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NOTCH2
Final classification
VUS
PM1PM2
NOTCH2
c.7354C>T
p.Gln2452Ter
This variant

NM_024408.3:c.7354C>T (p.Gln2452Ter) is a nonsense variant in the last exon of NOTCH2 that truncates the C-terminal portion of the PEST degradation domain.

Transcript
NM_024408.3
HGVS · transcript:coding
NM_024408.3:c.7354C>T
GRCh38
chr1:119915368 G>A
GRCh37
chr1:120457991 G>A
Basis gene-specific framework lacked a usable explicit final combination framework, so generic ACMG/AMP 2015 final-combination rules were applied as fallback; applied criteria: PM1 moderate, PM2 moderate; combination = 2 moderate, which maps to VUS.
gene-specific framework lacked a usable explicit final combination framework, so generic ACMG/AMP 2015 final-combination rules were applied as fallback; applied criteria: PM1 moderate, PM2 moderate; combination = 2 moderate, which maps to VUS.
Classification rationale
PM1PM2 VUS
NOTCH2 c.7354C>T

NM_024408.3:c.7354C>T (p.Gln2452Ter) is a nonsense variant in the last exon of NOTCH2 that truncates the C-terminal portion of the PEST degradation domain.1 The variant is absent from gnomAD v2.1 and v4.1, meeting PM2 at moderate strength.2 The truncation removes part of the PEST domain, a well-characterized functional domain responsible for NOTCH2 protein degradation, meeting PM1 at moderate strength.3 PVS1 is not met because NOTCH2 PEST domain truncations are established as gain-of-function (Hajdu-Cheney syndrome), not loss-of-function, and the alteration predicts NMD escape.4 No variant-specific functional data, de novo reports, segregation data, or ClinVar classifications are available. Remaining criteria are not met or not applicable. Overall evidence: 2 moderate pathogenic criteria (PM1 + PM2) with no benign criteria. This combination does not reach the threshold for Likely Pathogenic under generic ACMG/AMP 2015 rules (requires 2 moderate + 2 supporting, or 3 moderate, or 1 strong + 1-2 moderate). The variant is classified as a Variant of Uncertain Significance (VUS).5

PM1 + PM2 VUS
Gene diagram · NM_024408.3 · variants mapped to exon structure
NOTCH2 NM_024408.3
Fetching transcript structure from UCSC…
Applied criteria · 2 applied · 19 assessed
MetEvidence satisfies this criterion.
Not metEvaluated against available evidence; threshold not reached.
Not assessedApplies in principle, but no evidence was found to evaluate it.
N/ADoesn't apply to this variant type.
Applied · 2
Strength Supporting Moderate Strong Very strong
PM1 moderate Pathogenic
The variant p.Gln2452Ter truncates the C-terminal portion of the NOTCH2 PEST domain (approx. aa 2418-2472), a well-established functional domain responsible for ubiquitin-mediated protein degradation. PEST domain truncations in NOTCH2 are a characterized pathogenic mechanism causing Hajdu-Cheney syndrome (PMID:21378989) and have been identified in DLBCL (PMID:25314575). Truncation of this degradation domain leads to gain-of-function via increased NOTCH2 protein stability. A well-characterized functional domain in the literature satisfies PM1 for truncating variants that remove or disrupt it.
Variant truncates the PEST degradation domain (removes aa 2452-2472)PEST domain is a well-characterized functional domain controlling NOTCH2 protein turnoverPEST domain truncations are a known disease mechanism in Hajdu-Cheney syndrome and DLBCL
PM2 moderate Pathogenic
NM_024408.3:c.7354C>T is absent from gnomAD v2.1 and v4.1, meeting the PM2 threshold of allele frequency <0.1% in population databases.
Absent from gnomAD v2.1 (exomes)Absent from gnomAD v4.1 (genomes/exomes)Absent from gnomAD-Canada v1.0
Assessed · not applied · 19 not met · 0 not assessed
Pathogenic
PVS1 NM_024408.3:c.7354C>T is a nonsense variant (p.Gln2452Ter) in the last coding exon (exon 34/34), which escapes nonsense-mediated decay.
PS2 No de novo observation has been reported for NM_024408.3:c.7354C>T.
PS3 No variant-specific functional data exists for NM_024408.3:c.7354C>T (p.Gln2452Ter).
PS4 The variant is absent from ClinVar and gnomAD, so the prevalence in affected individuals versus controls cannot be assessed.
PM5 No same-residue comparator variants were identified via ClinVar harvesting.
PM6 No de novo report has been identified for NM_024408.3:c.7354C>T.
PP1 No segregation data are available for this variant.
PP3 SpliceAI predicts no significant splice impact (max delta score = 0.02).
PP4 No patient phenotype data are available for this assessment.
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 No data are available regarding this variant in healthy adult individuals.
BS3 No functional studies demonstrate a benign effect for this variant.
BS4 No segregation data are available.
BP2 No observation of this variant in trans with a known pathogenic variant has been reported.
BP4 Multiple lines of computational evidence do not suggest a benign impact.
BP5 No alternative molecular basis for disease has been identified in a case harboring this variant.
BP6 The variant is absent from ClinVar.
N/A · 4 PS1 · PP2 · BP1 · BP7
Research & evidence
Population frequency
gnomAD v4.1 screenshot
gnomAD v4.1
gnomAD v2.1 screenshot
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
Not observed in any ancestry group.
gnomAD v2.1
Absent · 0 / ?
0 hom
Not observed in any ancestry group.
gnomAD Canada 🇨🇦
Absent · 0 / ?
0 hom
Not observed in any ancestry group.
ClinVar screenshot
ClinVar
This variant is absent from ClinVar.
SpliceAI screenshot
In silico
SpliceAI predicts no significant splice impact for this variant (max delta score = 0.02). BayesDel score = 0.577639.
Functional / OncoKB screenshot
Functional Likely Oncogenic
OncoKB identified variant-specific curated literature and context relevant to functional review; biological-effect context: Likely Gain-of-function; curated oncogenicity label: Likely Oncogenic.
OncoKB ↗
COSMIC screenshot
COSMIC
Cancer hotspots screenshot
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.
Literature · how each cited paper was used
2papers cited
Each card is an audit: what was searched, what was found, whether it names the variant, which criteria it fed, and why.
Rule & framework references · cited for criterion definitions, not variant evidence
21378989 ↗ Truncating mutations in the last exon of NOTCH2 cause a rare skeletal disorder with osteoporosis.
25314575 ↗ The truncate mutation of Notch2 enhances cell proliferation through activating the NF-&#x3ba;B signal pathway in the diffuse large B-cell lymphomas.
Sources & reference links
8Sources
ClinVar
gnomAD v2.1
gnomAD v4.1
gnomAD-Canada
SpliceAI
OncoKB
COSMIC
Cancer hotspots