NM_033632.3:c.1436G>T

FBXW7 · NP_361014.1:p.(Arg479Leu) · NM_033632.3

GRCh37: chr4:153247366 C>A · GRCh38: chr4:152326214 C>A

Gene: FBXW7 Transcript: NM_033632.3

Final call

Likely Pathogenic

PS3 moderate PM1 moderate PM2 supporting PP3 supporting

Variant details

Gene

FBXW7

Transcript

NM_033632.3

Protein

NP_361014.1:p.(Arg479Leu)

gnomAD AF

ClinVar

Tier I - Strong

OncoKB

Likely Oncogenic

Classification rationale

Interpretation summary

Generated evidence synthesis

NM_033632.3:c.1436G>T (p.Arg479Leu) is a missense variant in exon 10 of FBXW7, located at residue 479 within the WD40 substrate recognition domain.

This variant is absent from gnomAD v2.1, v4.1, and gnomAD-Canada population databases, meeting PM2 at supporting strength.

The variant lies at a statistically significant mutational hotspot (cancerhotspots.org) within the WD40 domain, a well-characterized functional domain critical for FBXW7 substrate recognition. Mutations at residue 479 have been shown to disrupt FBXW7-substrate interactions across multiple studies, meeting PM1 at moderate strength.

Functional studies directly testing the R479L substitution in a co-immunoprecipitation assay (293T cells) demonstrated complete loss of FBXW7 interaction with its substrate DAB2IP, confirming disruption of substrate recognition function. This meets PS3 at moderate strength.

Multiple in silico tools support a deleterious effect: REVEL score 0.583 and SpliceAI max delta score 0.33 (acceptor loss prediction). This meets PP3 at supporting strength.

The variant has been reported in ClinVar (Variation ID: 4530538) as Tier I - Strong with a single submitter (1-star review status). It has been observed in somatic cancers (COSMIC COSV55899054, 18 counts) but lacks independent germline proband observations. These data are insufficient for PP5 or PS4.

Final determination: Generic ACMG/AMP 2015 fallback rules support a Likely Pathogenic classification based on the observed combination of pathogenic criteria.

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	PVS1 is restricted to null variants (nonsense, frameshift, canonical ±1,2 splice sites). NM_033632.3:c.1436G>T is a missense substitution (p.Arg479Leu) in exon 10 and does not fall into any PVS1 null-variant bucket per ClinGen SVI recommendations (PMC6185798).	pvs1_generic_framework
PS1	Not met	PS1 requires a different nucleotide change at the same codon producing the same amino acid change (p.Arg479Leu) that has been established as pathogenic. No alternative nucleotide change at c.1436 producing p.Arg479Leu was identified in ClinVar or the reviewed literature.
PS2	Not met	PS2 requires a de novo observation with confirmed maternity and paternity. No de novo data for NM_033632.3:c.1436G>T was identified in ClinVar submissions, the reviewed literature, or any other source.
PS3	Met	The R479L substitution was directly tested in a co-immunoprecipitation assay in 293T cells and demonstrated complete loss of FBXW7 interaction with its substrate DAB2IP, confirming disruption of substrate recognition function. This is a single study with direct variant testing using an indirect reporter-type assay, supporting moderate strength.	PMID:24912918
PS4	Not met	PS4 requires statistically significant enrichment in affected individuals or a substantial number of independent proband observations. This variant has been observed in COSMIC (18 somatic counts, COSV55899054) but these are somatic cancer observations. No independent germline proband count is available; ClinVar submissions could not be extracted (0 submissions parsed), and the reviewed literature did not identify any germline probands with this variant. PMID:25768946 (rhabdomyosarcoma genomics) was screened but the variant was not identified in the full text.	clinvar
PS5	Not met	PS5 requires the same amino acid change (p.Arg479Leu) to have been established as pathogenic via a different nucleotide change at the same codon. No alternative nucleotide change at codon 479 producing p.Arg479Leu was identified in ClinVar or the reviewed literature. The ClinVar record (Variation ID: 4530538) lists the variant under NM_001349798.2:c.1436G>T, not an alternative nucleotide change.
PM1	Met	The variant is located at residue Arg479 within the WD40 substrate recognition domain of FBXW7, a well-characterized critical functional domain. This residue is a statistically significant mutational hotspot per cancerhotspots.org. Functional studies (PMID:24912918, PMID:17646408, PMID:17646409) confirm that mutations at this position disrupt FBXW7 substrate binding. The variant lies in the WD40 repeat domain that mediates substrate recognition, and no benign variation is observed at this position in population databases.	PMID:24912918 PMID:17646408 PMID:17646409 gnomad_v2 gnomad_v4
PM2	Met	This variant is absent from gnomAD v2.1 (exomes), gnomAD v4.1 (exomes), and gnomAD-Canada v1.0. Allele frequency is below the 0.1% PM2 threshold for rare variant support in the generic ACMG framework.	gnomad_v2 gnomad_v4 gnomad_canada
PM5	Not met	PM5 requires a different pathogenic missense variant at the same amino acid residue (Arg479). The automated PM5 candidate search identified 0 same-residue pathogenic comparator variants in ClinVar. While R479Q has been reported in the literature (PMID:17646408, PMID:17646409) as a functionally damaging T-ALL-associated mutation, it has not been classified as pathogenic in ClinVar, and functional data from a sister variant does not independently satisfy PM5 without a clinical classification.	pm5_candidates
PM6	Not met	PM6 requires a de novo observation with confirmed maternity and paternity. No de novo data was identified for this variant in any reviewed source.
PP1	Not met	PP1 requires cosegregation of the variant with disease in multiple affected family members. No segregation data was available for this variant in ClinVar submissions or the reviewed literature.
PP2	Not met	PP2 applies when a gene has a low rate of benign missense variation and missense variants are a known disease mechanism. FBXW7 is a tumor suppressor with disease-associated missense variants in the WD40 domain; however, without a VCEP-specified z-score or missense constraint metric, PP2 cannot be automatically applied under the generic ACMG framework.
PP3	Met	Multiple lines of computational evidence support a deleterious effect: REVEL score of 0.583 (above the 0.5 threshold for pathogenicity) and SpliceAI predicts a possible splice alteration with a max delta score of 0.33 (acceptor loss). The variant also lies at a statistically significant mutational hotspot. BayesDel score is low at 0.125 but does not outweigh the preponderance of evidence from REVEL and SpliceAI.	revel spliceai bayesdel
PP4	Not met	PP4 requires the variant to be found in a patient with a phenotype highly specific for FBXW7-related disease. No patient-specific phenotype information was available for this variant. The ClinVar record lacks extractable submission details and no clinical phenotype data was identified in the reviewed literature.	clinvar
PP5	Not met	PP5 requires a reputable source (≥3-star ClinVar expert panel) to have classified the variant as pathogenic. The ClinVar record (Variation ID: 4530538) has a review status of 'criteria provided, single submitter' (1-star). The classification is 'Tier I - Strong,' which is a somatic AMP/ASCO/CAP tier, not an ACMG germline classification. Under the governing PP5 rule (≥3-star EP required), this does not meet the threshold for supporting strength. Submission details could not be extracted (0 submissions parsed).	clinvar
BA1	Not met	BA1 requires an allele frequency >1% in gnomAD. This variant is absent from gnomAD v2.1, v4.1, and gnomAD-Canada.	gnomad_v2 gnomad_v4 gnomad_canada
BS1	Not met	BS1 requires an allele frequency >0.3% in gnomAD. This variant is absent from all gnomAD datasets.	gnomad_v2 gnomad_v4
BS2	Not met	BS2 requires observation in a healthy adult at a frequency inconsistent with a fully penetrant disorder. The variant is absent from all population databases; no healthy adult observation exists.	gnomad_v2 gnomad_v4
BS3	Not met	BS3 requires well-established functional studies showing no damaging effect. The only functional study of this variant (PMID:24912918) demonstrated loss of FBXW7-DAB2IP interaction, confirming a damaging loss-of-function effect. No benign functional data exists.	PMID:24912918
BS4	Not met	BS4 requires lack of segregation in affected family members. No segregation data is available for this variant.
BP1	Not met	BP1 applies to missense variants in genes where only truncating variants cause disease. FBXW7-related neurodevelopmental syndrome and Wilms tumor predisposition are associated with both truncating and missense variants, particularly missense variants in the WD40 domain. Therefore BP1 does not apply.
BP2	Not met	BP2 requires observation in trans with a pathogenic variant for a fully penetrant dominant disorder. No such observation exists.
BP3	N/A	BP3 applies to in-frame deletions/insertions in repetitive regions; this is a missense substitution.
BP4	Not met	BP4 requires multiple lines of computational evidence suggesting no impact on gene product. REVEL score (0.583) and SpliceAI (max delta 0.33) both predict a deleterious effect. While BayesDel (0.125) is low, the preponderance of in silico evidence does not support a benign interpretation.	revel spliceai bayesdel
BP5	Not met	BP5 requires the variant to be found in a case with an alternate molecular basis for disease. No such evidence was identified.
BP6	Not met	BP6 requires a reputable source (≥3-star ClinVar EP) to have classified the variant as benign. The ClinVar record classifies this variant as 'Tier I - Strong' (pathogenic), not benign. Additionally, the review status is 1-star, not the required 3-star threshold.	clinvar
BP7	N/A	BP7 applies to synonymous variants predicted to have no splice impact. NM_033632.3:c.1436G>T is a missense variant (p.Arg479Leu), not a synonymous variant.
PM3	N/A	PM3 applies to recessive disorders where the variant is found in trans with another pathogenic variant. FBXW7-associated disease is autosomal dominant; no trans-configuration data is relevant.
PM4	N/A	PM4 applies to in-frame deletions/insertions or stop-loss variants causing protein length change. This is a missense substitution.

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