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PTCH1
Final classification
VUS
PTCH1 c.2438C>T · p.Pro813Leu
PTCH1

NM_000264.5:c.2438C>T (p.Pro813Leu) is a missense variant in exon 15 of PTCH1, a gene in which loss-of-function variants are an established cause of Gorlin syndrome (nevoid basal cell carcinoma syndrome).

Gene
PTCH1
Transcript
NM_000264.5
HGVS · transcript:coding
NM_000264.5:c.2438C>T
Consequence
N/A
GRCh38
chr9:95467238 G>A
GRCh37
chr9:98229520 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 moderate, BP4 supporting benign; combination = 1 moderate + 1 supporting benign, 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 moderate, BP4 supporting benign; combination = 1 moderate + 1 supporting benign, which maps to VUS.
Classification rationale
PM2 BP4 VUS
PTCH1 c.2438C>T

NM_000264.5:c.2438C>T (p.Pro813Leu) is a missense variant in exon 15 of PTCH1, a gene in which loss-of-function variants are an established cause of Gorlin syndrome (nevoid basal cell carcinoma syndrome).1 This variant is absent from gnomAD v2.1 and present at extremely low frequency in gnomAD v4.1 (4/1,612,430 alleles, AF=2.48e-6, 0 homozygotes), meeting PM2 at moderate strength.2 Multiple lines of computational evidence suggest no significant impact on the gene product: BayesDel score is 0.0037 (strongly predicts benign) and SpliceAI max delta is 0.01 (no splicing impact), meeting BP4 at supporting benign level.3 The variant has been reported in ClinVar as Uncertain significance by a single clinical laboratory (Labcorp/Invitae, SCV005813886). It has been observed somatically in COSMIC (COSV59468245, n=2) but this does not inform germline pathogenicity.4 No variant-specific functional studies, segregation data, case-control analyses, or de novo observations were identified. Five literature-triage papers (PMIDs 15604628, 20301330, 21304560, 26389210, 26389333) were reviewed; none mention NM_000264.5:c.2438C>T.5 Applying generic ACMG/AMP 2015 combination rules (PMID:25741868): one moderate pathogenic criterion (PM2) and one supporting benign criterion (BP4) are present. These do not meet the threshold for Likely Pathogenic, Likely Benign, Pathogenic, or Benign. The variant is classified as a Variant of Uncertain Significance.6

PM2 + BP4 VUS
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
      This variant is present in gnomAD v4.1 (AF= 2.48073e-06; MAF= 0.00025%, 4/1612430 alleles, homozygotes = 0) and has highest observed frequency in the European (non-Finnish) population (AF= 3.39134e-06; MAF= 0.00034%, 4/1179474 alleles, homozygotes = 0); grpmax FAF= 7.9e-07.
      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
      0.00025% · 4 / 1,612,430
      0 hom · FAF 7.9e-05%
      European (non-Finnish)
      4 / 1,179,474
      0.00034%
      + 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
      Not observed in any ancestry group.
      gnomAD Canada 🇨🇦
      Absent · 0 / ?
      0 hom
      Not observed in any ancestry group.
      ClinVar screenshot
      ClinVar
      This variant has been reported in ClinVar as Uncertain significance (1 clinical laboratory). (ClinVarID = 3705147)
      SpliceAI screenshot
      In silico
      SpliceAI predicts no significant splice impact for this variant (max delta score = 0.01). REVEL score = 0.656. BayesDel score = 0.00372277.
      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; COSV59468245, n = 2 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
      Triaged references · 5 PMIDs not cited in assessment
      15604628 ↗ Genetic cancer risk assessment and counseling: recommendations of the national society of genetic counselors. CLINVAR
      20301330 ↗ Nevoid Basal Cell Carcinoma Syndrome. CLINVAR
      21304560 ↗ Clinical utility gene card for: Gorlin syndrome. CLINVAR
      26389210 ↗ Genetics of Breast and Gynecologic Cancers (PDQ®): Health Professional Version. CLINVAR
      26389333 ↗ Genetics of Skin Cancer (PDQ®): Health Professional Version. CLINVAR