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PTCH1
Final classification
VUS
PM2BP4
PTCH1
c.2438C>T
p.Pro813Leu
This variant

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).

Transcript
NM_000264.5
HGVS · transcript:coding
NM_000264.5:c.2438C>T
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 applied · 20 assessed
MetEvidence satisfies this criterion.
Not metEvaluated against available evidence; threshold not reached.
Not assessedApplies in principle, but no evidence was found to evaluate it.
N/ADoesn't apply to this variant type.
Applied · 2
Strength Supporting Moderate Strong Very strong
PM2 moderate Pathogenic
This variant is absent from gnomAD v2.1 and is present at extremely low frequency in gnomAD v4.1 (4/1,612,430 alleles; AF=2.48e-6; 0 homozygotes; grpmax FAF=7.9e-7). The allele frequency of 0.00025% is well below the 0.1% PM2 threshold for non-VCEP frameworks. The submitting laboratory (Labcorp/Invitae) also applied PM2 for this variant.
gnomAD v2.1: absentgnomAD v4.1: 4/1612
BP4 supporting Benign
Multiple lines of computational evidence suggest this variant does not have a significant impact on the gene product. BayesDel score is 0.0037, which strongly predicts a benign effect. SpliceAI max delta is 0.01, indicating no predicted splicing alteration. The REVEL score of 0.656 is borderline and does not outweigh the preponderance of benign computational evidence.
BayesDel: 0.0037 (strongly predicts benign)SpliceAI max delta: 0.01 (no splice impact)REVEL: 0.656 (borderline
Assessed · not applied · 20 not met · 0 not assessed
Pathogenic
PS1 No known pathogenic missense variant at Pro813 arising from a different nucleotide change has been identified.
PS2 No de novo observation with confirmed maternity and paternity has been reported for this variant in any available source.
PS3 No well-established in vitro or in vivo functional studies demonstrate a damaging effect for NM_000264.5:c.2438C>T (p.Pro813Leu).
PS4 The prevalence of this variant in affected individuals has not been shown to be significantly increased compared to controls.
PM1 Residue Pro813 does not lie within a statistically significant mutational hotspot as determined by cancerhotspots.org.
PM6 No de novo observation (without confirmed parentage) has been reported for this variant in ClinVar, the reviewed literature, or any other source.
PP1 No co-segregation data are available for this variant.
PP2 While PTCH1 loss-of-function is an established disease mechanism for Gorlin syndrome, missense variants are also well-documented as causative in this disorder.
PP3 In silico predictions are conflicting and do not provide multiple lines of computational support for a deleterious effect.
PP4 No proband phenotype information is available.
PP5 No reputable source has classified this variant as pathogenic.
Benign
BA1 The allele frequency in gnomAD v4.1 is 2.48e-6 (0.00025%), far below the 1% BA1 threshold for non-VCEP frameworks.
BS1 The allele frequency in gnomAD v4.1 is 0.00025%, below the 0.3% BS1 threshold for non-VCEP frameworks.
BS2 This variant has not been observed in the homozygous state (0 homozygotes in gnomAD v4.1, 0 in v2.1) and no control population data demonstrate observation in healthy adults at a frequency that would meet BS2.
BS3 No well-established in vitro or in vivo functional studies demonstrate no damaging effect for this variant.
BS4 No segregation data are available for this variant.
BP1 Although PTCH1 loss-of-function is an established disease mechanism for Gorlin syndrome, missense variants in PTCH1 are also well-documented as causative.
BP2 No observation of this variant in trans with a known pathogenic PTCH1 variant has been reported.
BP5 No observation of this variant in a case with an alternative molecular basis for disease has been reported.
BP6 No reputable source has classified this variant as benign.
N/A · 6 PVS1 · PM3 · PM4 · PM5 · BP3 · BP7
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