rs118203597

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

Scores

Not classified

Clinical Significance

Pathogenic criteria provided, multiple submitters, no conflicts P:12O:2

Conservation

PhyloP100: 1.36
Variant links:
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
TSC1NM_000368.5 linkuse as main transcriptc.1904_1905delCA p.Thr635fs frameshift_variant 15/23 ENST00000298552.9 NP_000359.1 Q92574-1Q86WV8X5D9D2

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Protein Appris UniProt
TSC1ENST00000298552.9 linkuse as main transcriptc.1904_1905delCA p.Thr635fs frameshift_variant 15/231 NM_000368.5 ENSP00000298552.3 Q92574-1
TSC1ENST00000490179.4 linkuse as main transcriptc.1904_1905delCA p.Thr635fs frameshift_variant 16/243 ENSP00000495533.2 A0A2R8Y6S8

Frequencies

GnomAD3 genomes
Cov.:
32
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
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 submitterclinical testingLabcorp Genetics (formerly Invitae), LabcorpJun 05, 2023This 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 submitterresearchMolecular Biology Laboratory, Fundació PuigvertFeb 01, 2020- -
Pathogenic, no assertion criteria providedclinical testingDivision of Genomic Medicine, Department of Advanced Medicine, Medical Research Institute, Kanazawa Medical UniversityJun 09, 2020- -
Pathogenic, criteria provided, single submitterclinical testingConsultorio y Laboratorio de Neurogenética, Hospital JM Ramos Mejia-- -
Pathogenic, criteria provided, single submitterclinical testingInstitute of Human Genetics, University of Leipzig Medical CenterSep 06, 2022Criteria applied: PVS1,PS4,PM2_SUP -
Pathogenic, criteria provided, single submitterclinical testingMyriad Genetics, Inc.Feb 21, 2024This variant is considered pathogenic. This variant creates a frameshift predicted to result in premature protein truncation. -
Pathogenic, no assertion criteria providedliterature onlyOMIMMar 04, 1999- -
Pathogenic, criteria provided, single submitterclinical testingGenome-Nilou LabNov 07, 2021- -
Tuberous sclerosis syndrome Pathogenic:1Other:2
not provided, no classification providedcurationTuberous sclerosis database (TSC1)-- -
Pathogenic, criteria provided, single submitterclinical testingInstitute of Medical Genetics and Applied Genomics, University Hospital TübingenAug 29, 2023- -
not provided, no classification providedcurationTuberous sclerosis database (TSC1)-- -
not provided Pathogenic:1
Pathogenic, criteria provided, single submitterclinical testingAthena DiagnosticsNov 22, 2017- -
Hereditary cancer-predisposing syndrome Pathogenic:1
Pathogenic, criteria provided, single submitterclinical testingAmbry GeneticsJan 26, 2023The 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 submitterclinical testingSwedish National ChiCaP Initative, Genomic Medicine SwedenMay 01, 2024- -

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction

Splicing

Name
Calibrated prediction
Score
Prediction
SpliceAI score (max)
0.10
Details are displayed if max score is > 0.2

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

LitVar

Below is the list of publications found by LitVar. It may be empty.

Other links and lift over

dbSNP: rs118203597; hg19: chr9-135781059; API