16-2071534-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.1864C>T(p.Arg622Trp) variant causes a missense change. The variant allele was found at a frequency of 0.00000137 in 1,461,296 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a pathogenic outcome for this variant. Variant has been reported in ClinVar as Likely pathogenic (★★). Another variant affecting the same amino acid position, but resulting in a different missense (i.e. R622P) has been classified as Likely pathogenic.

• Frequency:
  • Genomes: not found (cov: 33)
  • Exomes 𝑓: 0.0000014 (0 hom.)
• Consequence: TSC2 NM_000548.5 missense
• Clinical Significance: Pathogenic/Likely pathogenic criteria provided, multiple submitters, no conflicts P:9 O:2
• Conservation: PhyloP100: 3.75

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 hotspot region, there are 2 aminoacids with missense pathogenic changes in the window of +-8 aminoacids around while only 5 benign, 13 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 chr16-2071535-G-C is described in ClinVar as [Conflicting_classifications_of_pathogenicity]. Clinvar id is 49775.We mark this variant Likely_pathogenic, oryginal submissions are: {not_provided=1, Uncertain_significance=2, Likely_pathogenic=1}.
• PP3: MetaRNN computational evidence supports a deleterious effect, 0.95
• PP5: Variant 16-2071534-C-T is Pathogenic according to our data. Variant chr16-2071534-C-T is described in ClinVar as [Likely_pathogenic]. Clinvar id is 64889.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr16-2071534-C-T is described in Lovd as [Pathogenic]. Variant chr16-2071534-C-T is described in Lovd as [Pathogenic]. Variant chr16-2071534-C-T is described in Lovd as [Likely_pathogenic].

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
TSC2	NM_000548.5	c.1864C>T	p.Arg622Trp	missense_variant	18/42	ENST00000219476.9

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
TSC2	ENST00000219476.9	c.1864C>T	p.Arg622Trp	missense_variant	18/42	5	NM_000548.5

Frequencies

GnomAD3 genomes Cov.: 33

GnomAD4 exome AF: 0.00000137 AC: 2 AN: 1461296 Hom.: 0 Cov.: 32 AF XY: 0.00000138 AC XY: 1 AN XY: 726972

Gnomad4 AFR exome AF: 0.00

Gnomad4 AMR exome AF: 0.00

Gnomad4 ASJ exome AF: 0.00

Gnomad4 EAS exome AF: 0.00

Gnomad4 SAS exome AF: 0.00

Gnomad4 FIN exome AF: 0.00

Gnomad4 NFE exome AF: 0.00000180

Gnomad4 OTH exome AF: 0.00

GnomAD4 genome Cov.: 33

Bravo AF: 0.00000378

EpiCase AF: 0.00

EpiControl AF: 0.0000593

ClinVar

Significance: Pathogenic/Likely pathogenic

Submissions summary: Pathogenic:9 Other:2

Revision: criteria provided, multiple submitters, no conflicts

Submissions by phenotype

Tuberous sclerosis 2 Pathogenic:6 Other:1

Likely 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	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. (I) 0115 - Variants in this gene are known to have variable expressivity. The p.(Arg622Trp) variant has been reported to result in a milder phenotype than other TSC2 variants (PMID: 28211972). (I) 0200 - Variant is predicted to result in a missense amino acid change from arginine to tryptophan. (I) 0251 - This variant is heterozygous. (I) 0301 - Variant is absent from gnomAD (both v2 and v3). (SP) 0309 - An alternative amino acid change at the same position has been observed in gnomAD (v2) (18 heterozygotes, 0 homozygotes). (I) 0501 - Missense variant consistently predicted to be damaging by multiple in silico tools or highly conserved with a major amino acid change. (SP) 0600 - Variant is located in the annotated tuberin domain (NCBI, PDB). (I) 0710 - Other missense variants comparable to the one identified in this case have inconclusive previous evidence for pathogenicity. Alternative changes at the same residue, to glutamine and proline, have previously been reported with conflicting classifications, included benign, VUS and pathogenic (ClinVar, PMID: 29476190). (I) 0801 - This variant has strong previous evidence of pathogenicity in unrelated individuals. The variant has previously been reported in a number of individuals with tuberous sclerosis-2 (MIM#613254), however the reported patients are considered to have a mild phenotype and do not always meet all the major criteria for diagnosis (ClinVar, HGMD, LOVD, PMIDs: 28211972, 31005478). (SP) 1002 - This variant has moderate functional evidence supporting abnormal protein function. Functional studies in transfected cells demonstrated a loss of function (PMID: 20633017). (SP) 1208 - Inheritance information for this variant is not currently available in this individual. (I) Legend: (SP) - Supporting pathogenic, (I) - Information, (SB) - Supporting benign -
Likely pathogenic, criteria provided, single submitter	clinical testing	Myriad Genetics, Inc.	Mar 13, 2024	This variant is considered likely pathogenic. This variant has been reported in multiple individuals with clinical features of gene-specific disease [PMID: 28211972, 29101226, 29933521, 36232477, 31005478]. Functional studies indicate this variant impacts protein function [PMID: 21309039, 20633017]. -
not provided, no classification provided	literature only	GeneReviews	-	- -
Likely pathogenic, criteria provided, single submitter	clinical testing	Revvity Omics, Revvity	Sep 07, 2021	- -
Likely pathogenic, criteria provided, single submitter	clinical testing	Genome-Nilou Lab	Nov 07, 2021	- -
Pathogenic, criteria provided, single submitter	clinical testing	Invitae	Jan 18, 2024	This sequence change replaces arginine, which is basic and polar, with tryptophan, which is neutral and slightly polar, at codon 622 of the TSC2 protein (p.Arg622Trp). This variant is not present in population databases (gnomAD no frequency). This missense change has been observed in individuals with clinical features of tuberous sclerosis complex (PMID: 21520333, 21846442, 22867869, 28211972). It has also been observed to segregate with disease in related individuals. ClinVar contains an entry for this variant (Variation ID: 64889). 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: 20633017, 21309039). This variant disrupts the p.Arg622 amino acid residue in TSC2. Other variant(s) that disrupt this residue have been observed in individuals with TSC2-related conditions (PMID: 29476190), which suggests that this may be a clinically significant amino acid residue. For these reasons, this variant has been classified as Pathogenic. -

TSC2-related disorder Pathogenic:1

Likely pathogenic, criteria provided, single submitter

clinical testing

PreventionGenetics, part of Exact Sciences

Aug 31, 2022

The TSC2 c.1864C>T variant is predicted to result in the amino acid substitution p.Arg622Trp. This variant was reported in individuals and families with tuberous sclerosis complex, some of whom had mild or atypical presentations (Table S1, van Eeghen et al. 2012. PubMed ID: 22867869; Farach et al. 2017. PubMed ID: 28211972). In vitro experimental studies suggest that this variant impacts protein function (Figure 3, Table S2, 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 and likely pathogenic in ClinVar (https://www.ncbi.nlm.nih.gov/clinvar/variation/64889/). This variant is interpreted as likely pathogenic. -

not provided Pathogenic:1

Likely pathogenic, criteria provided, single submitter

clinical testing

GeneDx

Feb 08, 2023

Variant has been observed in individuals with some features of TSC including cardiac rhabdomyomas, cortical tubers, epilepsy, and renal cysts but did not fulfill TSC clinical diagnostic criteria, and in unaffected and mildly affected relatives in the published literature and at GeneDx; this suggests this variant may be associated with reduced penetrance and/or a milder TSC phenotype (Chadha et al., 2011; Farach et al., 2017; Xiong et al., 2019; Borges et al., 2022); Reported previously in patients with TSC, however no further clinical details were provided (Hoogeveen-Westerveld et al. 2011; van Eeghen et al., 2013; Davis et al., 2017); Published functional studies indicate R622W destabilizes the TSC2 protein (Qin et al., 2010; 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: 34800434, 34740132, 31031587, 33011641, 21309039, 22867869, 28211972, 15798777, 29101226, 20633017, 21846442, 33327995, 36527179, 31005478) -

Hereditary cancer-predisposing syndrome Pathogenic:1

Pathogenic, criteria provided, single submitter

clinical testing

Ambry Genetics

Aug 27, 2020

The p.R622W pathogenic mutation (also known as c.1864C>T), located in coding exon 17 of the TSC2 gene, results from a C to T substitution at nucleotide position 1864. The arginine at codon 622 is replaced by tryptophan, an amino acid with dissimilar properties. This alteration has been identified in many individuals with clinical features suggestive of tuberous sclerosis including cardiac rhabdomyomas, renal angiomyolipomas, cortical tubers and cortical dysplasia (Farach LS et al. Am. J. Med. Genet. A, 2017 Mar;173:771-775; van Eeghen AM et al. Epilepsy Res., 2013 Jan;103:83-7; http://www.lovd.nl/TSC2). Evaluation of these families shows that the variant segregates with these disease features in multiple relatives; however, some carriers are unaffected or have subclinical manifestations of tuberous sclerosis, indicating it carries incomplete penetrance or a milder phenotype than classic TSC1/2 pathogenic mutations (Farach LS et al. Am. J. Med. Genet. A, 2017 Mar;173:771-775; Ambry internal data). Multiple functional studies have shown that this variant has defective TSC1 binding and stabilization as well as increased phosphorylation of S6K at residue T389 (Qin W et al. Brain Pathol., 2010 Nov;20:1096-105; Hoogeveen-Westerveld M et al. Hum. Mutat., 2011 Apr;32:424-35). 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 available evidence, this alteration is classified as a pathogenic mutation associated with reduced penetrance compared to other TSC2 mutations. -

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	0.61
BayesDel_addAF	Pathogenic	0.46	D
BayesDel_noAF	Pathogenic	0.43
Cadd	Pathogenic	28
Dann	Pathogenic	1.0
DEOGEN2	Pathogenic	0.93	D;.;.;.;.;.;.;.;.;.;.;.;D;.;D
Eigen	Uncertain	0.61
Eigen_PC	Uncertain	0.55
FATHMM_MKL	Uncertain	0.95	D
LIST_S2	Uncertain	0.97	D;D;D;D;D;D;D;D;D;D;D;D;D;D;D
M_CAP	Pathogenic	0.72	D
MetaRNN	Pathogenic	0.95	D;D;D;D;D;D;D;D;D;D;D;D;D;D;D
MetaSVM	Pathogenic	0.93	D
MutationAssessor	Pathogenic	3.0	M;.;.;.;M;M;.;.;.;M;.;M;.;.;.
MutationTaster	Benign	1.0	D;D;D;D;D;D;D
PrimateAI	Uncertain	0.71	T
PROVEAN	Pathogenic	-7.3	D;.;.;D;.;D;.;.;D;D;.;.;.;.;D
REVEL	Pathogenic	0.91
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		0.80		Gain of catalytic residue at L620 (P = 0.0044);Gain of catalytic residue at L620 (P = 0.0044);Gain of catalytic residue at L620 (P = 0.0044);.;Gain of catalytic residue at L620 (P = 0.0044);Gain of catalytic residue at L620 (P = 0.0044);Gain of catalytic residue at L620 (P = 0.0044);Gain of catalytic residue at L620 (P = 0.0044);.;Gain of catalytic residue at L620 (P = 0.0044);Gain of catalytic residue at L620 (P = 0.0044);Gain of catalytic residue at L620 (P = 0.0044);Gain of catalytic residue at L620 (P = 0.0044);Gain of catalytic residue at L620 (P = 0.0044);.;
MVP		0.98
ClinPred		0.99	D
GERP RS		4.5
RBP_binding_hub_radar		0.0
RBP_regulation_power_radar		1.7
Varity_R		0.83
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: rs397514914; hg19: chr16-2121535; COSMIC: COSV54779446; COSMIC: COSV54779446;