NM_000435.2:c.3452G>A

NOTCH3 · NP_000426.2:p.(Gly1151Glu) · NM_000435.2

GRCh37: chr19:15290183 C>T · GRCh38: chr19:15179372 C>T

Gene: NOTCH3 Transcript: NM_000435.2

Final call

VUS

PM2 supporting PP3 supporting

Variant details

Gene

NOTCH3

Transcript

NM_000435.2

Protein

NP_000426.2:p.(Gly1151Glu)

gnomAD AF

1.2390821375158139e-06 (v4.1)

ClinVar

OncoKB

Unknown Oncogenic Effect

Classification rationale

Interpretation summary

Generated evidence synthesis

NM_000435.2:c.3452G>A (p.Gly1151Glu) is a missense variant in NOTCH3, a gene in which missense variants are a well-established cause of CADASIL (cerebral autosomal dominant arteriopathy with subcortical infarcts and leukoencephalopathy).

This variant is ultra-rare in population databases, absent from gnomAD v2.1 and present in gnomAD v4.1 at an allele frequency of 1.24e-6 (2/1,614,098 alleles, 0 homozygotes), well below the 0.1% PM2 threshold (PM2_Supporting).

In silico analysis with REVEL yields a score of 0.866, predicting a damaging effect on the protein. BayesDel is borderline at 0.474, and SpliceAI predicts no splice impact (max delta 0.02) (PP3_Supporting).

No variant-specific functional data, de novo observations, case-control studies, segregation data, or ClinVar classifications are available for this variant. The variant is absent from ClinVar and has not been reported in COSMIC or literature.

With only two supporting-level pathogenic criteria (PM2_Supporting, PP3_Supporting) and no benign criteria met, the evidence is insufficient to classify this variant as pathogenic, likely pathogenic, benign, or likely benign under the ACMG/AMP 2015 framework. This variant is classified as a Variant of Uncertain Significance (VUS).

Final determination: Generic ACMG/AMP 2015 fallback rules do not meet benign, likely benign, likely pathogenic, or pathogenic combination thresholds, so the variant is classified as Variant of Uncertain Significance.

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	N/A	This variant (NM_000435.2:c.3452G>A, p.Gly1151Glu) is a missense substitution and does not fall into any ClinGen PVS1 null-variant bucket (nonsense, frameshift, or canonical ±1,2 splice consensus variants). The generic PVS1 framework is not applicable to missense variants.	pvs1_generic_framework pvs1_variant_assessment
PS1	Not met	No prior pathogenic variant resulting in the same amino acid change (p.Gly1151Glu) has been reported in ClinVar or the literature. There is no evidence that the same nucleotide change has been previously established as pathogenic.	clinvar
PS2	Not met	No de novo observation with confirmed paternity and maternity has been reported for this variant.
PS3	Not met	No variant-specific functional data are available for p.Gly1151Glu. OncoKB classifies this variant as having unknown oncogenic effect. No publications with functional characterization of this variant or a systematically characterized range that includes residue 1151 were identified.	oncokb
PS4	Not met	No case-control studies or prevalence data in affected individuals versus controls are available for this variant.
PS5	N/A	PS5 is not a standard ACMG/AMP 2015 criterion. In the canonical Richards et al. 2015 framework, same-residue different missense change is assessed under PM5. This criterion is not applicable under the generic ACMG/AMP framework used for this case.	generic_acmg_combination_rules
PM1	Not met	Residue G1151 is not located within a statistically significant mutational hotspot as determined by cancerhotspots.org. While NOTCH3 has well-characterized EGF-like repeat domains where pathogenic cysteine-altering variants cluster in CADASIL, G1151E is a glycine-to-glutamate change, not a cysteine-altering variant, and no domain-level functional data specific to this region were identified in the case materials that would independently support PM1.	oncokb
PM2	Met	This variant is absent from gnomAD v2.1 and present in gnomAD v4.1 at an ultra-rare allele frequency of 1.24e-6 (2/1,614,098 alleles, 0 homozygotes), well below the 0.1% PM2 threshold for non-VCEP adjudication.	gnomad_v2 gnomad_v4
PM5	Not met	No same-residue comparator variant (different missense change at p.Gly1151) with an established pathogenic classification was identified. The automated PM5 candidate search returned no candidates.	pm5_candidates clinvar
PM6	Not met	No de novo observation (without confirmation of paternity and maternity) has been reported for this variant.
PP1	Not met	No co-segregation data with disease in multiple affected family members are available for this variant.
PP2	Not assessed	PP2 requires demonstration that the gene has a low rate of benign missense variation (typically via a high missense Z-score) in a gene where missense variants are a common mechanism of disease. While NOTCH3 missense variants are a well-established mechanism in CADASIL, the missense constraint metric (Z-score) for NOTCH3 was not available in the provided evidence materials, precluding a definitive PP2 assessment.
PP3	Met	REVEL predicts a damaging effect with a score of 0.866 (above the 0.5 threshold). BayesDel score of 0.474 is borderline. SpliceAI reports no significant splice impact (max delta 0.02). At least one in silico predictor (REVEL) supports a deleterious effect on the gene product, meeting supporting-level PP3.	revel bayesdel spliceai
PP4	Not met	No patient phenotype or clinical data are available to assess whether the phenotype is highly specific for NOTCH3-related disease.
PP5	Not met	This variant is absent from ClinVar. No reputable source has classified this variant as pathogenic. The ClinVar global PP5/BP6 override rule (ClinVar 3-star expert panel → supporting) does not apply as no ClinVar entry exists.	clinvar
BA1	Not met	The allele frequency in gnomAD v4.1 is 1.24e-6 (0.000124%), far below the 1% BA1 threshold. This variant is ultra-rare, not common.	gnomad_v4
BS1	Not met	The allele frequency in gnomAD v4.1 is 1.24e-6, far below the 0.3% BS1 threshold for non-VCEP adjudication.	gnomad_v4
BS2	Not met	No evidence that this variant has been observed in healthy adults at an age when full penetrance of NOTCH3-related disease would be expected.
BS3	Not met	No well-established functional studies demonstrating no damaging effect on protein function or splicing are available for this variant. OncoKB reports unknown oncogenic effect; no publications report benign functional characterization.	oncokb
BS4	Not met	No segregation data in affected families are available to demonstrate lack of co-segregation with disease.
BP1	Not met	BP1 applies when a missense variant occurs in a gene where primarily truncating variants cause disease. CADASIL is primarily caused by missense (cysteine-altering) variants in NOTCH3, not truncating variants. BP1 does not apply.
BP2	Not met	No observation of this variant in trans with a known pathogenic variant in a gene associated with a fully penetrant dominant disorder has been reported.
BP4	Not met	REVEL predicts a damaging effect with a score of 0.866, contradicting benign in silico predictions. BayesDel score of 0.474 is borderline. The SpliceAI max delta score of 0.02 indicates no splice impact, but this alone is insufficient to meet BP4 when a primary pathogenicity predictor (REVEL) indicates a damaging effect.	revel bayesdel spliceai
BP5	Not met	No case has been reported where an alternative molecular basis for disease was identified in an individual carrying this variant, which would suggest the variant is not causative.
BP6	Not met	This variant is absent from ClinVar. No reputable source has classified this variant as benign. The ClinVar global PP5/BP6 override rule (ClinVar 3-star expert panel → supporting benign) does not apply as no ClinVar entry exists.	clinvar
BP7	N/A	BP7 is reserved for synonymous (silent) variants with no predicted splice impact. This variant (c.3452G>A, p.Gly1151Glu) is a missense substitution, not a synonymous variant.	spliceai
BP3	N/A	BP3 applies to in-frame insertions or deletions in repetitive regions. This is a single-nucleotide substitution.
PM3	N/A	PM3 is reserved for recessive disorders where the variant is observed in trans with a pathogenic variant. NOTCH3-associated CADASIL is an autosomal dominant disorder.
PM4	N/A	PM4 applies to protein-length-altering variants (non-frameshift indels, stop-loss, initiation codon). This is a missense substitution that does not alter protein length.

Disclaimer: The content and results provided by LYFE Sciences are for research and educational purposes only and must not be used as a substitute for professional medical judgment, diagnosis, or treatment. Always consult a qualified healthcare professional before making any clinical decisions.