rs775836288

Positions:

• chr19-15192389-G-A
• chr19-15192389-G-C
• chr19-15192389-G-T

Variant summary

Our verdict is Likely pathogenic. Variant got 6 ACMG points: 6P and 0B. PM1 PM2 PP3 PP5

The NM_000435.3(NOTCH3):​c.328C>T​(p.Arg110Cys) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000274 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 Conflicting classifications of pathogenicity (no stars). Another variant affecting the same amino acid position, but resulting in a different missense (i.e. R110H) has been classified as Likely benign.

• Frequency:
  • Genomes: not found (cov: 32)
  • Exomes 𝑓: 0.0000027 (0 hom.)
• Consequence: NOTCH3 NM_000435.3 missense
• Clinical Significance: Conflicting classifications of pathogenicity criteria provided, conflicting classifications P:10 U:1 O:1
• Conservation: PhyloP100: 0.897

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 Likely_pathogenic. Variant got 6 ACMG points.

• PM1: In a hotspot region, there are 4 aminoacids with missense pathogenic changes in the window of +-8 aminoacids around while only 1 benign, 5 uncertain in NM_000435.3
• PM2: Very rare variant in population databases, with high coverage
• PP3: MetaRNN computational evidence supports a deleterious effect, 0.787
• PP5: Variant 19-15192389-G-A is Pathogenic according to our data. Variant chr19-15192389-G-A is described in ClinVar as [Conflicting_classifications_of_pathogenicity]. Clinvar id is 447831.We mark this variant Likely_pathogenic, oryginal submissions are: {Pathogenic=10, Uncertain_significance=1, not_provided=1}.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
NOTCH3	NM_000435.3	c.328C>T	p.Arg110Cys	missense_variant	3/33	ENST00000263388.7
NOTCH3	XM_005259924.5	c.328C>T	p.Arg110Cys	missense_variant	3/32

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
NOTCH3	ENST00000263388.7	c.328C>T	p.Arg110Cys	missense_variant	3/33	1	NM_000435.3	P1
NOTCH3	ENST00000601011.1	c.325C>T	p.Arg109Cys	missense_variant	3/23	5

Frequencies

GnomAD3 genomes Cov.: 32

GnomAD4 exome AF: 0.00000274 AC: 4 AN: 1460660 Hom.: 0 Cov.: 40 AF XY: 0.00000275 AC XY: 2 AN XY: 726634

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: 0.00000360

Gnomad4 OTH exome AF: 0.00

GnomAD4 genome Cov.: 32

ClinVar

Significance: Conflicting classifications of pathogenicity

Submissions summary: Pathogenic:10 Uncertain:1 Other:1

Revision: criteria provided, conflicting classifications

Submissions by phenotype

not provided Pathogenic:6

Pathogenic, criteria provided, single submitter	clinical testing	Invitae	Dec 28, 2023	This sequence change replaces arginine, which is basic and polar, with cysteine, which is neutral and slightly polar, at codon 110 of the NOTCH3 protein (p.Arg110Cys). 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, 29363903, 29980472). It has also been observed to segregate with disease in related individuals. ClinVar contains an entry for this variant (Variation ID: 447831). 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	Jul 18, 2023	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 occurs as the most likely explanation for disease in a significant number of cases, suggesting this variant is associated with disease. This variant appears to segregate with disease in at least one family with CADASIL. 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	Jan 05, 2023	PP1, PP2, PP3, PP4, PM1, PM2, PS4 -
Pathogenic, criteria provided, single submitter	clinical testing	GeneDx	Jan 14, 2020	In silico analysis, which includes protein predictors and evolutionary conservation, supports a deleterious effect; This variant is associated with the following publications: (PMID: 32277177, 33061333, 31418856, 17996090, 26856460, 15387979, 9388399, 30311053, 28710804, 28991717, 24840674, 19167727, 25623805, 11706120, 25190493, 20935329, 29363903, 19174371, 19006080, 16730748, 11755616, 29188607, 29980472, 12721871) -
Pathogenic, criteria provided, single submitter	clinical testing	ARUP Laboratories, Molecular Genetics and Genomics, ARUP Laboratories	Jan 13, 2020	The NOTCH3 c.328C>T; p.Arg110Cys variant is reported in the literature in multiple individuals and families affected with CADASIL (Dichgans 2000, Hung 2018, Joutel 1997, Khan 2016, Opherk 2004, Peters 2005, Singhal 2004, Uyguner 2006, Wang 2011). This variant is reported in ClinVar (Variation ID: 447831), 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 110 is highly conserved, but computational analyses (SIFT: tolerated, PolyPhen-2: possibly damaging) predict conflicting effects of this variant on protein structure/function. However, this variant lies with an EGF-like repeat domain, and pathogenic variants resulting in the gain or loss of a cysteine residue are common in these repeats and are predicted to disrupt protein structure (Dichgans 2000, Joutel 2007). Based on available information, the p.Arg110Cys variant is considered to be pathogenic. References: Dichgans M et al. Small in-frame deletions and missense mutations in CADASIL: 3D models predict misfolding of Notch3 EGF-like repeat domains. Eur J Hum Genet. 2000 Apr;8(4):280-5. Hung LY et al. Genetic diagnosis of CADASIL in three Hong Kong Chinese patients: A novel mutation within the intracellular domain of NOTCH3. J Clin Neurosci. 2018 Oct;56:95-100. Joutel A et al. Strong clustering and stereotyped nature of Notch3 mutations in CADASIL patients. Lancet. 1997 Nov 22;350(9090):1511-5. Khan MT et al. Successful Use of Intravenous Tissue Plasminogen Activator as Treatment for a Patient with Cerebral Autosomal Dominant Arteriopathy with Subcortical Infarcts and Leukoencephalopathy: A Case Report and Review of Literature. J Stroke Cerebrovasc Dis. 2016 Apr;25(4):e53-7. 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. Peters N et al. Spectrum of mutations in biopsy-proven CADASIL: implications for diagnostic strategies. Arch Neurol. 2005 Jul;62(7):1091-4. Singhal S et al. The influence of genetic and cardiovascular risk factors on the CADASIL phenotype. Brain. 2004 Sep;127(Pt 9):2031-8. Uyguner ZO et al. The R110C mutation in Notch3 causes variable clinical features in two Turkish families with CADASIL syndrome. J Neurol Sci. 2006 Jul 15;246(1-2):123-30. Wang Z et al. NOTCH3 mutations and clinical features in 33 mainland Chinese families with CADASIL. J Neurol Neurosurg Psychiatry. 2011 May;82(5):534-9. -
Pathogenic, criteria provided, single submitter	clinical testing	CeGaT Center for Human Genetics Tuebingen	May 01, 2018	- -

Cerebral arteriopathy, autosomal dominant, with subcortical infarcts and leukoencephalopathy, type 1 Pathogenic:3 Uncertain:1 Other:1

Pathogenic, criteria provided, single submitter	clinical testing	Molecular Genetics, Royal Melbourne Hospital	May 05, 2023	This sequence change in NOTCH3 is predicted to replace arginine with cysteine at codon 110, p.(Arg110Cys). The arginine residue is moderately conserved (100 vertebrates, UCSC), and introduces an odd number of cysteine residues in the EGF-like repeat domain 2 which is expected to alter the disulfide bonds in this domain. There is a large physicochemical difference between arginine and cysteine. This variant is absent from the population database gnomAD v2.1 and v3.1. This variant has been reported in at least seven individuals with a clinical diagnosis of cerebral autosomal dominant arteriopathy with subcortical infarcts and leukoencephalopathy (CADASIL; PMID: 16730748, 9388399, 29363903, 33061333, 35775048). The variant has been reported to segregate with CADASIL in four affected family members from three unrelated families (PMID: 16730748, 29363903). Computational evidence predicts a deleterious effect for the missense substitution (REVEL = 0.757). Based on the classification scheme RMH Modified ACMG/AMP Guidelines v1.6.1, this variant is classified as PATHOGENIC. Following criteria are met: PS4, PM1, PP1_Moderate, PM2_Supporting, PP3. -
Uncertain significance, criteria provided, single submitter	clinical testing	Centre for Mendelian Genomics, University Medical Centre Ljubljana	Jan 09, 2019	This variant was classified as: Uncertain significance. The available evidence favors the pathogenic nature of this variant, however the currently available data is insufficient to conclusively support its pathogenic nature. Thus this variant is classified as Uncertain significance - favor pathogenic. The following ACMG criteria were applied in classifying this variant: PM2,PP2,PP3,PP5. -
Pathogenic, criteria provided, single submitter	clinical testing	Institute of Human Genetics, University of Leipzig Medical Center	Feb 26, 2024	Criteria applied: PS4,PM1,PM2_SUP,PP1,PP2,PP3 -
Pathogenic, criteria provided, single submitter	clinical testing	Mendelics	May 28, 2019	- -
not provided, no classification provided	phenotyping only	GenomeConnect - CureCADASIL	-	Variant identified in multiple registry participants. Variant interpreted as Pathogenic and reported on 02-13-2015 by lab or GTR ID 303161. Variant interpreted as Uncertain Significance and reported on 05-28-2021 by lab or GTR ID 500105. GenomeConnect - CFC International 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:1

Pathogenic, criteria provided, single submitter

clinical testing

PreventionGenetics, part of Exact Sciences

Nov 01, 2023

The NOTCH3 c.328C>T variant is predicted to result in the amino acid substitution p.Arg110Cys. This patient is heterozygous in the NOTHC3 gene for a sequence variant designated c.328C>T, which is predicted to result in the amino acid substitution p.Arg110Cys. This variant has been reported as causative for CADASIL in numerous patients and families (see for example Joutel et al. 1997. PubMed ID: 9388399; Wang et al. 2011. PubMed ID: 20935329). Of note, the vast majority of 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, where this patient’s variant is located. This patient’s variant alters a cysteine residue and is located in the extracellular EGF-like domain two. 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 has not been reported in a large population database (http://gnomad.broadinstitute.org), indicating this variant is rare. This variant is interpreted as pathogenic. -

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
AlphaMissense	Uncertain	0.48
BayesDel_addAF	Pathogenic	0.36	D
BayesDel_noAF	Pathogenic	0.28
CADD	Pathogenic	27
DANN	Pathogenic	1.0
DEOGEN2	Benign	0.32	T;T
Eigen	Uncertain	0.52
Eigen_PC	Uncertain	0.52
FATHMM_MKL	Pathogenic	0.97	D
LIST_S2	Uncertain	0.95	D;D
M_CAP	Pathogenic	0.51	D
MetaRNN	Pathogenic	0.79	D;D
MetaSVM	Uncertain	0.59	D
MutationAssessor	Uncertain	2.3	M;.
MutationTaster	Benign	1.0	D
PrimateAI	Pathogenic	0.81	D
PROVEAN	Uncertain	-2.9	D;.
REVEL	Pathogenic	0.76
Sift	Benign	0.10	T;.
Sift4G	Benign	0.090	T;T
Polyphen		1.0	D;.
Vest4		0.63
MutPred		0.67		Loss of MoRF binding (P = 0.015);.;
MVP		1.0
MPC		1.4
ClinPred		0.97	D
GERP RS		5.2
Varity_R		0.17
gMVP		0.72

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: rs775836288; hg19: chr19-15303200;