AXIN2 c.1985T>C, p.(Leu662Pro)

Reasoning

BP4 is applicable because NM_004655.4:c.1985T>C is a missense variant producing NP_004646.3:p.(Leu662Pro), so the missense REVEL path is used exclusively. The available REVEL score is 0.169. Under the supplied generic ClinGen SVI REVEL calibration, BP4 is supporting at <=0.29, moderate at <=0.183, and strong at <=0.016; 0.169 meets the moderate BP4 threshold but not the strong threshold. SpliceAI is not used because this is not an intronic, synonymous, or splice-region assessment, and BayesDel has no applicable generic calibration.

Rule

missense_only_revel; BP4 supporting <=0.29, moderate <=0.183, strong <=0.016

Evidence considered

• The variant is a missense substitution, NM_004655.4:c.1985T>C, producing NP_004646.3:p.(Leu662Pro); therefore REVEL is the sole applicable computational path.
• Local REVEL lookup reports a score of 0.169.
• The supplied ClinGen SVI REVEL calibration assigns BP4 supporting at <=0.29, moderate at <=0.183, and strong at <=0.016 (Pejaver et al. 2022, PMID:36413997); the score 0.169 meets moderate BP4.

Sources

Reasoning

Generic ACMG/AMP PM2 is not met. No AXIN2-specific or VCEP population threshold is available, so the supplied generic PM2 supporting threshold of allele frequency <=0.0001 applies. The variant is substantially more frequent than this threshold in all relevant datasets: gnomAD v2.1 AF 0.000967467, gnomAD v4.1 AF 0.0012045176848476137, gnomAD v2.1 non-cancer exomes AF 0.001018145422228358, and gnomAD v3.1 non-cancer genomes AF 0.0008784496040219477. The presence of homozygotes also does not support rarity-based PM2.

Rule

{'name': 'generic_acmg_pm2', 'threshold': 'allele frequency <=0.0001', 'strength_if_met': 'supporting', 'source': 'ClinGen SVI 2020 recommendation (PMID:25741868)'}

Evidence considered

• No applicable AXIN2 VCEP or gene-specific framework was available; generic ACMG/AMP defaults were therefore used.
• The supplied generic PM2 threshold is allele frequency <=0.0001, based on the ClinGen SVI recommendation to use PM2 at Supporting strength (ClinGen SVI 2020; PMID:25741868).
• gnomAD v2.1 reports AF 0.000967467 (268/277012 alleles; homozygotes 1), and gnomAD v4.1 reports AF 0.0012045176848476137 (1944/1613924 alleles; homozygotes 5).
• The specified non-cancer subsets report AF 0.001018145422228358 in gnomAD v2.1 non-cancer exomes (236/231794 alleles; homozygotes 1) and AF 0.0008784496040219477 in gnomAD v3.1 non-cancer genomes (130/147988 alleles; homozygotes 0).

Sources

Reasoning

PP3 is applicable because NM_004655.4:c.1985T>C is a missense variant producing NP_004646.3:p.(Leu662Pro), so the missense REVEL path is used exclusively. The available REVEL score is 0.169. Under the supplied generic ClinGen SVI REVEL calibration, PP3 requires at least 0.644 for supporting strength, 0.773 for moderate strength, or 0.932 for strong strength; 0.169 meets none of these pathogenic computational thresholds. SpliceAI is not used because this is not an intronic, synonymous, or splice-region assessment, and BayesDel has no applicable generic calibration.

Rule

missense_only_revel; PP3 supporting >=0.644, moderate >=0.773, strong >=0.932

Evidence considered

• The variant is a missense substitution, NM_004655.4:c.1985T>C, producing NP_004646.3:p.(Leu662Pro); therefore REVEL is the sole applicable computational path.
• Local REVEL lookup reports a score of 0.169.
• The supplied ClinGen SVI REVEL calibration assigns PP3 supporting at >=0.644, moderate at >=0.773, and strong at >=0.932 (Pejaver et al. 2022, PMID:36413997); the score 0.169 does not meet PP3.

Sources

Reasoning

Generic ACMG/AMP BA1 is not met. No AXIN2-specific or VCEP population threshold is available, so the supplied generic stand-alone threshold of allele frequency >=0.05 applies. The highest reported frequency is 0.00438596 (4/912 alleles in the Amish population in gnomAD v4.1), and the maximum group frequency is 0.00245618; both are below 0.05. The governing-source search found no applicable VCEP framework. The non-cancer datasets are also far below the BA1 threshold: gnomAD v2.1 non-cancer exomes AF 0.00101815 and gnomAD v3.1 non-cancer genomes AF 0.00087845.

Rule

{'name': 'generic_acmg_ba1', 'threshold': 'allele frequency >=0.05', 'source': 'ACMG/AMP 2015 (PMID:25741868)'}

Evidence considered

• No applicable AXIN2 VCEP or gene-specific framework was available; generic ACMG/AMP defaults were therefore used.
• The supplied generic BA1 threshold is allele frequency >=0.05 from ACMG/AMP 2015 (PMID:25741868).
• gnomAD v4.1 reports overall AF 0.0012045176848476137, group-maximum FAF 0.00245618, and highest subpopulation AF 0.0043859649122807015 in the Amish population (4/912 alleles; homozygotes 0).
• gnomAD v2.1 reports overall AF 0.000967467, group-maximum FAF 0.00145642, and highest subpopulation AF 0.0015455 in the European non-Finnish population (192/124232 alleles; homozygotes 0).
• The non-cancer subsets report AF 0.00101815 in gnomAD v2.1 non-cancer exomes (236/231794 alleles; homozygotes 1) and AF 0.00087845 in gnomAD v3.1 non-cancer genomes (130/147988 alleles; homozygotes 0).

Sources

Reasoning

Generic ACMG/AMP BS1 is not met. No AXIN2-specific or VCEP population threshold is available, so the supplied generic strong-benign threshold of allele frequency >=0.01 applies. The highest reported frequency is 0.00438596 (4/912 alleles in the Amish population in gnomAD v4.1), with group-maximum FAF 0.00245618; these are below 0.01. The non-cancer subset frequencies are likewise below this threshold: 0.00101815 in gnomAD v2.1 non-cancer exomes and 0.00087845 in gnomAD v3.1 non-cancer genomes.

Rule

{'name': 'generic_acmg_bs1', 'threshold': 'allele frequency >=0.01', 'source': 'Generic SVI default; Whiffin et al. 2017 (PMID:28518168)'}

Evidence considered

• No applicable AXIN2 VCEP or gene-specific framework was available; generic ACMG/AMP defaults were therefore used.
• The supplied generic BS1 threshold is allele frequency >=0.01, identified as the generic SVI default with per-gene derivation preferred (Whiffin et al. 2017, PMID:28518168).
• gnomAD v4.1 reports overall AF 0.0012045176848476137, group-maximum FAF 0.00245618, and highest subpopulation AF 0.0043859649122807015 in the Amish population (4/912 alleles; homozygotes 0).
• gnomAD v2.1 reports overall AF 0.000967467, group-maximum FAF 0.00145642, and highest subpopulation AF 0.0015455 in the European non-Finnish population (192/124232 alleles; homozygotes 0).
• The non-cancer subsets report AF 0.00101815 in gnomAD v2.1 non-cancer exomes and AF 0.00087845 in gnomAD v3.1 non-cancer genomes, both below 0.01.

Sources

Reasoning

PS1 requires a previously established pathogenic or likely pathogenic variant producing the same amino-acid change. The case identifies NM_004655.4:c.1985T>C as NP_004646.3:p.(Leu662Pro), but the available ClinVar record is conflicting and does not provide a validated same-amino-acid pathogenic comparator; the reviewed paper extracts contain no variant-specific evidence. Therefore PS1 cannot be adjudicated from the available evidence.

Rule

generic_acmg: requires_same_amino_acid_change_with_established_pathogenicity

Evidence considered

• The variant is NP_004646.3:p.(Leu662Pro).
• ClinVar variation 127939 has conflicting submissions, with no expert-panel assertion establishing a same-amino-acid pathogenic comparator.
• The reviewed paper extracts do not mention AXIN2 c.1985T>C or p.Leu662Pro.

Still missing

• A validated pathogenic or likely pathogenic variant with the same p.Leu662Pro amino-acid change is needed.

Sources

Reasoning

No case-specific evidence establishes that AXIN2 NM_004655.4:c.1985T>C (p.Leu662Pro) arose de novo in a proband. The available evidence contains no proband-level parental genotypes, validated maternity and paternity, or documented phenotype consistent with an AXIN2-related disorder; therefore PS2 cannot be assessed.

Evidence considered

• The case-specific records identify the variant as NM_004655.4:c.1985T>C (NP_004646.3:p.(Leu662Pro)) but provide no parental testing results or de novo assertion.
• No fetched paper in the reviewed extraction set reports this exact AXIN2 variant or provides proband-level de novo evidence.

Still missing

• Documented proband genotype and phenotype are needed.
• Molecular testing results for both biological parents, including confirmation of maternity and paternity, are needed.
• If parental samples are unavailable, a validated alternative establishing de novo status is needed.

Reasoning

No applicable AXIN2-specific VCEP specification was identified, so generic ACMG/AMP functional-evidence principles apply. The available case evidence identifies the variant as NM_004655.4:c.1985T>C (NP_004646.3:p.Leu662Pro), but contains no variant-specific functional assay result, assay methodology, quantitative effect, appropriate controls, or demonstration that the tested system is biologically relevant to AXIN2 function. The reviewed publications are general interpretation or clinical-testing sources and do not report a functional experiment for this variant. Therefore, PS3 cannot be assessed; there is no validated experimental evidence supporting a damaging effect and no basis for assigning supporting, moderate, or strong strength.

Evidence considered

• The case identifies NM_004655.4:c.1985T>C as NP_004646.3:p.Leu662Pro, but no variant-specific experimental functional result is provided.
• The reviewed literature sources provide general ACMG/AMP or clinical-testing information and do not report an assay for AXIN2 p.Leu662Pro.
• No AXIN2-specific VCEP specification was available; generic ACMG/AMP principles were therefore used.

Still missing

• A validated functional assay testing AXIN2 p.Leu662Pro is needed.
• Assay controls, quantitative results, biological relevance, and reproducibility are not documented.

Sources

Reasoning

No applicable AXIN2-specific VCEP framework was found, so generic ACMG/AMP guidance applies. PS4 requires significantly increased prevalence of the exact variant in affected individuals compared with appropriate controls, but the available evidence contains no affected-case/control counts, enrichment statistic, odds ratio, or variant-specific prevalence. The exact-variant papers reviewed do not mention NM_004655.4:c.1985T>C or NP_004646.3:p.(Leu662Pro), and ClinVar contains only laboratory submissions rather than an affected-case series.

Rule

Generic PS4: significantly increased prevalence of the exact variant in affected individuals versus appropriate controls; variant-specific case-control or comparable enrichment evidence is required.

Evidence considered

• No AXIN2-specific VCEP framework was available; generic ACMG/AMP guidance was therefore used.
• The reviewed papers PMID:25394175, PMID:29641532, and PMID:38136308 do not report the exact variant NM_004655.4:c.1985T>C or p.Leu662Pro and provide no case-control enrichment data.
• ClinVar variation 127939 has 18 submissions but zero expert-panel submissions; its laboratory submission summary cannot establish PS4.

Still missing

• An appropriately designed affected-case/control study or variant-specific prevalence estimate is required.

Sources

Reasoning

PM1 requires location in a well-established critical functional domain or mutational hotspot with little benign variation. No applicable AXIN2 VCEP or gene-specific framework was found, vcep_materials.json has no domain_tables entry for AXIN2, and the cancer-hotspot result reports no statistically significant hotspot at AXIN2 L662. No authoritative domain evidence places residue 662 in a critical functional region, so PM1 cannot be adjudicated.

Rule

generic_acmg: requires_well_established_critical_functional_domain_or_mutational_hotspot_with_little_benign_variation

Evidence considered

• No applicable AXIN2 VCEP specification or domain table was available.
• The cancer-hotspot query for AXIN2 L662 returned no statistically significant hotspot.
• OncoKB supplied only gene-level context and did not identify variant-specific reviewed functional evidence.

Still missing

• An authoritative AXIN2 critical-domain or hotspot source covering residue 662 is needed.

Sources

Reasoning

PM5 requires a novel missense change at a residue where another missense change has established pathogenicity. The case variant is p.Leu662Pro, but pm5_candidates.json contains no candidates and explicitly does not establish classic same-residue PM5 semantics. The available ClinVar and extracted literature evidence do not establish a pathogenic or likely pathogenic alternate missense change at Leu662; therefore PM5 cannot be adjudicated.

Rule

generic_acmg: requires_established_pathogenic_missense_variant_at_same_residue_with_different_amino_acid

Evidence considered

• The variant changes AXIN2 Leu662 to Pro.
• pm5_candidates.json reports zero same-residue candidates and does not establish classic PM5 semantics.
• ClinVar variation 127939 has conflicting submissions and no expert-panel pathogenic alternate at residue 662.

Still missing

• A validated pathogenic or likely pathogenic alternate missense variant at AXIN2 residue 662 is needed.

Sources

Reasoning

No case-specific or publication-based evidence supports an assumed de novo occurrence of AXIN2 NM_004655.4:c.1985T>C (p.Leu662Pro) without parental testing. The available records do not identify a proband, describe an apparently unaffected parent, or provide a clinical report documenting a de novo event; therefore PM6 cannot be assessed.

Evidence considered

• The case-specific records contain no clinical case narrative documenting this variant as apparently de novo.
• The reviewed paper extractions contain no exact-variant report providing PM6-type evidence.

Still missing

• A specific clinical case with a proband carrying the variant is needed.
• The report must document the relevant phenotype and the absence of a known family history.
• Parental testing status and the basis for any presumed de novo interpretation are needed.

Reasoning

No affected relatives carrying AXIN2 NM_004655.4:c.1985T>C (p.Leu662Pro), no informative meioses, and no unaffected relatives who lack the variant are documented. The available records also do not provide a family pedigree or phenotype assessments suitable for evaluating cosegregation; therefore PP1 cannot be assessed.

Evidence considered

• The case-specific records provide no family segregation study, relative genotypes, pedigree, or count of informative meioses.
• The reviewed publications do not report this exact variant in a family segregation analysis.

Still missing

• A pedigree with clinically characterized relatives is needed.
• Genotypes for affected and unaffected informative relatives are needed.
• The number of informative meioses and phenotype ascertainment details are needed.

Reasoning

PP2 requires that missense variation is a common disease mechanism in the relevant gene and that the gene has a low rate of benign missense variation. The available AXIN2 context describes a tumor-suppressor role and reported truncating mutations, but does not establish the generic PP2 prerequisites or a quantitative gene-specific missense mechanism. The variant-specific sources provide no such analysis, so PP2 cannot be adjudicated.

Rule

generic_acmg: requires_gene_with_high_rate_of_pathogenic_missense_variants_and_low_rate_of_benign_missense_variants

Evidence considered

• AXIN2 is described as a tumor suppressor involved in WNT signaling.
• The available gene-level context mentions truncating mutations but does not quantify pathogenic versus benign missense variation or establish PP2 applicability.
• No variant-specific paper finding establishes the PP2 gene-level prerequisites.

Still missing

• A validated AXIN2 missense-mechanism analysis documenting the PP2 gene-level prerequisites is needed.

Sources

Reasoning

No applicable AXIN2-specific VCEP framework was found, so generic ACMG/AMP guidance applies. PP4 requires a highly specific phenotype or family history consistent with a single-gene disorder, but the case evidence does not provide the patient's phenotype, diagnostic features, family history, or a documented AXIN2-related clinical presentation for this exact variant. A laboratory submission mentioning colorectal cancer frequency is not an independently documented patient phenotype and cannot establish PP4.

Rule

Generic PP4: the patient's phenotype or family history is highly specific for a disease with a single-gene etiology; phenotype specificity must be documented independently of the variant classification.

Evidence considered

• No AXIN2-specific VCEP framework was available; generic ACMG/AMP guidance was therefore used.
• The exact-variant ClinVar record includes a single-submitter laboratory signal mentioning colorectal cancer frequency, but it does not provide independently verifiable patient phenotype or family-history documentation.
• The reviewed literature provides no exact-variant clinical presentation for NM_004655.4:c.1985T>C / p.Leu662Pro.

Still missing

• Clinical phenotype and family-history documentation tied to the tested individual are required.

Sources

Reasoning

PP5 is restricted here to an exact-variant ClinVar expert-panel classification of Pathogenic or Likely pathogenic. ClinVar variation 127939 is an exact match, but the record has zero expert-panel submissions and reports conflicting laboratory submissions, including Likely benign, Benign, and Uncertain significance. Therefore no qualifying PP5 evidence is available; ordinary laboratory submissions and aggregate labels are excluded.

Rule

PP5: apply only when an exact-variant ClinVar expert panel classifies the variant as Pathogenic or Likely pathogenic; laboratory submissions, aggregate labels, and non-expert assertions do not qualify.

Evidence considered

• ClinVar variation 127939 exactly matches NM_004655.4:c.1985T>C (p.Leu662Pro).
• The ClinVar record reports zero expert-panel submissions and only laboratory submissions with conflicting classifications; these cannot trigger PP5.

Still missing

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

Sources

Reasoning

BS2 cannot be assessed from the available evidence. Generic BS2 requires observation of the variant in healthy adults, typically with a disease model and penetrance that make the observation informative. gnomAD reports homozygotes (1 in gnomAD v2.1, 5 in gnomAD v4.1, and 1 in the v2.1 non-cancer subset), but the available records do not establish that these individuals were healthy with respect to AXIN2-related disease, their ages, phenotype status, ascertainment, or penetrance. Therefore these homozygote counts cannot be converted into BS2 evidence without additional clinical context.

Rule

{'name': 'generic_acmg_bs2', 'requirement': 'variant observed in healthy adults in a disease model where that observation is informative', 'application': 'population homozygote counts alone do not establish healthy-adult observations'}

Evidence considered

• gnomAD v2.1 reports 1 total homozygote and gnomAD v4.1 reports 5 total homozygotes; gnomAD v2.1 non-cancer exomes reports 1 homozygote and gnomAD v3.1 non-cancer genomes reports 0.
• The population records do not provide individual-level health status, age at observation, AXIN2 phenotype assessment, ascertainment details sufficient for BS2, or penetrance calibration.

Still missing

• Phenotype and age information for the reported homozygotes is unavailable.
• The penetrance and disease-model assumptions needed to interpret healthy homozygotes for AXIN2-related disease are unavailable.

Sources

Reasoning

No applicable AXIN2-specific VCEP specification was identified, so generic ACMG/AMP functional-evidence principles apply. The available case evidence identifies the variant as NM_004655.4:c.1985T>C (NP_004646.3:p.Leu662Pro), but contains no variant-specific functional assay result showing normal function, assay methodology, quantitative effect, appropriate positive and negative controls, or demonstration that the tested system is biologically relevant to AXIN2 function. The reviewed publications are general interpretation or clinical-testing sources and do not report a functional experiment for this variant. Therefore, BS3 cannot be assessed; there is no validated experimental evidence supporting a benign functional effect and no basis for assigning supporting, moderate, or strong strength.

Evidence considered

• The case identifies NM_004655.4:c.1985T>C as NP_004646.3:p.Leu662Pro, but no variant-specific experimental functional result is provided.
• The reviewed literature sources provide general ACMG/AMP or clinical-testing information and do not report an assay for AXIN2 p.Leu662Pro.
• No AXIN2-specific VCEP specification was available; generic ACMG/AMP principles were therefore used.

Still missing

• A validated functional assay testing AXIN2 p.Leu662Pro is needed.
• Normal-function results, assay controls, biological relevance, and reproducibility are not documented.

Sources

Reasoning

No informative affected family members carrying AXIN2 NM_004655.4:c.1985T>C (p.Leu662Pro) are documented, and no unaffected relatives with reliable genotype and phenotype data are available for a non-segregation analysis. Consequently, there is no adequate evidence to determine whether the variant fails to segregate with disease, so BS4 cannot be assessed.

Evidence considered

• The case-specific records contain no family data showing affected individuals who lack the variant or any other valid non-segregation observation.
• The reviewed paper extractions provide no exact-variant family data relevant to BS4.

Still missing

• Clinically affected relatives and their genotypes are needed.
• Reliable phenotype assessments and genotypes for unaffected relatives are needed.
• Pedigree structure, age-related penetrance considerations, and informative meioses are needed.

Reasoning

BP1 requires a missense variant in a gene for which primarily truncating variants are known to cause disease. Although the available AXIN2 gene context mentions reported truncating mutations, it does not establish that disease-causing AXIN2 variation is primarily truncating or define the applicable disease mechanism. The variant-specific evidence does not resolve this gene-level requirement, so BP1 cannot be adjudicated.

Rule

generic_acmg: requires_missense_variant_in_gene_where_disease_causing_variants_are_predominantly_truncating

Evidence considered

• The variant is a missense substitution, p.Leu662Pro.
• Available AXIN2 context mentions truncating mutations but does not establish a primarily truncating disease mechanism for BP1.
• No variant-specific paper finding resolves the BP1 gene-level prerequisite.

Still missing

• A validated AXIN2 disease-mechanism source demonstrating that pathogenic variation is primarily truncating is needed.

Sources

Reasoning

No AXIN2-specific VCEP specification is available, so generic ACMG/AMP is used. BP2 requires direct observation of the variant with a pathogenic variant in cis for a dominant disorder or in trans with a pathogenic variant for a recessive disorder. The available evidence contains no affected-proband genotype, second pathogenic or likely pathogenic allele, parental testing, phase information, co-occurrence observation, or inheritance result for NM_004655.4:c.1985T>C (NP_004646.3:p.(Leu662Pro)). Population observations, ClinVar submissions, computational scores, and gene-level literature do not establish BP2. The criterion is therefore not assessed pending phase-resolved case evidence.

Evidence considered

• Generic BP2 requires documented co-occurrence with a pathogenic variant and known phase: cis for a dominant disorder or trans for a recessive disorder.
• The case evidence documents the isolated variant NM_004655.4:c.1985T>C (NP_004646.3:p.(Leu662Pro)) but no affected-proband second allele, co-occurrence, parental testing, or phase information.
• The reviewed exact-variant literature extractions contain no variant-specific phase, co-occurrence, segregation, or inheritance observation supporting BP2.
• ClinVar records classify the variant inconsistently and do not provide phase-resolved affected-proband evidence; those classifications were not used as evidence for BP2.

Still missing

• A phase-resolved affected-proband genotype showing a pathogenic or likely pathogenic AXIN2 allele in cis or trans.
• Parental or family testing establishing inheritance and phase of the two variants.
• A documented pathogenic or likely pathogenic classification for the co-occurring allele.

Sources

Reasoning

No applicable AXIN2-specific VCEP framework was found, so generic ACMG/AMP guidance applies. BP5 requires the affected phenotype to be explained by an alternative molecular basis, generally supported by a pathogenic variant in another gene or another established cause. The case evidence contains no documented alternative molecular diagnosis or relevant phenotype-based exclusion, and an aggregate benign ClinVar label cannot establish BP5.

Rule

Generic BP5: a pathogenic variant in another gene or other established alternative molecular cause explains the patient's phenotype, making this variant unlikely to be causal.

Evidence considered

• No AXIN2-specific VCEP framework was available; generic ACMG/AMP guidance was therefore used.
• The available case record contains no alternative pathogenic molecular finding or other established cause of the relevant phenotype.
• Conflicting single-submitter ClinVar classifications are not evidence of an alternative molecular basis.

Still missing

• A documented alternative molecular diagnosis explaining the phenotype is required.

Sources

Reasoning

BP6 is restricted here to an exact-variant ClinVar expert-panel classification of Benign or Likely benign. ClinVar variation 127939 is an exact match, but the record has zero expert-panel submissions and reports only laboratory submissions with conflicting classifications. Therefore no qualifying BP6 evidence is available; ordinary laboratory submissions and aggregate ClinVar labels are excluded.

Rule

BP6: apply only when an exact-variant ClinVar expert panel classifies the variant as Benign or Likely benign; laboratory submissions, aggregate labels, and non-expert assertions do not qualify.

Evidence considered

• ClinVar variation 127939 exactly matches NM_004655.4:c.1985T>C (p.Leu662Pro).
• The ClinVar record reports zero expert-panel submissions and only laboratory submissions with conflicting classifications; these cannot trigger BP6.

Still missing

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

Sources