rs201680145

chr19-15179052-G-Achr19-15179052-G-Cchr19-15179052-G-T

Variant summary

Our verdict is Benign. Variant got -8 ACMG points: 0P and 8B. BP4_Strong BS2

The NM_000435.3(NOTCH3):c.3691C>T(p.Arg1231Cys) variant causes a missense change. The variant allele was found at a frequency of 0.000478 in 1,614,208 control chromosomes in the GnomAD database, including 3 homozygotes. In-silico tool predicts a benign 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. R1231H) has been classified as Likely benign.

• Frequency:
  • Genomes: 𝑓 0.00023 (0 hom., cov: 33)
  • Exomes 𝑓: 0.00050 (3 hom.)
• Consequence: NOTCH3 NM_000435.3 missense
• Clinical Significance: Conflicting classifications of pathogenicity criteria provided, conflicting classifications P:4 U:9 B:1
• Conservation: PhyloP100: 4.97

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 Benign. Variant got -8 ACMG points.

• BP4: Computational evidence support a benign effect (MetaRNN=0.02636671).
• BS2: High AC in GnomAd at 36 AD gene.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
NOTCH3	NM_000435.3	c.3691C>T	p.Arg1231Cys	missense_variant	22/33	ENST00000263388.7
NOTCH3	XM_005259924.5	c.3535C>T	p.Arg1179Cys	missense_variant	21/32

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
NOTCH3	ENST00000263388.7	c.3691C>T	p.Arg1231Cys	missense_variant	22/33	1	NM_000435.3	P1
NOTCH3	ENST00000601011.1	c.3532C>T	p.Arg1178Cys	missense_variant	21/23	5
NOTCH3	ENST00000595045.1	n.527C>T		non_coding_transcript_exon_variant	2/3	2
NOTCH3	ENST00000600841.1	n.169C>T		non_coding_transcript_exon_variant	1/2	2

Frequencies

GnomAD3 genomes AF: 0.000236 AC: 36 AN: 152244 Hom.: 0 Cov.: 33

Gnomad AFR AF: 0.0000241

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.000393

Gnomad ASJ AF: 0.00

Gnomad EAS AF: 0.00

Gnomad SAS AF: 0.00414

Gnomad FIN AF: 0.00

Gnomad MID AF: 0.00

Gnomad NFE AF: 0.000118

Gnomad OTH AF: 0.000478

GnomAD3 exomes AF: 0.000887 AC: 222 AN: 250384 Hom.: 3 AF XY: 0.00112 AC XY: 152 AN XY: 135626

Gnomad AFR exome AF: 0.00

Gnomad AMR exome AF: 0.000637

Gnomad ASJ exome AF: 0.00

Gnomad EAS exome AF: 0.0000544

Gnomad SAS exome AF: 0.00536

Gnomad FIN exome AF: 0.00

Gnomad NFE exome AF: 0.000274

Gnomad OTH exome AF: 0.000654

GnomAD4 exome AF: 0.000504 AC: 737 AN: 1461846 Hom.: 3 Cov.: 36 AF XY: 0.000649 AC XY: 472 AN XY: 727224

Gnomad4 AFR exome AF: 0.0000299

Gnomad4 AMR exome AF: 0.000537

Gnomad4 ASJ exome AF: 0.00

Gnomad4 EAS exome AF: 0.00

Gnomad4 SAS exome AF: 0.00494

Gnomad4 FIN exome AF: 0.0000936

Gnomad4 NFE exome AF: 0.000194

Gnomad4 OTH exome AF: 0.000729

GnomAD4 genome AF: 0.000230 AC: 35 AN: 152362 Hom.: 0 Cov.: 33 AF XY: 0.000295 AC XY: 22 AN XY: 74500

Gnomad4 AFR AF: 0.0000240

Gnomad4 AMR AF: 0.000392

Gnomad4 ASJ AF: 0.00

Gnomad4 EAS AF: 0.00

Gnomad4 SAS AF: 0.00393

Gnomad4 FIN AF: 0.00

Gnomad4 NFE AF: 0.000118

Gnomad4 OTH AF: 0.000473

Alfa AF: 0.000232 Hom.: 0

Bravo AF: 0.000204

ESP6500AA AF: 0.00 AC: 0

ESP6500EA AF: 0.000116 AC: 1

ExAC AF: 0.000988 AC: 120

Asia WGS AF: 0.00231 AC: 8 AN: 3478

EpiCase AF: 0.000273

EpiControl AF: 0.000474

ClinVar

Significance: Conflicting classifications of pathogenicity

Submissions summary: Pathogenic:4 Uncertain:9 Benign:1

Revision: criteria provided, conflicting classifications

Submissions by phenotype

not provided Pathogenic:2 Uncertain:7 Benign:1

Benign, criteria provided, single submitter	clinical testing	CeGaT Center for Human Genetics Tuebingen	Dec 01, 2022	NOTCH3: PP2, BS1, BS2 -
Uncertain significance, criteria provided, single submitter	clinical testing	ARUP Laboratories, Molecular Genetics and Genomics, ARUP Laboratories	Oct 20, 2021	The NOTCH3 c.3691C>T; p.Arg1231Cys variant (rs201680145), is reported in the literature in individuals with CADASIL (Abou Al-Shaar 2016, Joutel 1997, Rinnoci 2013), and in an individual with Alzheimer's disease but no features of CADASIL (Guerreiro 2012). In one family affected with CADASIL, seven family members were found to be homozygous for the variant and had a slightly more severe phenotype than the six family members heterozygous for the variant (Abou Al-Shaar 2016). The p.Arg1231Cys variant is also reported in the ClinVar database (Variation ID: 216972). It is found in the general population with an overall allele frequency of 0.08% (225/281770 alleles, including 3 homozygotes), with an increased frequency of 0.5% in the South Asian population (Genome Aggregation Database). The arginine at codon 1231 is located in an EGF-like domain; most pathogenic NOTCH3 variants occur in exons 2-24 and either create or destroy a cysteine residue within an EGF-like domain (Rutten 2014). However, given the high frequency of this variant in the general population, and asymptomatic heterozygous carriers that have been reported, the clinical significance of this variant is uncertain at this time. References: Abou Al-Shaar H et al. Phenotypic comparison of individuals with homozygous or heterozygous mutation of NOTCH3 in a large CADASIL family. J Neurol Sci. 2016 Aug 15;367:239-43. Guerreiro RJ et al. Exome sequencing reveals an unexpected genetic cause of disease: NOTCH3 mutation in a Turkish family with Alzheimer's disease. Neurobiol Aging. 2012 May;33(5):1008.e17-23. Joutel A et al. Strong clustering and stereotyped nature of Notch3 mutations in CADASIL patients. Lancet. 1997 Nov 22;350(9090):1511-5. Rinnoci V et al. Cerebral hemorrhages in CADASIL: report of four cases and a brief review. J Neurol Sci. 2013 Jul 15;330(1-2):45-51. Rutten JW et al. Interpretation of NOTCH3 mutations in the diagnosis of CADASIL. Expert Rev Mol Diagn. 2014 Jun;14(5):593-603. -
Uncertain significance, criteria provided, single submitter	clinical testing	Athena Diagnostics	Sep 22, 2023	Available data are insufficient to determine the clinical significance of the variant at this time. The frequency of this variant in the general population is higher than would generally be expected for pathogenic variants in this gene. (Genome Aggregation Database (gnomAD), Cambridge, MA (URL: http://gnomad.broadinstitute.org)). This variant is statistically more frequent in affected individuals than in the general population and/or healthy controls. 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). -
Uncertain significance, criteria provided, single submitter	clinical testing	Mayo Clinic Laboratories, Mayo Clinic	Nov 08, 2022	PP2, PP4, PM1 -
Pathogenic, no assertion criteria provided	clinical testing	Laboratory of Diagnostic Genome Analysis, Leiden University Medical Center (LUMC)	-	- -
Uncertain significance, criteria provided, single submitter	clinical testing	Revvity Omics, Revvity	Nov 20, 2023	- -
Pathogenic, no assertion criteria provided	clinical testing	Clinical Genetics DNA and cytogenetics Diagnostics Lab, Erasmus MC, Erasmus Medical Center	-	- -
Uncertain significance, criteria provided, single submitter	clinical testing	Invitae	Dec 15, 2023	This sequence change replaces arginine, which is basic and polar, with cysteine, which is neutral and slightly polar, at codon 1231 of the NOTCH3 protein (p.Arg1231Cys). This variant is present in population databases (rs201680145, gnomAD 0.5%), including at least one homozygous and/or hemizygous individual. This missense change has been observed in individual(s) with cerebral arteriopathy with subcortical infarcts and leukoencephalopathy (PMID: 9388399, 12395806, 15229130, 19006080, 22664156, 23639391, 25326637, 31915071, 32128266, 33013620, 33712516). It has also been observed to segregate with disease in related individuals. ClinVar contains an entry for this variant (Variation ID: 216972). 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%. In summary, the available evidence is currently insufficient to determine the role of this variant in disease. Therefore, it has been classified as a Variant of Uncertain Significance. -
Uncertain significance, no assertion criteria provided	clinical testing	Department of Pathology and Laboratory Medicine, Sinai Health System	-	The NOTCH3 p.(Arg1231Cys) variant was identified in 3 of 206 proband chromosomes (frequency: 0.015) from individuals or families with Cerebral autosomal dominant arteriopathy with subcortical infarcts and leukoencephalopathy (CADASIL) or a strong suspicion of CADASIL and was not identified in 200 control chromosomes from healthy individuals (Testi_2012_PMID: 22664156; Joutel_1997_PMID: 9388399). The variant was also identified in dbSNP (ID: rs201680145), Clinvitae, Cosmic, MutDB, LOVD 3.0 and ClinVar (reported as pathogenic for CADASIL by UCLA Clinical Genomics Center and Genomic Research Center, Shahid Beheshti University of Medical Sciences however reported as a VUS by GeneDX and Athena Diagnostics Inc). The variant was identified in control databases in 225 of 281770 chromosomes (3 homozygous) at a frequency of 0.000799 increasing the likelihood this could be a low frequency benign variant (Genome Aggregation Database Feb 27, 2017). The variant was observed in the following populations: South Asian in 164 of 30614 chromosomes (freq: 0.005357), Latino in 22 of 35400 chromosomes (freq: 0.000622), Other in 4 of 7200 chromosomes (freq: 0.000556), European (non-Finnish) in 34 of 128480 chromosomes (freq: 0.000265) and East Asian in 1 of 19924 chromosomes (freq: 0.00005), while the variant was not observed in the African, Ashkenazi Jewish, and European (Finnish) populations. The R1231C variant was recently identified in the homozygous state in several members from a large family with CADASIL (Abou Al-Shaar_2016_PMID: 27423596). These homozygous individuals had phenotypic features that were within the spectrum of CADASIL, though on the slightly severe end compared to their affected family members with R1231C in the heterozygous state (Abou Al-Shaar_2016_ PMID: 27423596). The R1231C variant was also identified in a 55 year old patient with a sudden depressive episode as well as loss of ability to execute or carry out learned purposeful movements, expressive aphasia, and mild alterations in some cognitive domains such as attention and executive functions (Ungaro_2009_ PMID: 19259619). Valenti et al. (2008) reported an Italian patient with the Arg1231Cys mutation affected by CADASIL as well as a depressive episode at the age of 50 (Valenti_2008_PMID: 18384453). The p.Arg1231 residue is conserved in mammals but not in more distantly related organisms and computational analyses (PolyPhen-2, SIFT, AlignGVGD, BLOSUM, MutationTaster) suggest that the variant may impact the protein; however, this information is not predictive enough to assume pathogenicity. In summary, based on the above information the clinical significance of this variant cannot be determined with certainty at this time. This variant is classified as a variant of uncertain significance. -
Uncertain significance, criteria provided, single submitter	clinical testing	GeneDx	Aug 30, 2016	The R1231C variant in the NOTCH3 gene has been reported previously in association with CADASIL (Joutel et al., 1997; Rinnoci et al., 2013; Abou Al-Shaar et al., 2016). The R1231C variant was recently identified in the homozygous state in several members from a large family with CADASIL (Abou Al-Shaar et al., 2016). These homozygous individuals had phenotypic features that were within the spectrum of CADASIL, though on the slightly severe end compared to their affected family members with R1231C in the heterozygous state (Abou Al-Shaar et al., 2016). The R1231C variant was also identified by whole exome sequencing in an individual with Alzheimer's disease and no features of CADASIL, which the authors conclude either leads to questions of the pathogenicity of R1231C or broadens the phenotypic spectrum associated with this variant (Guerreiro et al., 2012). The R1231C variant is a non-conservative amino acid substitution, which is likely to impact secondary protein structure as these residues differ in polarity, charge, size and/or other properties. While this substitution occurs at a position that is not conserved across species, in silico analysis predicts this variant is probably damaging to the protein structure/function. However, the R1231C variant was observed in 0.58% of alleles from individuals of South Asian background, including three homozygous individuals, in the Exome Aggregation Consortium (ExAC) data set, indicating it may be a rare benign variant in this population. We have also identified many unaffected individuals who are heterozygous for the R1231C variant at GeneDx. As the R1231C variant is observed with significant frequency among unaffected individuals in the ExAC data set and at GeneDx, we now interpret R1231C as a variant of uncertain significance. -

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

Pathogenic, criteria provided, single submitter	clinical testing	Genomic Research Center, Shahid Beheshti University of Medical Sciences	Dec 03, 2017	- -
Pathogenic, criteria provided, single submitter	clinical testing	UCLA Clinical Genomics Center, UCLA	May 27, 2014	- -
Uncertain significance, criteria provided, single submitter	clinical testing	Mendelics	May 28, 2019	- -
Uncertain significance, criteria provided, single submitter	clinical testing	MGZ Medical Genetics Center	Apr 21, 2022	- -

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
AlphaMissense	Uncertain	0.39
BayesDel_addAF	Benign	-0.12	T
BayesDel_noAF	Uncertain	0.060
Cadd	Pathogenic	27
Dann	Pathogenic	1.0
DEOGEN2	Uncertain	0.72	D;D
Eigen	Uncertain	0.37
Eigen_PC	Uncertain	0.28
FATHMM_MKL	Pathogenic	0.99	D
LIST_S2	Benign	0.48	T;T
M_CAP	Pathogenic	0.62	D
MetaRNN	Benign	0.026	T;T
MetaSVM	Uncertain	0.48	D
MutationAssessor	Pathogenic	3.4	M;.
MutationTaster	Benign	1.0	D
PrimateAI	Benign	0.32	T
PROVEAN	Pathogenic	-4.7	D;.
REVEL	Pathogenic	0.70
Sift	Benign	0.074	T;.
Sift4G	Uncertain	0.012	D;D
Polyphen		0.84	P;.
Vest4		0.80
MVP		0.88
MPC		1.2
ClinPred		0.16	T
GERP RS		3.9
Varity_R		0.43
gMVP		0.58

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: rs201680145; hg19: chr19-15289863; COSMIC: COSV54649464; COSMIC: COSV54649464;