rs118203597
Positions:
Variant summary
Our verdict is Pathogenic. Variant got 18 ACMG points: 18P and 0B. PVS1PM2PP5_Very_Strong
The NM_000368.5(TSC1):c.1904_1905delCA(p.Thr635fs) variant causes a frameshift change involving the alteration of a non-conserved nucleotide. The variant was absent in control chromosomes in GnomAD project. Variant has been reported in ClinVar as Pathogenic (★★). Variant results in nonsense mediated mRNA decay.
Frequency
Genomes: not found (cov: 32)
Consequence
TSC1
NM_000368.5 frameshift
NM_000368.5 frameshift
Scores
Not classified
Clinical Significance
Conservation
PhyloP100: 1.36
Genes affected
TSC1 (HGNC:12362): (TSC complex subunit 1) This gene is a tumor suppressor gene that encodes the growth inhibitory protein hamartin. The encoded protein interacts with and stabilizes the GTPase activating protein tuberin. This hamartin-tuberin complex negatively regulates mammalian target of rapamycin complex 1 (mTORC1) signaling which is a major regulator of anabolic cell growth. This protein also functions as a co-chaperone for Hsp90 that inhibits its ATPase activity. This protein functions as a facilitator of Hsp90-mediated folding of kinase and non-kinase clients, including TSC2 and thereby preventing their ubiquitination and proteasomal degradation. Mutations in this gene have been associated with tuberous sclerosis and lymphangioleiomyomatosis. [provided by RefSeq, May 2022]
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ACMG classification
Classification made for transcript
Verdict is Pathogenic. Variant got 18 ACMG points.
PVS1
Loss of function variant, product undergoes nonsense mediated mRNA decay. LoF is a known mechanism of disease.
PM2
Very rare variant in population databases, with high coverage;
PP5
Variant 9-132905672-CTG-C is Pathogenic according to our data. Variant chr9-132905672-CTG-C is described in ClinVar as [Pathogenic]. Clinvar id is 5100.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr9-132905672-CTG-C is described in Lovd as [Pathogenic]. Variant chr9-132905672-CTG-C is described in Lovd as [Pathogenic]. Variant chr9-132905672-CTG-C is described in Lovd as [Pathogenic].
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
TSC1 | NM_000368.5 | c.1904_1905delCA | p.Thr635fs | frameshift_variant | 15/23 | ENST00000298552.9 | NP_000359.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
TSC1 | ENST00000298552.9 | c.1904_1905delCA | p.Thr635fs | frameshift_variant | 15/23 | 1 | NM_000368.5 | ENSP00000298552.3 | ||
TSC1 | ENST00000490179.4 | c.1904_1905delCA | p.Thr635fs | frameshift_variant | 16/24 | 3 | ENSP00000495533.2 |
Frequencies
GnomAD3 genomes Cov.: 32
GnomAD3 genomes
Cov.:
32
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome Cov.: 32
GnomAD4 genome
Cov.:
32
ClinVar
Significance: Pathogenic
Submissions summary: Pathogenic:12Other:2
Revision: criteria provided, multiple submitters, no conflicts
LINK: link
Submissions by phenotype
Tuberous sclerosis 1 Pathogenic:8
Pathogenic, criteria provided, single submitter | clinical testing | Labcorp Genetics (formerly Invitae), Labcorp | Jun 05, 2023 | This sequence change creates a premature translational stop signal (p.Thr635Argfs*52) in the TSC1 gene. It is expected to result in an absent or disrupted protein product. Loss-of-function variants in TSC1 are known to be pathogenic (PMID: 10227394, 17304050). For these reasons, this variant has been classified as Pathogenic. ClinVar contains an entry for this variant (Variation ID: 5100). This variant is also known as 2122delAC. This premature translational stop signal has been observed in individual(s) with tuberous sclerosis complex (TSC) (PMID: 9242607, 10053179, 21520333). This variant is not present in population databases (gnomAD no frequency). - |
Pathogenic, criteria provided, single submitter | research | Molecular Biology Laboratory, Fundació Puigvert | Feb 01, 2020 | - - |
Pathogenic, no assertion criteria provided | clinical testing | Division of Genomic Medicine, Department of Advanced Medicine, Medical Research Institute, Kanazawa Medical University | Jun 09, 2020 | - - |
Pathogenic, criteria provided, single submitter | clinical testing | Consultorio y Laboratorio de Neurogenética, Hospital JM Ramos Mejia | - | - - |
Pathogenic, criteria provided, single submitter | clinical testing | Institute of Human Genetics, University of Leipzig Medical Center | Sep 06, 2022 | Criteria applied: PVS1,PS4,PM2_SUP - |
Pathogenic, criteria provided, single submitter | clinical testing | Myriad Genetics, Inc. | Feb 21, 2024 | This variant is considered pathogenic. This variant creates a frameshift predicted to result in premature protein truncation. - |
Pathogenic, no assertion criteria provided | literature only | OMIM | Mar 04, 1999 | - - |
Pathogenic, criteria provided, single submitter | clinical testing | Genome-Nilou Lab | Nov 07, 2021 | - - |
Tuberous sclerosis syndrome Pathogenic:1Other:2
not provided, no classification provided | curation | Tuberous sclerosis database (TSC1) | - | - - |
Pathogenic, criteria provided, single submitter | clinical testing | Institute of Medical Genetics and Applied Genomics, University Hospital Tübingen | Aug 29, 2023 | - - |
not provided, no classification provided | curation | Tuberous sclerosis database (TSC1) | - | - - |
not provided Pathogenic:1
Pathogenic, criteria provided, single submitter | clinical testing | Athena Diagnostics | Nov 22, 2017 | - - |
Hereditary cancer-predisposing syndrome Pathogenic:1
Pathogenic, criteria provided, single submitter | clinical testing | Ambry Genetics | Jan 26, 2023 | The c.1904_1905delCA pathogenic mutation, located in coding exon 13 of the TSC1 gene, results from a deletion of two nucleotides at nucleotide positions 1904 to 1905, causing a translational frameshift with a predicted alternate stop codon (p.T635Rfs*52). This alteration has been observed in multiple individuals with a personal history that is consistent with TSC1-related disease (Au KS et al. Genet Med, 2007 Feb;9:88-100; Ding Y et al. Front Genet, 2020 Mar;11:204; Dong X et al. J Med Genet, 2020 Aug;57:558-566; Meng Y et al. J Hum Genet, 2021 Mar;66:227-236). This variant is considered to be rare based on population cohorts in the Genome Aggregation Database (gnomAD). In addition to the clinical data presented in the literature, this alteration is expected to result in loss of function by premature protein truncation or nonsense-mediated mRNA decay. As such, this alteration is interpreted as a disease-causing mutation. - |
TSC1-related disorder Pathogenic:1
Pathogenic, criteria provided, single submitter | clinical testing | Swedish National ChiCaP Initative, Genomic Medicine Sweden | May 01, 2024 | - - |
Computational scores
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SpliceAI score (max)
Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at