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.

31 entries on 1 page. Showing entries 1 - 31.
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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     

Remarks     

Disease     

ID_report     

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Consanguinity     

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Owner     
+/. 10 c.989dup r.(?) p.(Ser331Glufs*10) Tuberin binding domain - Unknown - pathogenic (dominant) g.135786880dup g.132911493dup 1210insT - TSC1_000067 1bp duplication of T unpublished - - Unknown - - SmlI+, AlwNI- - - DNA DHPLC Blood - TSC - unpublished 3rd case reported; patient has TSC1 c.965T>C F - - - - - - - 1 Rosemary Ekong
+/. 10 c.989dup r.(?) p.(Ser331Glufs*10) Tuberin binding domain - Unknown - pathogenic (dominant) g.135786880dup g.132911493dup 1210_1211ins/dupT - TSC1_000067 1bp duplication of T unpublished - - Unknown - - SmlI+, AlwNI- - - DNA DHPLC Blood - TSC - unpublished patient has TSC1 variants (c.965T>C and c.1335A>G) and TSC2 variants (c.5202T>C, c.5161-10A>C and c.5397G>C) ? - - - - - - - 1 Rosemary Ekong
+/. 10 c.989dup r.(?) p.(Ser331Glufs*10) Tuberin binding domain - Unknown - pathogenic (dominant) g.135786880dup g.132911493dup 1210insT - TSC1_000067 1bp duplication of T unpublished - - Unknown - - SmlI+, AlwNI- - - DNA DHPLC Blood - TSC - unpublished different patient ? - - - - - - - 1 Rosemary Ekong
+/. 10 c.989dup r.(?) p.(Ser331Glufs*10) Tuberin binding domain - Unknown - pathogenic (dominant) g.135786880dup g.132911493dup 1210insT - TSC1_000067 1bp duplication of T PubMed: vanSlegtenhorst, 1999; PubMed: Sancak, 2005 - - Germline - 2/2 individuals tested have the variant SmlI+, AlwNI- - - DNA SSCA Blood - TSC - PubMed: vanSlegtenhorst, 1999; PubMed: Sancak, 2005 diagnosed with definite TSC; same patient reported in both papers ? - - - - - - - 2 Rosemary Ekong
+/. 10 c.989dup r.(?) p.(Ser331Glufs*10) Tuberin binding domain - Unknown - pathogenic (dominant) g.135786880dup g.132911493dup 1210insT, 330L-FS-X at 340 - TSC1_000067 1bp duplication of T originally in Kwaitkowski database - - Unknown - 2/2 individuals tested have the variant SmlI+, AlwNI- - - DNA SEQ Blood - TSC - originally in Kwaitkowski database variant seen 2 times ? - - - - - - - 2 Rosemary Ekong
+/. 10 c.989dup r.(?) p.(Ser331Glufs*10) Tuberin binding domain - Unknown - pathogenic (dominant) g.135786880dup g.132911493dup 1210insT, 311SerFS-340X - TSC1_000067 1bp duplication of T PubMed: Zhang, 1999 - - Germline - - SmlI+, AlwNI- - - DNA SSCA Blood - TSC - PubMed: Zhang, 1999 familial case ? - Japan - - - - - 1 Rosemary Ekong
+/. 10 c.989dup r.(?) p.(Ser331Glufs*10) Tuberin binding domain - Unknown - pathogenic (dominant) g.135786880dup g.132911493dup 1210insT - TSC1_000067 1bp duplication of T PubMed: Sancak, 2005 - - Unknown - - SmlI+, AlwNI- - - DNA SEQ Blood - TSC - PubMed: Sancak, 2005 different patient; sporadic case; diagnosed with definite TSC ? - - - - - - - 1 Rosemary Ekong
+/. 10 c.989dup r.(?) p.(Ser331Glufs*10) Tuberin binding domain - Unknown - pathogenic (dominant) g.135786880dup g.132911493dup 1210insT - TSC1_000067 1bp duplication of T PubMed: Sancak, 2005 - - Unknown - - SmlI+, AlwNI- - - DNA SEQ Blood - TSC - PubMed: Sancak, 2005 different patient; diagnosed with definite TSC ? - - - - - - - 1 Rosemary Ekong
+/. 10 c.989dup r.(?) p.(Ser331Glufs*10) Tuberin binding domain - Unknown - pathogenic (dominant) g.135786880dup g.132911493dup - - TSC1_000067 1bp duplication of T unpublished - - De novo - 1/3 individuals tested have the variant SmlI+, AlwNI- - - DNA SEQ Blood - TSC - unpublished 1 affected individual in 1 generation; parents tested and variant not found ? - - - - - - - 1 Rosemary Ekong
+/. 10 c.989dup r.(?) p.(Ser331Glufs*10) Tuberin binding domain - Unknown - pathogenic (dominant) g.135786880dup g.132911493dup - - TSC1_000067 1bp duplication of T unpublished - - Germline - 3/5 individuals tested have the variant SmlI+, AlwNI- - - DNA SEQ Blood - TSC - unpublished 3 affected individuals in 2 generations; variant is de novo in the proband as parents of proband tested and variant not found ? - - - - - - - 3 Rosemary Ekong
+/. 10 c.989dup r.(?) p.(Ser331Glufs*10) Tuberin binding domain - Unknown - pathogenic (dominant) g.135786880dup g.132911493dup - - TSC1_000067 1bp duplication of T; found with TSC1 intronic variant c.1998-66A>G unpublished - - De novo - 1/3 individuals tested have the variant SmlI+, AlwNI- - - DNA SEQ Blood - TSC - unpublished 1 affected individual in 1 generation; proband a de novo TSC1 frameshift c.989dup which is absent in both parents; proband also has the TSC1 intronic variant c.1998-66A>G which is present in one healthy parent and a sibling ? - - - - - - - 1 Rosemary Ekong
+/. 10 c.989dup r.(?) p.(Ser331Glufs*10) Tuberin binding domain - Unknown - pathogenic (dominant) g.135786880dup g.132911493dup - - TSC1_000067 1bp duplication of T unpublished - - De novo - 1/3 individuals tested have the variant SmlI+, AlwNI- - - DNA SEQ Blood - TSC - unpublished 1 affected individual in 1 generation; parents tested and variant not found ? - - - - - - - 1 Rosemary Ekong
+/. 10 c.989dup r.(?) p.(Ser331Glufs*10) Tuberin binding domain - Unknown - pathogenic (dominant) g.135786880dup g.132911493dup - - TSC1_000067 1bp duplication of T unpublished - - De novo - 1/3 individuals tested have the variant SmlI+, AlwNI- - - DNA SEQ Blood - TSC - unpublished 1 affected individual in 1 generation; parents tested and variant not found ? - - - - - - - 1 Rosemary Ekong
+/. 10 c.989dup r.(?) p.(Ser331Glufs*10) Tuberin binding domain - Unknown - pathogenic (dominant) g.135786880dup g.132911493dup c.989dupT - TSC1_000067 1bp duplication of T; found with TSC2 missense c.3281C>T unpublished - - Unknown - - SmlI+, AlwNI- - - DNA SEQ Blood - TSC - unpublished patient has TSC2 missense c.3281C>T and TSC1 frameshift c.989dup ? - - - - - - - 1 Rosemary Ekong
+/. 10 c.989dup r.(?) p.(Ser331Glufs*10) Tuberin binding domain - Unknown - pathogenic (dominant) g.135786880dup g.132911493dup c.989dupT - TSC1_000067 1bp duplication of T; complete screen; MLPA kits P124 (TSC1), P046B2 (TSC2) used unpublished - - De novo - 1/3 individuals tested have the variant SmlI+, AlwNI- - - DNA MLPA, SEQ Blood - TSC - unpublished both parents tested and variant not found; referred for diagnostic TS testing F - - - - - - - 1 Rosemary Ekong
+/. 10 c.989dup r.(?) p.(Ser331Glufs*10) Tuberin binding domain - Unknown - pathogenic (dominant) g.135786880dup g.132911493dup c.989dupT - TSC1_000067 1bp duplication of T; complete screen; MLPA kits P124 (TSC1), P046B2 (TSC2) used unpublished - - Unknown - 1/3 individuals tested have the variant SmlI+, AlwNI- - - DNA MLPA, SEQ Blood - TSC - unpublished both parents tested and variant not found; one parent with facial angiofibroma possibly mosaic M - - - - - - - 1 Rosemary Ekong
+/. 10 c.989dup r.(?) p.(Ser331Glufs*10) Tuberin binding domain - Unknown - pathogenic (dominant) g.135786880dup g.132911493dup c.989_990dupT, 330dupfs - TSC1_000067 1bp duplication of T; found with with TSC2 silent variant c.990G>A; reported as disease-associated mutation; entire TSC1 and TSC2 genes sequenced; TSC1/TSC2 MLPA done unpublished - - De novo - 1/3 individuals tested have the variant SmlI+, AlwNI- - - DNA MLPA, SEQ Blood - TSC - unpublished TS affected with TSC1 frameshift c.989dup and TSC2 silent variant c.990G>A; TSC2 c.990G>A inherited from one of the unaffected parents; both unaffected parents tested and TSC1 c.989dup absent in both M - - - - - - - 1 Rosemary Ekong
+?/. 10 c.989dup r.(?) p.(Ser331Glufs*10) Tuberin binding domain - Unknown - likely pathogenic (dominant) g.135786880dup g.132911493dup NM_000368.4:c.989_990insT - TSC1_000067 1bp duplication of T unpublished - - Unknown - - SmlI+, AlwNI- - - DNA SEQ-NG-I Blood - TSC - unpublished no information M - - Asian - - - - 1 Rosemary Ekong
+/. 10 c.989dup r.(?) p.(Ser331Glufs*10) Tuberin binding domain - Unknown - pathogenic (dominant) g.135786880dup g.132911493dup c.989dupT - TSC1_000067 1bp duplication of T PubMed: Kwiatkowski, 2015 - - Unknown - - SmlI+, AlwNI- - - DNA SEQ Blood - TSC - PubMed: Kwiatkowski, 2015 patient has subependymal giant cell astrocytomas associated with tuberous sclerosis complex ? - - - - - - - 1 Rosemary Ekong
+/. 10 c.989dup r.(?) p.(Ser331Glufs*10) Tuberin binding domain - Maternal (confirmed) - pathogenic (dominant) g.135786880dup g.132911493dup - - TSC1_000067 1bp duplication of T unpublished - - Germline - 3/5 individuals tested have the variant SmlI+, AlwNI- - - DNA DHPLC, SEQ Blood - TSC - unpublished a parent and a child of the proband have the same variant; 2 siblings tested negative F - - - - - - - 3 Rosemary Ekong
+/. 10 c.989dup r.(?) p.(Ser331Glufs*10) Tuberin binding domain - Unknown - pathogenic (dominant) g.135786880dup g.132911493dup - - TSC1_000067 1bp duplication of T unpublished - - Unknown - 1/2 individuals tested have the variant SmlI+, AlwNI- - - DNA DHPLC, SEQ Blood - TSC - unpublished the one parent tested is negative for the variant F - - - - - - - 1 Rosemary Ekong
+/. 10 c.989dup r.(?) p.(Ser331Glufs*10) Tuberin binding domain - Unknown - pathogenic (dominant) g.135786880dup g.132911493dup - - TSC1_000067 1bp duplication of T unpublished - - Unknown - 1/2 individuals tested have the variant SmlI+, AlwNI- - - DNA DHPLC, SEQ Blood - TSC - unpublished variant absent in relative tested M - - - - - - - 1 Rosemary Ekong
+/. 10 c.989dup r.(?) p.(Ser331Glufs*10) Tuberin binding domain - Unknown - pathogenic (dominant) g.135786880dup g.132911493dup - - TSC1_000067 1bp duplication of T unpublished - - Unknown - 1/2 individuals tested have the variant SmlI+, AlwNI- - - DNA DHPLC, SEQ Blood - TSC - unpublished sibling tested negative F - - - - - - - 1 Rosemary Ekong
+/. 10 c.989dup r.(?) p.(Ser331Glufs*10) Tuberin binding domain - Unknown - pathogenic (dominant) g.135786880dup g.132911493dup c.989dupT - TSC1_000067 1bp duplication of T; found with TSC2 missense c.3986G>A PubMed: Rosset, 2017 - - Germline - 2/2 individuals tested have the variant SmlI+, AlwNI- - - DNA SEQ-NG-IT Blood - TSC - PubMed: Rosset, 2017 patient has TSC1 frameshift c.989dup and TSC2 missense c.3986G>A ? - Brazil - - - - - 2 Rosemary Ekong
+/+ 10 c.989dup r.(?) p.(Ser331Glufs*10) Tuberin binding domain - Unknown - pathogenic (dominant) g.135786880dup g.132911493dup - - TSC1_000067 1bp duplication of T - - - SUMMARY record - - SmlI+, AlwNI- - - - - - - - - - - - - - - - - - - - -
+/. - c.989dup r.(?) p.(Ser331GlufsTer10) - - Unknown - pathogenic g.135786880dup g.132911493dup TSC1(NM_000368.4):c.989dupT (p.S331Efs*10) - TSC1_000067 VKGL data sharing initiative Nederland - - - CLASSIFICATION record - - - - - - - - - - - - - - - - - - - - - - -
+/. 10 c.989dup r.(?) p.(Ser331Glufs*10) Tuberin binding domain - Unknown - pathogenic (dominant) g.135786880dup g.132911493dup 989dupT - TSC1_000067 1bp duplication of T unpublished - - Germline ? - - - - DNA MCA, SEQ Blood - TSC - unpublished patient with refractory seizures; parents not tested F ? - - - - - - 1 Rosemary Ekong
+/. 10 c.989dup r.(?) p.(Ser331Glufs*10) Tuberin binding domain - Unknown - pathogenic (dominant) g.135786880dup g.132911493dup 989dupT - TSC1_000067 1bp duplication of T unpublished - - Germline ? - - - - DNA MCA, SEQ Blood - TSC - unpublished parents not tested F ? - - - - - - 1 Rosemary Ekong
+/. 10 c.989dup r.(?) p.(Ser331Glufs*10) Tuberin binding domain - Unknown - pathogenic (dominant) g.135786880dup g.132911493dup c.989dupT, 1210-1211 ins/dup T - TSC1_000067 1bp duplication of T unpublished - - Germline ? 1/2 individuals tested have the variant - - - DNA DHPLC Blood - TSC - unpublished one parent - reported to have non-specific hyperintense MRI changes in frontal lobes and an incidental finding - does not have the variant M ? - - - - - - 1 Rosemary Ekong
+/. 10 c.989dup r.(?) p.(Ser331Glufs*10) - - Unknown - pathogenic (dominant) g.135786880dup g.132911493dup c.989_990insT, p(.L330fs) - TSC1_000067 variant at 44% MAF; somatic variants in other genes found (not specified) PubMed: Giannikou, 2020 - - Somatic ? - - - - DNA SEQ-NG-I Brain whole exome analysis of Subependymal giant cell astrocytomas, median coverage = 443x TSC SEGA-S9 PubMed: Giannikou, 2020 patient had surgery at 17y M ? - - - - - - 1 Rosemary Ekong
+/. 10 c.989dup r.(?) p.(Ser331Glufs*10) - - Unknown ACMG pathogenic g.135786880dup g.132911493dup - - TSC1_000067 - - - rs118203478 Germline ? - - - - DNA SEQ Blood Sanger Sequencing TSC - - - M ? 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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