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.1 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.2 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.3 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.4 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).5
FBXW7
Final classification
VUS
FBXW7 c.1514G>T · p.Arg505Leu
FBXW7
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.
gene-specific framework lacked a usable explicit final combination framework, so generic ACMG/AMP 2015 final-combination rules were applied as fallback; applied criteria: PS3 supporting, PM1 moderate, PM2 supporting; combination = 1 moderate + 2 supporting, which maps to VUS.
Classification rationale
PS3PM1PM2
VUS
FBXW7 c.1514G>T
PS3 + PM1 + PM2
→
VUS
5
generic_acmg_combination_rules
Gene diagram
· NM_033632.3 · variants mapped to exon structure
FBXW7
NM_033632.3
Fetching transcript structure from UCSC…
Applied criteria · 3 applied · 19 assessed
Applied · 3
Strength
Supporting
Moderate
Strong
Very strong
✓
PS3
supporting
review
Pathogenic
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: R505C mutation in FBXW7 WD40 domain abolishes NICD binding and MYC degradation in co-immunoprecipitation and ubiquitination assays.Same residue (Arg505) different substitutionfunctional effect direction is clearly damaging and consistent with loss-of-function mechanism.
✓
PM1
moderate
Pathogenic
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: The WD40 domain (exons 7–11) is the substrate-binding domainArg505 is one of three key arginine residues critical for substrate recognition.cancerhotspots.org: Residue is in a statistically significant hotspot.
✓
PM2
supporting
Pathogenic
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 v4.1: 1/1613302 alleles (AF = 6.2e-07)
Assessed · not applied
Pathogenic
PS1
No pathogenic or likely pathogenic variant with the same amino acid change (p.Arg505Leu) has been identified in ClinVar or the literature.
PS2
No de novo data are available for this variant.
PS4
The variant is absent from ClinVar and no case-control or case-series data are available.
PM5
No different pathogenic missense variant at the same amino acid position (Arg505) has been identified in ClinVar with a pathogenic or likely pathogenic classification.
PM6
No de novo reports are available for this variant.
PP1
No segregation data are available for this variant.
PP2
No gene-level missense constraint metric (HCI prior, gnomAD missense Z-score, or observed/expected ratio) is available for FBXW7.
PP3
In silico predictions do not provide multiple converging lines of evidence for a deleterious effect.
PP4
No specific phenotypic data are available for this variant.
PP5
This variant is absent from ClinVar.
Benign
BA1
The gnomAD v4.1 allele frequency of 6.2e-07 (0.00006%) is far below the BA1 threshold of 1%.
BS1
The gnomAD v4.1 allele frequency of 6.2e-07 (0.00006%) is far below the BS1 threshold of 0.3%.
BS2
No data are available on observation of this variant in healthy adults.
BS3
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.
BS4
No segregation data are available to evaluate lack of co-segregation with disease.
BP1
FBXW7 germline disease is not caused exclusively by truncating variants.
BP4
While SpliceAI predicts no splicing impact (max delta = 0.13), the REVEL score of 0.601 suggests a potential deleterious effect on protein function.
BP5
No data are available on observation of this variant in a case with an alternate molecular basis for disease.
BP6
This variant is absent from ClinVar.
N/A · 3
PVS1 · BP2 · BP7
Research & evidence
Population frequency
gnomAD v4.1
gnomAD v2.1
v4.1
This variant is present in gnomAD v4.1 (AF= 6.19847e-07; MAF= 0.00006%, 1/1613302 alleles, homozygotes = 0) and has highest observed frequency in the European (non-Finnish) population (AF= 8.47801e-07; MAF= 0.00008%, 1/1179522 alleles, homozygotes = 0).
v2.1
Absent from gnomAD v2.1.
🇨🇦 CA
Absent from gnomAD-Canada v1.0.
Allele frequency by ancestry
three datasets · side by side
gnomAD v4.1
6.2e-05%
· 1 / 1,613,302
0 hom
0 hom
European (non-Finnish) 1 / 1,179,522 |
8.5e-05% |
+ 9 not observed (Remaining individuals, Admixed American, European (Finnish), Amish, East Asian, Middle Eastern, South Asian, Ashkenazi Jewish, African/African American)
gnomAD v2.1
Absent
· 0 / ?
0 hom
0 hom
Not observed in any ancestry group.
gnomAD Canada 🇨🇦
Absent
· 0 / ?
0 hom
0 hom
Not observed in any ancestry group.
In silico
SpliceAI predicts no significant splice impact for this variant (max delta score = 0.13). REVEL score = 0.601. BayesDel score = 0.235507.
Functional
Oncogenic
OncoKB identified variant-specific curated literature and context relevant to functional review; biological-effect context: Loss-of-function; curated oncogenicity label: Oncogenic.
COSMIC
Cancer hotspots
Somatic evidence
Hotspot
COSMIC
This variant lies in a statistically significant hotspot. This variant has previously been reported in somatic cancers (COSMIC; COSV55908371, n = 36 times).
Hotspots
This variant lies in a statistically significant hotspot.
Literature · how each cited paper was used
1papers cited
Each card is an audit: what was searched, what was found, whether it names the variant, which criteria it fed, and why.
FBW7 mutations in leukemic cells mediate NOTCH pathway activation and resistance to gamma-secretase inhibitors.
Searched
c.1514G>Tp.Arg505LeuR505Lc.1513C>TR505C505 R→C
Found
Demonstrates that FBW7 (FBXW7) R505C mutations in the WD40 domain disrupt binding to NOTCH1 intracellular domain (NICD) and impair MYC degradation in T-ALL cell lines. The R505C mutant acts as a dominant-negative allele. The paper reports R505C (p.Arg505Cys, NM_033632:c.1513C>T) in Jurkat, HSB2, and PEER T-ALL cell lines, but does not report the R505L (c.1514G>T) variant under review.
Variant
◇ Residue / gene-level — variant not named
Applied to
→PM1 supports · met
→PS3 supports · met
Why
Provides functional evidence that mutation of Arg505 in the FBXW7 WD40 domain disrupts substrate binding. Used to support PS3 at supporting strength (same residue, different substitution; not a systematic range study) and PM1 at moderate strength (establishes WD40 domain as critical functional domain).
Each of the seven cell lines with increased levels of NICD but without C-terminal truncating mutations in NOTCH1 (RPMI8402, CEM, BE13, DU528, HSB2, Jurkat, and PEER) harbored either a mutation in FBW7 or homozygous deletion of the gene.
Location Table I (T-ALL cell line FBW7 mutations); Results section 'FBW7 is mutated in T-ALL cell lines and primary samples'; Methods section 'Plasmids and transient transfections' (R505C mutant construction) · Context Co-immunoprecipitation, ubiquitination assays, and pulse-chase experiments in 293a and K562 cells; T-ALL cell lines Jurkat (R505C heterozygous) and HSB2 (R505C heterozygous) · full text
Sources & reference links