rs1174625611

Positions:

• chr19-15192218-G-A
• chr19-15192218-G-T

Variant summary

Our verdict is Pathogenic. Variant got 14 ACMG points: 14P and 0B. PM1 PP3_Strong PP5_Very_Strong

The NM_000435.3(NOTCH3):​c.421C>T​(p.Arg141Cys) variant causes a missense change. The variant allele was found at a frequency of 0.0000048 in 1,456,966 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: 0.0000048 (0 hom.)
• Consequence: NOTCH3 NM_000435.3 missense
• Clinical Significance: Pathogenic criteria provided, multiple submitters, no conflicts P:11 O:1
• Conservation: PhyloP100: 5.57

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 disulfide_bond (size 16) in uniprot entity NOTC3_HUMAN there are 18 pathogenic changes around while only 0 benign (100%) in NM_000435.3
• PP3: MetaRNN computational evidence supports a deleterious effect, 0.977
• PP5: Variant 19-15192218-G-A is Pathogenic according to our data. Variant chr19-15192218-G-A is described in ClinVar as [Pathogenic]. Clinvar id is 447846.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr19-15192218-G-A is described in Lovd as [Pathogenic].

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
NOTCH3	NM_000435.3	c.421C>T	p.Arg141Cys	missense_variant	4/33	ENST00000263388.7	NP_000426.2
NOTCH3	XM_005259924.5	c.421C>T	p.Arg141Cys	missense_variant	4/32		XP_005259981.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
NOTCH3	ENST00000263388.7	c.421C>T	p.Arg141Cys	missense_variant	4/33	1	NM_000435.3	ENSP00000263388	P1
NOTCH3	ENST00000601011.1	c.418C>T	p.Arg140Cys	missense_variant	4/23	5		ENSP00000473138

Frequencies

GnomAD3 genomes Cov.: 32

GnomAD4 exome AF: 0.00000480 AC: 7 AN: 1456966 Hom.: 0 Cov.: 40 AF XY: 0.00000276 AC XY: 2 AN XY: 724556

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: 0.00000630

Gnomad4 OTH exome AF: 0.00

GnomAD4 genome Cov.: 32

ClinVar

Significance: Pathogenic

Submissions summary: Pathogenic:11 Other:1

Revision: criteria provided, multiple submitters, no conflicts

Submissions by phenotype

not provided Pathogenic:7

Pathogenic, criteria provided, single submitter	clinical testing	ARUP Laboratories, Molecular Genetics and Genomics, ARUP Laboratories	Aug 11, 2023	The NOTCH3 c.421C>T; p.Arg141Cys variant is reported in the literature in numerous individuals with clinical diagnoses or personal and family histories indicative of CADASIL (Cappelli 2009, Joutel 1997, Kusaba 2007, Lee 2006, Murakami 2001, Onder 2017, Yadav 2013) and familial studies demonstrate that the variant cosegregates with disease (Murakami 2001, Yadav 2013). This variant is reported in ClinVar (Variation ID: 447846), and it is absent from general population databases (Exome Variant Server, Genome Aggregation Database), indicating it is not a common polymorphism. The arginine at codon 141 is highly conserved and computational analyses (SIFT, PolyPhen-2) predict that this variant is deleterious. Furthermore, this variant creates an additional cysteine in an EGF-like repeat domain, which is thought to lead to abnormal disulfide bridge formation and perturb protein function (Joutel 1997, Rutten 2016). Consistent with this notion, functional studies indicate that the p.Arg141Cys variant aggregates in the cytoplasm and is not efficiently processed and trafficked to the plasma membrane (Karlstrom 2002). Based on available information, this variant is considered to be pathogenic. References: Cappelli A et al. High recurrence of the R1006C NOTCH3 mutation in central Italian patients with cerebral autosomal dominant arteriopathy with subcortical infarcts and leukoencephalopathy (CADASIL). Neurosci Lett. 2009 Sep 22;462(2):176-8. Joutel A et al. Strong clustering and stereotyped nature of Notch3 mutations in CADASIL patients. Lancet. 1997 Nov 22;350(9090):1511-5. Karlstrom H et al. A CADASIL-mutated Notch 3 receptor exhibits impaired intracellular trafficking and maturation but normal ligand-induced signaling. Proc Natl Acad Sci U S A. 2002 Dec 24;99(26):17119-24. Kusaba T et al. Renal involvement in cerebral autosomal dominant arteriopathy with subcortical infarcts and leukoencephalopathy (CADASIL). Clin Nephrol. 2007 Mar;67(3):182-7. Lee YC et al. Cerebral autosomal dominant arteriopathy with subcortical infarcts and leukoencephalopathy: two novel mutations in the NOTCH3 gene in Chinese. J Neurol Sci. 2006 Jul 15;246(1-2):111-5. Murakami T et al. Two Japanese CADASIL families with a R141C mutation in the Notch3 gene. Intern Med. 2001 Nov;40(11):1144-8. Onder H et al. R141C Mutation of NOTCH3 Gene in Cerebral Autosomal Dominant Arteriopathy with Subcortical Infarcts and Leukoencephalopathy. J Neurosci Rural Pract. 2017 Apr-Jun;8(2):301-303. Rutten JW et al. Archetypal NOTCH3 mutations frequent in public exome: implications for CADASIL. Ann Clin Transl Neurol. 2016 Sep 28;3(11):844-853. Yadav S et al. The first Indian-origin family with genetically proven cerebral autosomal dominant arteriopathy with subcortical infarcts and leukoencephalopathy (CADASIL). J Stroke Cerebrovasc Dis. 2013 Jan;22(1):28-31. -
Pathogenic, criteria provided, single submitter	clinical testing	GeneDx	Mar 21, 2023	Published functional studies demonstrate a damaging effect on cell surface expression and protein trafficking (Karlstrom et al., 2002).; 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: 31680059, 32188464, 17390743, 11757773, 16580020, 21737310, 19576955, 12482954, 15981641, 17235124, 10227618, 10371548, 11102981, 16009764, 11755616, 15364702, 9388399, 15229130, 10712431, 31433517, 32277177, 36047879, 34741685) -
Pathogenic, criteria provided, single submitter	clinical testing	Athena Diagnostics	Dec 20, 2022	This variant has been identified in multiple unrelated individuals with clinical features of CADASIL. This variant has not been reported in large, multi-ethnic general populations (Genome Aggregation Database (gnomAD), Cambridge, MA (URL: http://gnomad.broadinstitute.org)). This variant has been previously reported as c.499C>T. Assessment of experimental evidence suggests this variant results in abnormal protein function. (PMID: 12482954) 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	Mayo Clinic Laboratories, Mayo Clinic	Jun 14, 2023	PP1, PP2, PP3, PM1, PM2, PS3, PS4 -
Pathogenic, criteria provided, single submitter	clinical testing	CeGaT Center for Human Genetics Tuebingen	Jun 01, 2022	NOTCH3: PM1:Strong, PM2, PS4:Moderate, PP2, PP4 -
Pathogenic, criteria provided, single submitter	clinical testing	Clinical Genetics Laboratory, Skane University Hospital Lund	May 27, 2022	- -
Pathogenic, criteria provided, single submitter	clinical testing	Labcorp Genetics (formerly Invitae), Labcorp	Jan 25, 2024	This sequence change replaces arginine, which is basic and polar, with cysteine, which is neutral and slightly polar, at codon 141 of the NOTCH3 protein (p.Arg141Cys). 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: 9388399, 11757773, 16580020). It has also been observed to segregate with disease in related individuals. ClinVar contains an entry for this variant (Variation ID: 447846). 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. -

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

not provided, no classification provided	phenotyping only	GenomeConnect - CureCADASIL	-	Variant interpreted as Pathogenic and reported most recently on 05/13/2013 by Lab or GTR ID 1012. The variant was also interpreted as Pathogenic by Lab or GTR ID 239772 on 80-16-2017. 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. -
Pathogenic, criteria provided, single submitter	clinical testing	MGZ Medical Genetics Center	Jan 20, 2022	- -
Pathogenic, criteria provided, single submitter	clinical testing	3billion	Jan 03, 2022	The variant was co-segregated with Cerebral arteriopathy with subcortical infarcts and leukoencephalopathy 1 in multiple affected family members with additional meioses meeting moderate evidence levels (PMID: 11757773, 21737310, PP1_M). The variant has been observed in multiple (>3) similarly affected unrelated individuals (PMID: 11757773, 21737310, 19576955, 16580020, 28479817, PS4_S). Functional studies provide strong evidence of the variant having a damaging effect on the gene or gene product (PMID: 12482954, PS3_S). In silico tool predictions suggest damaging effect of the variant on gene or gene product (REVEL: 0.874, 3CNET: 0.861, PP3_P). A missense variant is a common mechanism associated with Cerebral arteriopathy with subcortical infarcts and leukoencephalopathy 1 (PP2_P). It is not observed in the gnomAD v2.1.1 dataset (PM2_M). Therefore, this variant is classified as pathogenic according to the recommendation of ACMG/AMP guideline. -

NOTCH3-related disorder Pathogenic:1

Pathogenic, no assertion criteria provided

clinical testing

PreventionGenetics, part of Exact Sciences

Jul 15, 2024

The NOTCH3 c.421C>T variant is predicted to result in the amino acid substitution p.Arg141Cys. This variant has been reported as causative for CADASIL in numerous unrelated patients, and functional studies support its pathogenicity (see, for example, Joutel et al. Lancet. 1997. PubMed ID: 9388399; Karlström et al. 2002. PubMed ID: 12482954; Cappelli et al. 2009. PubMed ID: 19576955). At PreventionGenetics, we previously identified this variant in other patients with a diagnosis of CADASIL. 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 alters a cysteine residue and is located in the extracellular EGF-like domain three. 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). We classify this variant 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 27, 2021

- -

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
AlphaMissense	Uncertain	0.51
BayesDel_addAF	Pathogenic	0.28	D
BayesDel_noAF	Pathogenic	0.16
CADD	Pathogenic	32
DANN	Pathogenic	1.0
DEOGEN2	Pathogenic	0.82	D;D
Eigen	Pathogenic	0.70
Eigen_PC	Uncertain	0.66
FATHMM_MKL	Pathogenic	1.0	D
LIST_S2	Benign	0.82	T;D
M_CAP	Pathogenic	0.78	D
MetaRNN	Pathogenic	0.98	D;D
MetaSVM	Pathogenic	0.96	D
MutationAssessor	Benign	1.9	L;.
MutationTaster	Benign	1.0	D
PrimateAI	Uncertain	0.54	T
PROVEAN	Uncertain	-3.6	D;.
REVEL	Pathogenic	0.87
Sift	Benign	0.031	D;.
Sift4G	Uncertain	0.038	D;D
Polyphen		1.0	D;.
Vest4		0.85
MutPred		0.86		Gain of sheet (P = 0.1208);.;
MVP		1.0
MPC		1.5
ClinPred		0.96	D
GERP RS		5.0
Varity_R		0.53
gMVP		0.60

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: rs1174625611; hg19: chr19-15303029; COSMIC: COSV54638194;