rs201118034

chr19-15187315-G-Achr19-15187315-G-Cchr19-15187315-G-T

Variant summary

Our verdict is Uncertain significance. Variant got 5 ACMG points: 10P and 5B. PM1 PP5_Very_Strong BP4 BS2

The NM_000435.3(NOTCH3):c.1630C>T(p.Arg544Cys) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000595 in 1,613,780 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 12/21 in silico tools predict a benign 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. R544H) has been classified as Uncertain significance.

• Frequency:
  • Genomes: 𝑓 0.000039 (0 hom., cov: 33)
  • Exomes 𝑓: 0.000062 (0 hom.)
• Consequence: NOTCH3 NM_000435.3 missense
• Clinical Significance: Pathogenic/Likely pathogenic criteria provided, multiple submitters, no conflicts P:11 O:1
• Conservation: PhyloP100: 0.546

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 Uncertain_significance. Variant got 5 ACMG points.

• PM1: In a hotspot region, there are 2 aminoacids with missense pathogenic changes in the window of +-8 aminoacids around while only 2 benign, 4 uncertain in NM_000435.3
• PP5: Variant 19-15187315-G-A is Pathogenic according to our data. Variant chr19-15187315-G-A is described in ClinVar as [Likely_pathogenic]. Clinvar id is 546089.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr19-15187315-G-A is described in Lovd as [Likely_pathogenic]. Variant chr19-15187315-G-A is described in Lovd as [Pathogenic].
• BP4: Computational evidence support a benign effect (MetaRNN=0.017121106).. Strength limited to SUPPORTING due to the PP5.
• BS2: High AC in GnomAd at 6 AD gene.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
NOTCH3	NM_000435.3	c.1630C>T	p.Arg544Cys	missense_variant	11/33	ENST00000263388.7
NOTCH3	XM_005259924.5	c.1630C>T	p.Arg544Cys	missense_variant	11/32

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
NOTCH3	ENST00000263388.7	c.1630C>T	p.Arg544Cys	missense_variant	11/33	1	NM_000435.3	P1
NOTCH3	ENST00000601011.1	c.1627C>T	p.Arg543Cys	missense_variant	11/23	5

Frequencies

GnomAD3 genomes AF: 0.0000394 AC: 6 AN: 152192 Hom.: 0 Cov.: 33

Gnomad AFR AF: 0.00

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.00

Gnomad ASJ AF: 0.00

Gnomad EAS AF: 0.000770

Gnomad SAS AF: 0.00

Gnomad FIN AF: 0.00

Gnomad MID AF: 0.00

Gnomad NFE AF: 0.0000147

Gnomad OTH AF: 0.000479

GnomAD3 exomes AF: 0.000320 AC: 80 AN: 250312 Hom.: 0 AF XY: 0.000288 AC XY: 39 AN XY: 135504

Gnomad AFR exome AF: 0.00

Gnomad AMR exome AF: 0.0000289

Gnomad ASJ exome AF: 0.00

Gnomad EAS exome AF: 0.00414

Gnomad SAS exome AF: 0.0000981

Gnomad FIN exome AF: 0.00

Gnomad NFE exome AF: 0.00

Gnomad OTH exome AF: 0.00

GnomAD4 exome AF: 0.0000616 AC: 90 AN: 1461470 Hom.: 0 Cov.: 33 AF XY: 0.0000674 AC XY: 49 AN XY: 727074

Gnomad4 AFR exome AF: 0.00

Gnomad4 AMR exome AF: 0.0000224

Gnomad4 ASJ exome AF: 0.0000383

Gnomad4 EAS exome AF: 0.00151

Gnomad4 SAS exome AF: 0.000244

Gnomad4 FIN exome AF: 0.00

Gnomad4 NFE exome AF: 0.00000270

Gnomad4 OTH exome AF: 0.0000662

GnomAD4 genome AF: 0.0000394 AC: 6 AN: 152310 Hom.: 0 Cov.: 33 AF XY: 0.0000269 AC XY: 2 AN XY: 74482

Gnomad4 AFR AF: 0.00

Gnomad4 AMR AF: 0.00

Gnomad4 ASJ AF: 0.00

Gnomad4 EAS AF: 0.000771

Gnomad4 SAS AF: 0.00

Gnomad4 FIN AF: 0.00

Gnomad4 NFE AF: 0.0000147

Gnomad4 OTH AF: 0.000474

Alfa AF: 0.0000474 Hom.: 0

Bravo AF: 0.0000642

ExAC AF: 0.000264 AC: 32

ClinVar

Significance: Pathogenic/Likely pathogenic

Submissions summary: Pathogenic:11 Other:1

Revision: criteria provided, multiple submitters, no conflicts

Submissions by phenotype

not provided Pathogenic:5

Likely pathogenic, criteria provided, single submitter	clinical testing	Revvity Omics, Revvity	Sep 30, 2021	- -
Pathogenic, criteria provided, single submitter	clinical testing	Invitae	Nov 21, 2023	This sequence change replaces arginine, which is basic and polar, with cysteine, which is neutral and slightly polar, at codon 544 of the NOTCH3 protein (p.Arg544Cys). This variant is present in population databases (rs201118034, gnomAD 0.4%), and has an allele count higher than expected for a pathogenic variant. This missense change has been observed in individual(s) with cerebral arteriopathy with subcortical infarcts and leukoencephalopathy (PMID: 16717210, 19242647, 26308724, 30906334, 31792094). It is commonly reported in individuals of East Asian ancestry (PMID: 19242647). ClinVar contains an entry for this variant (Variation ID: 546089). 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. -
Pathogenic, criteria provided, single submitter	clinical testing	Athena Diagnostics	May 22, 2023	This variant is the most common variant associated with CADASIL in the East Asian population (PMID: 25692567, 26308724, 31792094), and is statistically more frequent in affected individuals than in the general population and/or healthy controls (Genome Aggregation Database (gnomAD), Cambridge, MA (URL: http://gnomad.broadinstitute.org)). Reports of this variant in asymptomatic individuals, as well as affected heterozygous and homozygous patients, suggests this variant may have reduced penetrance (PMID: 26308724, 30199759, 30656190, 31792094). This variant occurs as the most likely explanation for disease in a significant number of cases, suggesting this variant is associated with disease. 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). -
Likely pathogenic, criteria provided, single submitter	clinical testing	ARUP Laboratories, Molecular Genetics and Genomics, ARUP Laboratories	Apr 01, 2020	The NOTCH3 c.1630C>T; p.Arg544Cys variant (rs201118034) is reported in the literature in several individuals with CADASIL and segregates with disease in families (Choi 2013, Liao 2015, Tang 2018, Yoon 2015). The variant exhibits a founder effect in Asians (Liao 2015) and is reported in the East Asian population with an allele frequency of 0.4% (79/19916 alleles) in the Genome Aggregation Database. The variant is reported as pathogenic or likely pathogenic by several sources in the ClinVar database (Variation ID: 546089). The arginine at codon 544 computational analyses (SIFT: Tolerated, PolyPhen-2: Possibly Damaging) predict conflicting effects of this variant on protein structure/function. However, this variant creates a cysteine in an EGF-like domain and most pathogenic NOTCH3 variants create or destroy a cysteine residue within an EGF-like domain (Rutten 2014); thus, the p.Arg544Cys variant is consistent with the predominant mechanism of disease in NOTCH3. Considering available information, this variant is classified as likely pathogenic. REFERENCES Choi JC et al. Diversity of stroke presentation in CADASIL: study from patients harboring the predominant NOTCH3 mutation R544C. J Stroke Cerebrovasc Dis. 2013 Feb;22(2):126-31. Liao YC et al. Characterization of CADASIL among the Han Chinese in Taiwan: Distinct Genotypic and Phenotypic Profiles. PLoS One. 2015 Aug 26;10(8):e0136501. Rutten JW et al. Interpretation of NOTCH3 mutations in the diagnosis of CADASIL. Expert Rev Mol Diagn. 2014 Jun;14(5):593-603. Tang SC et al. Prevalence and clinical characteristics of stroke patients with p.R544C NOTCH3 mutation in Taiwan. Ann Clin Transl Neurol. 2018 Nov 20;6(1):121-128. Yoon CW et al. NOTCH3 variants in patients with subcortical vascular cognitive impairment: a comparison with typical CADASIL patients. Neurobiol Aging. 2015 Aug;36(8):2443.e1-7. -
Likely pathogenic, criteria provided, single submitter	clinical testing	GeneDx	Apr 06, 2020	In silico analysis, which includes protein predictors and evolutionary conservation, supports that this variant does not alter protein structure/function; This variant is associated with the following publications: (PMID: 24344756, 25095812, 21852154, 28549449, 31515791, 23847153, 18207319, 24480794, 19252787, 23602593, 16580020, 17135568, 10371548, 26002683, 22133740, 24139282, 27844030, 25105908, 26671140, 28710804, 26308724, 25692567, 25959358, 19242647, 30199759, 30656190, 31792094, 32410215, 32277177) -

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

Pathogenic, criteria provided, single submitter	clinical testing	Mendelics	May 04, 2022	- -
Pathogenic, criteria provided, single submitter	clinical testing	Illumina Laboratory Services, Illumina	Apr 05, 2019	The NOTCH3 c.1630C>T (p.Arg544Cys) missense variant has been reported extensively in the literature, particularly in individuals affected with cerebral autosomal dominant arteriopathy with subcortical infarcts and leukoencephalopathy (CADASIL) of Asian descent, where the variant appears to be a founder variant (Lee et al. 2009; Choi et al. 2013; Liao et al. 2015). Across a selection of the available literature, the p.Arg544Cys variant has been identified in 155 individuals affected with CADASIL, including four individuals who were homozygous for the variant (Oberstein et al. 1999; Lee et al. 2009b; Choi et al. 2013; Soong et al. 2013; Kim et al. 2014; Liao et al. 2015). Of note, the expressivity of CADASIL varies in age of onset, severity of clinical symptoms and progression of disease (Rutten et al. 2000). The p.Arg544Cys variant was absent from 100 controls and is reported at a frequency of 0.003821 in the East Asian population of the Genome Aggregation Database. Based on the evidence, the p.Arg544Cys variant is classified as pathogenic for cerebral autosomal dominant arteriopathy with subcortical infarcts and leukoencephalopathy. This variant was observed by ICSL as part of a predisposition screen in an ostensibly healthy population. -
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: 0105 - The mechanism of disease for this gene is not clearly established. Both loss of function and dominant negative have been suggested as mechanisms in CADASIL (MIM#125310), however lateral meningocele syndrome (MIM#130720) results from a gain of function (OMIM). (I) 0107 - This gene is associated with autosomal dominant disease. (I) 0115 - Variants in this gene are known to have variable expressivity. The p.(Arg544Cys) variant is associated with a later age of onset and milder clinical features than other NOTCH3 variants (GeneReviews, PMID: 26308724). (I) 0200 - Variant is predicted to result in a missense amino acid change from arginine to cysteine. (I) 0251 - This variant is heterozygous. (I) 0309 - Alternative amino acid changes at the same position have been observed in gnomAD (v3) (8 heterozygotes, 0 homozygotes). (I) 0310 - Variant is present in gnomAD (v2) >=0.001 and <0.01 for a dominant condition (83 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) 0604 - Variant is not located in an established domain, motif, hotspot or informative constraint region. (I) 0801 - This variant has very strong previous evidence of pathogenicity in unrelated individuals. This is considered to be a founder variant in East Asian populations and is one of the most common NOTCH3 variants, having been identified in over 100 individuals and families with CADASIL (MIM#125310) (ClinVar, HGMD, LOVD, PMIDs: PMID: 26308724, 30656190). (SP) 1102 - Strong phenotype match for this individual. (SP) 1208 - Inheritance information for this variant is not currently available in this individual. (I) Legend: (SP) - Supporting pathogenic, (I) - Information, (SB) - Supporting benign -
Pathogenic, criteria provided, single submitter	clinical testing	3billion	Jan 03, 2022	The variant known to cause Cerebral arteriopathy with subcortical infarcts and leukoencephalopathy 1 in an autosomal dominant inheritance pattern. The variant the most common variant associated with CADASIL in the East Asian population (PMID: 25692567, 26308724, 31792094). It has been observed in multiple (>3) similarly affected unrelated individuals(PMID: 32277177, 30906334, 25692567, 26308724, 31792094, PS4_S). A missense variant is a common mechanism associated with Cerebral arteriopathy with subcortical infarcts and leukoencephalopathy 1 (PP2_P). Therefore, this variant is classified as pathogenic according to the recommendation of ACMG/AMP guideline. -
not provided, no classification provided	literature only	GeneReviews	-	- -

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

Likely pathogenic, criteria provided, single submitter

clinical testing

Fulgent Genetics, Fulgent Genetics

Nov 06, 2021

- -

Cerebral autosomal dominant arteriopathy with subcortical infarcts and leukoencephalopathy Pathogenic:1

Pathogenic, criteria provided, single submitter

clinical testing

Women's Health and Genetics/Laboratory Corporation of America, LabCorp

Dec 23, 2021

Variant summary: NOTCH3 c.1630C>T (p.Arg544Cys) results in a non-conservative amino acid change at a location bordered between the EGFR-13 and EGFR-14 domains (IPR000742) of the encoded protein sequence. This is different from other cysteine involving mutations residing within an EGFR domain and therefore, comparing with other cysteine-involving NOTCH3 mutations, R544C may result in a milder conformational change of NOTCH3 molecules and consequently a milder clinical phenotype (Liao_2015). Gain/loss of cysteine residues in the EGFr domains in NOTCH3 have been shown to be typical mutations of CADASIL and NOTCH3-related disorders (reviewed by Mizuno_2020). Five of five in-silico tools predict a damaging effect of the variant on protein function. The variant allele was found at a frequency of 0.00032 in 250312 control chromosomes, particularly at a frequency of 0.0041 within the East Asian subpopulation in the gnomAD database. c.1630C>T has been reported in the literature in multiple individuals/families (mainly of East Asian origin) affected with CADASIL and NOTCH3-Related Disorders (example: Oberstein_1999, Kim_2006, Soong_2013, Liao_2015). Asymptomatic individuals with the variant have also been reported within affected families (example: Kim_2006, Liao_2015). Recent data suggest that CADASIL is much more prevalent than previously suspected and the NOTCH3 clinical spectrum must be considerably broader, ranging from classic CADASIL to a much milder small-vessel disease, or possibly even non-penetrance (Hack RJ, Rutten J, Lesnik Oberstein SAJ. CADASIL. 2000 Mar 15 [Updated 2019 Mar 14]. In: Adam MP, Ardinger HH, Pagon RA, et al., editors. GeneReviews [Internet]. Seattle (WA): University of Washington, Seattle; 1993-2021). These data indicate that the variant is very likely to be associated with disease. To our knowledge, no experimental evidence demonstrating an impact on protein function has been reported. Seven ClinVar submitters have assessed this variant since 2014: four have classified the variant as likely pathogenic and three as pathogenic. Based on the evidence outlined above, the variant was classified as pathogenic. -

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
AlphaMissense	Benign	0.28
BayesDel_addAF	Benign	-0.24	T
BayesDel_noAF	Benign	-0.12
Cadd	Benign	22
Dann	Uncertain	1.0
DEOGEN2	Benign	0.26	T;T
Eigen	Benign	0.14
Eigen_PC	Benign	0.027
FATHMM_MKL	Benign	0.37	N
LIST_S2	Uncertain	0.93	D;D
M_CAP	Pathogenic	0.34	D
MetaRNN	Benign	0.017	T;T
MetaSVM	Uncertain	0.53	D
MutationAssessor	Uncertain	2.1	M;.
MutationTaster	Benign	0.95	D
PrimateAI	Benign	0.32	T
PROVEAN	Benign	-2.4	N;.
REVEL	Uncertain	0.57
Sift	Benign	0.052	T;.
Sift4G	Uncertain	0.042	D;T
Polyphen		0.84	P;.
Vest4		0.43
MVP		1.0
MPC		0.97
ClinPred		0.11	T
GERP RS		3.3
Varity_R		0.50
gMVP		0.83

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: rs201118034; hg19: chr19-15298126; COSMIC: COSV54658002;