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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
      Population frequency
      Overall AF
      4 / 1,611,580
      0.00025%
      Highest · South Asian
      0.0044%
      Homozygotes
      0
      grpmax FAF
      0.0014%
      Allele frequency by ancestry — gnomAD v4.1
      observed in 1 of 9 groups
      AncestryAllele countFrequencyHomozygotes
      South Asian 4 / 91,070 0.0044% 0
      Admixed American 0 / 60,038
      European (Finnish) 0 / 62,936
      Amish 0 / 910
      East Asian 0 / 44,856
      Middle Eastern 0 / 6,056
      Ashkenazi Jewish 0 / 29,600
      African/African American 0 / 75,054
      European (non-Finnish) 0 / 1,178,604
      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.
      Overall AF
      2 / 246,054
      0.00081%
      Highest · South Asian
      0.0065%
      Homozygotes
      0
      grpmax FAF
      0.0011%
      Allele frequency by ancestry — gnomAD v2.1
      observed in 1 of 8 groups
      AncestryAllele countFrequencyHomozygotes
      South Asian 2 / 30,568 0.0065% 0
      African/African American 0 / 14,988
      Admixed American 0 / 34,508
      Ashkenazi Jewish 0 / 9,946
      East Asian 0 / 18,226
      European (Finnish) 0 / 21,610
      European (non-Finnish) 0 / 110,170
      Remaining individuals 0 / 6,038
      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.
      This variant is absent from gnomAD-Canada.
      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 · 8 PMIDs triaged · 7 high-priority
      8papers screened
      Papers triaged by theme: functional/splicing/segregation/case_observation. high_priority_papers include abstract snippets. Use these to support PS3/BS3/PS4/PP1/PP3/PP5.
      15604628 ↗ case observation
      Genetic cancer risk assessment and counseling: recommendations of the national society of genetic counselors.
      These cancer genetic counseling recommendations describe the medical, psychosocial, and ethical ramifications of identifying at-risk individuals through cancer risk assessment with or without genetic testing. They were developed by members of the Practice Issues Subcommittee of the National Society of Genetic Counselors Cancer Genetic Counseling Special Interest Group. The information contained in
      PP5PS4
      20301330 ↗ case observation
      Untitled reference
      PP5PS4
      21304560 ↗ case observation
      Clinical utility gene card for: Gorlin syndrome.
      PP5PS4
      25394175 ↗ case observation
      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.
      The practice guidelines of the American College of Medical Genetics and Genomics (ACMG) and the National Society of Genetic Counselors (NSGC) are developed by members of the ACMG and NSGC to assist medical geneticists, genetic counselors, and other health-care providers in making decisions about appropriate management of genetic concerns, including access to and/or delivery of services. Each pract
      PP5PS4
      26389210 ↗ case observation
      Untitled reference
      PP5PS4
      26389258 ↗ case observation
      Untitled reference
      PP5PS4
      26389333 ↗ case observation
      Untitled reference
      PP5PS4
      28492532 ↗ background review
      Sherloc: a comprehensive refinement of the ACMG-AMP variant classification criteria.
      PP5PS4
      Sources & reference links
      7Sources
      ClinVar
      gnomAD v2.1
      gnomAD v4.1
      SpliceAI
      OncoKB
      COSMIC
      Cancer hotspots