NM_005631.4:c.1604G>T (p.Trp535Leu) is absent from all population databases including gnomAD v2.1, v4.1, and gnomAD-Canada, with an allele frequency of 0.0%.1 W535L is a well-established constitutively active gain-of-function variant in SMO, demonstrated in Smo−/− MEFs to activate Hedgehog signaling (GLI1 reporter) in the absence of ligand and to confer strong resistance to the SMO inhibitor vismodegib (IC50 >320 nM vs wildtype ~8 nM).2 W535 is located at position 7.55 in transmembrane helix VII, a conserved tryptophan residue critical for maintaining SMO autoinhibition. Structural studies confirm that mutation of this residue disrupts the inactive receptor conformation, producing constitutive activation.3 W535L lies within a statistically significant mutational hotspot and no benign variation is observed at this residue in population databases.4 REVEL in silico prediction score of 0.922 strongly supports a deleterious effect.5 Applying generic ACMG/AMP 2015 final classification combination rules (PMID:25741868): Two moderate criteria (PS3, PM1) plus two supporting criteria (PM2, PP3) meet the threshold for Likely Pathogenic.6
SMO
Final classification
Likely Pathogenic
SMO c.1604G>T · p.Trp535Leu
SMO
NM_005631.4:c.1604G>T (p.Trp535Leu) is absent from all population databases including gnomAD v2.1, v4.1, and gnomAD-Canada, with an allele frequency of 0.0%.
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 moderate, PM1 moderate, PM2 supporting, PP3 supporting; combination = 2 moderate + 2 supporting, which maps to Likely Pathogenic.
Classification rationale
PS3PM1PM2PP3
Likely Pathogenic
SMO c.1604G>T
PS3 + PM1 + PM2 + PP3
→
Likely Pathogenic
5
revel
6
generic_acmg_combination_rules
Gene diagram
· NM_005631.4 · variants mapped to exon structure
SMO
NM_005631.4
Fetching transcript structure from UCSC…
Applied criteria · 4 met · select any tile
Met
Not met
Not assessed
N/A
Strength
very strong
supporting
Pathogenic evidence
PVS
PS
PM
PP
Benign evidence
BA
BS
BP
—
—
—
Rationale
Select a criterion.
Sources
Evidence used
Gaps remaining
Rule
—
Research & evidence
Population frequency · supports pathogenic
gnomAD v4.1
gnomAD v2.1
v4.1
Absent from gnomAD v4.1.
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
Absent
· 0 / ?
0 hom
0 hom
Not observed in any ancestry group.
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.
ClinVar
This variant is present in ClinVar (Variation ID: 8117); submission details unavailable.
In silico
SpliceAI predicts no significant splice impact for this variant (max delta score = 0.00). REVEL score = 0.922. BayesDel score = 0.462622.
Functional
Likely Oncogenic
OncoKB identified variant-specific curated literature and context relevant to functional review; biological-effect context: Gain-of-function; curated oncogenicity label: Likely 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; COSV50824509, n = 36 times).
Hotspots
This variant lies in a statistically significant hotspot.
Literature · how each cited paper was used
3papers cited
Each card is an audit: what was searched, what was found, whether it names the variant, which criteria it fed, and why.
Structure of the human smoothened receptor bound to an antitumour agent.
Searched
c.1604G>Tp.Trp535LeuW535LW535Trp535535
Found
Crystal structure of the human SMO receptor 7TM domain at 2.5 Å resolution reveals that W535, located at position 7.55 in helix VII, is a conserved tryptophan critical for receptor autoinhibition. The paper notes that mutation of W535 leads to a constitutively active SMO receptor, providing structural basis for the gain-of-function effect.
Variant
✓ Names this variant — characterised directly
Applied to
→PM1 supports · met
→PS3 supports · met
Why
Variant-specific structural context confirmed; W535 is identified as a critical autoinhibitory residue. Provides structural mechanistic support for PM1 and PS3 assessments.
W535 7.55 in helix VII. The latter tryptophan, conserved among class F and superimposable with the location of the NPxxY motif of class A, is shown to play an important role in receptor activation, as mutation of W535 7.55 leads to a constitutively active SMO receptor.
Location Results section: 'Homology with Frizzled family receptors'; Figure 6 · Context X-ray crystallography of human SMO 7TM domain bound to LY2940680 antagonist; structural analysis · full text
Smoothened variants explain the majority of drug resistance in basal cell carcinoma.
Searched
c.1604G>Tp.Trp535LeuW535LW535Trp535535
Found
W535L identified in 3/30 vismodegib-resistant BCCs and 1/36 untreated BCCs. Functional characterization in Smo−/− MEFs demonstrated W535L is constitutively active (GLI1 reporter activation without SHH ligand), confers high-level vismodegib resistance (IC50 >320 nM vs wildtype ~8 nM), and provides a selective growth advantage under drug treatment. In paired pre/post-treatment biopsies, W535L subclones present at low allele fraction before treatment were enriched during therapy, confirming its role in acquired resistance.
Variant
✓ Names this variant — characterised directly
Applied to
→PS3 supports · met
Why
Variant-specific functional data confirmed in multiple independent assays. Primary evidence for PS3 assessment demonstrating constitutive activity, drug resistance, and selective growth advantage. Somatic cohort data noted but insufficient for germline PS4.
W535L in another three resistant BCCs. Also known as SMO-M2, W535L is a known oncogenic mutation present at low rates in sporadic BCCs and can drive tumor progression in the absence of PTCH1 loss.
Location Results: 'Exome sequencing identifies recurrent SMO mutations in resistant BCC'; Figure 2B, 2E, 4A-F, 5A · Context Smo−/− mouse embryonic fibroblasts (MEFs), GLI-luciferase reporter assays, ASZ001 BCC cell line competition assays (mCherry/GFP), patient-derived BCC sequencing · full text
Activating Smoothened mutations in sporadic basal-cell carcinoma.
Searched
c.1604G>Tp.Trp535LeuW535LTrp535535
Found
Original identification of W535L (SMO-M2) as a constitutively active Smoothened mutation in sporadic basal cell carcinomas. W535L was shown to activate Hedgehog signaling in the absence of PTCH1 loss and contribute to BCC tumorigenesis.
Variant
✓ Names this variant
Applied to
→PS3 supports · met
Why
Variant confirmed in original publication; foundational reference for W535L as activating SMO mutation. Cited in PS3 assessment.
W535L is a known oncogenic mutation present at low rates in sporadic BCCs and can drive tumor progression in the absence of PTCH1 loss (Xie et al., 1998).
Location Confirmed via explicit citation in Atwood et al. 2015 (PMID:25759020), which states: 'Also known as SMO-M2, W535L is a known oncogenic mutation present at low rates in sporadic BCCs and can drive tumor progression in the absence of PTCH1 loss (Xie et al., 1998).' · Context Functional characterization in cell-based Hedgehog signaling assays
Sources & reference links