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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 applied · 21 assessed
Applied · 2
Strength Supporting Moderate Strong Very strong
PM2 supporting Pathogenic
NM_000264.5:c.1085C>T is absent from all population databases: gnomAD v2.1 (exomes), gnomAD v4.1 (exomes), and gnomAD-Canada v1.0 (genomes). Allele frequency is 0.0% in all populations, meeting PM2 at supporting level for a missense variant in an autosomal dominant disorder.
Absent from gnomAD v2.1 (0 alleles)absent from gnomAD v4.1 (0 alleles)absent from gnomAD-Canada v1.0 (0 alleles)
PP3 supporting Pathogenic
REVEL predicts a damaging effect with a score of 0.809 (well above the 0.5 threshold). BayesDel score is 0.454 (borderline, just below 0.5). SpliceAI predicts no significant splice impact (max delta = 0.11). The REVEL meta-predictor, which integrates multiple individual in silico tools, strongly supports a deleterious effect, meeting PP3 at supporting level.
REVEL: 0.809 (damaging)BayesDel: 0.454 (borderline)SpliceAI max delta: 0.11 (no splice impact)
Assessed · not applied
Pathogenic
PS1 No established pathogenic variant at the same amino acid residue (Thr362) has been identified in ClinVar or the literature to support PS1.
PS2 No published reports of de novo occurrence of NM_000264.5:c.1085C>T with confirmed paternity and maternity were identified in the literature or exploratory evidence search.
PS3 No well-established functional studies demonstrating a damaging effect of p.Thr362Ile on PTCH1 protein function have been identified.
PS4 No controlled case-control data or proband counts are available to demonstrate that the prevalence of this variant in affected individuals is significantly increased compared to controls.
PM1 Residue 362 is not located in a statistically significant mutational hotspot as assessed by cancerhotspots.org (residue_significant: false).
PM5 No pathogenic or likely pathogenic missense variants at the same amino acid residue (Thr362) have been identified in ClinVar to serve as comparator variants.
PM6 No reports of de novo occurrence of NM_000264.5:c.1085C>T without confirmation of paternity were identified in the literature or databases.
PP1 No published data demonstrating co-segregation of NM_000264.5:c.1085C>T with Gorlin syndrome or other PTCH1-associated phenotypes in affected families have been identified.
PP2 HCI prior probability scores are not available for PTCH1, so a low rate of benign missense variation cannot be computationally established.
PP4 No patient phenotype or family history data were provided for this case.
PP5 No reputable source has recently reported NM_000264.5:c.1085C>T as pathogenic.
Benign
BA1 NM_000264.5:c.1085C>T is absent from gnomAD v2.1, v4.1, and gnomAD-Canada.
BS1 NM_000264.5:c.1085C>T is absent from all population databases (allele frequency 0.0%), well below the BS1 threshold of >0.3% for non-VCEP assessment.
BS2 No observations of NM_000264.5:c.1085C>T in healthy adult individuals have been reported.
BS3 No well-established functional studies demonstrating no damaging effect of p.Thr362Ile on PTCH1 protein function have been identified.
BS4 No reports of lack of segregation of NM_000264.5:c.1085C>T with disease in affected families have been identified.
BP1 BP1 applies when a missense variant occurs in a gene for which primarily truncating variants are known to cause disease.
BP2 No observations of NM_000264.5:c.1085C>T in trans with a pathogenic PTCH1 variant or in cis with a pathogenic variant in any inheritance pattern have been reported.
BP4 REVEL score of 0.809 predicts a damaging effect, not a benign effect.
BP5 No observation of NM_000264.5:c.1085C>T in a case with an alternate molecular basis for disease has been reported.
BP6 No reputable source has reported NM_000264.5:c.1085C>T as benign.
N/A · 5 PVS1 · PM3 · PM4 · BP3 · BP7
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