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     

Segregation     

Frequency     

Re-site     

VIP     

Methylation     

Template     

Technique     

Tissue     

Remarks     

Disease     

ID_report     

Reference     

Remarks     

Gender     

Consanguinity     

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Population     

Age at death     

VIP     

Data_av     

Treatment     

Panel size     

Owner     
+/. 17 c.2111_2112del r.(?) p.(Tyr704*) - - Unknown - pathogenic (dominant) g.135779135_135779136del g.132903748_132903749del 2332delAT - TSC1_000136 2bp deletion of AT PubMed: van Slegtenhorst, 1997, PubMed: Young, 1998; PubMed: Jeganathan, 2002 - - Unknown - - BspCNI+, DdeI+ - - DNA SSCA Blood - TSC - PubMed: van Slegtenhorst, 1997, PubMed: Young, 1998; PubMed: Jeganathan, 2002 sporadic case ? - - - - - - - 1 Rosemary Ekong
+/. 17 c.2111_2112del r.(?) p.(Tyr704*) - - Unknown - pathogenic (dominant) g.135779135_135779136del g.132903748_132903749del 2332delAT - TSC1_000136 2bp deletion of AT PubMed: van Slegtenhorst, 1997, PubMed: Ali, 1998 - - Unknown - 1/3 individuals tested have the variant BspCNI+, DdeI+ - - DNA HD, SSCA Blood - TSC - PubMed: van Slegtenhorst, 1997, PubMed: Ali, 1998 sporadic case; TSC1-linked by linkage data; variant not seen in parents ? - - - - - - - 1 Rosemary Ekong
+/. 17 c.2111_2112del r.(?) p.(Tyr704*) - - Unknown - pathogenic (dominant) g.135779135_135779136del g.132903748_132903749del c.2111_2112delAT, p.Y703fsX1 - TSC1_000136 2bp deletion of AT; found with TSC2 c.5017G>C PubMed: Ali, 2005 - - Germline - 2/2 individuals tested have the variant BspCNI+, DdeI+ - - DNA SSCA Blood - TSC - PubMed: Ali, 2005 familial case; patient has TSC1 nonsense c.2111_2112del and TSC2 missense c.5017G>C ? - India - - - - - 2 Rosemary Ekong
+/. 17 c.2111_2112del r.(?) p.(Tyr704*) - - Unknown - pathogenic (dominant) g.135779135_135779136del g.132903748_132903749del - - TSC1_000136 2bp deletion of AT; found in blinded analysis PubMed: Dabora, 1998 - - Unknown - - BspCNI+, DdeI+ - - DNA DGGE Blood - TSC - PubMed: Dabora, 1998 patient has TSC1 c.965T>C andTSC1 c.1335A>G ? - - - - - - - 1 Rosemary Ekong
+/. 17 c.2111_2112del r.(?) p.(Tyr704*) - - Unknown - pathogenic (dominant) g.135779135_135779136del g.132903748_132903749del c.2111_2112delAT - TSC1_000136 2bp deletion of AT PubMed: Au, 2007 - - Unknown - - BspCNI+, DdeI+ - - DNA SEQ Blood - TSC - PubMed: Au, 2007 another sporadic case ? - - - - - - - 1 Rosemary Ekong
+/. 17 c.2111_2112del r.(?) p.(Tyr704*) - - Unknown - pathogenic (dominant) g.135779135_135779136del g.132903748_132903749del c.2111_2112delAT - TSC1_000136 2bp deletion of AT PubMed: Au, 2007 - - Unknown - - BspCNI+, DdeI+ - - DNA SEQ Blood - TSC - PubMed: Au, 2007 sporadic case ? - - - - - - - 1 Rosemary Ekong
+/. 17 c.2111_2112del r.(?) p.(Tyr704*) - - Unknown - pathogenic (dominant) g.135779135_135779136del g.132903748_132903749del - - TSC1_000136 2bp deletion of AT unpublished - - Germline - 3/3 individuals tested have the variant BspCNI+, DdeI+ - - DNA SEQ Blood - TSC - unpublished 3 affected individuals in 2 generations tested and all 3 patients have the variant; variant cosegregates with TS in family ? - - - - - - - 3 Rosemary Ekong
+/. 17 c.2111_2112del r.(?) p.(Tyr704*) - - Unknown - pathogenic (dominant) g.135779135_135779136del g.132903748_132903749del 704fs - TSC1_000136 2bp Deletion of AT; reported as a frameshift; entire TSC1 and TSC2 genes sequenced; deletion test not done unpublished - - Unknown - - BspCNI+, DdeI+ - - DNA SEQ Blood - TSC - unpublished TS affected M - - - - - - - 1 Rosemary Ekong
+/. 17 c.2111_2112del r.(?) p.(Tyr704*) - - Unknown - pathogenic (dominant) g.135779135_135779136del g.132903748_132903749del - - TSC1_000136 2bp Deletion of AT unpublished - - Unknown - - BspCNI+, DdeI+ - - DNA DHPLC, SEQ Blood - TSC - unpublished No other family member tested F - - - - - - - 1 Rosemary Ekong
+/. 17 c.2111_2112del r.(?) p.(Tyr704*) - - Unknown - pathogenic (dominant) g.135779135_135779136del g.132903748_132903749del - - TSC1_000136 2bp Deletion of AT unpublished - - Unknown - 1/2 individuals tested have the variant BspCNI+, DdeI+ - - DNA DHPLC, SEQ Blood - TSC - unpublished affected parent and grandparent of the proband were unavailable for testing; a child of the proband tested negative F - - - - - - - 1 Rosemary Ekong
+/. 17 c.2111_2112del r.(?) p.(Tyr704*) - - Unknown - pathogenic (dominant) g.135779135_135779136del g.132903748_132903749del - - TSC1_000136 2bp deletion of AT unpublished - - Unknown - - BspCNI+, DdeI+ - - DNA MLPA, SEQ-NG-I Blood - TSC - unpublished parents not tested F - - - - - - - 1 Rosemary Ekong
+/. 17 c.2111_2112del r.(?) p.(Tyr704*) - - Unknown - pathogenic (dominant) g.135779135_135779136del g.132903748_132903749del c.2111_2112delAT, p.Tyr704Ter - TSC1_000136 2bp deletion of AT; variant confirmed by Sanger sequencing PubMed: Papadopoulou, 2018 - - Unknown - - BspCNI+, DdeI+ - - DNA SEQ, SEQ-NG-R Blood - TSC - PubMed: Papadopoulou, 2018 sporadic case; patient diagnosed with TSC at 2yrs, last reviewed at 9yrs; has refractory seizures F - - - - - - - 1 Rosemary Ekong
+/+ 17 c.2111_2112del r.(?) p.(Tyr704*) - - Unknown - pathogenic (dominant) g.135779135_135779136del g.132903748_132903749del - - TSC1_000136 2bp deletion of AT - - - SUMMARY record - - BspCNI+, DdeI+ - - - - - - - - - - - - - - - - - - - -
+/. 17 c.2111_2112del r.(?) p.(Tyr704*) - - Unknown - pathogenic (dominant) g.135779135_135779136del g.132903748_132903749del 2111_2112delAT, g.135779134_135779135del (hg19), g.2072254_2072255del (hg38) - TSC1_000136 - PubMed: He, 2020 - - Germline/De novo (untested) - - - - - DNA SEQ-NG - - TSC1 09 PubMed: He 2020 - F - China - - - - - 1 Lang He
+/. 17 c.2111_2112del r.(?) p.(Tyr704*) - - Unknown - pathogenic (dominant) g.135779135_135779136del g.132903748_132903749del c.2111_2112delAT - TSC1_000136 2bp Deletion of AT; NGS read depth >500x PubMed: Tyburczy, 2015; PubMed: Giannikou, 2019 - - De novo - 1/3 individuals tested have the variant BspCNI+, DdeI+ - - DNA SEQ-NG-I, PE Blood, normal skin SNaPshot TSC - PubMed: Tyburczy, 2015; PubMed: Giannikou, 2019 4 year old TSC patient with NMI status (previous Sanger SEQ and TSC2 MLPA negative); reported as mosaic (4.7% MAF); sporadic case with no FH of TS; both parents tested and variant not found M - - - - - - - 1 Rosemary Ekong
+/. 17 c.2111_2112del r.(?) p.(Tyr704*) - - Unknown - pathogenic (dominant) g.135779134_135779135del - - - TSC1_000136 2bp deletion of AT unpublished - - Germline ? - - - - DNA DHPLC, SEQ Blood Diagnostic testing TSC - unpublished No other family member tested F ? - - - - - - 1 Rosemary Ekong
+/. 17 c.2111_2112del r.(?) p.(Tyr704*) - - Unknown - pathogenic (dominant) g.135779134_135779135del g.132903747_132903748del c.2111_2112delAT - TSC1_000136 2bp deletion of AT unpublished - - Germline ? 1/3 individuals tested have the variant - - - DNA SEQ-NG-I, SEQ Blood Illumina TruSight Cancer panel used TSC - unpublished clinical diagnosis of TSC; child and sibling of index tested; variant absent in both; parents not tested M ? - - - - - - 1 Rosemary Ekong
+/. 17 c.2111_2112del r.(?) p.(Tyr704*) - - Maternal (confirmed) ACMG pathogenic (dominant) g.135779135_135779136del g.132903748_132903749del - - TSC1_000136 - PubMed: Ogorek, 2020 - - Germline ? - - - - DNA SEQ-NG-I Blood Targeted massive parallel sequencing, mean target coverage of 327× to 1614× (median 716×) TSC 01-030 PubMed: Ogorek, 2020 infant with TSC; one parent also has TSC; patient had first subclinical/clinical seizures at day 162 during the study M ? - - - - - - 2 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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