NM_033632.3:c.1514G>T

FBXW7 · NP_361014.1:p.(Arg505Leu) · NM_033632.3

GRCh37: chr4:153247288 C>A · GRCh38: chr4:152326136 C>A

Gene: FBXW7 Transcript: NM_033632.3

Final call

VUS

PS3 supporting PM1 moderate PM2 supporting

Variant details

Gene

FBXW7

Transcript

NM_033632.3

Protein

NP_361014.1:p.(Arg505Leu)

gnomAD AF

6.19846749089755e-07 (v4.1)

ClinVar

OncoKB

Oncogenic

Classification rationale

Interpretation summary

Generated evidence synthesis

NM_033632.3:c.1514G>T (p.Arg505Leu) is a missense variant in exon 10 of FBXW7, affecting a critical arginine residue in the WD40 substrate-recognition domain.

The variant is extremely rare in population databases, with a single heterozygous observation among 1,613,302 alleles in gnomAD v4.1 (AF = 6.2e-07), meeting PM2 at supporting strength.

The variant is located at Arg505 in the WD40 beta-propeller domain, a well-characterized functional domain critical for substrate recognition and ubiquitination. Mutations at this residue have been shown to disrupt NOTCH1 and MYC binding (PMID:17646409), and the residue is a statistically significant cancer hotspot, meeting PM1 at moderate strength.

Functional studies of an R505C substitution at the same residue demonstrate that mutation of Arg505 impairs FBXW7 substrate binding, producing a dominant-negative allele. While the exact variant (R505L) was not directly tested and the study characterized only three specific arginine residues rather than a systematic range, the functional data at the same position supports a deleterious effect, meeting PS3 at supporting strength.

Applying the generic ACMG/AMP 2015 final classification combination rules (PMID:25741868), one moderate criterion (PM1) plus two supporting criteria (PM2, PS3) is insufficient to reach likely pathogenic classification, which requires at minimum either two moderate criteria or one moderate plus four supporting criteria. The 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	NM_033632.3:c.1514G>T is a missense variant (p.Arg505Leu), not a null variant. The variant falls outside the generic PVS1 null-variant buckets of nonsense, frameshift, or canonical ±1,2 splice consensus variants per ClinGen SVI PVS1 recommendations (PMC6185798).	pvs1_generic_framework pvs1_variant_assessment
PS1	Not met	No pathogenic or likely pathogenic variant with the same amino acid change (p.Arg505Leu) has been identified in ClinVar or the literature. PS1 requires an established pathogenic variant resulting in the identical amino acid change via a different nucleotide alteration.	clinvar
PS2	Not assessed	No de novo data are available for this variant. PS2 requires confirmation that the variant occurred de novo with both maternity and paternity confirmed.
PS3	Met	Functional data from PMID:17646409 demonstrate that mutation of Arg505 (specifically R505C) in the FBXW7 WD40 substrate-recognition domain disrupts binding to NOTCH1 intracellular domain (NICD) and impairs MYC degradation, producing a dominant-negative allele. The exact variant (R505L) was not directly tested and the study characterized only three specific arginine residues rather than a systematic range, limiting PS3 to supporting strength under the calibration framework.	PMID:17646409
PS4	Not assessed	The variant is absent from ClinVar and no case-control or case-series data are available. PS4 requires significantly increased prevalence in affected individuals compared with controls.
PS5	Not met	No alternative nucleotide change at the same position resulting in the same amino acid change (p.Arg505Leu) has been established as pathogenic. PS5 requires a proven pathogenic variant producing the same missense change through a different nucleotide substitution.	clinvar
PM1	Met	The variant affects Arg505, a critical arginine residue within the WD40 beta-propeller substrate-recognition domain of FBXW7. PMID:17646409 demonstrates that mutations at Arg505 (along with Arg465 and Arg479) in this domain disrupt substrate binding to NOTCH1 and MYC, and the residue is identified as a statistically significant cancer hotspot (cancerhotspots.org). PM1 is applied at moderate strength based on location in a well-characterized functional domain without benign variation.	PMID:17646409 oncokb
PM2	Met	The variant is extremely rare in population databases. gnomAD v4.1 reports a single allele among 1,613,302 total alleles (AF = 6.2e-07; MAF = 0.00006%) in the European (non-Finnish) population, with zero homozygotes. The variant is absent from gnomAD v2.1 and gnomAD-Canada v1.0. This is well below the PM2 threshold of 0.1% under generic ACMG/AMP.	gnomad_v4 gnomad_v2 gnomad_canada
PM5	Not met	No different pathogenic missense variant at the same amino acid position (Arg505) has been identified in ClinVar with a pathogenic or likely pathogenic classification. While PMID:17646409 reports an R505C mutation in somatic T-ALL cell lines, this is not a ClinVar-classified germline pathogenic variant and does not satisfy PM5 requirements under generic ACMG/AMP.	pm5_candidates clinvar
PM6	Not assessed	No de novo reports are available for this variant. PM6 requires confirmation of a de novo occurrence with maternity and paternity confirmed, without confirmation through any other means.
PP1	Not assessed	No segregation data are available for this variant. PP1 requires co-segregation of the variant with disease in multiple affected family members.
PP2	Not assessed	No gene-level missense constraint metric (HCI prior, gnomAD missense Z-score, or observed/expected ratio) is available for FBXW7. While FBXW7 germline missense variants are a known disease mechanism (PMID:35395208), PP2 requires explicit constraint data demonstrating a low rate of benign missense variation, which is not available in the case materials.
PP3	Not met	In silico predictions do not provide multiple converging lines of evidence for a deleterious effect. REVEL score of 0.601 is borderline and falls below the more stringent threshold of 0.75. BayesDel score of 0.235 is below the standard damaging threshold of 0.27 (noAF version). SpliceAI predicts no splicing impact (max delta = 0.13). Only one of three computational tools (REVEL) provides equivocal support, which is insufficient for PP3 under generic ACMG/AMP.	revel bayesdel spliceai
PP4	Not assessed	No specific phenotypic data are available for this variant. PP4 requires that the patient's phenotype or family history is highly specific for a disease with a single genetic etiology.
PP5	Not met	This variant is absent from ClinVar. PP5 requires a pathogenic or likely pathogenic classification from a reputable source (3-star expert panel or equivalent). No such classification exists for this variant.	clinvar
BA1	Not met	The gnomAD v4.1 allele frequency of 6.2e-07 (0.00006%) is far below the BA1 threshold of 1%. This variant is too rare in the general population to qualify as a common benign polymorphism.	gnomad_v4
BS1	Not met	The gnomAD v4.1 allele frequency of 6.2e-07 (0.00006%) is far below the BS1 threshold of 0.3%. This variant is too rare to be considered a benign polymorphism with frequency exceeding disease prevalence.	gnomad_v4
BS2	Not assessed	No data are available on observation of this variant in healthy adults. BS2 requires observation in a healthy adult individual for a recessive, X-linked, or fully penetrant dominant disorder.
BS3	Not met	The only available functional study (PMID:17646409) demonstrates that mutations at Arg505 in FBXW7 disrupt substrate binding and produce a dominant-negative effect, consistent with a damaging rather than benign functional impact. No well-established functional studies show no deleterious effect.	PMID:17646409
BS4	Not assessed	No segregation data are available to evaluate lack of co-segregation with disease. BS4 requires observation that the variant does not segregate with disease in affected family members.
BP1	Not met	FBXW7 germline disease is not caused exclusively by truncating variants. Multiple publications (PMID:35395208, PMID:42111496) establish that missense variants clustering in the WD40 domain are a common mechanism of FBXW7-related neurodevelopmental disorder. BP1 is only applicable when a gene's disease mechanism is primarily through truncating variants.
BP2	N/A	No observation of this variant in trans with a known pathogenic FBXW7 variant. BP2 requires observation in trans with a dominant pathogenic variant for a fully penetrant dominant disorder, or in cis with a pathogenic variant in a recessive disorder.
BP4	Not met	While SpliceAI predicts no splicing impact (max delta = 0.13), the REVEL score of 0.601 suggests a potential deleterious effect on protein function. BP4 requires multiple lines of computational evidence to suggest no impact on gene or gene product, which is not satisfied when one tool suggests a deleterious effect.	revel bayesdel spliceai
BP5	Not assessed	No data are available on observation of this variant in a case with an alternate molecular basis for disease. BP5 requires the variant to be found in a case with a clear alternate cause of disease.
BP6	Not met	This variant is absent from ClinVar. BP6 requires a benign or likely benign classification from a reputable source (3-star expert panel or equivalent). No such classification exists.	clinvar
BP7	N/A	NM_033632.3:c.1514G>T is a missense variant (p.Arg505Leu), not a synonymous variant. BP7 applies exclusively to synonymous variants with no predicted splicing impact and non-conserved nucleotides.

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