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.

36 entries on 1 page. Showing entries 1 - 36.
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ClinVar ID     
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+/. - c.3598C>T r.(?) p.(Arg1200Trp) - - Unknown - pathogenic g.2130366C>T g.2080365C>T TSC2(NM_000548.3):c.3598C>T (p.R1200W) - TSC2_000056 VKGL data sharing initiative Nederland - - - CLASSIFICATION record - - - - - - - - - - - - - - - - - - - - - - -
+/. 30 c.3598C>T - p.Arg1200Trp - - Unknown - NA g.2130366C>T g.2080365C>T - - TSC2_000056 assay using TSC2 null cells showed T389/S6K ratio significantly increased compared to wild type TSC2 and the same as the pathogenic TSC2 R611Q variant; TSC1 and TSC2 signals significantly reduced compared to wild type TSC2; variant disrupts TSC2 function PubMed: Hoogeveen-Westerveld, 2011 - - In vitro (cloned) - - - - - - - - - - - - - - - - - - - - - - -
+/+ 30 c.3598C>T r.(?) p.(Arg1200Trp) - - Unknown - pathogenic (dominant) g.2130366C>T g.2080365C>T - - TSC2_000056 - - - rs45438205 SUMMARY record - 1/31378 alleles BpmI+, AvaII- - - - - - - - - - - - - - - - - - - - -
+/. 30 c.3598C>T r.(?) p.(Arg1200Trp) - - Unknown - pathogenic g.2130366C>T g.2080365C>T 3616C>T - TSC2_000056 reported as pathogenic unpublished - - Germline - - +BpmI, MspI- - - DNA DHPLC Blood - TSC - unpublished - ? - - - - - - - 1 Rosemary Ekong
+/. 30 c.3598C>T r.(?) p.(Arg1200Trp) - - Unknown - pathogenic g.2130366C>T g.2080365C>T 3616C>T - TSC2_000056 - unpublished - - De novo - - +BpmI, MspI- - - DNA DHPLC Blood - TSC - unpublished 2nd case reported; variant not seen in parents ? - - - - - - - 1 Rosemary Ekong
+/. 30 c.3598C>T r.(?) p.(Arg1200Trp) - - Unknown - pathogenic g.2130366C>T g.2080365C>T - - TSC2_000056 - PubMed: Au, 2007 - - Germline - - +BpmI, MspI- - - DNA SEQ Blood - TSC HOU53-002 PubMed: Au, 2007 2nd case ? - - - - - - - 2 Rosemary Ekong
+/. 30 c.3598C>T r.(?) p.(Arg1200Trp) - - Unknown - pathogenic g.2130366C>T g.2080365C>T - - TSC2_000056 found with TSC2 missense c.4225C>T PubMed: Au, 2007 - - De novo - - +BpmI, MspI- - - DNA SEQ Blood - TSC TS00-270 PubMed: Au, 2007 patient with two TSC2 missense variants (c.3598C>T and c.4225C>T); TSC2 c.3598C>T reported not found in parents; inheritance of TSC2 missense c.4225C>T not indicated ? - - - - - - - 1 Rosemary Ekong
+/. 30 c.3598C>T r.(?) p.(Arg1200Trp) - - Unknown - pathogenic g.2130366C>T g.2080365C>T - - TSC2_000056 - originally Kwiatkowski database - - Germline - - +BpmI, MspI- - - DNA ? Blood - TSC - originally Kwiatkowski database no parental DNA available for testing; variant seen 2 times ? - - - - - - - 1 Rosemary Ekong
+/. 30 c.3598C>T r.(?) p.(Arg1200Trp) - - Unknown - pathogenic g.2130366C>T g.2080365C>T 3616C>T, Arg1199Trp - TSC2_000056 - PubMed: Wilson, 1996 - - Germline - - +BpmI, MspI- - - DNA, RNA SSCA Blood - TSC TSC-001 PubMed: Wilson, 1996 - ? - - - - - - - 2 Rosemary Ekong
+/. 30 c.3598C>T r.(?) p.(Arg1200Trp) - - Unknown - pathogenic g.2130366C>T g.2080365C>T - - TSC2_000056 both TSC1 and TSC2 genes tested unpublished - - Germline - - +BpmI, MspI- - - DNA SEQ Blood - TSC - unpublished one parent tested and variant not found; M - - Middle East - - - - 1 Rosemary Ekong
+/. 30 c.3598C>T r.(?) p.(Arg1200Trp) - - Unknown - pathogenic g.2130366C>T g.2080365C>T - - TSC2_000056 - PubMed: Sancak, 2005, PubMed: Hoogeveen-Westerveld, 2011 - - Germline - - +BpmI, MspI- - - DNA SEQ Blood - TSC - PubMed: Sancak, 2005, PubMed: Hoogeveen-Westerveld, 2011 4 different patients ? - - - - - - - 8 Rosemary Ekong
+/. 30 c.3598C>T r.(?) p.(Arg1200Trp) - - Unknown - pathogenic g.2130366C>T g.2080365C>T - - TSC2_000056 - PubMed: Hoogeveen-Westerveld, 2011 - - Germline - - +BpmI, MspI- - - DNA SEQ Blood - TSC - PubMed: Hoogeveen-Westerveld, 2011 2 different sporadic patients; one patient is indicated as sporadic ? - - - - - - - 2 Rosemary Ekong
-/. 30 c.3598C>T r.(?) p.(Arg1200Trp) - - Unknown - benign g.2130366C>T g.2080365C>T exon 30, p.Arg1200Trp (CGG>TGG) - TSC2_000056 variant identified in epilepsy panel test unpublished - - De novo - - +BpmI, MspI- - - DNA SEQ-NG-I Blood - TSC - unpublished de novo case initially evaluated for infantile epilepsy M - United States white - - - - 1 Rosemary Ekong
+/. 30 c.3598C>T r.(?) p.(Arg1200Trp) - - Unknown - pathogenic g.2130366C>T g.2080365C>T - - TSC2_000056 - PubMed: van Eeghen, 2012 - - Germline - - +BpmI, MspI- - - DNA SEQ Blood - TSC - PubMed: van Eeghen, 2012 5 affected in same family; 4/5 do not have infantile spasms or other epilepsy types, 1/5 has other epilepsy types without infantile spasms; all 5 have other TS features (not described as paper is focused on epilepsy) ? - - - - - - - 5 Rosemary Ekong
+/. 30 c.3598C>T r.(?) p.(Arg1200Trp) - - Unknown - pathogenic g.2130366C>T g.2080365C>T - - TSC2_000056 - PubMed: van Eeghen, 2012 - - Germline - - +BpmI, MspI- - - DNA SEQ Blood - TSC - PubMed: van Eeghen, 2012 4 different patients; 3/4 have other epilepsy types without infantile spasms, 1/4 does not have infantile spasms or other epilepsy types; all 4 patients have other TS features (not described as paper is focused on epilepsy) ? - - - - - - - 4 Rosemary Ekong
+/. 30 c.3598C>T r.(?) p.(Arg1200Trp) - - Unknown - pathogenic g.2130366C>T g.2080365C>T - - TSC2_000056 found with TSC2 intronic variant c.2545+26G>A PubMed: Hoogeveen-Westerveld, 2011 - - Germline - - +BpmI, MspI- - - DNA SEQ Blood - TSC - PubMed: Hoogeveen-Westerveld, 2011 patient has pathogenic TSC2 missense c.3598C>T and TSC2 intronic variant c.2545+26G>A ? - - - - - - - 1 Rosemary Ekong
+/. 30 c.3598C>T r.(?) p.(Arg1200Trp) - - Unknown - pathogenic g.2130366C>T g.2080365C>T - - TSC2_000056 - PubMed: Au, 1998, PubMed: Au, 2007, PubMed: Hoogeveen-Westerveld, 2013 - - Germline - - +BpmI, MspI- - - DNA SEQ Blood - TSC HOU11/HOU11-04 PubMed: Au, 1998, PubMed: Au, 2007, PubMed: Hoogeveen-Westerveld, 2013 7 individuals in extended 2 generation family tested and all have TSC2 missense variant c.3598C>T; index reported here does not have TSC2 missense variant c.3434C>T, but one of the affected family members does have TSC2 missense variant c.3434C>T; African-American M - United States African-American - - - - 1 Rosemary Ekong
?/. 30 c.3598C>T r.(?) p.(Arg1200Trp) - - Unknown - VUS g.2130366C>T g.2080365C>T - - TSC2_000056 reported as variant of unknown functional significance unpublished - - Germline - - +BpmI, MspI- - - DNA SEQ Blood - TSC - unpublished familail case; sibling and one parent affected; affected parent has seizures and white patches; unclear if both tested; referred for diagnostic TS testing M - - - - - - - 1 Rosemary Ekong
+/. 30 c.3598C>T r.(?) p.(Arg1200Trp) - - Unknown - pathogenic g.2130366C>T g.2080365C>T - - TSC2_000056 - unpublished - - Germline - - +BpmI, MspI- - - DNA SEQ, MLPA Blood - TSC - unpublished patient diagnosed with clinical TS; parents not tested M - - - - - - - 1 Rosemary Ekong
+/. 30 c.3598C>T r.(?) p.(Arg1200Trp) - - Unknown - pathogenic g.2130366C>T g.2080365C>T - - TSC2_000056 - unpublished - - Germline - - +BpmI, MspI- - - DNA SEQ, MLPA Blood - TSC - unpublished FH of HM in 4 generations including child of index; mild features in affecteds; parents or other family members have not been tested F - - - - - - - 1 Rosemary Ekong
+/. 30 c.3598C>T r.(?) p.(Arg1200Trp) - - Unknown - pathogenic g.2130366C>T g.2080365C>T - - TSC2_000056 reported as disease-associated variant; found with TSC2 missense variants c.4225C>T; entire TSC1 and TSC2 genes sequenced; TSC MLPA done unpublished - - Germline - - +BpmI, MspI- - - DNA SEQ, MLPA Blood - TSC - unpublished TS affected with two TSC2 missense variants c.3598C>T and c.4225C>T M - - - - - - - 1 Rosemary Ekong
+/. 30 c.3598C>T r.(?) p.(Arg1200Trp) - - Unknown - pathogenic g.2130366C>T g.2080365C>T - - TSC2_000056 entire TSC1 and TSC2 genes sequenced; TSC MLPA done unpublished - - De novo - - +BpmI, MspI- - - DNA SEQ Blood - TSC - unpublished 1 affected in 1 generation; parents tested and variant not found ? - - - - - - - 1 Rosemary Ekong
+/. 30 c.3598C>T r.(?) p.(Arg1200Trp) - - Unknown - pathogenic g.2130366C>T g.2080365C>T - - TSC2_000056 - unpublished - - De novo - - +BpmI, MspI- - - DNA DHPLC, SEQ Amniocytes - TSC - unpublished prenatally diagnosed cardiac rhabdomyoma in index; both parents and a sibling tested negative ? - - - - - - - 1 Rosemary Ekong
+/. 30 c.3598C>T r.(?) p.(Arg1200Trp) - - Paternal (confirmed) - pathogenic g.2130366C>T g.2080365C>T - - TSC2_000056 - unpublished - - Germline - - +BpmI, MspI- - - DNA DHPLC, SEQ Blood - TSC - unpublished variant is present in one parent, but absent in the other parent and a relative ? - - - - - - - 2 Rosemary Ekong
+/. 30 c.3598C>T r.(?) p.(Arg1200Trp) - - Maternal (confirmed) - pathogenic g.2130366C>T g.2080365C>T - - TSC2_000056 - unpublished - - Germline - - +BpmI, MspI- - - DNA DHPLC, SEQ Blood - TSC - unpublished variant is present in 4 other family members - an affected sibling, another sibling and one child of this 2nd sibling and one of the parents; the other parent and two relatives tested negative M - - - - - - - 5 Rosemary Ekong
+/. 30 c.3598C>T r.(?) p.(Arg1200Trp) - - Unknown - pathogenic g.2130366C>T g.2080365C>T - - TSC2_000056 - unpublished - - Germline - - +BpmI, MspI- - - DNA DHPLC, SEQ Blood - TSC - unpublished No other family member tested M - - - - - - - 1 Rosemary Ekong
+/. 30 c.3598C>T r.(?) p.(Arg1200Trp) - - Unknown - pathogenic g.2130366C>T g.2080365C>T - - TSC2_000056 - unpublished - - Germline - - +BpmI, MspI- - - DNA SEQ Blood - TSC - unpublished patient with clinical diagnosis of TS; one parent has dental pits and white spot; one sibling has white spots; none of the family members were tested ? - - - - - - - 1 Rosemary Ekong
+/. 30 c.3598C>T r.(?) p.(Arg1200Trp) - - Unknown - pathogenic g.2130366C>T g.2080365C>T - - TSC2_000056 found with TSC2 missense c.4066G>T; reported that variant absent in the 105 ethnicity-matched healthy Chinese subjects (with no history of TSC) used as controls PubMed: Yu, 2017 - - Germline - - - - - DNA SEQ Blood - TSC 11 PubMed: Yu, 2017 15mth old patient with onset of seizures at 8mths; has two TSC2 missense variants (TSC2 c.3598C>T and TSC2 c.4066G>T); inheritance of variant not determined as family members not available for testing F - China - - - - - 1 Rosemary Ekong
+/. 30 c.3598C>T r.(?) p.(Arg1200Trp) - - Unknown - pathogenic g.2130366C>T g.2080365C>T - - TSC2_000056 - PubMed: Pannu, 2017 - - Germline - - - - - DNA SEQ Blood - TSC - PubMed: Pannu, 2017 38 year old asymptomatic mother (index) diagnosed with TSC and multifocal micronodular pneumocyte hyperplasia (MMPH); her baby confirmed as TS affected; no clinical signs of TSC in other family members; 2 out of 4 siblings of index tested negative for variant; CT chest negative for typical LAM lesions; brain MRI consistent with diagnosis of TSC F - (United States) white - - - - 2 Rosemary Ekong
+/. 30 c.3598C>T r.(?) p.(Arg1200Trp) - - Unknown - pathogenic g.2130366C>T g.2080365C>T - - TSC2_000056 - unpublished - rs45438205 Germline - - - - - DNA SEQ Blood - TSC - unpublished - ? - - - - - - - 1 Rosemary Ekong
+/. 30 c.3598C>T r.(?) p.(Arg1200Trp) - - Unknown - pathogenic g.2130366C>T g.2080365C>T - - TSC2_000056 - PubMed: Overwater 2016 - - Germline - - - - - DNA SEQ Blood - TSC - PubMed: Overwater 2016 - ? - - - - - - - 2 Rosemary Ekong
+/. 30 c.3598C>T r.(?) p.(Arg1200Trp) - - Paternal (confirmed) ACMG pathogenic (dominant) g.2130366C>T g.2080365C>T - - TSC2_000056 - PubMed: Ding, 2020 - - Germline - - - - - DNA SEQ - - TSC 50 PubMed: Ding, 2020 - F - China - - - - - 1 Yifeng Ding
+/. 30 c.3598C>T r.(?) p.(Arg1200Trp) - - Unknown ACMG pathogenic (dominant) g.2130366C>T g.2080365C>T exon 29 - TSC2_000056 - PubMed: Ogorek, 2020 - - Germline ? - - - - DNA SEQ-NG-I Blood Targeted massive parallel sequencing, mean target coverage of 327× to 1614× (median 716×) TSC 01-052 PubMed: Ogorek, 2020 infant; no history of TSC in the family; patient had first subclinical/clinical seizures at day 482 during the study M ? - - - - - - 1 Rosemary Ekong
+/. 30 c.3598C>T r.(?) p.(Arg1200Trp) - - Unknown ACMG pathogenic (dominant) g.2130366C>T g.2080365C>T - - TSC2_000056 - PubMed: Ye, 2022 - - Germline - - - - - DNA SEQ-NG Blood - TSC - PubMed: Ye, 2022 - M - - - - - - - 1 Zimeng Ye
+/. 30 c.3598C>T r.(?) p.(Arg1200Trp) - - Maternal (confirmed) ACMG pathogenic (dominant) g.2130366C>T g.2080365C>T - - TSC2_000056 - PubMed: Milon 2024; PubMed: Milon 2024 - - Germline - - - - - DNA SEQ, SEQ-NG-IT Amniocytes - TSC - PubMed: Milon 2024; PubMed: Milon 2024 no family history of TSC; prenatally diagnosed cardiac rhabdomyoma (single), cortical tubers (≥2, multiple) and subependymal nodules (≥2, multiple); one parent has variant in mosaic 6.7% and has 2 achromic macules, other parent negative; termination of pregnancy at 33+2 - - - - - - - - 1 Sarah Prestwich
+/. 30 c.3598C>T r.? p.(Arg1200Trp) - - Unknown - pathogenic (dominant) g.2130366C>T g.2080365C>T - - TSC2_000056 somatic variant; found with TSC1 missense c.236A>G and TSC2 splice variant c.225+1G>T PubMed: Tao 2025 - - Somatic - - - - - DNA SEQ-NG Kidney tumour DNA from paraffin block, customized 1021-gene cancer panel used on the Geneplus-2000 platform, 500X average sequencing coverage RCC Case 3 PubMed: Tao 2025 patient with renal cell carcinoma and both hemangioblastoma-like and fibromyomatous stroma-like regions; all variants were found in both regions of the tumour F - China - - - - - 1 Rosemary Ekong
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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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