rs137852642

chr19-15192242-G-Achr19-15192242-G-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_000435.3(NOTCH3):c.397C>T(p.Arg133Cys) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000207 in 1,450,026 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. R133H) has been classified as Likely benign.

• Frequency:
  • Genomes: not found (cov: 32)
  • Exomes 𝑓: 0.0000021 (0 hom.)
• Consequence: NOTCH3 NM_000435.3 missense
• Clinical Significance: Pathogenic/Likely pathogenic criteria provided, multiple submitters, no conflicts P:15 O:2
• Conservation: PhyloP100: 3.36

Genes affected

NOTCH3 (HGNC:7883): (notch receptor 3) This gene encodes the third discovered human homologue of the Drosophilia melanogaster type I membrane protein notch. In Drosophilia, notch interaction with its cell-bound ligands (delta, serrate) establishes an intercellular signalling pathway that plays a key role in neural development. Homologues of the notch-ligands have also been identified in human, but precise interactions between these ligands and the human notch homologues remains to be determined. Mutations in NOTCH3 have been identified as the underlying cause of cerebral autosomal dominant arteriopathy with subcortical infarcts and leukoencephalopathy (CADASIL). [provided by RefSeq, Jul 2008]

ACMG classification

Verdict is Pathogenic. Variant got 18 ACMG points.

• PM1: In a hotspot region, there are 3 aminoacids with missense pathogenic changes in the window of +-8 aminoacids around while only 1 benign, 3 uncertain in NM_000435.3
• PM2: Very rare variant in population databases, with high coverage
• PM5: Other missense variant is known to change same aminoacid residue: Variant chr19-15192241-C-A is described in ClinVar as [Likely_pathogenic]. Clinvar id is 1687327.Status of the report is criteria_provided_single_submitter, 1 stars.
• PP3: MetaRNN computational evidence supports a deleterious effect, 0.945
• PP5: Variant 19-15192242-G-A is Pathogenic according to our data. Variant chr19-15192242-G-A is described in ClinVar as [Likely_pathogenic]. Clinvar id is 9225.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr19-15192242-G-A is described in Lovd as [Pathogenic]. Variant chr19-15192242-G-A is described in Lovd as [Pathogenic].

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
NOTCH3	NM_000435.3	c.397C>T	p.Arg133Cys	missense_variant	4/33	ENST00000263388.7
NOTCH3	XM_005259924.5	c.397C>T	p.Arg133Cys	missense_variant	4/32

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
NOTCH3	ENST00000263388.7	c.397C>T	p.Arg133Cys	missense_variant	4/33	1	NM_000435.3	P1
NOTCH3	ENST00000601011.1	c.394C>T	p.Arg132Cys	missense_variant	4/23	5

Frequencies

GnomAD3 genomes Cov.: 32

GnomAD3 exomes AF: 0.00000451 AC: 1 AN: 221490 Hom.: 0 AF XY: 0.00000829 AC XY: 1 AN XY: 120636

Gnomad AFR exome AF: 0.00

Gnomad AMR exome AF: 0.00

Gnomad ASJ exome AF: 0.00

Gnomad EAS exome AF: 0.00

Gnomad SAS exome AF: 0.00

Gnomad FIN exome AF: 0.0000517

Gnomad NFE exome AF: 0.00

Gnomad OTH exome AF: 0.00

GnomAD4 exome AF: 0.00000207 AC: 3 AN: 1450026 Hom.: 0 Cov.: 39 AF XY: 0.00000278 AC XY: 2 AN XY: 720456

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: 0.0000387

Gnomad4 NFE exome AF: 9.03e-7

Gnomad4 OTH exome AF: 0.00

GnomAD4 genome Cov.: 32

ClinVar

Significance: Pathogenic/Likely pathogenic

Submissions summary: Pathogenic:15 Other:2

Revision: criteria provided, multiple submitters, no conflicts

Submissions by phenotype

Cerebral arteriopathy, autosomal dominant, with subcortical infarcts and leukoencephalopathy, type 1 Pathogenic:6 Other:2

not provided, no classification provided	phenotyping only	GenomeConnect - CureCADASIL	-	Variant interpreted as Pathogenic and most recently reported on 09-17-2018 by Lab or GTR ID 1012. Variant also interpreted as Pathogenic and reported on 05-12-2019 by GTR ID 500035. GenomeConnect-CureCADASIL assertions are reported exactly as they appear on the patient-provided report from the testing laboratory. Registry team members make no attempt to reinterpret the clinical significance of the variant. -
not provided, no classification provided	literature only	GeneReviews	-	- -
Pathogenic, criteria provided, single submitter	clinical testing	Neuberg Centre For Genomic Medicine, NCGM	-	The missense variant p.R133C in NOTCH3 (NM_000435.3) has been observed with multiple affected individuals with CADASIL (Takahashi K, Peters N et al).The variant has been submitted to ClinVar as Pathogenic.The missense variant c.397C>T (p.R133C) in NOTCH3 (NM_000435.3) is observed in 1/19354 (0.0052%) alleles from individuals of Finnish background in the gnomAD dataset (Exome Aggregation Consortium et al., 2016), but was not seen in the homozygous state The p.R133C missense variant is predicted to be damaging by both SIFT and PolyPhen2. The nucleotide c.397 in NOTCH3 is predicted conserved by GERP++ and PhyloP across 100 vertebrates. For these reasons, this variant has been classified as Pathogenic. -
Pathogenic, no assertion criteria provided	literature only	OMIM	Aug 01, 2009	- -
Pathogenic, criteria provided, single submitter	clinical testing	Centre for Mendelian Genomics, University Medical Centre Ljubljana	Jan 01, 2016	This variant was classified as: Pathogenic. The following ACMG criteria were applied in classifying this variant: PS1,PM1,PM2,PP2,PP3. -
Pathogenic, criteria provided, single submitter	clinical testing	Institute of Human Genetics Munich, Klinikum Rechts Der Isar, TU München	Dec 21, 2020	- -
Pathogenic, criteria provided, single submitter	clinical testing	Laboratory of Medical Genetics, National & Kapodistrian University of Athens	Oct 01, 2021	PM1, PM2, PP2, PP3, PP5 -
Likely pathogenic, criteria provided, single submitter	clinical testing	Institute of Human Genetics, University of Leipzig Medical Center	Apr 20, 2018	- -

not provided Pathogenic:6

Pathogenic, criteria provided, single submitter	clinical testing	Athena Diagnostics	Feb 28, 2022	The frequency of this variant in the general population is consistent with pathogenicity (Genome Aggregation Database (gnomAD), Cambridge, MA (URL: http://gnomad.broadinstitute.org)). This variant has been identified in at least one individual with cerebral arteriopathy with subcortical infarcts and leukoencephalopathy (CADASIL). 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. The variant causes protein aggregation and ER retention, resulting in impaired cell proliferation (PMID: 19825845). This variant alters a critical location within the protein, and is expected to severely affect function and cause disease. Greater than 90% of pathogenic variants identified in NOTCH3 involve the gain or loss of a cysteine residue within the epidermal growth factor (EGF)-like repeat domain. -
Pathogenic, criteria provided, single submitter	clinical testing	Mayo Clinic Laboratories, Mayo Clinic	Jun 29, 2022	PP3, PP4, PP5, PM1, PS3, PS4 -
Pathogenic, criteria provided, single submitter	clinical testing	GeneDx	Aug 31, 2023	Published functional studies suggest that the R133C impacts protein function (Opherk et al., 2009; Takahashi et al., 2010; Wollenweber et al., 2015); 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: 10854111, 26261665, 11771160, 25819272, 15378071, 15364702, 16009764, 9388399, 15350543, 19417009, 19825845, 10969905, 11715067, 15716553, 22623959, 22019870, 11486103, 25604251, 28334938, 28534048, 10371548, 12810003, 11755616, 31571467, 31554780, 30402942, 31720972, 34335700, 34008892, 15143298, 10609671, 36047879, 32555735, 34741685, 10766655, 30392756, 16877080, 32277177, 24844136) -
Pathogenic, criteria provided, single submitter	clinical testing	CeGaT Center for Human Genetics Tuebingen	Jul 01, 2021	- -
Pathogenic, criteria provided, single submitter	clinical testing	ARUP Laboratories, Molecular Genetics and Genomics, ARUP Laboratories	Apr 21, 2022	The NOTCH3 c.397C>T; p.Arg133Cys variant (rs137852642) has been described in multiple individuals affected with CADASIL (Joutel 1997, Maclean 2005, Mykkanen 2004). This variant is reported as pathogenic or likely pathogenic in ClinVar (Variation ID: 9225), and is absent from general population databases (1000 Genomes Project, Exome Variant Server, and Genome Aggregation Database), indicating it is not a common polymorphism. The arginine at codon 133 is moderately conserved, and computational algorithms (PolyPhen-2, SIFT) predict that this variant is deleterious. In vitro characterization of this variant protein demonstrates increased spontaneous multimerization compared to wild-type (Opherk 2009). Based on available information, this variant is considered to be pathogenic. References: Joutel A et al. Strong clustering and stereotyped nature of Notch3 mutations in CADASIL patients. Lancet. 1997 Nov 22;350(9090):1511-5. Maclean A et al. Spontaneous lobar haemorrhage in CADASIL. J Neurol Neurosurg Psychiatry. 2005 Mar;76(3):456-7. Mykkanen K et al. Detection of the founder effect in Finnish CADASIL families. Eur J Hum Genet. 2004 Oct;12(10):813-9. Opherk C et al. CADASIL mutations enhance spontaneous multimerization of NOTCH3. Hum Mol Genet. 2009 Aug 1;18(15):2761-7. -
Pathogenic, criteria provided, single submitter	clinical testing	Invitae	Dec 01, 2023	This sequence change replaces arginine, which is basic and polar, with cysteine, which is neutral and slightly polar, at codon 133 of the NOTCH3 protein (p.Arg133Cys). This variant is not present in population databases (gnomAD no frequency). This missense change has been observed in individuals with CADASIL (PMID: 10969905, 22019870, 28334938). ClinVar contains an entry for this variant (Variation ID: 9225). 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) performed at Invitae indicates that this missense variant is expected to disrupt NOTCH3 protein function with a positive predictive value of 95%. For these reasons, this variant has been classified as Pathogenic. -

Recurrent subcortical infarcts Pathogenic:1

Likely pathogenic, criteria provided, single submitter

clinical testing

Centre for Mendelian Genomics, University Medical Centre Ljubljana

Nov 28, 2013

- -

NOTCH3-related condition Pathogenic:1

Pathogenic, criteria provided, single submitter

clinical testing

PreventionGenetics, part of Exact Sciences

Feb 03, 2023

The NOTCH3 c.397C>T variant is predicted to result in the amino acid substitution p.Arg133Cys. This variant has been reported as causative for CADASIL in numerous affected individuals and its pathogenicity is supported by functional studies (Joutel et al. 1997. PubMed ID: 9388399; Wollenweber et al. 2015. PubMed ID: 25604251). Of note, the vast majority of CADASIL-causing variants in the NOTCH3 gene are predicted to result in the gain or loss of cysteine residues in the extracellular domain of the protein, as seen in this patient. At PreventionGenetics, we have previously detected this variant in other affected individuals. This variant is reported in 0.0052% of alleles in individuals of European (Finnish) descent in gnomAD (http://gnomad.broadinstitute.org/variant/19-15303053-G-A) and is interpreted as pathogenic/likely pathogenic by multiple laboratories in ClinVar (https://www.ncbi.nlm.nih.gov/clinvar/variation/9225/). This variant is interpreted as pathogenic. -

Lateral meningocele syndrome;C3809084:Myofibromatosis, infantile, 2;C4551768:Cerebral arteriopathy, autosomal dominant, with subcortical infarcts and leukoencephalopathy, type 1 Pathogenic:1

Pathogenic, criteria provided, single submitter

clinical testing

North West Genomic Laboratory Hub, Manchester University NHS Foundation Trust

Apr 27, 2020

Criteria Codes: PS3_Str PS4_Mod PM1_Str PP1_Str PP2 -

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
AlphaMissense	Uncertain	0.41
BayesDel_addAF	Pathogenic	0.27	D
BayesDel_noAF	Pathogenic	0.15
Cadd	Pathogenic	31
Dann	Pathogenic	1.0
DEOGEN2	Uncertain	0.69	D;D
Eigen	Uncertain	0.61
Eigen_PC	Uncertain	0.57
FATHMM_MKL	Pathogenic	0.98	D
LIST_S2	Benign	0.32	T;T
M_CAP	Pathogenic	0.58	D
MetaRNN	Pathogenic	0.94	D;D
MetaSVM	Pathogenic	0.83	D
MutationAssessor	Benign	1.7	L;.
MutationTaster	Benign	1.0	A
PrimateAI	Uncertain	0.62	T
PROVEAN	Uncertain	-3.7	D;.
REVEL	Pathogenic	0.86
Sift	Benign	0.046	D;.
Sift4G	Uncertain	0.052	T;D
Polyphen		0.99	D;.
Vest4		0.71
MutPred		0.84		Gain of catalytic residue at S135 (P = 0.064);.;
MVP		1.0
MPC		1.4
ClinPred		0.96	D
GERP RS		5.0
Varity_R		0.63
gMVP		0.71

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: rs137852642; hg19: chr19-15303053;