16-2088293-C-T

Position:

• chr16-2088293-C-T

Variant summary

Our verdict is Pathogenic. Variant got 18 ACMG points: 18P and 0B. PM1 PM2 PM5 PP3_Strong PP5_Very_Strong

The NM_000548.5(TSC2):​c.5227C>T​(p.Arg1743Trp) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant was absent in control chromosomes in GnomAD project. In-silico tool predicts a pathogenic outcome for this variant. Variant has been reported in ClinVar as Pathogenic (★★). Another variant affecting the same amino acid position, but resulting in a different missense (i.e. R1743G) has been classified as Likely pathogenic.

• Frequency: Genomes: not found (cov: 34)
• Consequence: TSC2 NM_000548.5 missense
• Clinical Significance: Pathogenic criteria provided, multiple submitters, no conflicts P:12 O:1
• Conservation: PhyloP100: 1.84

Genes affected

TSC2 (HGNC:12363): (TSC complex subunit 2) This gene is a tumor suppressor gene that encodes the growth inhibitory protein tuberin. Tuberin interacts with hamartin to form the TSC protein complex which functions in the control of cell growth. This TSC protein complex negatively regulates mammalian target of rapamycin complex 1 (mTORC1) signaling which is a major regulator of anabolic cell growth. Mutations in this gene have been associated with tuberous sclerosis and lymphangioleiomyomatosis. [provided by RefSeq, May 2022]

ACMG classification

Verdict is Pathogenic. Variant got 18 ACMG points.

• PM1: In a domain Rap-GAP (size 227) in uniprot entity TSC2_HUMAN there are 284 pathogenic changes around while only 47 benign (86%) in NM_000548.5
• PM2: Very rare variant in population databases, with high coverage
• PM5: Other missense variant is known to change same aminoacid residue: Variant chr16-2088293-C-G is described in Lovd as [Likely_pathogenic].
• PP3: MetaRNN computational evidence supports a deleterious effect, 0.989
• PP5: Variant 16-2088293-C-T is Pathogenic according to our data. Variant chr16-2088293-C-T is described in ClinVar as [Pathogenic]. Clinvar id is 49471.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr16-2088293-C-T is described in Lovd as [Pathogenic]. Variant chr16-2088293-C-T is described in Lovd as [Pathogenic]. Variant chr16-2088293-C-T is described in Lovd as [Likely_pathogenic].

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
TSC2	NM_000548.5	c.5227C>T	p.Arg1743Trp	missense_variant	41/42	ENST00000219476.9	NP_000539.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
TSC2	ENST00000219476.9	c.5227C>T	p.Arg1743Trp	missense_variant	41/42	5	NM_000548.5	ENSP00000219476

Frequencies

GnomAD3 genomes Cov.: 34

GnomAD4 exome Cov.: 34

GnomAD4 genome Cov.: 34

ClinVar

Significance: Pathogenic

Submissions summary: Pathogenic:12 Other:1

Revision: criteria provided, multiple submitters, no conflicts

Submissions by phenotype

Tuberous sclerosis 2 Pathogenic:7

Pathogenic, criteria provided, single submitter	clinical testing	Center of Genomic medicine, Geneva, University Hospital of Geneva	Dec 06, 2016	- -
Pathogenic, criteria provided, single submitter	clinical testing	Genome-Nilou Lab	Nov 07, 2021	- -
Pathogenic, criteria provided, single submitter	clinical testing	Division of Genomic Medicine, Department of Advanced Medicine, Medical Research Institute, Kanazawa Medical University	Jul 10, 2020	- -
Pathogenic, criteria provided, single submitter	clinical testing	Illumina Laboratory Services, Illumina	Jul 28, 2023	The TSC2 c.5227C>T (p.Arg1743Trp) missense variant, also known as R1720W, has been identified in individuals with a phenotype consistent with tuberous sclerosis complex including, in a de novo state in at least one individual (PMID: 32211034; 35918040; 34403804). This variant is not observed in version 2.1.1 or version 3.1.2 of the Genome Aggregation Database. A functional study conducted in human cell lines demonstrated that this variant impacts protein function (PMID: 18854862). Additionally, a different amino acid substitution at the same codon (p.Arg1743Gln) has been reported in individuals with tuberous sclerosis complex and is classified as pathogenic by several submitters in ClinVar (Variation ID: 49960). Multiple lines of computational evidence suggest the variant may impact the gene or gene product. This variant was identified in a de novo state. Based on the available evidence, the c.5227C>T (p.Arg1743Trp) variant is classified as pathogenic for tuberous sclerosis complex. -
Pathogenic, criteria provided, single submitter	clinical testing	Institute of Human Genetics, University of Leipzig Medical Center	Dec 14, 2022	This variant was identified as de novo (maternity and paternity confirmed)._x000D_ Criteria applied: PS2_VSTR, PS4, PM5_STR, PS3_MOD, PM1_SUP, PM2_SUP, PP3, PP4 -
Pathogenic, criteria provided, single submitter	clinical testing	Labcorp Genetics (formerly Invitae), Labcorp	Jan 09, 2024	This sequence change replaces arginine, which is basic and polar, with tryptophan, which is neutral and slightly polar, at codon 1743 of the TSC2 protein (p.Arg1743Trp). This variant is not present in population databases (gnomAD no frequency). This missense change has been observed in individual(s) with tuberous sclerosis, epilepsy and/or infantile spasms (PMID: 12111193, 16114042, 16981987, 22867869, 27174333, 29476190, 29500070, 29801666). In at least one individual the variant was observed to be de novo. This variant is also known as R1720W. ClinVar contains an entry for this variant (Variation ID: 49471). Advanced modeling of protein sequence and biophysical properties (such as structural, functional, and spatial information, amino acid conservation, physicochemical variation, residue mobility, and thermodynamic stability) has been performed at Invitae for this missense variant, however the output from this modeling did not meet the statistical confidence thresholds required to predict the impact of this variant on TSC2 protein function. Experimental studies have shown that this missense change affects TSC2 function (PMID: 18854862, 21309039, 23955302). This variant disrupts the p.Arg1743 amino acid residue in TSC2. Other variant(s) that disrupt this residue have been determined to be pathogenic (PMID: 10732801, 16114042, 18854862, 20165957). This suggests that this residue is clinically significant, and that variants that disrupt this residue are likely to be disease-causing. For these reasons, this variant has been classified as Pathogenic. -
Pathogenic, criteria provided, single submitter	clinical testing	Victorian Clinical Genetics Services, Murdoch Childrens Research Institute	May 06, 2021	Based on the classification scheme VCGS_Germline_v1.3.4, this variant is classified as Pathogenic. Following criteria are met: 0102 - Loss of function is a known mechanism of disease in this gene and is associated with tuberous sclerosis-2 (MIM#613254). (I) 0107 - This gene is associated with autosomal dominant disease. Heterozygous variants are associated with tuberous sclerosis-2 (MIM#613254). Additionally, somatic variants are associated with lymphangioleiomyomatosis (MIM#606690). (I) 0254 - This variant is suspected mosaic. Low level mosaicism was detected in somatic tissues tested in a research setting. (I) 0200 - Variant is predicted to result in a missense amino acid change from arginine to tryptophan. (I) 0301 - Variant is absent from gnomAD (both v2 and v3). (SP) 0501 - Missense variant consistently predicted to be damaging by multiple in silico tools and highly conserved with a major amino acid change. (SP) 0600 - Variant is located in the annotated Rap-GAP domain (UniProt). (I) 0701 - Other missense variants comparable to the one identified in this case have very strong previous evidence for pathogenicity. Alternate changes at the same residue, to glycine, glutamine, leucine and proline have previously been reported as pathogenic (ClinVar, LOVD). (SP) 0801 - This variant has strong previous evidence of pathogenicity in unrelated individuals. The variant has previously been reported as pathogenic in multiple individuals with tuberous sclerosis, some of whom were shown to be de novo (ClinVar, LOVD, PMID: 19369101, PMID: 27859028). (SP) 1002 - This variant has moderate functional evidence supporting abnormal protein function. Cells transfected with the variant have been shown to result in a loss of protein function (ClinVar, PMID: 21309039). (SP) 1208 - Inheritance information for this variant is not currently available in this individual. (I) Legend: (SP) - Supporting pathogenic, (I) - Information, (SB) - Supporting benign -

not provided Pathogenic:2

Pathogenic, criteria provided, single submitter	clinical testing	GeneDx	Nov 09, 2022	Published functional studies demonstrate a damaging effect indicating that p.R1743W disrupts the TSC1-TSC2 complex (Coevoets et al., 2009; Hoogeveen-Westerveld et al., 2011); Not observed at significant frequency in large population cohorts (gnomAD); In silico analysis supports that this missense variant has a deleterious effect on protein structure/function; This variant is associated with the following publications: (PMID: 17536269, 20165957, 15798777, 21309039, 16114042, 25782670, 22867869, 21510812, 12111193, 16981987, 27174333, 23955302, 28178598, 29500070, 28065512, 29476190, 29801666, 19369101, 10732801, 30787465, 32005694, 34403804, 34849272, 32211034, 33528079, PMC9266619, 32555378, 18854862) -
Pathogenic, criteria provided, single submitter	clinical testing	Athena Diagnostics	Aug 01, 2018	Not found in the total gnomAD dataset, and the data is high quality. Located in potentially critical domain of the protein. This variant occurs as the most likely explanation for disease in a significant number of internal cases, suggesting this variant is associated with disease. Assessment of experimental evidence suggests this variant results in abnormal protein function. 5 de novo cases with parental identity not confirmed, plus case with parental identity confirmed. -

Lymphangiomyomatosis;C1846385:Isolated focal cortical dysplasia type II;C1860707:Tuberous sclerosis 2 Pathogenic:1

Pathogenic, criteria provided, single submitter

clinical testing

Fulgent Genetics, Fulgent Genetics

Oct 31, 2018

- -

TSC2-related disorder Pathogenic:1

Pathogenic, criteria provided, single submitter

clinical testing

PreventionGenetics, part of Exact Sciences

Jun 07, 2023

The TSC2 c.5227C>T variant is predicted to result in the amino acid substitution p.Arg1743Trp. This variant has been reported in individuals with tuberous sclerosis complex, with at least one de novo occurrence reported (Langkau et al. 2002. PubMed ID: 12111193; Rendtorff et al. 2005. PubMed ID: 16114042; Hung et al. 2006. PubMed ID: 16981987; Coevoets et al. 2008. PubMed ID: 18854862; Suspitsin et al. 2018. PubMed ID: 29476190; Papadopoulou et al. 2018. PubMed ID: 29500070). In vitro experimental studies suggest this variant impacts protein function (Coevoets et al. 2009. PubMed ID: 18854862; Referred to as "R1720W", Hoogeveen-Westerveld et al. 2011. PubMed ID: 21309039). This variant has not been reported in a large population database (http://gnomad.broadinstitute.org), indicating this variant is rare. It is interpreted as pathogenic in ClinVar (https://www.ncbi.nlm.nih.gov/clinvar/variation/49471/). This variant is interpreted as pathogenic. -

Hereditary cancer-predisposing syndrome Pathogenic:1

Pathogenic, criteria provided, single submitter

clinical testing

Ambry Genetics

Jun 19, 2016

The p.R1743W pathogenic mutation (also known as c.5227C>T), located in coding exon 40 of the TSC2 gene, results from a C to T substitution at nucleotide position 5227. The arginine at codon 1743 is replaced by tryptophan, an amino acid with dissimilar properties. This mutation has been described in two unrelated individuals with TSC who had infantile spasms and epilepsy (van Eeghen AM et al. Epilepsy Res. 2013;103(1):83-7). Another disease-causing mutation, p.R1743Q, has been described in the same codon. Analyses via in-cell western assay and transfection-based immunoblot assay showed reduced expression of the mutant p.R1743W and p.R1743Q TSC2 proteins compared to wild-type (Coevoets R et al. Eur. J. Hum. Genet. 2009;17(3):301-10, Hoogeveen-Westerveld M et al. Hum. Mutat. 2011;32(4):424-35). Based on the supporting evidence, p.R1743W is interpreted as a disease-causing mutation. -

Tuberous sclerosis syndrome Other:1

not provided, no classification provided

curation

Tuberous sclerosis database (TSC2)

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Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
AlphaMissense	Pathogenic	1.0
BayesDel_addAF	Pathogenic	0.52	D
BayesDel_noAF	Pathogenic	0.51
CADD	Uncertain	25
DANN	Uncertain	1.0
DEOGEN2	Pathogenic	0.96	D;.;.;.;.;.;.;.;.;.;.;.;D;.;D
Eigen	Uncertain	0.35
Eigen_PC	Benign	0.18
FATHMM_MKL	Benign	0.64	D
LIST_S2	Pathogenic	0.98	D;D;D;D;D;D;D;D;D;D;D;D;D;D;D
M_CAP	Pathogenic	0.95	D
MetaRNN	Pathogenic	0.99	D;D;D;D;D;D;D;D;D;D;D;D;D;D;D
MetaSVM	Pathogenic	1.1	D
MutationAssessor	Pathogenic	3.4	M;.;.;.;.;.;.;.;.;.;.;.;.;.;.
MutationTaster	Benign	1.0	D;D;D;D;D;D;D
PrimateAI	Uncertain	0.79	T
PROVEAN	Pathogenic	-7.3	D;.;.;D;.;D;.;.;D;D;.;.;.;.;D
REVEL	Pathogenic	0.93
Sift	Pathogenic	0.0	D;.;.;D;.;D;.;.;D;D;.;.;.;.;D
Sift4G	Pathogenic	0.0	D;.;.;D;.;D;.;.;D;D;.;.;.;.;D
Polyphen		1.0	D;.;.;.;D;D;.;.;D;D;.;.;.;.;.
Vest4		0.93
MutPred		0.90		Loss of disorder (P = 0.0247);.;.;.;.;.;.;.;.;.;.;.;.;.;.;
MVP		1.0
ClinPred		0.99	D
GERP RS		0.035
RBP_binding_hub_radar		0.0
RBP_regulation_power_radar		1.7
Varity_R		0.90
gMVP		0.91

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.0		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

Other links and lift over

dbSNP: rs45517412; hg19: chr16-2138294; COSMIC: COSV51918349; COSMIC: COSV51918349;