - - Germline - 1% - - - 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
-/. 23 c.2580T>C r.(?) p.(Phe860=) Hamartin binding domain - Unknown - benign g.2125834T>C g.2075833T>C - - TSC2_000054 frequency in HapMap: CEU f(T)=0.9, YRI f(T)=0.925, CHB and JPT non-polymorphic; APPLERA_GI: f(T)=0.934 - - rs13337626 Germline - - - - - DNA ? Blood - Healthy/Control - - HapMap: CEU f(T)=0.9, YRI f(T)=0.925, CHB and JPT non-polymorphic; APPLERA_GI: f(T)=0.934; rs13337626; ? - - - - - - - 1 Rosemary Ekong
-/. 23 c.2580T>C r.(?) p.(Phe860=) Hamartin binding domain - Unknown - benign g.2125834T>C g.2075833T>C c.2580C>T - TSC2_000054 - PubMed: Au, 2007 - - Germline - - - - - DNA ? Blood - TSC - PubMed: Au, 2007 - ? - - - - - - - 1 Rosemary Ekong
-/. 23 c.2580T>C r.(?) p.(Phe860=) Hamartin binding domain - Unknown - benign g.2125834T>C g.2075833T>C - - TSC2_000054 variant reported also in CEPHs (numbers in CEPH not indicated) PubMed: Niida, 1999 - - Germline - 3/124 cases tested have the variant - - - DNA SSCA Blood - TSC group PubMed: Niida, 1999 seen in 3 patients ? - - - - - - - 3 Rosemary Ekong
-/. 23 c.2580T>C r.(?) p.(Phe860=) Hamartin binding domain - Unknown - benign g.2125834T>C g.2075833T>C - - TSC2_000054 - originally Kwiatkowski database - - Germline - 2.20% - - - DNA ? Blood - TSC - originally Kwiatkowski database - ? - - - - - - - 1 Rosemary Ekong
-/. 23 c.2580T>C r.(?) p.(Phe860=) Hamartin binding domain - Unknown - benign g.2125834T>C g.2075833T>C 2598T>C - TSC2_000054 variant seen in cDNA; normal controls not screened PubMed: Wilson, 1996 - - Germline - 1/60 chromosomes amongst TSC patients - - - DNA, RNA SSCA Blood - TSC - PubMed: Wilson, 1996 TSC patient with variant ? - - - - - - - 1 Rosemary Ekong
-/. 23 c.2580T>C r.(?) p.(Phe860=) Hamartin binding domain - Unknown - benign g.2125834T>C g.2075833T>C - - TSC2_000054 - unpublished - - Germline - - - - - DNA SEQ Blood - TSC - unpublished - ? - - - - - - - 1 Rosemary Ekong
-/. 23 c.2580T>C r.(?) p.(Phe860=) Hamartin binding domain - Unknown - benign g.2125834T>C g.2075833T>C - - TSC2_000054 - PubMed: Badri, 2013 - - Somatic - - - - - DNA SEQ-NG-R, MLPA, SEQ Lung - LAM 9034 PubMed: Badri, 2013 patient has sporadic LAM ? - - - - - - - 1 Rosemary Ekong
-/. 23 c.2580T>C r.(?) p.(Phe860=) Hamartin binding domain - Unknown - benign g.2125834T>C g.2075833T>C 2598T>C - TSC2_000054 found with TSC2 in-frame deletion c.2369_2371del and 4 other TSC2 variants (c.2546-12C>T, c.2639+44C>G, c.3884-56C>G and c.5161-10A>C) unpublished - - Germline - - - - - 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
-/. 23 c.2580T>C r.(?) p.(Phe860=) Hamartin binding domain - Unknown - benign g.2125834T>C g.2075833T>C 2598T>C, 860F - TSC2_000054 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 - - - - - DNA SSCA, SEQ Brain tumour - ? - PubMed: Becker, 2001 patient has ganglioglioma and chronic epilepsy ? - - - - - - - 1 Rosemary Ekong
-/. 23 c.2580T>C r.(?) p.(Phe860=) Hamartin binding domain - Unknown - benign g.2125834T>C g.2075833T>C - - TSC2_000054 reported het frequency in submitted data = <5% unpublished - rs13337626 Germline - - - - - DNA SEQ Blood - TSC - unpublished variant in probands ? - - - - - - - 7 Rosemary Ekong
-/. 23 c.2580T>C r.2580u>c p.Phe860= Hamartin binding domain - Unknown - benign g.2125834T>C g.2075833T>C - - TSC2_000054 found with other TSC2 variants - intronic (c.976-63G>A, c.1600-14C>T, c.2546-12C>T, c.2639+44C>G, c.5161-10A>C, c.5260-49C>T, c.5260-25C>G) and silent (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
-/. 23 c.2580T>C r.2580u>c p.Phe860= Hamartin binding domain - Unknown - benign g.2125834T>C g.2075833T>C - - TSC2_000054 found with other TSC2 variants - intronic (c.1600-14C>T, c.2546-12C>T, c.2639+44C>G, c.5161-10A>C) and silent (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
-/. 23 c.2580T>C r.(?) p.(Phe860=) Hamartin binding domain - Unknown - benign g.2125834T>C g.2075833T>C F860, exon 22 - TSC2_000054 - unpublished - - Germline ? - - - - DNA MCA, SEQ Blood - - - unpublished patient with clinical diagnosis of TSC; parents not tested F ? - - - - - - 1 Rosemary Ekong
-/- 23 c.2580T>C r.(?) p.(Phe860=) Hamartin binding domain - Unknown - benign g.2125834T>C g.2075833T>C - - TSC2_000054 - - - rs13337626 SUMMARY record - 22175/308774 alleles, 852 homozygotes - - - - - - - - - - - - - - - - - - - - -
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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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