PTCH1 c.324A>G, p.(Ile108Met)

Reasoning

The variant is rare but not absent in population databases: gnomAD v4.1 overall allele frequency is 0.01618%, gnomAD v2.1 is 0.00886%, and gnomAD-Canada is 0.01090%. These are below the generic non-VCEP PM2 cutoff of 0.1%, so PM2 is met at supporting strength. The observed homozygote in gnomAD v4.1 is recorded separately under BS2 and does not change the frequency calculation.

Rule

Generic fallback used here: PM2 supporting when the variant is rare in population databases with allele frequency below 0.1%; absence is not required under this case's non-VCEP operating threshold.

Evidence considered

• gnomAD v4.1 reports 261/1,613,260 alleles (AF 0.000161784; 0.01618%) and one homozygote.
• gnomAD v2.1 reports 25/282,050 alleles (AF 0.0000886368; 0.00886%) with no homozygotes; gnomAD-Canada reports 2/18,342 alleles (AF 0.000109039; 0.01090%) with no homozygotes.
• The exact variant was reported with MAF 0.00008 in the clinical cohort publication, consistent with rarity, but the population-database observations are the primary basis for PM2.
• Generic non-VCEP operating threshold used for this case: PM2 applies when allele frequency is below 0.1%; no PTCH1 VCEP specification was available.

Sources

Reasoning

BS2 is supported by one homozygous observation in gnomAD v4.1 for this PTCH1 missense variant, a pattern that is inconsistent with a highly penetrant autosomal-dominant PTCH1 disorder. The evidence is appropriately limited to supporting strength because gnomAD phenotype, age, and clinical ascertainment for the homozygous individual are not available, and the relevant PTCH1 disorder can show incomplete penetrance. The exact variant was also inherited from an unaffected mother in a clinical cohort, although that observation is not equivalent to a documented healthy-control cohort.

Rule

Generic BS2: observation of the variant in a healthy adult or in a homozygous state when the disease is expected to be fully penetrant and dominant supports benign evidence. Apply cautiously when phenotype and penetrance are incompletely characterized.

Evidence considered

• gnomAD v4.1 reports one homozygote among 1,613,260 alleles; the single homozygote is also present in the Remaining individuals subgroup.
• The exact p.Ile108Met variant was inherited from an unaffected mother in the reported Lausanne cohort, and the authors explicitly discuss incomplete penetrance in the context of PTCH1-related clinical features.
• Because the database homozygote is not phenotyped in the case bundle, this is supporting rather than stronger BS2 evidence and warrants human review.

Still missing

• The gnomAD v4.1 homozygous individual's age, phenotype, and clinical follow-up are unavailable.
• The case bundle does not provide a PTCH1-specific penetrance model or disease-prevalence calculation for this allele.

Sources

Reasoning

The variant is NP_000255.2:p.(Ile108Met), and PMID:32074614 reports the same protein change in one proband. However, that report does not establish the variant as pathogenic: the proband had no Gorlin-Goltz features, the variant was inherited from an unaffected mother, and the paper does not provide a prior pathogenic classification or disease-specific evidence sufficient for PS1. Therefore, an established pathogenic same-amino-acid change is not demonstrated.

Rule

Generic ACMG/AMP PS1: same amino-acid change as a previously established pathogenic variant; the matching protein change must itself be supported as pathogenic rather than merely reported.

Evidence considered

• PMID:32074614 explicitly reports PTCH1 c.324A>G / p.Ile108Met in one of 124 CHH/KS probands, but describes inheritance from an unaffected mother and does not establish a pathogenic same-amino-acid comparator for PS1.

Still missing

• No independently established pathogenic interpretation for NP_000255.2:p.Ile108Met was identified.

Sources

Reasoning

No applicable PTCH1 VCEP or gene-specific framework was available, so generic ACMG/AMP criteria were used. The case evidence reports that PTCH1 p.Ile108Met is not in a statistically significant cancer hotspot, and no curated variant-specific domain or critical functional region supporting PM1 was identified. Gene-level PTCH1 tumor-suppressor context alone is insufficient for PM1.

Rule

Generic ACMG/AMP PM1: variant located in a mutational hot spot and/or critical, well-established functional domain without benign variation; a gene-level disease association alone does not satisfy PM1.

Evidence considered

• Cancer Hotspots returned no statistically significant hotspot row for PTCH1 I108.
• OncoKB provided gene-level PTCH1 context but no variant-specific reviewed functional evidence or critical-domain annotation for I108M.

Still missing

• No curated PTCH1 domain or critical functional-region annotation for residue 108 was available in the case bundle.

Sources

Reasoning

The consolidated evidence bundle contains no confirmed pathogenic or likely pathogenic missense comparator at PTCH1 residue 108 and no usable same-residue PM5 candidate collection. PMID:32074614 reports p.Ile108Met itself and other PTCH1 variants at residues 1192 and 1203, not alternate missense changes at residue 108. PM5 therefore is not met.

Rule

Generic ACMG/AMP PM5: a novel missense change at a residue where a different missense change has been previously established to be pathogenic; the comparator must be an appropriate pathogenic/likely pathogenic same-residue variant.

Evidence considered

• The case bundle's PM5 candidate summary reports zero same-residue candidates and states that classic same-residue PM5 semantics could not be confirmed safely.
• PMID:32074614 lists PTCH1 p.Ser1203Arg, p.Arg1192Ser, and p.Ile108Met; it does not report an alternate missense change at residue 108 established as pathogenic.

Still missing

• No confirmed pathogenic alternate missense variant at PTCH1 residue 108 was identified.

Sources

Reasoning

PTCH1 NM_000264.5:c.324A>G is a missense variant, p.(Ile108Met), so the applicable generic non-VCEP pathway is REVEL only. Its REVEL score of 0.603 is between the PP3 threshold (>0.750) and BP4 threshold (<0.250); therefore it is in the calibrated gray zone and does not meet PP3. The SpliceAI max delta score (0.014) is not used to assign PP3 for this missense variant, avoiding cross-mechanism double counting.

Rule

generic_acmg_non_vcep_missense_REVEL: PP3 if REVEL >0.750; BP4 if REVEL <0.250; otherwise neither. Use only this missense mechanism and do not use SpliceAI independently.

Evidence considered

• REVEL score for the normalized genomic variant is 0.603.
• The generic non-VCEP missense rule uses REVEL only: PP3 requires >0.750 and BP4 requires <0.250; the published ClinGen SVI calibration for these REVEL cutoffs is Pejaver et al., 2022, PMID:36413997.
• SpliceAI max delta score is 0.014 (DS_AG 0.014, DS_DG 0.012), predicting no significant splice impact; because this is a missense variant, the generic rule does not use SpliceAI for PP3/BP4.
• PMID:32074614 reports p.Ile108Met with mixed legacy protein-prediction results (deleterious by at least one program, tolerated/neutral by others); this is not an independently calibrated PP3 result and does not override the REVEL-based generic rule.

Sources

Reasoning

The variant does not reach the generic benign stand-alone frequency threshold of 1%. The highest reported allele frequency is 0.000448359 (0.04484%) in a gnomAD v4.1 subpopulation, and the overall gnomAD v4.1 allele frequency is 0.000161784 (0.01618%).

Rule

Generic fallback: BA1 requires allele frequency greater than 1% in an appropriate population database; no VCEP specification was available for PTCH1.

Evidence considered

• gnomAD v4.1 reports 261/1,613,260 alleles, allele frequency 0.000161784, with a maximum subpopulation frequency of 28/62,450 alleles (0.000448359; 0.04484%).
• gnomAD v2.1 reports 25/282,050 alleles (0.0000886368; 0.00886%), and gnomAD-Canada reports 2/18,342 alleles (0.000109039; 0.01090%).
• All observed frequencies are below 0.01, so the generic BA1 threshold is not met.

Sources

Reasoning

The variant does not exceed the generic BS1 frequency threshold of 0.3%. The highest observed frequency is 0.04484% in a gnomAD v4.1 subpopulation, well below 0.3%.

Rule

Generic fallback used here: BS1 requires allele frequency greater than 0.3%; no PTCH1 VCEP specification was available.

Evidence considered

• gnomAD v4.1 reports an overall allele frequency of 0.000161784 (0.01618%) and a maximum subpopulation frequency of 0.000448359 (0.04484%).
• gnomAD v2.1 reports a maximum listed subpopulation allele frequency of 0.000163016 (0.01630%), and gnomAD-Canada reports 0.000109039 (0.01090%).
• The maximum observed frequency is below the generic BS1 threshold of 0.3%; no disease-prevalence or penetrance model in the case bundle establishes a lower PTCH1-specific BS1 threshold.

Sources

Reasoning

PTCH1 NM_000264.5:c.324A>G is a missense variant, p.(Ile108Met), so the applicable generic non-VCEP pathway is REVEL only. Its REVEL score of 0.603 is between the PP3 threshold (>0.750) and BP4 threshold (<0.250); therefore it is in the calibrated gray zone and does not meet BP4. The low SpliceAI score is not a BP4 assignment for a missense variant under the governing generic rule.

Rule

generic_acmg_non_vcep_missense_REVEL: PP3 if REVEL >0.750; BP4 if REVEL <0.250; otherwise neither. Use only this missense mechanism and do not use SpliceAI independently.

Evidence considered

• REVEL score for the normalized genomic variant is 0.603.
• The generic non-VCEP missense rule uses REVEL only: PP3 requires >0.750 and BP4 requires <0.250; the published ClinGen SVI calibration for these REVEL cutoffs is Pejaver et al., 2022, PMID:36413997.
• SpliceAI max delta score is 0.014, but this splice predictor is not applied as BP4 to a missense variant under the generic rule.

Sources

Reasoning

No de novo occurrence is documented for NM_000264.5:c.324A>G. The available case report states that the variant was inherited from the proband's unaffected mother, so PS2 cannot be applied.

Evidence considered

• PMID:32074614 reports p.Ile108Met in one male CHH/Kallmann syndrome proband and states that the proband inherited the variant from his unaffected mother; this is evidence against a de novo event, not evidence for PS2.

Still missing

• No documented trio testing demonstrating confirmed de novo occurrence.

Sources

Reasoning

No validated variant-specific functional assay demonstrating a damaging effect was identified. The only paper in the bundle that directly reports PTCH1 p.Ile108Met describes a cohort observation, inheritance from an unaffected mother, and in-silico predictions, but no functional assay. Generic ACMG/AMP PS3 therefore cannot be applied.

Rule

Generic ACMG/AMP 2015 PS3 requires well-established functional studies showing a damaging effect; no strength calibration is possible without validated assay data.

Evidence considered

• OncoKB reports no variant-specific reviewed functional evidence for PTCH1 p.I108M.
• PMID:32074614 reports p.Ile108Met in one proband and provides in-silico predictions and maternal inheritance, but the extracted study context is whole-exome sequencing and computational assessment rather than a functional assay.

Still missing

• A validated variant-specific functional assay with appropriate positive and negative controls, quantitative results, and demonstrated biological relevance is not available in the case evidence bundle.

Sources

Reasoning

The exact variant was observed in one Kallmann syndrome/congenital hypogonadotropic hypogonadism proband, but no case-control comparison or statistically interpretable enrichment data are available.

Evidence considered

• PMID:32074614 reports p.Ile108Met in one male proband among 124 unrelated CHH/KS probands; the paper provides no control count or case-control statistical analysis for this variant.

Still missing

• A case-control study or other appropriately controlled enrichment analysis for PTCH1 c.324A>G is needed.

Sources

Reasoning

No apparently de novo occurrence with incomplete parental testing is reported. The available report documents inheritance from an unaffected mother, and no other de novo case is provided.

Evidence considered

• PMID:32074614 explicitly states that the p.Ile108Met proband inherited the variant from his unaffected mother; therefore the report does not support PM6.

Still missing

• No case with an apparently de novo variant and incomplete parental testing.

Sources

Reasoning

No affected relatives carrying the variant, informative meioses, or family-level segregation data are reported. The single reported proband was from a CHH/Kallmann syndrome cohort without Gorlin-Goltz syndrome features, and the variant was inherited from an unaffected mother.

Evidence considered

• PMID:32074614 describes one p.Ile108Met proband and reports inheritance from an unaffected mother; it does not report affected relatives carrying the variant or segregation across informative meioses.

Still missing

• No pedigree with affected relatives and informative variant testing.
• No documented number of informative meioses or co-segregating affected carriers.

Sources

Reasoning

No PTCH1-specific framework or quantitative missense-constraint and benign-missense-rate assessment was available to establish that PTCH1 has a low rate of benign missense variation and a high proportion of pathogenic missense variants. The bundle supports PTCH1 loss of function as a germline disease mechanism, but that does not by itself satisfy generic PP2.

Rule

Generic ACMG/AMP PP2: missense variant in a gene with a low rate of benign missense variation and a high proportion of pathogenic missense variants.

Evidence considered

• The case bundle indicates a PTCH1 loss-of-function germline mechanism, but provides no validated PTCH1 missense-spectrum analysis meeting the generic PP2 requirement.

Still missing

• A validated gene-level assessment of benign missense tolerance and the proportion of pathogenic PTCH1 missense variants is unavailable.

Reasoning

The reported proband had isolated Kallmann syndrome/congenital hypogonadotropic hypogonadism without Gorlin-Goltz syndrome features. This single observation does not establish a highly specific PTCH1-associated phenotype for the exact variant, and no phenotype for the present individual is supplied.

Evidence considered

• PMID:32074614 describes the p.Ile108Met carrier as one of three KS probands without clinical features of Gorlin-Goltz syndrome and reports maternal inheritance from an unaffected mother.

Still missing

• Detailed phenotype data for the present individual are needed.
• Evidence that the observed phenotype is highly specific for PTCH1-related disease, including differential diagnoses and molecular testing results, is needed.

Sources

Reasoning

No exact-variant ClinVar expert-panel Pathogenic or Likely pathogenic classification is present.

Evidence considered

• ClinVar lists no expert-panel submissions for this exact variant; the available assertions are single-submitter Likely benign or uncertain significance and cannot be used for PP5.

Still missing

• An exact-variant ClinVar expert-panel Pathogenic or Likely pathogenic classification is required.

Sources

Reasoning

No validated variant-specific functional assay demonstrating a normal or benign effect was identified. The directly relevant publication reports clinical and in-silico observations only and does not provide a controlled functional experiment. Generic ACMG/AMP BS3 therefore cannot be applied.

Rule

Generic ACMG/AMP 2015 BS3 requires well-established functional studies showing no damaging effect or normal function; no strength calibration is possible without validated assay data.

Evidence considered

• OncoKB reports no variant-specific reviewed functional evidence for PTCH1 p.I108M.
• PMID:32074614 reports p.Ile108Met in one proband and provides in-silico predictions and maternal inheritance, but the extracted study context is whole-exome sequencing and computational assessment rather than a functional assay.

Still missing

• A validated variant-specific functional assay with appropriate controls, quantitative normal-function results, and demonstrated assay relevance is not available in the case evidence bundle.

Sources

Reasoning

The variant was inherited from an unaffected mother and the proband reportedly had no Gorlin-Goltz syndrome features, but the report concerns a possible CHH/Kallmann phenotype rather than an established PTCH1-associated Gorlin phenotype. This does not establish formal lack of segregation of the variant with a defined familial disease phenotype, so BS4 is not applied.

Evidence considered

• PMID:32074614 reports that the p.Ile108Met proband had no Gorlin-Goltz syndrome features and inherited the variant from an unaffected mother; this raises a non-segregation concern but is insufficient for BS4 because no established familial PTCH1 disease phenotype and no informative pedigree are provided.

Still missing

• No pedigree establishing a defined PTCH1-associated disease phenotype in affected relatives.
• No systematic assessment of the mother's age, clinical features, or penetrance-relevant findings.
• No multiple informative affected/non-affected relatives tested for the variant.

Sources

Reasoning

PTCH1 loss of function is supported as a germline disease mechanism, but the case bundle does not establish that disease-causing PTCH1 variants are primarily truncating or provide a validated missense-benign framework. The single report of p.Ile108Met being inherited from an unaffected mother is not sufficient on its own to apply BP1.

Rule

Generic ACMG/AMP BP1: missense variant in a gene for which primarily truncating variants are known to cause disease; gene-wide variant-type predominance must be established.

Evidence considered

• PMID:32074614 reports p.Ile108Met in a CHH/KS proband inherited from an unaffected mother, but this observation does not establish the gene-wide variant-type pattern required for BP1.
• The bundle supports PTCH1 loss of function as a disease mechanism, but does not provide the gene-wide evidence that PTCH1 disease is primarily caused by truncating variants.

Still missing

• No validated PTCH1 variant-spectrum analysis demonstrates that disease is primarily caused by truncating rather than missense variants.
• No sufficient independent benign evidence for p.Ile108Met was identified.

Sources

Reasoning

No qualifying co-occurrence evidence was identified. The available exact-variant publication reports inheritance from an unaffected mother but does not report another pathogenic or benign PTCH1 variant in the same individual, nor does it establish cis or trans phase. An unaffected transmitting parent is not, by itself, BP2 evidence.

Rule

Generic BP2: the variant is observed in trans with a pathogenic variant for a dominant disorder or in cis with a pathogenic variant for a recessive disorder; phase and the relevant co-occurring allele must be documented.

Evidence considered

• PMID:32074614 reports p.Ile108Met in one proband and inheritance from an unaffected mother, but reports no co-occurring PTCH1 variant and no cis/trans phase information.
• The available case evidence does not provide a documented benign or pathogenic allele in cis or trans with the evaluated variant.

Still missing

• No documented co-occurring PTCH1 variant in cis or trans was found.
• No phase-resolved family or proband data were available to evaluate BP2.

Sources

Reasoning

No evidence identifies an independent molecular diagnosis that fully explains the phenotype in an individual carrying this variant.

Still missing

• A documented alternate molecular diagnosis and phenotype correlation for the same individual are needed.

Reasoning

No exact-variant ClinVar expert-panel Benign or Likely benign classification is present.

Evidence considered

• ClinVar lists no expert-panel submissions for this exact variant; single-submitter Likely benign assertions and the aggregate ClinVar label cannot be used for BP6.

Still missing

• An exact-variant ClinVar expert-panel Benign or Likely benign classification is required.

Sources