Variant classification summary

NM_005631.4:c.1604G>T

SMO · NP_005622.1:p.(Trp535Leu) · NM_005631.4

GRCh37: chr7:128850341 G>T · GRCh38: chr7:129210500 G>T

Gene: SMO Transcript: NM_005631.4

Final call

Likely Pathogenic

PS3 moderate PM1 moderate PM2 supporting PP3 supporting

Variant details

Gene

SMO

Transcript

NM_005631.4

Protein

NP_005622.1:p.(Trp535Leu)

gnomAD AF

ClinVar

OncoKB

Likely Oncogenic

Classification rationale

Interpretation summary

Generated evidence synthesis

1

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%.

2

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).

3

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.

4

W535L lies within a statistically significant mutational hotspot and no benign variation is observed at this residue in population databases.

5

REVEL in silico prediction score of 0.922 strongly supports a deleterious effect.

6

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.

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	NM_005631.4:c.1604G>T is a missense variant (p.Trp535Leu). It does not fall into the default 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 prior pathogenic variant at codon 535 with a different nucleotide change producing the same amino acid (Trp535Leu) has been identified. No other pathogenic missense change at this codon is reported in ClinVar.	clinvar
PS2	N/A	No de novo occurrence data (with confirmed maternity and paternity) available for this variant. The single ClinVar submission (OMIM, SCV000028794) is derived from literature only in a somatic context.	clinvar
PS3	Met	Well-established functional studies demonstrate that W535L is a constitutively active gain-of-function variant in SMO. In Smo−/− MEFs, W535L drives Hedgehog pathway activation (GLI1 reporter) in the absence of ligand, confers strong resistance to the SMO inhibitor vismodegib (IC50 >320 nM vs wildtype IC50 ~8 nM), and provides a selective growth advantage to tumor cells under vismodegib treatment. W535L was originally identified as an activating mutation in sporadic BCCs (Xie et al. 1998) and confirmed in multiple independent studies. At the structural level, W535 is a conserved tryptophan (7.55) in helix VII critical for maintaining SMO autoinhibition; its mutation disrupts this regulatory mechanism. Functional evidence is robust and replicated across independent laboratories, but all studies are in somatic/cancer models; germline functional data are not available.	PMID:9422511 PMID:25759020 PMID:23636324 oncokb
PS4	Not met	No germline case-control data demonstrating statistically significant enrichment of W535L in affected individuals versus population controls. All reported observations are somatic: 36 occurrences in COSMIC, 3/30 resistant BCCs and 1/36 untreated BCCs (Atwood et al. 2015), and original discovery in sporadic BCCs (Xie et al. 1998). Somatic prevalence data do not satisfy PS4 for germline variant interpretation.	PMID:25759020 PMID:9422511
PS5	N/A	No reputable germline source has recently reported this variant as pathogenic with unavailable evidence. The single ClinVar submission (OMIM, SCV000028794) classifies as Pathogenic in a somatic context with no assertion criteria provided and does not constitute a reputable germline source.	clinvar
PM1	Met	W535 is located in a statistically significant mutational hotspot (Cancer Hotspots) within a critical functional domain. It resides in transmembrane helix VII at position 7.55, a conserved tryptophan essential for SMO autoinhibition. Mutation of this residue is shown to produce constitutive receptor activation (Wang et al. 2013). No benign variation is observed at this residue in population databases.	PMID:23636324 gnomad_v2 gnomad_v4
PM2	Met	NM_005631.4:c.1604G>T is absent from all population databases: gnomAD v2.1 (exomes), gnomAD v4.1 (exomes + genomes), and gnomAD-Canada v1.0 (genomes). Allele frequency in all populations is 0.0%, well below the 0.1% PM2 threshold for non-VCEP assessment.	gnomad_v2 gnomad_v4 gnomad_canada
PM5	N/A	No alternative pathogenic missense variant at codon 535 has been identified in ClinVar or published literature. PM5 candidate harvesting returned zero same-residue comparator variants. The PM5 criterion cannot be applied without a confirmed pathogenic comparator at the same residue.	pm5_candidates clinvar
PM6	N/A	No de novo observation (assumed or confirmed) of W535L has been reported in a germline context. All reported occurrences are somatic.
PP1	Not met	No cosegregation data are available for this variant. No family studies with multiple affected members have been reported.
PP2	Not met	Insufficient evidence to establish that SMO has a low rate of benign missense variation. The HCI prior score is not available for SMO. While missense gain-of-function variants are a recognized mechanism in SMO, gene-level missense constraint metrics are not established.
PP3	Met	REVEL predicts a strongly deleterious effect (score 0.922). BayesDel score (0.463) is borderline. SpliceAI predicts no splice impact (max delta 0.00), consistent with a purely missense effect. The high REVEL score provides in silico support for pathogenicity.	revel bayesdel spliceai
PP4	Not met	No patient phenotype or family history information is available for this variant assessment. The variant was submitted to ClinVar by OMIM in a somatic BCC context without detailed clinical information.
PP5	Not met	The single ClinVar submission (OMIM, SCV000028794) classifies the variant as Pathogenic but with review status 'no assertion criteria provided' in a somatic context. This does not satisfy PP5 requirements for a reputable germline source with supporting evidence. No CSPEC/VCEP classification exists for SMO.	clinvar
BA1	Not met	The variant is absent from all population databases (gnomAD v2.1, v4.1, gnomAD-Canada). Allele frequency is 0.0%, far below the 1% BA1 threshold.	gnomad_v2 gnomad_v4 gnomad_canada
BS1	Not met	The variant is absent from gnomAD. Allele frequency is 0.0%, far below the 0.3% BS1 threshold for non-VCEP assessment.	gnomad_v2 gnomad_v4 gnomad_canada
BS2	Not met	The variant is absent from population databases, providing no evidence of observation in healthy adults. No healthy adult carriers have been reported.	gnomad_v2 gnomad_v4 gnomad_canada
BS3	Not met	Well-established functional studies demonstrate the OPPOSITE of a benign effect: W535L is a constitutively active gain-of-function variant that drives Hedgehog pathway activation in the absence of ligand and confers strong resistance to SMO inhibitors. These findings are incompatible with a benign functional interpretation.	PMID:9422511 PMID:25759020 PMID:23636324
BS4	Not met	No cosegregation data are available to assess lack of segregation in affected family members.
BP1	Not met	Missense gain-of-function variants are a recognized disease mechanism for SMO. W535L is a well-characterized activating mutation, and the SMO gene is not limited to a truncating-only disease mechanism.	PMID:9422511 PMID:25759020
BP2	Not met	No phasing data are available to assess whether this variant has been observed in trans with a pathogenic variant or in cis with a pathogenic variant.
BP3	N/A	The variant is a single-nucleotide substitution, not an in-frame deletion/insertion in a repetitive region.
BP4	Not met	REVEL score of 0.922 strongly predicts a deleterious effect, contradicting BP4 requirements for multiple lines of computational evidence suggesting no impact. SpliceAI predicts no splice effect (max delta 0.00) but this alone is insufficient when REVEL strongly supports pathogenicity.	revel bayesdel spliceai
BP5	Not met	No data available to demonstrate that this variant is found in a case with an alternate molecular basis for disease.
BP6	Not met	No reputable source has reported this variant as benign. The single ClinVar submission classifies it as Pathogenic (somatic).	clinvar
BP7	N/A	NM_005631.4:c.1604G>T is a missense variant (p.Trp535Leu), not a synonymous variant. BP7 applies exclusively to synonymous variants with no predicted splice impact.

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