NM_017617.5:c.3225G>A (p.Trp1075Ter) is a nonsense variant in NOTCH1 predicted to undergo nonsense-mediated decay, meeting PVS1 at very strong strength.1 The variant is absent from all gnomAD population databases (v2.1, v4.1, gnomAD-Canada), meeting PM2 at supporting strength.2 No variant-specific functional studies, de novo observations, case-control data, or cosegregation evidence are available. ClinVar contains no entry for this variant.3 Five publications identified via OncoKB discuss NOTCH1 loss-of-function in squamous cell carcinoma at the gene level, but none mention NM_017617.5:c.3225G>A specifically. COSMIC reports two somatic occurrences (COSV53100468) without functional characterization.4 The met criteria are PVS1 (very_strong) and PM2 (supporting). Under generic ACMG/AMP 2015 combination rules, one very-strong criterion plus one supporting criterion does not meet the threshold for Pathogenic (requires 1 Strong, 2 Moderate, or 1 Moderate + 1 Supporting in addition to PVS1) or Likely Pathogenic (requires at least PVS1 + 1 Moderate). The variant is classified as Variant of Uncertain Significance (VUS).5
NOTCH1
Final classification
VUS
NOTCH1 c.3225G>A · p.Trp1075Ter
NOTCH1
NM_017617.5:c.3225G>A (p.Trp1075Ter) is a nonsense variant in NOTCH1 predicted to undergo nonsense-mediated decay, meeting PVS1 at very strong strength.
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, PM2 supporting; combination = 1 very strong + 1 supporting, which maps to VUS.
Classification rationale
PVS1PM2
VUS
NOTCH1 c.3225G>A
PVS1 + PM2
→
VUS
1
pvs1_generic_framework ↗pvs1_gene_context
5
generic_acmg_combination_rules
Gene diagram
· NM_017617.5 · variants mapped to exon structure
NOTCH1
NM_017617.5
Fetching transcript structure from UCSC…
Applied criteria · 2 applied · 19 assessed
Applied · 2
Strength
Supporting
Moderate
Strong
Very strong
✓
PVS1
very strong
Pathogenic
Nonsense variant NM_017617.5:c.3225G>A (p.Trp1075Ter) in exon 20/34 of NOTCH1 creates a premature termination codon predicted to trigger nonsense-mediated decay (NMD). Under PMC6185798, nonsense variants in genes where loss of function is an established disease mechanism are assigned PVS1 at full strength. NOTCH1 loss of function is supported for germline disease (Aortic Valve Disease 1, Adams-Oliver syndrome, congenital heart defects). The variant is absent from gnomAD and the stop codon is >50bp upstream of the last exon-exon junction, favoring NMD. The truncation removes all intracellular signaling domains including ANK repeats, TAD, and PEST.
Nonsense variant at codon 1075 in exon 20/34Germline LoF mechanism established for NOTCH1 (AOVD1Adams-Oliver syndrome)
✓
PM2
supporting
Pathogenic
The variant is absent from all gnomAD population databases (v2.1 exomes, v4.1 exomes, and gnomAD-Canada v1.0 genomes), meeting the PM2 threshold of allele frequency <0.1% in population databases under generic ACMG rules.
Absent from gnomAD v2.1 (0 alleles)Absent from gnomAD v4.1 (0 alleles)Absent from gnomAD-Canada v1.0 (0 alleles)
Assessed · not applied
Pathogenic
PS1
No established pathogenic variant at this nucleotide position with the same predicted protein change (p.Trp1075Ter).
PS2
No de novo testing data (maternity and paternity confirmation) provided for this case.
PS3
No variant-specific functional assay data exist for NM_017617.5:c.3225G>A (p.Trp1075Ter).
PS4
No case-control comparison data or disease-specific prevalence statistics provided for this variant in the phenotype associated with NOTCH1 germline disease.
PM1
The nonsense variant at position 1075 lies within the EGF repeat region of NOTCH1, which is functionally critical for ligand binding (Delta/Serrate).
PM6
No de novo observation data (with or without confirmation of paternity/maternity) provided for this variant.
PP1
No family cosegregation data provided for this variant.
PP3
SpliceAI predicts no splice impact (max delta score = 0.00).
PP4
No patient phenotype data provided to evaluate whether the clinical presentation is highly specific for NOTCH1-related disease (AOVD1, Adams-Oliver syndrome, congenital heart defects).
PP5
The variant is absent from ClinVar.
Benign
BA1
The variant is absent from gnomAD v2.1 and v4.1.
BS1
The variant is absent from gnomAD.
BS2
The variant is absent from gnomAD.
BS3
No well-established functional studies demonstrate a neutral effect for this variant.
BS4
No family segregation data available to evaluate lack of cosegregation with disease.
BP2
No data on observation in trans with a known pathogenic variant in NOTCH1 (autosomal dominant AOVD1/Adams-Oliver syndrome).
BP4
SpliceAI predicts no splicing impact (max delta = 0.00), indicating no cryptic splice site creation or disruption.
BP5
No data on an alternate molecular basis for disease in an individual carrying this variant.
BP6
The variant is absent from ClinVar.
N/A · 7
PM3 · PM4 · PM5 · PP2 · BP1 · BP3 · BP7
Research & evidence
Population frequency
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 = 0.00). 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 previously been reported in somatic cancers (COSMIC; COSV53100468, n = 2 times).
Hotspots
This variant does not lie in a statistically significant hotspot.
Sources & reference links
Triaged references · 5 PMIDs not cited in assessment
1657403 ↗
Specific EGF repeats of Notch mediate interactions with Delta and Serrate: implications for Notch as a multifunctional receptor.
ONCOKB
21798897 ↗
Exome sequencing of head and neck squamous cell carcinoma reveals inactivating mutations in NOTCH1.
ONCOKB
22006338 ↗
Loss-of-function mutations in Notch receptors in cutaneous and lung squamous cell carcinoma.
ONCOKB