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).1 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.2 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.3
NOTCH3
Final classification
Pathogenic
NOTCH3 c.5032G>T · p.Glu1678Ter
NOTCH3
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).
gene-specific framework lacked a usable explicit final combination framework, so generic ACMG/AMP 2015 final-combination rules were applied as fallback; applied criteria: PVS1 very strong, PM1 moderate, PM2 supporting; combination = 1 very strong + 1 moderate + 1 supporting, which maps to Pathogenic.
Classification rationale
PVS1PM1PM2
Pathogenic
NOTCH3 c.5032G>T
PVS1 + PM1 + PM2
→
Pathogenic
1
pvs1_generic_framework ↗pvs1_gene_context
Gene diagram
· NM_000435.2 · variants mapped to exon structure
NOTCH3
NM_000435.2
Fetching transcript structure from UCSC…
Applied criteria · 3 applied · 17 assessed
Applied · 3
Strength
Supporting
Moderate
Strong
Very strong
✓
PVS1
very strong
Pathogenic
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).
Nonsense variant at c.5032 (exon 27/33) predicted to trigger NMDNOTCH3 LoF mechanism supported by germline disease literature (PMID:41196431PMID:41947304)
✓
PM1
moderate
Pathogenic
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.
Truncation removes ANK repeat domain and PEST domain in the NOTCH3 ICDANK repeats required for transcriptional activationPEST domain regulates protein stability
✓
PM2
supporting
Pathogenic
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.
Absent from gnomAD v2.1 (AF = 0)Absent from gnomAD v4.1 (AF = 0)Absent from gnomAD-Canada v1.0 (AF = 0)
Assessed · not applied
Pathogenic
PS2
No de novo observation was identified for NM_000435.2:c.5032G>T in any source.
PS3
No variant-specific functional data exists for NM_000435.2:c.5032G>T.
PS4
The variant has not been reported in affected individuals.
PM5
No pathogenic missense variant at codon 1678 was identified.
PM6
No de novo observation was identified for NM_000435.2:c.5032G>T.
PP1
No segregation data are available for this variant.
PP3
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.
PP4
No patient phenotype or family history data were submitted with this variant.
PP5
NM_000435.2:c.5032G>T is absent from ClinVar.
Benign
BA1
The variant is absent from gnomAD v2.1, v4.1, and gnomAD-Canada (AF=0).
BS1
The variant is absent from all population databases (AF=0).
BS2
The variant is absent from gnomAD; no homozygous observations exist in healthy adults.
BS3
No functional data demonstrating a neutral or benign effect for NM_000435.2:c.5032G>T were identified.
BS4
No segregation data are available to assess lack of cosegregation with disease.
BP2
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.
BP5
No alternative molecular basis for disease was identified because no patient case data with a different causative variant were available for comparison.
BP6
NM_000435.2:c.5032G>T is absent from ClinVar.
N/A · 5
PS1 · PP2 · BP1 · BP4 · BP7
Research & evidence
Population frequency · supports pathogenic
gnomAD v4.1
gnomAD v2.1
v4.1
Absent from gnomAD v4.1.
v2.1
Absent from gnomAD v2.1.
🇨🇦 CA
Absent from gnomAD-Canada v1.0.
Allele frequency by ancestry
three datasets · side by side
gnomAD v4.1
Absent
· 0 / ?
0 hom
0 hom
Not observed in any ancestry group.
gnomAD v2.1
Absent
· 0 / ?
0 hom
0 hom
Not observed in any ancestry group.
gnomAD Canada 🇨🇦
Absent
· 0 / ?
0 hom
0 hom
Not observed in any ancestry group.
In silico
SpliceAI predicts no significant splice impact for this variant (max delta score = 0.16). BayesDel score = 0.66.
Functional
Likely Oncogenic
OncoKB identified variant-specific curated literature and context relevant to functional review; biological-effect context: Likely Loss-of-function; curated oncogenicity label: Likely Oncogenic.
COSMIC
Cancer hotspots
Somatic evidence
Not in COSMIC / hotspots
COSMIC
This variant does not lie in a statistically significant hotspot. This variant has not previously been reported in somatic cancers (COSMIC).
Hotspots
This variant does not lie in a statistically significant hotspot.
Sources & reference links
Triaged references · 2 PMIDs not cited in assessment
19825845 ↗
Mutations in NOTCH3 cause the formation and retention of aggregates in the endoplasmic reticulum, leading to impaired cell proliferation.
ONCOKB
25870235 ↗
Homozygous NOTCH3 null mutation and impaired NOTCH3 signaling in recessive early-onset arteriopathy and cavitating leukoencephalopathy.
ONCOKB