Full data view for gene TSC1

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_000368.4 transcript reference sequence.

18 entries on 1 page. Showing entries 1 - 18.
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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     

Origin     

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Frequency     

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Methylation     

Template     

Technique     

Tissue     

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Disease     

ID_report     

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Consanguinity     

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Owner     
-/. - c.2392-35T>C r.(=) p.(=) - - Unknown - benign g.135777121A>G g.132901734A>G TSC1(NM_000368.4):c.2392-35T>C - TSC1_000158 VKGL data sharing initiative Nederland - - - CLASSIFICATION record - - - - - - - - - - - - - - - - - - - - - - -
-/. 18i c.2392-35T>C r.spl p.(=) - - Unknown - benign g.135777121A>G g.132901734A>G - - TSC1_000158 reported as a polymorphism; found with TSC2 frameshift c.2765dup PubMed: Au 2007 - - Unknown - - BseRI+ - - DNA SEQ Blood - TSC - PubMed: Au 2007 patient has TSC2 frameshift c.2765dup and TSC1 c.2392-35T>C ? - - - - - - - 1 Rosemary Ekong
-/. 18i c.2392-35T>C r.spl p.(=) - - Unknown - benign g.135777121A>G g.132901734A>G - - TSC1_000158 reported as a polymorphism; found with TSC2 nonsense c.3685C>T PubMed: Au 2007 - - Unknown - - BseRI+ - - DNA SEQ Blood - TSC - PubMed: Au 2007 patient has TSC2 nonsense c.3685C>T and TSC1 variant c.2392-35T>C ? - - - - - - - 1 Rosemary Ekong
-/. 18i c.2392-35T>C r.spl p.(=) - - Unknown - benign g.135777121A>G g.132901734A>G - - TSC1_000158 reported as a polymorphism; found with TSC1 c.989_990del PubMed: Au 2007 - - Unknown - - BseRI+ - - DNA SEQ Blood - TSC - PubMed: Au 2007 patient has TSC1 c.989_990del and TSC1 c.2392-35T>C (described as a non-pathogenic splice variant) ? - - - - - - - 1 Rosemary Ekong
-/. 18i c.2392-35T>C r.spl p.(=) - - Unknown - benign g.135777121A>G g.132901734A>G - - TSC1_000158 - PubMed: Hung, 2006 - - Unknown - 9/84 individuals tested have the variant BseRI+ - - DNA HD Blood - TSC - PubMed: Hung, 2006 tested in 84 TSC patients and 100 healthy Taiwanese volunteers; frequency refers to the number among TSC patients (9/84) ? - Taiwan - - - - - 9 Rosemary Ekong
-/. 18i c.2392-35T>C r.spl p.(=) - - Unknown - benign g.135777121A>G g.132901734A>G 2613-35T>C - TSC1_000158 - PubMed: Niida, 1999 - - Unknown - 21/112 individuals tested have the variant BseRI+ - - DNA SSCA Blood - TSC - PubMed: Niida, 1999 frequency = 21/112 patient samples ? - - - - - - - 21 Rosemary Ekong
-/. 18i c.2392-35T>C r.spl p.(=) - - Unknown - benign g.135777121A>G g.132901734A>G - - TSC1_000158 reported as a polymorphism; found with TSC2 c.5228G>A PubMed: Au 2007 - - Unknown - - BseRI+ - - DNA SEQ Blood - TSC - PubMed: Au 2007 patient has TSC2 c.5228G>A and TSC1 c.2392-35T>C ? - - - - - - - 1 Rosemary Ekong
-/. 18i c.2392-35T>C r.spl p.(=) - - Unknown - benign g.135777121A>G g.132901734A>G 2613-35T>C - TSC1_000158 variant found in blinded analysis; described as a polymorphism PubMed: Dabora, 1998 - - Unknown - - BseRI+ - - DNA DGGE Blood - TSC - PubMed: Dabora, 1998 patient has TSC1 missense c.2425G>C ? - - - - - - - 1 Rosemary Ekong
-/. 18i c.2392-35T>C r.spl p.(=) - - Unknown - benign g.135777121A>G g.132901734A>G - - TSC1_000158 reported as a polymorphism PubMed: Au 2007 - - Unknown - - BseRI+ - - DNA SEQ Blood - TSC - PubMed: Au 2007 - ? - - - - - - - 1 Rosemary Ekong
+/. 18i c.2392-35T>C r.2392_2433del p.(Thr798_Arg811del) Coiled-coil domain - Unknown - pathogenic (dominant) g.135777121A>G g.132901734A>G IVS18-35T>C - TSC1_000158 in-frame deletion of 42bp in exon 19, but sequence not specified PubMed: Mayer, 1999 - - Unknown - - BseRI+ - - RNA PTT Blood - TSC - PubMed: Mayer, 1999 sporadic case ? - - - - - - - 1 Rosemary Ekong
-/. 18i c.2392-35T>C r.spl p.(=) - - Unknown - benign g.135777121A>G g.132901734A>G - - TSC1_000158 found with known TSC1 variants c.965T>C and c.1335A>G; unpublished - - Unknown - - BseRI+ - - DNA DHPLC Blood - TSC - unpublished no definite mutation found; ? - - - - - - - 1 Rosemary Ekong
-/. 18i c.2392-35T>C r.spl p.(=) - - Unknown - benign g.135777121A>G g.132901734A>G - - TSC1_000158 seen with known TSC1 (c.965T>C, c.1335A>G) and TSC2 variants (c.482-3C>T, c.1578C>T, c.1600-39C>T, c.5161-10A>C, c.5260-25C>G) unpublished - - Unknown - - BseRI+ - - DNA DHPLC Blood - TSC - unpublished no definite mutation found but 7 other polymorphisms seen; ? - - - - - - - 1 Rosemary Ekong
-/. 18i c.2392-35T>C r.spl p.(=) - - Unknown - benign g.135777121A>G g.132901734A>G I-18 - TSC1_000158 reported as polymorphism unpublished - rs11243931 Unknown - - BseRI+ - - DNA SEQ Blood - TSC - unpublished no other variant found in the proband with this intronic variant; parents not tested for intronic variant ? - - - - - - - 1 Rosemary Ekong
-/. 18i c.2392-35T>C r.spl p.(=) - - Unknown - benign g.135777121A>G g.132901734A>G 2613-35 - TSC1_000158 variant found with TSC1 missense c.2425G>C in an unaffected parent unpublished - rs11243931 Unknown - 1/2 individuals tested have the variant BseRI+ - - DNA HD, SEQ Blood - Healthy/Control - unpublished this unaffected parent has TSC1 intronic variant c.2392-35T>C and TSC1 missense c.2425G>C; the affected child inherited TSC1 missense c.2425G>C but not TSC1 intronic variant c.2392-35T>C; affected child also has TSC2 in-frame deletion c.4912_4914del that is not present in this unaffected parent M - - - - - - - 1 Rosemary Ekong
-/. 18i c.2392-35T>C r.spl p.(=) - - Unknown - benign g.135777121A>G g.132901734A>G - - TSC1_000158 found with TSC1 variants (c.965T>C and c.1439-37C>T) and TSC2 c.2713C>T PubMed: Avgeris, 2017 - - Unknown - 1/4 individuals tested have the variant BseRI+ - - DNA SEQ Blood - TSC - PubMed: Avgeris, 2017 patient has TSC1 variants (c.965T>C, c.1439-37C>T and c.2392-35T>C) and TSC2 c.2713C>T; both parents and another family member tested and TSC2 c.2713C>T was absent; inheritance of other variants not indicated; reported that paternity testing not performed M - Greece Albanian - - - - 1 Rosemary Ekong
-/. 18i c.2392-35T>C r.spl p.(=) - - Unknown - benign g.135777121A>G g.132901734A>G - - TSC1_000158 found with TSC1 variants c.965T>C, c.1142-33A>G, c.1335A>G, c.1439-37C>T and TSC2 c.5313G>C PubMed: Avgeris, 2017 - - Unknown - - BseRI+ - - DNA SEQ Blood - TSC - PubMed: Avgeris, 2017 patient has TSC2 silent variant c.5313G>C and TSC1 variants (c.965T>C, c.1142-33A>G, c.1335A>G, c.1439-37C>T, c.2392-35T>C); reported that no definite disease-causing variant found, no other family member tested F - Greece Greek - - - - 1 Rosemary Ekong
-/- 18i c.2392-35T>C r.2392_2433del p.(Thr798_Arg811del) Coiled-coil domain affects splicing Unknown - benign g.135777121A>G g.132901734A>G - - TSC1_000158 in-frame deletion of 42bp from exon 19 seen in cDNA - - rs11243931 SUMMARY record - 46869/306882 alleles, 3735 homozygotes - - - - - - - - - - - - - - - - - - - - -
-/. 18i c.2392-35T>C r.(=) p.(=) - - Unknown ACMG benign g.135777121A>G g.132901734A>G - - TSC1_000158 found with TSC1 c.2332del - - - Germline - - - - - DNA SEQ Blood Sanger Sequencing TSC - - - F ? Brazil - - - - - 1 Luiz Gustavo Dufner de Almeida
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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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