NM_024408.3:c.782T>G

NOTCH2 · NP_077719.2:p.(Ile261Ser) · NM_024408.3

GRCh37: chr1:120529675 A>C · GRCh38: chr1:119987052 A>C

Gene: NOTCH2 Transcript: NM_024408.3

Final call

VUS

PM2 supporting

Variant details

Gene

NOTCH2

Transcript

NM_024408.3

Protein

NP_077719.2:p.(Ile261Ser)

gnomAD AF

ClinVar

Uncertain significance

OncoKB

Unknown Oncogenic Effect

Classification rationale

Interpretation summary

Generated evidence synthesis

NM_024408.3:c.782T>G (p.Ile261Ser) is absent from gnomAD v2.1, v4.1, and gnomAD-Canada population databases (0 alleles), meeting PM2 at supporting strength.

This variant has been reported in ClinVar (Variation ID 591665) as Uncertain significance by a single clinical testing laboratory (Labcorp Genetics, criteria provided, single submitter); no submitter has classified it as pathogenic or benign.

No published functional studies, de novo observations, case-control enrichment, or family segregation data exist for this specific variant.

In silico predictions are discordant: REVEL (0.80) supports a deleterious effect while BayesDel (0.402) does not; SpliceAI predicts no splicing impact (max delta 0.02). Neither PP3 nor BP4 can be applied.

PVS1 is not applicable as this is a missense variant outside the null-variant buckets defined by ClinGen SVI PVS1 recommendations (PMC6185798).

The only applicable criterion is PM2 (supporting); one supporting pathogenic criterion is insufficient to classify this variant above Variant of Uncertain Significance per ACMG/AMP 2015 combination rules.

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 is a missense variant (c.782T>G, p.Ile261Ser) and does not fall into the generic PVS1 null-variant buckets of nonsense, frameshift, or canonical ±1,2 splice consensus variants. Per ClinGen SVI PVS1 recommendations (PMC6185798), the generic PVS1 decision tree does not apply to this variant class.	pvs1_generic_framework pvs1_variant_assessment
PS1	Not met	No pathogenic variant with the same amino acid change (Ile261Ser) has been established in NOTCH2. PS1 requires a different nucleotide change resulting in the same amino acid change as an established pathogenic variant, which is not available.	clinvar
PS2	Not met	No de novo occurrence confirmed by both maternity and paternity testing has been reported. Exploratory search of ClinVar, Decipher, and published literature identified no de novo evidence for NM_024408.3:c.782T>G.	clinvar
PS3	Not met	No well-established in vitro or in vivo functional studies have been performed specifically on the I261S substitution. OncoKB identified no variant-specific functional evidence, and the exploratory literature search found no functional assays testing this variant.	oncokb
PS4	Not met	PS4 requires statistically significant enrichment of the variant in affected individuals compared with controls. Although the variant is absent from gnomAD, no case-control studies have been conducted, and absence from population databases alone is insufficient to meet PS4.	gnomad_v2 gnomad_v4
PS5	N/A	PS5 requires a different nucleotide change leading to the same amino acid change as an established pathogenic variant. No pathogenic variant resulting in Ile261Ser via a different nucleotide substitution has been reported.	clinvar
PM1	Not assessed	Residue Ile261 lies within an EGF-like repeat domain (exon 5 of NOTCH2), which is critical for ligand binding and where pathogenic missense variants have been reported in Alagille syndrome. However, domain-level missense tolerance data (e.g., MetaDome, gnomAD regional missense constraint) have not been reviewed to confirm the absence of benign missense variation in this specific EGF repeat region, which is required for PM1 application.
PM2	Met	NM_024408.3:c.782T>G is absent from gnomAD v2.1, gnomAD v4.1, and gnomAD-Canada v1.0 (0 alleles across all population databases). The allele frequency (0) is below the PM2 threshold of <0.1% for a rare variant in a dominant disorder gene.	gnomad_v2 gnomad_v4
PM5	Not met	No pathogenic missense variant at the same amino acid residue (Ile261) with a different amino acid change has been identified. The PM5 candidate collection confirmed 0 same-residue comparator variants in ClinVar.	pm5_candidates clinvar
PM6	Not met	No de novo event (without confirmed maternity/paternity) has been reported. Exploratory search of ClinVar, Decipher, and literature identified no de novo observations for this variant.	clinvar
PP1	Not met	No co-segregation data with disease in multiple affected family members is available. No family studies or pedigree analyses involving this variant have been reported.
PP2	Not assessed	While missense variants in NOTCH2 are a known disease mechanism (Alagille syndrome type 2, Hajdu-Cheney syndrome), gene-level missense constraint metrics (e.g., gnomAD missense Z-score, observed/expected ratio) have not been evaluated to confirm a low rate of benign missense variation in NOTCH2, which is required for PP2 application per ACMG/AMP 2015 guidelines.
PP3	Not met	In silico predictions are discordant. REVEL predicts a deleterious effect (score 0.80, above 0.5 threshold), but BayesDel does not support a deleterious effect (score 0.402, below 0.5 threshold). SpliceAI predicts no splicing impact (max delta score 0.02). Multiple lines of computational evidence do not uniformly support a deleterious effect, as required for PP3.	revel bayesdel spliceai
PP4	Not met	No patient phenotype or family history data are available for this case. PP4 requires the patient's phenotype or family history to be highly specific for a disease with a single genetic etiology.
PP5	Not met	This variant is classified as Uncertain significance in ClinVar (Variation ID 591665) by a single clinical submitter (Labcorp Genetics, criteria provided, single submitter). No reputable source has reported this variant as pathogenic. The ClinVar-submitted PMIDs (25741868 and 28492532) are methodology papers that do not mention or evaluate this specific variant.	clinvar PMID:25741868 PMID:28492532
BA1	Not met	The variant is absent from gnomAD v2.1, v4.1, and gnomAD-Canada (allele frequency = 0). The BA1 threshold of >1% allele frequency is not met.	gnomad_v2 gnomad_v4
BS1	Not met	The variant is absent from all population databases (allele frequency = 0). The BS1 threshold of >0.3% allele frequency is not met.	gnomad_v2 gnomad_v4
BS2	Not met	No observations of this variant in healthy adult controls at significant frequency have been reported. The variant has not been observed in trans with a pathogenic variant for a fully penetrant dominant disorder.	gnomad_v2 gnomad_v4
BS3	Not met	No well-established in vitro or in vivo functional studies have demonstrated no damaging effect for the I261S substitution. OncoKB identified no variant-specific functional evidence, and the exploratory literature search found no functional studies evaluating this variant's effect on NOTCH2 signaling.	oncokb
BS4	Not met	No evidence of non-segregation with disease in affected families is available. No family studies or pedigree analyses involving this variant have been reported.
BP1	N/A	BP1 applies to missense variants in genes where primarily truncating variants cause disease. NOTCH2 harbors both missense (Alagille syndrome type 2, Hajdu-Cheney syndrome) and truncating pathogenic variants, so the BP1 prerequisite is not satisfied.	pvs1_gene_context
BP2	Not met	No observation of this variant in trans with a pathogenic variant for a fully penetrant dominant disorder has been reported. NOTCH2-related disorders are autosomal dominant, and BP2 would require observation in trans with a known pathogenic variant without clinical consequence.
BP4	Not met	In silico predictions are discordant. While BayesDel (score 0.402) weakly suggests no impact and SpliceAI predicts no splicing effect (max delta 0.02), REVEL predicts a deleterious effect (score 0.80). Multiple lines of computational evidence do not uniformly suggest no impact on the gene product, as required for BP4.	revel bayesdel spliceai
BP5	Not met	No observation of this variant in a case with an alternate molecular basis for disease has been reported. BP5 requires the variant to be found in a patient with a different established genetic cause for their phenotype.
BP6	Not met	No reputable source has reported this variant as benign. The ClinVar classification is Uncertain significance (Variation ID 591665), not benign or likely benign. BP6 requires a reputable source to report the variant as benign.	clinvar
BP7	N/A	This is a missense variant (c.782T>G, p.Ile261Ser), not a synonymous variant. BP7 applies only to synonymous (silent) variants predicted to have no impact on splicing via computational assessment.

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