NM_000435.2:c.5032G>T

NOTCH3 · NP_000426.2:p.(Glu1678Ter) · NM_000435.2

GRCh37: chr19:15281224 C>A · GRCh38: chr19:15170413 C>A

Gene: NOTCH3 Transcript: NM_000435.2

Final call

Pathogenic

PVS1 very strong PM1 moderate PM2 supporting

Variant details

Gene

NOTCH3

Transcript

NM_000435.2

Protein

NP_000426.2:p.(Glu1678Ter)

gnomAD AF

ClinVar

OncoKB

Likely Oncogenic

Classification rationale

Interpretation summary

Generated evidence synthesis

PVS1 (very strong): NM_000435.2:c.5032G>T is a nonsense variant in exon 27 of 33, predicted to produce a premature termination codon at p.Glu1678Ter and trigger nonsense-mediated decay. NOTCH3 loss-of-function is established as a germline disease mechanism, satisfying PVS1 at very strong level under the ClinGen SVI PVS1 framework (PMC6185798).

PM1 (moderate): The nonsense variant truncates the NOTCH3 intracellular domain, removing the ankyrin repeat domain essential for transcriptional activation and the PEST domain that regulates protein stability. These are well-characterized, functionally critical domains.

PM2 (supporting): The variant is absent from gnomAD v2.1, v4.1, and gnomAD-Canada (AF=0), meeting the PM2 threshold of <0.1% allele frequency in population databases.

Final determination: Generic ACMG/AMP 2015 fallback rules support a Pathogenic classification based on the observed combination of very strong, strong, moderate, and supporting pathogenic criteria.

Criteria assessment

ACMG/AMP criteria review

Criteria shown when status is available

All criteria require review: For research and educational purposes only.

Criterion	Status	Rationale	Evidence used
PVS1	Met	Nonsense variant NM_000435.2:c.5032G>T (p.Glu1678Ter) in exon 27 of 33 introduces a premature termination codon predicted to trigger nonsense-mediated decay or produce a truncated protein lacking the C-terminal 644 amino acids including the ANK repeat and PEST domains. NOTCH3 loss-of-function is established as a germline disease mechanism by recent literature demonstrating recessive LoF variants cause early-onset arteriopathy and trans LoF variants modify CADASIL severity. Assessed under ClinGen SVI PVS1 framework (PMC6185798).	pvs1_generic_framework pvs1_gene_context pvs1_variant_assessment
PS1	N/A	PS1 applies to missense variants where a different nucleotide change produces the same amino acid substitution; not applicable to nonsense variants.
PS2	Not met	No de novo observation was identified for NM_000435.2:c.5032G>T in any source. The variant is absent from ClinVar and the reviewed literature.
PS3	Not met	No variant-specific functional data exists for NM_000435.2:c.5032G>T. The two publications reviewed (PMID:19825845, PMID:25870235) do not test or mention this variant. No systematic range characterization encompassing position 1678 was identified.
PS4	Not met	The variant has not been reported in affected individuals. It is absent from ClinVar and was not identified in any case report or cohort study in the reviewed literature. No case-control data are available.	clinvar
PS5	N/A	PS5 requires a variant detected in trans with a pathogenic variant for a recessive disorder. CADASIL is autosomal dominant; PS5 does not apply.
PM1	Met	The nonsense variant at p.Glu1678Ter is located in the NOTCH3 intracellular domain and truncates the protein, removing the ankyrin repeat domain and the PEST degradation domain — both well-characterized functional regions essential for NOTCH3 transcriptional activity and protein turnover. The truncated ICD is critical for Notch signaling, consistent with PM1 domain-level application.	PMID:19825845
PM2	Met	NM_000435.2:c.5032G>T is absent from gnomAD v2.1, v4.1, and gnomAD-Canada, with an allele frequency of 0 in all population databases. This is well below the PM2 threshold of <0.1% for non-VCEP frameworks.	gnomad_v2 gnomad_v4 gnomad_canada
PM5	Not met	No pathogenic missense variant at codon 1678 was identified. The PM5 candidate search returned no comparators for same-residue analysis. PM5 requires a different pathogenic amino acid change at the same residue, which was not found.	pm5_candidates
PM6	Not met	No de novo observation was identified for NM_000435.2:c.5032G>T. The variant is absent from ClinVar and the reviewed literature provides no de novo data.
PP1	Not met	No segregation data are available for this variant. Neither ClinVar nor the reviewed literature provides cosegregation information.
PP2	N/A	PP2 applies to missense variants in genes with a low rate of benign missense variation and where missense variants are a common disease mechanism. This is a nonsense variant.
PP3	Not met	BayesDel score of 0.66 is consistent with a deleterious prediction, but in silico pathogenicity predictors are calibrated for missense variants and are not validated for nonsense variants. Applying PP3 would double-count the evidence already captured by PVS1. SpliceAI predicts no splice impact (max delta 0.16). REVEL score is unavailable.	bayesdel spliceai
PP4	Not met	No patient phenotype or family history data were submitted with this variant. PP4 requires the patient's phenotype to be specific for and consistent with the gene's disease spectrum.
PP5	Not met	NM_000435.2:c.5032G>T is absent from ClinVar. No expert panel or reputable source has classified this variant as pathogenic.	clinvar
BA1	Not met	The variant is absent from gnomAD v2.1, v4.1, and gnomAD-Canada (AF=0). BA1 requires an allele frequency greater than 1% in any population database.	gnomad_v2 gnomad_v4 gnomad_canada
BS1	Not met	The variant is absent from all population databases (AF=0). BS1 requires an allele frequency greater than 0.3% for a dominant disorder.	gnomad_v2 gnomad_v4 gnomad_canada
BS2	Not met	The variant is absent from gnomAD; no homozygous observations exist in healthy adults. For a fully penetrant dominant disorder like CADASIL, BS2 requires observation of the variant in healthy adult controls or in a homozygous state in population databases.	gnomad_v2 gnomad_v4
BS3	Not met	No functional data demonstrating a neutral or benign effect for NM_000435.2:c.5032G>T were identified. The reviewed publications do not test this variant.
BS4	Not met	No segregation data are available to assess lack of cosegregation with disease. The variant has not been reported in any family study.
BP1	N/A	BP1 applies to missense variants in genes where only truncating variants are known to cause disease. This is a nonsense (truncating) variant, and NOTCH3 CADASIL is primarily caused by missense variants.
BP2	Not met	No observation of this variant in trans with a pathogenic NOTCH3 variant or in cis with a pathogenic variant in any inheritance pattern was identified.
BP4	N/A	BP4 applies to computational evidence suggesting no impact on gene product for missense and splice variants. In silico predictors are not calibrated for nonsense variants; applying BP4 to a stop-gain is not meaningful. BayesDel score 0.66 does not support a benign effect.
BP5	Not met	No alternative molecular basis for disease was identified because no patient case data with a different causative variant were available for comparison.
BP6	Not met	NM_000435.2:c.5032G>T is absent from ClinVar. No trusted source has reported this variant as benign. BP6 requires a reputable source classification as benign.	clinvar
BP7	N/A	BP7 applies to synonymous variants at non-conserved positions where splice prediction algorithms predict no impact. This is a nonsense variant.

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