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.

17 entries on 1 page. Showing entries 1 - 17.
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Effect     

Exon     

AscendingDNA change (cDNA)     

RNA change     

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Owner     
-?/. - c.5383C>T r.(?) p.(Arg1795Cys) - - Unknown - likely benign g.2138570C>T g.2088569C>T TSC2(NM_000548.3):c.5383C>T (p.R1795C, p.(Arg1795Cys)), TSC2(NM_000548.5):c.5383C>T (p.R1795C) - TSC2_000666 VKGL data sharing initiative Nederland - - - CLASSIFICATION record - - - - - - - - - - - - - - - - - - - - - - -
-?/. - c.5383C>T r.(?) p.(Arg1795Cys) - - Unknown - likely benign g.2138570C>T g.2088569C>T TSC2(NM_000548.3):c.5383C>T (p.R1795C, p.(Arg1795Cys)), TSC2(NM_000548.5):c.5383C>T (p.R1795C) - TSC2_000666 VKGL data sharing initiative Nederland - - - CLASSIFICATION record - - - - - - - - - - - - - - - - - - - - - - -
-/. - c.5383C>T r.(?) p.(Arg1795Cys) - - Unknown - benign g.2138570C>T g.2088569C>T TSC2(NM_000548.3):c.5383C>T (p.R1795C, p.(Arg1795Cys)), TSC2(NM_000548.5):c.5383C>T (p.R1795C) - TSC2_000666 VKGL data sharing initiative Nederland - - - CLASSIFICATION record - - - - - - - - - - - - - - - - - - - - - - -
-?/. 41 c.5383C>T r.(?) p.(Arg1795Cys) - - Maternal (confirmed) - likely benign g.2138570C>T g.2088569C>T - - TSC2_000666 - Papuc et al., unpublished - rs45517423 Germline - - - - - DNA SEQ-NG-I blood WES EE 68944 - - M no Switzerland - - - - - 1 Anaïs Begemann
-?/. 42 c.5383C>T - p.Arg1795Cys - - Unknown - NA g.2138570C>T g.2088569C>T - - TSC2_000666 S6K T389 phosphorylation not significantly higher than wild type TSC2, but is significantly lower than pathogenic TSC variant PubMed: Hoogeveen-Westerveld, 2011 - - In vitro (cloned) - - - - - - - - - - - - - - - - - - - - - - -
-?/. - c.5383C>T r.(?) p.(Arg1795Cys) - - Unknown - likely benign g.2138570C>T g.2088569C>T TSC2(NM_000548.3):c.5383C>T (p.R1795C, p.(Arg1795Cys)), TSC2(NM_000548.5):c.5383C>T (p.R1795C) - TSC2_000666 VKGL data sharing initiative Nederland - - - CLASSIFICATION record - - - - - - - - - - - - - - - - - - - - - - -
?/. - c.5383C>T r.(?) p.(Arg1795Cys) - - Unknown - VUS g.2138570C>T g.2088569C>T TSC2(NM_000548.3):c.5383C>T (p.R1795C, p.(Arg1795Cys)), TSC2(NM_000548.5):c.5383C>T (p.R1795C) - TSC2_000666 VKGL data sharing initiative Nederland - - - CLASSIFICATION record - - - - - - - - - - - - - - - - - - - - - - -
?/. 42 c.5383C>T r.(?) p.(Arg1795Cys) - - Unknown - VUS g.2138570C>T g.2088569C>T 5401C>T, Arg1795Cys - TSC2_000666 listed as unclassified variant PubMed: Langkau, 2002 - - Germline - - -HaeII, HhaI- - - DNA SSCA Blood - TSC T1280A PubMed: Langkau, 2002 unique; listed as unclassified variant as parental DNA unavailable for testing ? - - - - - - - 1 Rosemary Ekong
+/. 42 c.5383C>T r.(?) p.(Arg1795Cys) - - Unknown - pathogenic g.2138570C>T g.2088569C>T - - TSC2_000666 variant reported not seen in 50 controls or 35 patients with TSC or sporadic LAM; considered disease-causing by authors variant reported not seen in 50 controls; no TSC1 variant seen PubMed: Strizheva, 2001 - - Germline - - -HaeII, HhaI- - - DNA SSCA Blood - TSC 479 PubMed: Strizheva, 2001 TSC patient with symptomatic LAM; father unaffected but mother carries same variant; mother appears unaffected and has never been screened for TSC ? - - - - - - - 1 Rosemary Ekong
-/. 42 c.5383C>T r.(?) p.(Arg1795Cys) - - Unknown - benign g.2138570C>T g.2088569C>T - - TSC2_000666 reported as a rare variant originally Kwiatkowski database - - Germline - - -HaeII, HhaI- - - DNA ? Blood - TSC - originally Kwiatkowski database seen in 2 cases; reported that 1/2 patients had confirmed variant (variant not specified) ? - - - - - - - 2 Rosemary Ekong
-?/. 42 c.5383C>T r.(?) p.(Arg1795Cys) - - Unknown - likely benign g.2138570C>T g.2088569C>T 5332C>T, R1772C - TSC2_000666 variant reported without exon 32; found with TSC2 in-frame deletion c.2458_2460del PubMed: Sancak, 2005, PubMed: Nellist, 2008, PubMed: Hoogeveen-Westerveld, 2011 - - Germline - - -HaeII, HhaI- - - DNA SSCA, SEQ, DGGE Blood - TSC Family 1 PubMed: Sancak, 2005, PubMed: Nellist, 2008, PubMed: Hoogeveen-Westerveld, 2011 index case had in utero cardiac rhabdomyoma; did not meet diagnostic TSC criteria; 2 healthy siblings; patient has both TSC2 in-frame deletion c.2459_2461del and TSC2 missense c.5383C>T; both parents tested; index inherited one variant from each parent; parent with p.Ile820del variant has very mild disease; no somatic mosaicism seen in index case or parents tested but not excluded; no DNA from other relatives ? - - - - - - - 2 Rosemary Ekong
?/. 42 c.5383C>T r.(?) p.(Arg1795Cys) - - Paternal (confirmed) - VUS g.2138570C>T g.2088569C>T - - TSC2_000666 reported as of unknown significance; TSC2 MLPA done and TSC2 deletion absent; TSC1 MLPA not done; TSC1 & TSC2 genes sequenced unpublished - rs45517423 Germline - - -HaeII, HhaI- - - DNA SEQ, MLPA Blood - TSC - unpublished TS affected; both parents reported as unaffected; one of the unaffected parents has the variant; other unaffected parent does not have the variant F - - - - - - - 2 Rosemary Ekong
-/. 42 c.5383C>T r.(?) p.(Arg1795Cys) - - Maternal (confirmed) - benign g.2138570C>T g.2088569C>T - - TSC2_000666 - unpublished - - Germline - - -HaeII, HhaI- - - DNA SEQ Blood - TSC - unpublished variant inherited from a healthy parent; definite disease-causing variant not seen in proband ? - - - - - - - 2 Rosemary Ekong
-/. 42 c.5383C>T r.(?) p.(Arg1795Cys) - - Unknown - benign g.2138570C>T g.2088569C>T - - TSC2_000666 found with TSC2 missense c.3599G>C unpublished - - Germline - - -HaeII, HhaI- - - DNA SEQ Blood - TSC - unpublished 1 affected in 1 generation; patient has 2 TSC2 missense variants (c.3599G>C and c.5383C>T); parents tested for TSC2 c.3599G>C and variant not found; inheritance of TSC2 c.5383C>T not indicated ? - - - - - - - 1 Rosemary Ekong
?/. - c.5383C>T r.(?) p.(Arg1795Cys) - - Parent #1 - VUS g.2138570C>T g.2088569C>T - - TSC2_000666 conflicting interpretations of pathogenicity; 3 heterozygous, no homozygous; Clinindb (India) PubMed: Narang 2020, Journal: Narang 2020 - rs45517423 Germline - 3/2795 individuals - - - DNA arraySNP - Infinium Global Screening Array v1.0 ? - PubMed: Narang 2020, Journal: Narang 2020 analysis 2794 individuals (India) - - India - - - - - 3 Mohammed Faruq
-?/. 42 c.5383C>T r.(?) p.(Arg1795Cys) - - Unknown - likely benign g.2138570C>T g.2088569C>T exon 41 - TSC2_000666 somatic variant unpublished - - Germline ? - - - - DNA SEQ-NG-I, SEQ Skin Illumina TruSight Cancer panel used TSC - unpublished patient with clinical diagnosis of TSC; Parents not tested F ? - - - - - - 1 Rosemary Ekong
-/- 42 c.5383C>T r.(?) p.(Arg1795Cys) - - Unknown - benign g.2138570C>T g.2088569C>T - - TSC2_000666 - - - rs45517423 SUMMARY record - 438/303470 alleles, 1 homozygote HaeII-, HhaI- - - - - - - - - - - - - - - - - - - - -
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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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