Starting
Initialising…
0%
PTCH1
Final classification
VUS
PTCH1 c.1085C>T · p.Thr362Ile
PTCH1

NM_000264.5:c.1085C>T (p.Thr362Ile) is a missense variant in PTCH1, a gene in which heterozygous pathogenic variants cause Gorlin syndrome (nevoid basal cell carcinoma syndrome), an autosomal dominant tumor-predisposition disorder.

Gene
PTCH1
Transcript
NM_000264.5
HGVS · transcript:coding
NM_000264.5:c.1085C>T
Consequence
N/A
GRCh38
chr9:95479130 G>A
GRCh37
chr9:98241412 G>A
Basis gene-specific framework lacked a usable explicit final combination framework, so generic ACMG/AMP 2015 final-combination rules were applied as fallback; applied criteria: PM2 supporting, PP3 supporting; combination = 2 supporting, which maps to VUS.
gene-specific framework lacked a usable explicit final combination framework, so generic ACMG/AMP 2015 final-combination rules were applied as fallback; applied criteria: PM2 supporting, PP3 supporting; combination = 2 supporting, which maps to VUS.
Classification rationale
PM2PP3 VUS
PTCH1 c.1085C>T

NM_000264.5:c.1085C>T (p.Thr362Ile) is a missense variant in PTCH1, a gene in which heterozygous pathogenic variants cause Gorlin syndrome (nevoid basal cell carcinoma syndrome), an autosomal dominant tumor-predisposition disorder.1 The variant is absent from all population databases queried: gnomAD v2.1, gnomAD v4.1, and gnomAD-Canada v1.0 (allele frequency 0.0% in all populations). This absence meets PM2 at supporting level.2 REVEL in silico meta-predictor scores the variant as 0.809, predicting a damaging effect on protein function. BayesDel scores 0.454 (borderline). SpliceAI predicts no significant splicing impact (max delta = 0.11). These computational predictions meet PP3 at supporting level.3 The variant has been observed once in somatic cancers (COSMIC COSV59504254) but has not been reported in ClinVar as a germline variant, and no functional studies, de novo reports, segregation data, or case-control studies for this variant were identified in the literature.4 No other ACMG/AMP criteria are met. PVS1 is not applicable because this is a missense variant and SpliceAI does not predict a null effect. PS1-PS5, PM1, PM5, PM6, PP1-PP2, PP4-PP5, BA1, BS1-BS4, BP1-BP7 are either not met or not applicable. Applying the generic ACMG/AMP 2015 final combination rules (Richards et al. 2015, PMID:25741868), two supporting-level pathogenic criteria (PM2_Supporting, PP3_Supporting) are insufficient to reach Likely Pathogenic classification. The variant is classified as a Variant of Uncertain Significance (VUS).5

PM2 + PP3 VUS
1 pvs1_gene_context
3 revelbayesdelspliceai ↗
5 generic_acmg_combination_rules
Gene diagram · NM_000264.5 · variants mapped to exon structure
PTCH1 NM_000264.5
Fetching transcript structure from UCSC…
Applied criteria · 2 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
      gnomAD v4.1 screenshot
      gnomAD v4.1
      gnomAD v2.1 screenshot
      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
      Not observed in any ancestry group.
      gnomAD v2.1
      Absent · 0 / ?
      0 hom
      Not observed in any ancestry group.
      gnomAD Canada 🇨🇦
      Absent · 0 / ?
      0 hom
      Not observed in any ancestry group.
      ClinVar screenshot
      ClinVar
      This variant is absent from ClinVar.
      SpliceAI screenshot
      In silico
      SpliceAI predicts no significant splice impact for this variant (max delta score = 0.11). REVEL score = 0.809. BayesDel score = 0.454212.
      Functional / OncoKB screenshot
      Functional Unknown Oncogenic Effect
      OncoKB did not identify variant-specific reviewed functional evidence for this variant; gene-level curated context is available for reviewer follow-up. PTCH1, a tumor suppressor and inhibitor of the hedgehog pathway, is recurrently mutated in basal cell carcinoma.
      OncoKB ↗
      COSMIC screenshot
      COSMIC
      Cancer hotspots screenshot
      Cancer hotspots
      Somatic evidence Not in COSMIC / hotspots
      COSMIC
      This variant does not lie in a statistically significant hotspot. This variant has previously been reported in somatic cancers (COSMIC; COSV59504254, n = 1 times).
      Hotspots
      This variant does not lie in a statistically significant hotspot.
      Sources & reference links
      8Sources
      ClinVar
      gnomAD v2.1
      gnomAD v4.1
      gnomAD-Canada
      SpliceAI
      OncoKB
      COSMIC
      Cancer hotspots