19-15192134-G-A

Position:

• chr19-15192134-G-A

Variant summary

Our verdict is Pathogenic. Variant got 14 ACMG points: 14P and 0B. PM1 PM2 PP3_Moderate PP5_Very_Strong

The NM_000435.3(NOTCH3):​c.505C>T​(p.Arg169Cys) variant causes a missense change involving the alteration of a conserved nucleotide. The variant allele was found at a frequency of 0.00000205 in 1,460,660 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 Pathogenic (★★).

• Frequency:
  • Genomes: not found (cov: 32)
  • Exomes 𝑓: 0.0000021 (0 hom.)
• Consequence: NOTCH3 NM_000435.3 missense
• Clinical Significance: Pathogenic criteria provided, multiple submitters, no conflicts P:15 O:1
• Conservation: PhyloP100: 7.94

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 14 ACMG points.

• PM1: In a domain EGF-like 4; calcium-binding (size 37) in uniprot entity NOTC3_HUMAN there are 37 pathogenic changes around while only 1 benign (97%) in NM_000435.3
• PM2: Very rare variant in population databases, with high coverage
• PP3: MetaRNN computational evidence supports a deleterious effect, 0.922
• PP5: Variant 19-15192134-G-A is Pathogenic according to our data. Variant chr19-15192134-G-A is described in ClinVar as [Pathogenic]. Clinvar id is 9219.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr19-15192134-G-A is described in Lovd as [Pathogenic]. Variant chr19-15192134-G-A is described in Lovd as [Likely_pathogenic].

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
NOTCH3	NM_000435.3	c.505C>T	p.Arg169Cys	missense_variant	4/33	ENST00000263388.7	NP_000426.2
NOTCH3	XM_005259924.5	c.505C>T	p.Arg169Cys	missense_variant	4/32		XP_005259981.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
NOTCH3	ENST00000263388.7	c.505C>T	p.Arg169Cys	missense_variant	4/33	1	NM_000435.3	ENSP00000263388.1
NOTCH3	ENST00000601011.1	c.502C>T	p.Arg168Cys	missense_variant	4/23	5		ENSP00000473138.1

Frequencies

GnomAD3 genomes Cov.: 32

GnomAD4 exome AF: 0.00000205 AC: 3 AN: 1460660 Hom.: 0 Cov.: 40 AF XY: 0.00000275 AC XY: 2 AN XY: 726678

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: 0.0000166

GnomAD4 genome Cov.: 32

ClinVar

Significance: Pathogenic

Submissions summary: Pathogenic:15 Other:1

Revision: criteria provided, multiple submitters, no conflicts

Submissions by phenotype

not provided Pathogenic:7

Pathogenic, criteria provided, single submitter	clinical testing	Mayo Clinic Laboratories, Mayo Clinic	Sep 05, 2024	PP1, PP2, PP4, PM1, PM2_moderate, PS3, PS4 -
Pathogenic, criteria provided, single submitter	clinical testing	Labcorp Genetics (formerly Invitae), Labcorp	Oct 04, 2023	This sequence change replaces arginine, which is basic and polar, with cysteine, which is neutral and slightly polar, at codon 169 of the NOTCH3 protein (p.Arg169Cys). This variant is not present in population databases (gnomAD no frequency). This missense change has been observed in individuals with cerebral arteriopathy with subcortical infarcts and leukoencephalopathy (PMID: 12754354, 25412914, 28334938). It has also been observed to segregate with disease in related individuals. ClinVar contains an entry for this variant (Variation ID: 9219). 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. Experimental studies have shown that this missense change affects NOTCH3 function (PMID: 21940951). For these reasons, this variant has been classified as Pathogenic. -
Pathogenic, criteria provided, single submitter	clinical testing	Athena Diagnostics	Nov 15, 2022	This variant has been identified in multiple unrelated individuals with CADASIL. This variant has not been reported in large, multi-ethnic general populations (http://gnomad.broadinstitute.org). This variant alters a critical location within the protein, and is expected to severely affect function and cause disease. Greater than 90% of NOTCH3 pathogenic variants associated with CADASIL involve the gain or loss of a cysteine residue within the epidermal growth factor (EGF)-like repeat domain (PMID: 32457593, 20301673). -
Pathogenic, criteria provided, single submitter	clinical testing	GeneDx	Sep 25, 2020	Reported in individuals with CADASIL in published literature, including one family with an atypical presentation with symptoms of autoimmunity (Joutel et al., 1996; Joutel et al., 1997; Paraskevas et al., 2014); Published studies demonstrate that knock out mice with the R170C variant, which corresponds to R169C in humans, develop features of CADASIL (Wallays et al., 2011; Cognat et al., 2014; Joutel et al., 2010); Not observed in large population cohorts (Lek et al., 2016); 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: 32277177, 32581362, 31753008, 32344328, 31418856, 30014602, 25412914, 20071773, 11909813, 28334938, 9388399, 12754354, 15287509, 8878478, 24425116, 21940951, 32765252) -
Pathogenic, criteria provided, single submitter	clinical testing	CeGaT Center for Human Genetics Tuebingen	Sep 01, 2023	NOTCH3: PM1:Strong, PM2, PS4:Moderate, PP2, PP4, PS3:Supporting -
Pathogenic, criteria provided, single submitter	clinical testing	ARUP Laboratories, Molecular Genetics and Genomics, ARUP Laboratories	Oct 30, 2023	The NOTCH3 c.505C>T; p.Arg169Cys variant (rs28933696) is reported in the medical literature in individuals with CADASIL (Lynch 2017, Opherk 2004, Paraskevas 2014). Additionally, a mouse model with this variant shows hallmarks of disease (Cognat 2014). The variant is described in the ClinVar database (Variation ID: 9219) and is absent from the Genome Aggregation Database, indicating it is not a common polymorphism. Computational analyses predict that this variant is deleterious (REVEL: 0.726). Considering available information, this variant is classified as pathogenic. References: Cognat E et al. Archetypal Arg169Cys mutation in NOTCH3 does not drive the pathogenesis in cerebral autosomal dominant arteriopathy with subcortical infarcts and leucoencephalopathy via a loss-of-function mechanism. Stroke. 2014 Mar;45(3):842-9. PMID: 24425116. Lynch DS et al. Clinical and genetic characterization of leukoencephalopathies in adults. Brain. 2017 May 1;140(5):1204-1211. PMID: 28334938. Opherk C et al. Long-term prognosis and causes of death in CADASIL: a retrospective study in 411 patients. Brain. 2004 Nov;127(Pt 11):2533-9. PMID: 15364702. Paraskevas GP et al. CADASIL and autoimmunity: coexistence in a family with the R169C mutation at exon 4 of the NOTCH3 gene. Cerebrovasc Dis. 2014;38(4):302-7. PMID: 25412914 -
Pathogenic, criteria provided, single submitter	clinical testing	Institute of Medical Genetics and Applied Genomics, University Hospital Tübingen	Sep 15, 2021	- -

Cerebral arteriopathy, autosomal dominant, with subcortical infarcts and leukoencephalopathy, type 1 Pathogenic:4 Other:1

Pathogenic, no assertion criteria provided	literature only	OMIM	Nov 22, 1997	- -
Pathogenic, criteria provided, single submitter	clinical testing	Institute of Human Genetics, University of Leipzig Medical Center	Jan 16, 2018	- -
Pathogenic, criteria provided, single submitter	clinical testing	MGZ Medical Genetics Center	Sep 07, 2022	- -
Pathogenic, criteria provided, single submitter	clinical testing	DASA	Mar 05, 2022	Well-established in vitro or in vivo functional studies supportive of a damaging effect on the gene or gene product (PMID: 24425116) - The c.505C>T;p.(Arg169Cys) missense variant has been observed in affected individual(s) and ClinVar contains an entry for this variant (ClinVar ID: 9219; PMID: 28334938; PMID: 25412914) - PS4. The variant is located in a mutational hot spot and/or critical and well-established functional domain (EGF_CA; hEGF) - PM1. This variant is not present in population databases (rs28933696- gnomAD; ABraOM no frequency - http://abraom.ib.usp.br/) - PM2. The variant co-segregated with disease in multiple affected family members (PMID: 25412914) - PP1. Multiple lines of computational evidence support a deleterious effect on the gene or gene product - PP3. In summary, the currently available evidence indicates that the variant is pathogenic. -
not provided, no classification provided	phenotyping only	GenomeConnect - CureCADASIL	-	Variant interpreted as Pathogenic and reported on 07-16-2019 by lab or GTR ID University of Washington Laboratory for Precision Diagnostics. 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. Phenotypic details are available under supporting information. -

NOTCH3-related disorder Pathogenic:2

Pathogenic, no assertion criteria provided	clinical testing	PreventionGenetics, part of Exact Sciences	Jul 01, 2024	The NOTCH3 c.505C>T variant is predicted to result in the amino acid substitution p.Arg169Cys. This variant has been observed in numerous patients with CADASIL and is located in a mutation hotspot (Ni et al. 2022. PubMed ID: 35822697). Its pathogenicity is supported by functional studies (Lynch et al. 2017. PubMed ID: 28334938; Wallays et al. 2011. PubMed ID: 21940951). This variant has not been reported in a large population database, indicating this variant is rare. Most CADASIL causing variants in the NOTCH3 gene result in the gain or loss of one or more cysteine residues in the extracellular domain of the protein, as seen in this patient. This patient’s variant adds a cysteine residue and is located in the extracellular EGF-like domain 4. Pathogenic variants in EGF-like domains 1-6 appear to be fully penetrant and are usually associated with the classical CADASIL phenotype. However, there is variability in disease severity (OMIM #125310; Rutten et al. 2016. PubMed ID: 27844030; Rutten et al. 2019. PubMed ID: 30032161). This variant is interpreted as pathogenic. -
Pathogenic, criteria provided, single submitter	clinical testing	Women's Health and Genetics/Laboratory Corporation of America, LabCorp	Jul 23, 2024	Variant summary: NOTCH3 c.505C>T (p.Arg169Cys) results in a non-conservative amino acid change in the encoded protein sequence. Five of five in-silico tools predict a damaging effect of the variant on protein function. The variant was absent in 247840 control chromosomes. c.505C>T has been reported in the literature in multiple individuals affected with NOTCH3-Related Disorders (example, Thijs_2003, Mukai_2020). These data indicate that the variant is very likely to be associated with disease. At least one publication reports experimental evidence, which suggests this variant may affect protein function in a knock-in mouse model (Wallays_2011). The following publications have been ascertained in the context of this evaluation (PMID: 21940951, 32277177, 12754354). ClinVar contains an entry for this variant (Variation ID: 9219). Based on the evidence outlined above, the variant was classified 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

Fulgent Genetics, Fulgent Genetics

Jul 28, 2021

- -

Stroke disorder;C0338480:Migraine without aura Pathogenic:1

Likely pathogenic, no assertion criteria provided

research

NIHR Bioresource Rare Diseases, University of Cambridge

-

- -

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
AlphaMissense	Benign	0.19
BayesDel_addAF	Pathogenic	0.22	D
BayesDel_noAF	Uncertain	0.080
CADD	Pathogenic	26
DANN	Pathogenic	1.0
DEOGEN2	Uncertain	0.61	D;D
Eigen	Uncertain	0.31
Eigen_PC	Uncertain	0.38
FATHMM_MKL	Pathogenic	0.98	D
LIST_S2	Uncertain	0.88	D;D
M_CAP	Pathogenic	0.46	D
MetaRNN	Pathogenic	0.92	D;D
MetaSVM	Uncertain	0.62	D
MutationAssessor	Benign	1.1	L;.
PrimateAI	Benign	0.31	T
PROVEAN	Uncertain	-4.3	D;.
REVEL	Pathogenic	0.73
Sift	Uncertain	0.011	D;.
Sift4G	Uncertain	0.0060	D;T
Polyphen		0.99	D;.
Vest4		0.88
MutPred		0.81		Loss of glycosylation at T173 (P = 0.1693);.;
MVP		0.98
MPC		1.3
ClinPred		0.95	D
GERP RS		4.9
Varity_R		0.38
gMVP		0.42

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.030		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: rs28933696; hg19: chr19-15302945; COSMIC: COSV54627527;