rs142031490
Variant summary
Our verdict is Uncertain significance. Variant got 3 ACMG points: 3P and 0B. PM1PP3
The NM_000435.3(NOTCH3):c.133G>C(p.Asp45His) variant causes a missense change. The variant allele was found at a frequency of 0.00000993 in 1,611,474 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 Uncertain significance (★★). Synonymous variant affecting the same amino acid position (i.e. D45D) has been classified as Likely benign.
Frequency
Consequence
NM_000435.3 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Uncertain_significance. Variant got 3 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
NOTCH3 | NM_000435.3 | c.133G>C | p.Asp45His | missense_variant | 2/33 | ENST00000263388.7 | |
NOTCH3 | XM_005259924.5 | c.133G>C | p.Asp45His | missense_variant | 2/32 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
NOTCH3 | ENST00000263388.7 | c.133G>C | p.Asp45His | missense_variant | 2/33 | 1 | NM_000435.3 | P1 | |
NOTCH3 | ENST00000601011.1 | c.130G>C | p.Asp44His | missense_variant | 2/23 | 5 |
Frequencies
GnomAD3 genomes ? AF: 0.0000132 AC: 2AN: 151962Hom.: 0 Cov.: 30
GnomAD3 exomes AF: 0.00000818 AC: 2AN: 244642Hom.: 0 AF XY: 0.00 AC XY: 0AN XY: 133686
GnomAD4 exome AF: 0.00000959 AC: 14AN: 1459512Hom.: 0 Cov.: 34 AF XY: 0.00000826 AC XY: 6AN XY: 725994
GnomAD4 genome ? AF: 0.0000132 AC: 2AN: 151962Hom.: 0 Cov.: 30 AF XY: 0.0000135 AC XY: 1AN XY: 74218
ClinVar
Submissions by phenotype
not provided Uncertain:3
Uncertain significance, criteria provided, single submitter | clinical testing | Athena Diagnostics | Aug 08, 2023 | Available data are insufficient to determine the clinical significance of the variant at this time. This variant is statistically more frequent in the patient population than in the general population, which is weak evidence this variant may be disease causing. This variant has been identified in cis with NOTCH3 c.154G>A in published literature, general population data, and our internal patient data (PMID: 31836585, The Genome Aggregation Database (gnomAD), Athena Diagnostics internal data). Computational tools disagree on the variant's effect on normal protein function. 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 29, 2022 | BP1 - |
Uncertain significance, criteria provided, single submitter | clinical testing | Invitae | Jan 15, 2024 | This sequence change replaces aspartic acid, which is acidic and polar, with histidine, which is basic and polar, at codon 45 of the NOTCH3 protein (p.Asp45His). This variant is present in population databases (rs142031490, gnomAD 0.002%). This missense change has been observed in individual(s) with clinical features of NOTCH3-related conditions (PMID: 31836585, 31915071). ClinVar contains an entry for this variant (Variation ID: 447782). 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) has been performed at Invitae for this missense variant, however the output from this modeling did not meet the statistical confidence thresholds required to predict the impact of this variant on NOTCH3 protein function. 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. - |
Cerebral autosomal dominant arteriopathy with subcortical infarcts and leukoencephalopathy Uncertain:1Other:1
Uncertain significance, no assertion criteria provided | clinical testing | Molecular Genetics Laboratory, BC Children's and BC Women's Hospitals | Jul 02, 2021 | - - |
not provided, no classification provided | phenotyping only | GenomeConnect - CureCADASIL | - | Variant interpreted as Uncertain significance and reported on 10-23-2020 by lab or GTR ID London Health Sciences Centre/St. Joseph's Health Care London, Pathology and Laboratory Medicine. 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. - |
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | ARUP Laboratories, Molecular Genetics and Genomics, ARUP Laboratories | Mar 07, 2019 | The NOTCH3 c.133G>C; p.Asp45His variant (rs142031490) is reported in the literature in cis to a p.Gly52Arg missense variant in individual affected with cerebral small vessel disease with a family history of stroke and migraines (Tan 2018). The p.Asp45His variant is reported in ClinVar (Variation ID: 447782), and it is found on only two chromosomes (2/244642 alleles) in the Genome Aggregation Database. The aspartate at codon 45 is highly conserved, but computational analyses (SIFT: damaging, PolyPhen-2: benign) predict conflicting effects of this variant on protein structure/function. Structural modeling suggests this variant may perturb the secondary structure of EGF domain 1 and influence the orientation of a cysteine residue involved in a critical disulfide bond, though further studies would be required to determine a functional effect (Tan 2018). Given the lack of clinical and functional data, the significance of the p.Asp45His variant is uncertain at this time. References: Tan, YYR. Genetics of Cerebral Small Vessel Disease (Doctoral thesis). 2018. https://doi.org/10.17863/CAM.30570 - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at