NM_000435.2:c.3257A>C

NOTCH3 · NP_000426.2:p.(Asp1086Ala) · NM_000435.2

GRCh37: chr19:15290953 T>G · GRCh38: chr19:15180142 T>G

Gene: NOTCH3 Transcript: NM_000435.2

Final call

VUS

PM2 supporting

Variant details

Gene

NOTCH3

Transcript

NM_000435.2

Protein

NP_000426.2:p.(Asp1086Ala)

gnomAD AF

ClinVar

OncoKB

Unknown Oncogenic Effect

Classification rationale

Interpretation summary

Generated evidence synthesis

NM_000435.2:c.3257A>C (p.Asp1086Ala) is a missense variant in NOTCH3 exon 20. This variant is absent from large population databases (gnomAD v2.1, v4.1, and gnomAD-Canada; PM2_supporting). No pathogenic or benign criteria beyond PM2_supporting are met. The variant is not cysteine-altering and lies outside known mutational hotspots. No functional, segregation, de novo, case-control, or clinical classification data are available. Based on ACMG/AMP 2015 generic classification rules (PMID:25741868), a single supporting pathogenic criterion (PM2_supporting) is insufficient to reach Likely Pathogenic or any other classification tier. 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	Missense substitution (p.Asp1086Ala); does not fall into PVS1 null-variant categories (nonsense, frameshift, or canonical ±1,2 splice consensus variants). Per ClinGen SVI PVS1 recommendations (PMC6185798), generic PVS1 framework does not apply.	pvs1_generic_framework
PS1	Not assessed	No previously established pathogenic variant at amino acid residue 1086 has been identified in ClinVar or the literature to support PS1.
PS2	Not assessed	No de novo evidence with both maternity and paternity confirmed is available in ClinVar or the literature for this variant.
PS3	Not assessed	No variant-specific functional evidence (in vitro or in vivo) demonstrating a damaging effect is available in the literature, ClinVar, or OncoKB curated sources.
PS4	Not assessed	No case-control or prevalence data comparing affected vs. unaffected individuals are available for this variant.
PS5	Not assessed	No de novo evidence without confirmed maternity/paternity is available in ClinVar or the literature for this variant.
PM1	Not met	Residue Asp1086 is not located in a statistically significant mutational hotspot (Cancer Hotspots: not significant). The variant does not alter a cysteine residue within an EGF-like repeat domain, which is the hallmark pathogenic mechanism in NOTCH3-associated CADASIL.
PM2	Met	This variant is absent from large population databases including gnomAD v2.1, gnomAD v4.1, and gnomAD-Canada v1.0 (allele frequency 0.0%), meeting PM2 threshold of <0.1% allele frequency.	gnomad_v2 gnomad_v4 gnomad_canada
PM5	N/A	No same-residue comparator missense variant with established pathogenicity was identified in ClinVar or literature; PM5 candidate harvesting returned no candidates.
PM6	Not assessed	No de novo evidence without confirmed paternity/maternity is available in ClinVar or the literature for this variant.
PP1	Not assessed	No cosegregation data with disease in multiple affected family members are available for this variant.
PP2	Not met	The variant is a non-cysteine missense change (Asp1086Ala) in NOTCH3. Although NOTCH3 missense variants cause CADASIL, the established disease mechanism is specifically cysteine-altering variants within EGF-like repeat domains. HCI prior constraint data is not available for NOTCH3 to assess the gene's benign missense variation rate. Insufficient evidence to support PP2.
PP3	Not met	REVEL score of 0.744 is borderline but not supported by BayesDel (0.07, below deleterious threshold). SpliceAI predicts no splice impact (max delta 0.05). Insufficient multi-tool computational consensus to support a deleterious prediction.	revel bayesdel spliceai
PP4	Not assessed	No phenotype or family history data specific to this variant are available to assess whether the patient's presentation is highly specific for NOTCH3-related disease.
PP5	Not assessed	This variant is absent from ClinVar; no reputable source has classified it as pathogenic.
BA1	Not met	This variant is absent from gnomAD v2.1, v4.1, and gnomAD-Canada (allele frequency 0.0%). Does not meet BA1 threshold of >1%.	gnomad_v2 gnomad_v4 gnomad_canada
BS1	Not met	This variant is absent from gnomAD v2.1, v4.1, and gnomAD-Canada (allele frequency 0.0%). Does not meet BS1 threshold of >0.3%.	gnomad_v2 gnomad_v4 gnomad_canada
BS2	Not assessed	No evidence of observation in a healthy adult individual in trans with a known pathogenic NOTCH3 variant is available.
BS3	Not assessed	No variant-specific functional studies (in vitro or in vivo) demonstrating no damaging effect are available in the literature, ClinVar, or OncoKB.
BS4	Not assessed	No family segregation data are available to assess lack of segregation with disease.
BP1	Not met	NOTCH3-associated disease (CADASIL) is primarily caused by missense variants, not truncating variants. BP1 is not applicable for genes where missense variants are the predominant disease mechanism.
BP2	Not assessed	No evidence of observation in trans with a known dominant pathogenic NOTCH3 variant is available.
BP4	Not met	REVEL score of 0.744 is above 0.5, indicating a prediction of deleterious effect. Computational evidence does not support no impact on gene product, and therefore BP4 is not met.	revel bayesdel spliceai
BP5	Not assessed	No evidence of an alternate molecular basis for disease in a case carrying this variant is available.
BP6	Not assessed	This variant is absent from ClinVar; no reputable source has classified it as benign.
BP7	N/A	Variant is a missense substitution (c.3257A>C, p.Asp1086Ala), not a synonymous variant. BP7 does not apply.

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.