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PTCH1
Final classification
VUS
PTCH1 c.4033C>G · p.Arg1345Gly
PTCH1

NM_000264.5:c.4033C>G (p.Arg1345Gly) is a missense variant in PTCH1, a gene in which loss-of-function variants cause Gorlin syndrome (nevoid basal cell carcinoma syndrome) via an autosomal dominant haploinsufficiency mechanism.

Gene
PTCH1
Transcript
NM_000264.5
HGVS · transcript:coding
NM_000264.5:c.4033C>G
Consequence
N/A
GRCh38
chr9:95447223 G>C
GRCh37
chr9:98209505 G>C
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, BP6 supporting; combination = 1 supporting + 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 supporting, BP6 supporting; combination = 1 supporting + 1 supporting benign, which maps to VUS.
Classification rationale
PM2 BP6 VUS
PTCH1 c.4033C>G

NM_000264.5:c.4033C>G (p.Arg1345Gly) is a missense variant in PTCH1, a gene in which loss-of-function variants cause Gorlin syndrome (nevoid basal cell carcinoma syndrome) via an autosomal dominant haploinsufficiency mechanism. This variant is present at extremely low frequency in gnomAD v2.1 (AF=0.00081%, 2/246054 alleles) and gnomAD v4.1 (AF=0.00025%, 4/1611580 alleles), meeting PM2_Supporting (ClinGen SVI threshold ≤0.002%).1 Computational predictors are uninformative or weakly benign: BayesDel score is -0.078 (benign range), SpliceAI delta is 0.00, and REVEL is not available. This does not meet thresholds for PP3 or BP4.2 In ClinVar, Labcorp Genetics (formerly Invitae) has classified this variant as Benign (SCV001497416, criteria provided), while Ambry Genetics has classified it as Uncertain significance (SCV002619761). The Benign classification from a reputable clinical laboratory supports BP6_Supporting.3 No functional studies, segregation data, de novo reports, case-control data, or variant-specific publications were identified for this variant. PVS1, PS1-PS5, PM1, PM5, PM6, PP1-PP5, and the benign criteria BA1, BS1-BS4, BP1-BP2, BP4-BP5, BP7 are either not met or not applicable. The evidence profile yields one supporting pathogenic criterion (PM2_Supporting) and one supporting benign criterion (BP6_Supporting). Per generic ACMG/AMP 2015 combination rules (PMID:25741868), conflicting evidence with equal weight on both sides results in a classification of Variant of Uncertain Significance (VUS).4

PM2 + BP6 VUS
2 bayesdelspliceai ↗
4 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
      This variant is present in gnomAD v4.1 (AF= 2.48204e-06; MAF= 0.00025%, 4/1611580 alleles, homozygotes = 0) and has highest observed frequency in the South Asian population (AF= 4.39223e-05; MAF= 0.00439%, 4/91070 alleles, homozygotes = 0); grpmax FAF= 1.425e-05.
      v2.1
      This variant is present in gnomAD v2.1 (AF= 8.1283e-06; MAF= 0.00081%, 2/246054 alleles, homozygotes = 0) and has highest observed frequency in the South Asian population (AF= 6.54279e-05; MAF= 0.00654%, 2/30568 alleles, homozygotes = 0); grpmax FAF= 1.083e-05.
      🇨🇦 CA
      This variant is absent from gnomAD-Canada.
      Allele frequency by ancestry
      three datasets · side by side
      gnomAD v4.1
      0.00025% · 4 / 1,611,580
      0 hom · FAF 0.0014%
      South Asian
      4 / 91,070
      0.0044%
      + 9 not observed (Remaining individuals, Admixed American, European (Finnish), Amish, East Asian, Middle Eastern, Ashkenazi Jewish, African/African American, European (non-Finnish))
      gnomAD v2.1
      0.00081% · 2 / 246,054
      0 hom · FAF 0.0011%
      South Asian
      2 / 30,568
      0.0065%
      + 7 not observed (African/African American, Admixed American, Ashkenazi Jewish, East Asian, European (Finnish), European (non-Finnish), Remaining individuals)
      gnomAD Canada 🇨🇦
      Absent · 0 / ?
      0 hom
      Not observed in any ancestry group.
      ClinVar screenshot
      ClinVar
      This variant has been reported in ClinVar as Benign (1 clinical laboratory) and as Uncertain significance (1 clinical laboratory). (ClinVarID = 1010368)
      SpliceAI screenshot
      In silico
      SpliceAI predicts no significant splice impact for this variant (max delta score = 0.00). BayesDel score = -0.0783339.
      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; COSV59465944, n = 3 times).
      Hotspots
      This variant does not lie 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. 7 further PMIDs triaged but not cited — see Sources & References.
      Sherloc: a comprehensive refinement of the ACMG-AMP variant classification criteria.
      Found
      Structured finding pending for this record — see source link.
      Applied to
      BP6 supports · met
      Sources & reference links
      7Sources
      ClinVar
      gnomAD v2.1
      gnomAD v4.1
      SpliceAI
      OncoKB
      COSMIC
      Cancer hotspots
      Triaged references · 7 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
      25394175 ↗ A practice guideline from the American College of Medical Genetics and Genomics and the National Society of Genetic Counselors: referral indications for cancer predisposition assessment. CLINVAR
      26389210 ↗ Genetics of Breast and Gynecologic Cancers (PDQ®): Health Professional Version. CLINVAR
      26389258 ↗ Cancer Genetics Risk Assessment and Counseling (PDQ®): Health Professional Version. CLINVAR
      26389333 ↗ Genetics of Skin Cancer (PDQ®): Health Professional Version. CLINVAR