16-2088294-G-A

Position:

• chr16-2088294-G-A

Variant summary

Our verdict is Pathogenic. Variant got 22 ACMG points: 22P and 0B. PS1 PM1 PM2 PM5 PP3_Strong PP5_Very_Strong

The NM_000548.5(TSC2):​c.5228G>A​(p.Arg1743Gln) variant causes a missense change involving the alteration of a 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 Likely pathogenic (★★). Another nucleotide change resulting in same amino acid change has been previously reported as Pathogenicin Lovd. Another variant affecting the same amino acid position, but resulting in a different missense (i.e. R1743W) has been classified as Pathogenic.

• Frequency: Genomes: not found (cov: 34)
• Consequence: TSC2 NM_000548.5 missense
• Clinical Significance: Pathogenic/Likely pathogenic criteria provided, multiple submitters, no conflicts P:13 O:1
• Conservation: PhyloP100: 9.73

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 22 ACMG points.

• PS1: Transcript NM_000548.5 (TSC2) is affected with MISSENSE_VARIANT having same AA change as one Pathogenic present in Lovd
• PM1: In a hotspot region, there are 2 aminoacids with missense pathogenic changes in the window of +-8 aminoacids around while only 6 benign, 16 uncertain 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-T is described in ClinVar as [Pathogenic]. Clinvar id is 49471.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.
• PP3: MetaRNN computational evidence supports a deleterious effect, 0.989
• PP5: Variant 16-2088294-G-A is Pathogenic according to our data. Variant chr16-2088294-G-A is described in ClinVar as [Likely_pathogenic]. Clinvar id is 49960.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr16-2088294-G-A is described in Lovd as [Pathogenic]. Variant chr16-2088294-G-A is described in Lovd as [Benign]. Variant chr16-2088294-G-A is described in Lovd as [Likely_pathogenic]. Variant chr16-2088294-G-A is described in Lovd as [Pathogenic].

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
TSC2	NM_000548.5	c.5228G>A	p.Arg1743Gln	missense_variant	41/42	ENST00000219476.9

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
TSC2	ENST00000219476.9	c.5228G>A	p.Arg1743Gln	missense_variant	41/42	5	NM_000548.5

Frequencies

GnomAD3 genomes Cov.: 34

GnomAD4 exome Cov.: 34

GnomAD4 genome Cov.: 34

ClinVar

Significance: Pathogenic/Likely pathogenic

Submissions summary: Pathogenic:13 Other:1

Revision: criteria provided, multiple submitters, no conflicts

Submissions by phenotype

not provided Pathogenic:7

Pathogenic, criteria provided, single submitter	clinical testing	CeGaT Center for Human Genetics Tuebingen	Aug 01, 2021	- -
Pathogenic, criteria provided, single submitter	clinical testing	Athena Diagnostics	Jun 02, 2020	Predicted to have a damaging effect on the protein. Assessment of experimental evidence suggests this variant results in abnormal protein function. 2 de novo cases with parental identity confirmed, plus 2 unconfirmed cases. -
Pathogenic, no assertion criteria provided	clinical testing	Clinical Genetics DNA and cytogenetics Diagnostics Lab, Erasmus MC, Erasmus Medical Center	-	- -
Pathogenic, criteria provided, single submitter	clinical testing	ARUP Laboratories, Molecular Genetics and Genomics, ARUP Laboratories	Jun 09, 2018	The TSC2 c.5228G>A; p.Arg1743Gln variant (rs45507199), also known as R1720Q, is reported in multiple individuals affected with tuberous sclerosis complex and has been reported as a de novo variant (Coevoets 2009, Hoogeveen-Westerveld 2011, Overwater 2016, Qin 2010, see LOVD TSC2 database). Functional analyses show the variant disrupts the TSC1-TSC2 complex and affects downstream signaling (Coevoets 2009, Hoogeveen-Westerveld 2011, Overwater 2016). This variant is classified as pathogenic in ClinVar (Variation ID: 49960), as well as another variant at this codon (p.Arg1743Trp, Variation ID: 49471). The p.Arg1743Gln variant is absent from the general population databases (1000 Genomes Project, Exome Variant Server, and Genome Aggregation Database), indicating it is not a common polymorphism. The arginine at codon 1743 is highly conserved and computational analyses (SIFT, PolyPhen-2) predict that this variant is deleterious. Based on available information, the p.Arg1743Gln variant is considered to be pathogenic. REFERENCES LOVD TSC2 database link: http://chromium.lovd.nl/LOVD2/TSC/variants.php?select_db=TSC2&action=search_all&search_Variant%2FDNA=c.5228G%3EA Coevoets R et al. A reliable cell-based assay for testing unclassified TSC2 gene variants. Eur J Hum Genet. 2009 Mar;17(3):301-10. Hoogeveen-Westerveld M et al. Functional assessment of variants in the TSC1 and TSC2 genes identified in individuals with Tuberous Sclerosis Complex. Hum Mutat. 2011 Apr;32(4):424-35. Overwater IE et al. Genotype and brain pathology phenotype in children with tuberous sclerosis complex. Eur J Hum Genet. 2016 Dec;24(12):1688-1695. Qin W et al. Ultra deep sequencing detects a low rate of mosaic mutations in tuberous sclerosis complex. Hum Genet. 2010 Mar;127(5):573-82. -
Pathogenic, no assertion criteria provided	clinical testing	Diagnostic Laboratory, Department of Genetics, University Medical Center Groningen	-	- -
Pathogenic, criteria provided, single submitter	clinical testing	Mayo Clinic Laboratories, Mayo Clinic	Dec 08, 2022	PP3, PP4, PM2, PM5, PS3, PS4 -
Pathogenic, criteria provided, single submitter	clinical testing	GeneDx	Sep 19, 2022	Published functional studies demonstrate that R1743Q disrupts the TSC1-TSC2 complex (Coevoets et al., 2009; Hoogeveen-Westerveld et al., 2011); In silico analysis supports that this missense variant has a deleterious effect on protein structure/function; Not observed at significant frequency in large population cohorts (gnomAD); This variant is associated with the following publications: (PMID: 16981987, 22867869, 20165957, 18854862, 21309039, 10732801, 27406250, 16237225, 16114042, 17304050, 29801666, 30036593, 29655203, 31847710, 32555378, 32211034, 31447099, 33935721, 33532864, 34403804) -

Tuberous sclerosis 2 Pathogenic:4

Likely pathogenic, criteria provided, single submitter	clinical testing	Genome-Nilou Lab	Nov 07, 2021	- -
Pathogenic, criteria provided, single submitter	clinical testing	Invitae	Jan 20, 2024	This sequence change replaces arginine, which is basic and polar, with glutamine, which is neutral and polar, at codon 1743 of the TSC2 protein (p.Arg1743Gln). This variant is not present in population databases (gnomAD no frequency). This missense change has been observed in individual(s) with tuberous sclerosis (PMID: 10732801, 16114042, 18854862, 20165957, 21309039). In at least one individual the variant was observed to be de novo. ClinVar contains an entry for this variant (Variation ID: 49960). 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). 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: 10205261, 16981987, 18854862, 25782670). 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	Division of Genomic Medicine, Department of Advanced Medicine, Medical Research Institute, Kanazawa Medical University	Jul 10, 2020	- -
Likely pathogenic, criteria provided, single submitter	research	Molecular Biology Laboratory, Fundació Puigvert	Feb 01, 2020	- -

Tuberous sclerosis syndrome Pathogenic:1 Other:1

not provided, no classification provided	curation	Tuberous sclerosis database (TSC2)	-	- -
Pathogenic, criteria provided, single submitter	clinical testing	Laboratory for Molecular Medicine, Mass General Brigham Personalized Medicine	May 04, 2018	The Arg1743Gln variant in TSC2 was absent from large population studies but has been reported in at least 10 individuals with tuberous sclerosis (Gilbert 1998, Rendtorff 2005, Hung 2006, Qin 2010, van Eeghen 2013, Overwater 2016). In 2 of those individuals, the variant was reported to have occurred de novo (Rendtorff 2005, Overwater 2016). Different missense substitutions at this codon (p.Arg1743 Pro), (p.Arg1743Trp), and (p.Arg1743Gly) have been reported in individuals with tuberous sclerosis (HGMD database). In vitro functional studies provide some evi dence that the p.Arg1743Gln variant may impact protein function (Coevoets 2009, Hoogeveen-Westerveld 2011, Overwater 2016). However, these types of assays may n ot accurately represent biological function. Computational prediction tools and conservation analysis suggest that the p.Arg1743Gln variant may impact the prot ein, though this information is not predictive enough to determine pathogenicity . In summary, this variant meets criteria to be classified as pathogenic for tub erous sclerosis in an autosomal dominant manner based upon presence in multiple affected individuals, absence from controls, in vitro functional evidence, and p redicted impact on protein. ACMG/AMP Criteria applied: PS2; PM5; PS4_Moderate; P M2; PS3_Moderate. -

Hereditary cancer-predisposing syndrome Pathogenic:1

Likely pathogenic, criteria provided, single submitter

clinical testing

Ambry Genetics

Jun 22, 2018

The p.R1743Q variant (also known as c.5228G>A), located in coding exon 40 of the TSC2 gene, results from a G to A substitution at nucleotide position 5228. The arginine at codon 1743 is replaced by glutamine, an amino acid with highly similar properties. This variant has been detected in multiple individual's with a clinical diagnosis of TSC (Gilbert JR et al. Neurogenetics. 1998 Aug;1:267-72; Au KS et al. Genet. Med. 2007 Feb;9:88-100; van Eeghen AM et al. Epilepsy Res. 2013 Jan;103:83-7). Functional studies have shown that the p.R1743Q variant leads to significantly reduced protein expression and disrupts the normal formation of the TSC1 and TSC2 complex (Coevoets R et al. Eur. J. Hum. Genet. 2009 Mar;17:301-10; Hoogeveen-Westerveld M et al. Hum. Mutat. 2011 Apr;32:424-35; Overwater IE et al. Eur. J. Hum. Genet. 2016 12;24:1688-1695). Of note, this variant is also referred to as p.R1720Q (c. 5177G>A) in some literature. This amino acid position is highly conserved in available vertebrate species. In addition, this alteration is predicted to be deleterious by in silico analysis. Based on the majority of available evidence to date, this variant is likely to be pathogenic. -

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
AlphaMissense	Pathogenic	0.98
BayesDel_addAF	Pathogenic	0.58	D
BayesDel_noAF	Pathogenic	0.59
CADD	Pathogenic	32
DANN	Pathogenic	1.0
DEOGEN2	Pathogenic	0.96	D;.;.;.;.;.;.;.;.;.;.;.;D;.;D
Eigen	Pathogenic	0.83
Eigen_PC	Pathogenic	0.73
FATHMM_MKL	Uncertain	0.96	D
LIST_S2	Uncertain	0.97	D;D;D;D;D;D;D;D;D;D;D;D;D;D;D
M_CAP	Pathogenic	0.98	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	0.67	T
PROVEAN	Uncertain	-3.6	D;.;.;D;.;D;.;.;D;D;.;.;.;.;D
REVEL	Pathogenic	0.96
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		0.92
MutPred		0.92		Loss of MoRF binding (P = 0.0739);.;.;.;.;.;.;.;.;.;.;.;.;.;.;
MVP		0.99
ClinPred		1.0	D
GERP RS		4.2
RBP_binding_hub_radar		0.0
RBP_regulation_power_radar		1.1
Varity_R		0.85
gMVP		0.89

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: rs45507199; hg19: chr16-2138295; COSMIC: COSV51913895; COSMIC: COSV51913895;