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.

27 entries on 1 page. Showing entries 1 - 27.
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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     

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Frequency     

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Methylation     

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Technique     

Tissue     

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Disease     

ID_report     

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Consanguinity     

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+/. - c.2509_2512del r.(?) p.(Asn837ValfsTer11) - - Unknown - pathogenic g.135776217_135776220del g.132900830_132900833del TSC1(NM_000368.4):c.2509_2512delAACA (p.N837Vfs*11), TSC1(NM_000368.5):c.2509_2512delAACA (p.N837Vfs*11) - TSC1_000233 VKGL data sharing initiative Nederland - - - CLASSIFICATION record - - - - - - - - - - - - - - - - - - - - - - -
+/. 20 c.2509_2512del r.(?) p.(Asn837Valfs*11) Coiled-coil domain - Unknown - pathogenic (dominant) g.135776217_135776220del g.132900830_132900833del 2729delAACA - TSC1_000233 4bp deletion of AACA PubMed: vanSlegtenhorst, 1999 - - Germline - 2/2 individuals tested have the variant BspCNI+, DdeI+ - - DNA SSCA Blood - TSC - PubMed: vanSlegtenhorst, 1999 - ? - - - - - - - 2 Rosemary Ekong
+/. 20 c.2509_2512del r.(?) p.(Asn837Valfs*11) Coiled-coil domain - Unknown - pathogenic (dominant) g.135776217_135776220del g.132900830_132900833del 2730del4 - TSC1_000233 4bp deletion of AACA Yates 1998, unpublished - - Germline - 2/2 individuals tested have the variant BspCNI+, DdeI+ - - DNA SEQ Blood - TSC - Yates, 1998, Unpublished familial case ? - - - - - - - 2 Rosemary Ekong
+/. 20 c.2509_2512del r.(?) p.(Asn837Valfs*11) Coiled-coil domain - Unknown - pathogenic (dominant) g.135776217_135776220del g.132900830_132900833del c.2509_2512delAACA - TSC1_000233 4bp deletion of AACA; reported that variant not detected by SSCA PubMed: Au, 2007 - - Germline - - BspCNI+, DdeI+ - - DNA SEQ Blood - TSC - PubMed: Au, 2007 familial case ? - - - - - - - 1 Rosemary Ekong
+/. 20 c.2509_2512del r.(?) p.(Asn837Valfs*11) Coiled-coil domain - Unknown - pathogenic (dominant) g.135776217_135776220del g.132900830_132900833del c.2509_2512delAACA - TSC1_000233 4bp deletion of AACA PubMed: Au, 2007 - - Unknown - - BspCNI+, DdeI+ - - DNA SEQ Blood - TSC - PubMed: Au, 2007 authors confirm variant found in sporadic case ? - - - - - - - 1 Rosemary Ekong
+/. 20 c.2509_2512del r.(?) p.(Asn837Valfs*11) Coiled-coil domain - Unknown - pathogenic (dominant) g.135776217_135776220del g.132900830_132900833del c.2508_2511del, 2729–2108delAAAC, 2729delAAAC - TSC1_000233 4bp deletion of AACA (according to HGVS nomenclature) reported as deletion of AAAC; found with TSC1 missense c.3322G>A PubMed: Kwiatkowska, 1998; PubMed: Dabora, 1998; PubMed: Dabora, 2001 - - Unknown - - BspCNI+, DdeI+ - - DNA DGGE, DHPLC, HD, SSCA Blood - TSC - PubMed: Kwiatkowska, 1998; PubMed: Dabora, 1998; PubMed: Dabora, 2001 patient also has TSC1 missense c.3322G>A and TSC1 frameshift c.2509_2512del; parents unavailable for testing ? - - - - - - - 1 Rosemary Ekong
+/. 20 c.2509_2512del r.(?) p.(Asn837Valfs*11) Coiled-coil domain - Unknown - pathogenic (dominant) g.135776217_135776220del g.132900830_132900833del c.2508_2511del; S836FS>847X - TSC1_000233 4bp deletion of AACA (according to HGVS nomenclature) reported as deletion of AAAC PubMed: Yamamoto, 2002 - - Unknown - - BspCNI+, DdeI+ - - DNA SSCA Blood - TSC - PubMed: Yamamoto, 2002 sporadic case ? - Japan - - - - - 1 Rosemary Ekong
+/. 20 c.2509_2512del r.(?) p.(Asn837Valfs*11) Coiled-coil domain - Unknown - pathogenic (dominant) g.135776217_135776220del g.132900830_132900833del - - TSC1_000233 4bp deletion of AACA; Chinese paper with English abstract; information on variant taken from Zhao, 2006 PubMed: Feng, 2003 - - Unknown - - BspCNI+, DdeI+ - - DNA SSCA Blood - TSC - PubMed: Feng, 2003 - ? - China - - - - - 1 Rosemary Ekong
+/. 20 c.2509_2512del r.(?) p.(Asn837Valfs*11) Coiled-coil domain - Unknown - pathogenic (dominant) g.135776217_135776220del g.132900830_132900833del 2507_2510 del 4bp - TSC1_000233 4bp deletion of AACA (according to HGVS nomenclature) reported as deletion of AAAC unpublished - - Unknown - - BspCNI+, DdeI+ - - DNA DHPLC Blood - TSC - unpublished - F - - - - - - - 1 Rosemary Ekong
+/. 20 c.2509_2512del r.(?) p.(Asn837Valfs*11) Coiled-coil domain - Unknown - pathogenic (dominant) g.135776217_135776220del g.132900830_132900833del - - TSC1_000233 4bp deletion of AACA; found with TSC1 missense c.2194C>T unpublished - - Germline - 2/2 individuals tested have the variant BspCNI+, DdeI+ - - DNA SEQ Blood - TSC - unpublished seen in 2 affected individuals in 2 generations; proband has TSC1 missense c.2194C>T and a familial TSC1 frameshift c.2509_2512del seen in another family member, but parents were not available for testing ? - - - - - - - 2 Rosemary Ekong
+/. 20 c.2509_2512del r.(?) p.(Asn837Valfs*11) Coiled-coil domain - Unknown - pathogenic (dominant) g.135776217_135776220del g.132900830_132900833del - - TSC1_000233 4bp deletion of AACA unpublished - - De novo - 1/3 individuals tested have the variant BspCNI+, DdeI+ - - DNA SEQ Blood - TSC - unpublished 1 affected individual in 1 generation; parents tested and variant not found ? - - - - - - - 1 Rosemary Ekong
+/. 20 c.2509_2512del r.(?) p.(Asn837Valfs*11) Coiled-coil domain - Unknown - pathogenic (dominant) g.135776217_135776220del g.132900830_132900833del - - TSC1_000233 4bp deletion of AACA; found with TSC1 missense c.2285A>G unpublished - - De novo - 1/3 individuals tested have the variant BspCNI+, DdeI+ - - DNA SEQ Blood - TSC - unpublished 1 affected individual in 1 generation; proband has TSC1 frameshift c.2509_2512del and TSC1 missense c.2285A>G; both parents are negative for c.2509_2512del, but one of the healthy parents has TSC1 missense c.2285A>G ? - - - - - - - 1 Rosemary Ekong
+/. 20 c.2509_2512del r.(?) p.(Asn837Valfs*11) Coiled-coil domain - Unknown - pathogenic (dominant) g.135776217_135776220del g.132900830_132900833del c.2509del4, c.2509_2512delAACA - TSC1_000233 4bp deletion of AACA PubMed: Sancak, 2005 - - Unknown - 4/4 individuals tested have the variant BspCNI+, DdeI+ - - DNA SEQ Blood - TSC - PubMed: Sancak, 2005 4 patients; 3/4 diagnosed with definite TSC; 1/4 indicated as sporadic ? - - - - - - - 4 Rosemary Ekong
+/. 20 c.2509_2512del r.(?) p.(Asn837Valfs*11) Coiled-coil domain - Unknown - pathogenic (dominant) g.135776217_135776220del g.132900830_132900833del c.2509_2512delAACA - TSC1_000233 4bp deletion of AACA PubMed: Jansen, 2008 - - Unknown - 2/2 individuals tested have the variant BspCNI+, DdeI+ - - DNA SEQ Blood - TSC - PubMed: Jansen, 2008 2 cases; different to those reported in Sancak, 2005 ? - - - - - - - 2 Rosemary Ekong
+/. 20 c.2509_2512del r.(?) p.(Asn837Valfs*11) Coiled-coil domain - Unknown - pathogenic (dominant) g.135776217_135776220del g.132900830_132900833del 2509_2512delAACA - TSC1_000233 4bp deletion of AACA unpublished - - Unknown - 1/2 individuals tested have the variant BspCNI+, DdeI+ - - DNA SEQ Blood - TSC - unpublished one parent tested and variant not found; other parent not tested M - - - - - - - 1 Rosemary Ekong
+/. 20 c.2509_2512del r.(?) p.(Asn837Valfs*11) Coiled-coil domain - Unknown - pathogenic (dominant) g.135776217_135776220del g.132900830_132900833del c.2509_2512delAACA - TSC1_000233 4bp deletion of AACA unpublished - - De novo - 1/3 individuals tested have the variant BspCNI+, DdeI+ - - DNA SEQ Blood - TSC - unpublished both parents tested and variant not found; referred for TS M - - - - - - - 1 Rosemary Ekong
+/. 20 c.2509_2512del r.(?) p.(Asn837Valfs*11) Coiled-coil domain - Paternal (confirmed) - pathogenic (dominant) g.135776217_135776220del g.132900830_132900833del c.2508_2511del - TSC1_000233 4bp deletion of AACA (according to HGVS nomenclature) reported as deletion of AAAC unpublished - - Germline - 3/6 individuals tested have the variant BspCNI+, DdeI+ - - DNA DHPLC, SEQ Blood - TSC - unpublished proband, affected parent and one child of the proband have the same variant; 2 other children and a sibling tested negative; affected sibling was not tested M - - - - - - - 3 Rosemary Ekong
+/. 20 c.2509_2512del r.(?) p.(Asn837Valfs*11) Coiled-coil domain - Unknown - pathogenic (dominant) g.135776217_135776220del g.132900830_132900833del c.2508_2511del - TSC1_000233 4bp deletion of AACA (according to HGVS nomenclature) reported as deletion of AAAC unpublished - - Unknown - 1/2 individuals tested have the variant BspCNI+, DdeI+ - - DNA DHPLC, SEQ Blood - TSC - unpublished an unaffected child tested negative M - - - - - - - 1 Rosemary Ekong
+/. 20 c.2509_2512del r.(?) p.(Asn837Valfs*11) Coiled-coil domain - Unknown - pathogenic (dominant) g.135776217_135776220del g.132900830_132900833del c.2508_2511del - TSC1_000233 4bp deletion of AACA (according to HGVS nomenclature) reported as deletion of AAAC unpublished - - Unknown - - BspCNI+, DdeI+ - - DNA DHPLC, SEQ Blood - TSC - unpublished affected sibling, parent, grandparent and 1 other relative were not tested. F - - - - - - - 1 Rosemary Ekong
+/. 20 c.2509_2512del r.(?) p.(Asn837Valfs*11) Coiled-coil domain - Unknown - pathogenic (dominant) g.135776217_135776220del g.132900830_132900833del - - TSC1_000233 4bp deletion of AACA unpublished - - Unknown - - BspCNI+, DdeI+ - - DNA DHPLC, SEQ Blood - TSC - unpublished No other family member tested M - - - - - - - 1 Rosemary Ekong
+/+ 20 c.2509_2512del r.(?) p.(Asn837Valfs*11) Coiled-coil domain - Unknown - pathogenic (dominant) g.135776217_135776220del g.132900830_132900833del - - TSC1_000233 4bp deletion of AACA - - - SUMMARY record - - DdeI+, HpyCH4III- - - - - - - - - - - - - - - - - - - - -
+/. 20 c.2509_2512del r.(?) p.(Asn837Valfs*11) - - Maternal (confirmed) ACMG pathogenic (dominant) g.135776217_135776220del g.132900830_132900833del - - TSC1_000233 - PubMed: Ding, 2020 - - Germline - - - - - DNA SEQ - - TSC 11 PubMed: Ding, 2020 - M - China - - - - - 1 Yifeng Ding
+/. 20 c.2509_2512del r.(?) p.(Asn837Valfs*11) - - Unknown - pathogenic (dominant) g.135776215_135776218del - - - TSC1_000233 4bp deletion of AACA unpublished - - Germline ? - - - - DNA DHPLC, SEQ Blood Diagnostic testing TSC - unpublished No other family member tested F ? - - - - - - 1 Rosemary Ekong
+/. 20 c.2509_2512del r.(?) p.(Asn837Valfs*11) Coiled-coil domain - Unknown - pathogenic (dominant) g.135776215_135776218del g.132900828_132900831del 2507_2510delTTTG - TSC1_000233 4bp deletion of AACA unpublished - - De novo ? 1/3 individuals tested have the variant - - - DNA MCA, SEQ Blood - TSC - unpublished TS affected; both parents tested and variant absent in parents F ? - - - - - - 1 Rosemary Ekong
+/. 20 c.2509_2512del r.(?) p.(Asn837Valfs*11) Coiled-coil domain - Unknown - pathogenic (dominant) g.135776215_135776218del g.132900828_132900831del p.(Asn837fs) - TSC1_000233 4bp deletion of AACA; MLPA normal unpublished - - Germline ? - - - - DNA SEQ-NG-I, SEQ Blood Illumina TruSight Cancer panel used TSC - unpublished patient with clinical diagnosis of TSC; parents not tested M ? - - - - - - 1 Rosemary Ekong
+/. - c.2509_2512del r.(?) p.(Asn837ValfsTer11) - - Unknown - pathogenic g.135776217_135776220del - TSC1(NM_000368.4):c.2509_2512delAACA (p.N837Vfs*11), TSC1(NM_000368.5):c.2509_2512delAACA (p.N837Vfs*11) - TSC1_000233 VKGL data sharing initiative Nederland - - - CLASSIFICATION record - - - - - - - - - - - - - - - - - - - - - - -
+/. 20 c.2509_2512del r.(?) p.(Asn837Valfs*11) Coiled-coil domain - Unknown - pathogenic (dominant) g.135776217_135776220del g.132900830_132900833del c.2508_2511del - TSC1_000233 4bp deletion of AACA (according to HGVS nomenclature) reported as deletion of AAAC; found with TSC1 missense c.1342C>T and TSC2 silent variant c.1869C>T unpublished - - De novo - 1/3 individuals tested have the variant BspCNI+, DdeI+ - - DNA DHPLC, SEQ Blood - TSC - unpublished patient has TSC1 missense c.1342C>T, TSC1 frameshift c.2509_2512del and TSC2 silent variant c.1869C>T; both parents tested for TSC1 c.2509_2512del and TSC2 c.1869C>T; TSC1 c.2509_2512del is absent in both parents, but one parent has TSC2 c.1869C>T; inheritance of TSC1 c.1342C>T not tested F - - - - - - - 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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