ABL1 c.944C>T, p.Thr315Ile

Reasoning

The variant is ABL1 p.Thr315Ile (BCR-ABL T315I; c-ABL T334I in the isoform-1b numbering used in the study). PMID:18794843 directly tested the corresponding gatekeeper substitution using site-directed mutagenesis and orthogonal biochemical, cellular, and in vivo assays. The mutant showed increased kinase activity and autophosphorylation, robust survival and rapid IL-3-independent BaF3-cell proliferation, and leukemia with leukocytosis and splenomegaly in injected mice. These biologically relevant assays provide reproducible, concordant evidence of an activating/damaging effect on ABL1 function. Moderate strength is assigned because the evidence is strong and orthogonal but the extracted record does not document validation in a clinical diagnostic laboratory or all assay-control details required for the most well-established level.

Rule

Well-established in vitro or in vivo functional studies supportive of a damaging effect on the gene or gene product. ... Functional studies that have been validated and shown to be reproducible and robust in a clinical diagnostic laboratory setting are considered the most well-established.

Evidence considered

• Activation of tyrosine kinases by mutation of the gatekeeper threonine, PMID:18794843: the corresponding ABL1 gatekeeper substitution was evaluated by site-directed mutagenesis, kinase autophosphorylation and cellular phosphotyrosine assays, BaF3 IL-3-independent survival and proliferation assays, mouse xenograft/injection experiments, and inhibitor testing.
• The study reports that c-ABL-T334I supported robust survival and rapid IL-3-independent proliferation of BaF3 cells and caused leukemia with leukocytosis and splenomegaly in injected mice; T334I is the isoform-1b numbering equivalent of ABL1 T315I.

Still missing

• The available extraction does not document clinical diagnostic-laboratory validation or complete assay-control details.

Sources

Reasoning

PM2 is met at supporting strength. NM_005157.6:c.944C>T (ABL1 p.Thr315Ile) is absent from gnomAD v2.1 and gnomAD v4.1, and the reported non-cancer subsets also show absence. This is below the generic PM2 supporting threshold of <=0.0001 and supports rarity in population controls; no population frequency or homozygote is reported.

Rule

PM2: Absent from controls (or at extremely low frequency if recessive) in Exome Sequencing Project, 1000 Genomes or Exome Aggregation Consortium. ... PM2 (supporting): <= 0.0001 — SVI recommendation to downgrade PM2 to Supporting (ClinGen SVI 2020) (PMID:25741868)

Evidence considered

• gnomAD v2.1 all-comers: variant absent.
• gnomAD v4.1 all-comers: variant absent.
• The case evidence also reports absence from the gnomAD v2.1 non-cancer and gnomAD v3.1 non-cancer datasets; no allele count, allele frequency, or homozygote is reported.
• Generic calibration threshold supplied for PM2 supporting: <=0.0001, attributed in the governing prompt to the ClinGen SVI recommendation (PMID:25741868).

Sources

Reasoning

PS4 is not met. The literature_pass.json PS4 candidate (PMID:24976289) was checked against its abstract and does not mention ABL1 p.Thr315Ile/c.944C>T or provide affected-case and unaffected/population-control counts. No case-control comparison, odds ratio, confidence interval, or matched-ancestry gnomAD case-frequency comparison is available, so the ACMG/AMP requirement of OR or RR >5.0 with a confidence interval excluding 1.0 is not demonstrated.

Rule

The prevalence of the variant in affected individuals is significantly increased compared to the prevalence in controls. ... Note 1: Relative risk (RR) or odds ratio (OR), as obtained from case-control studies, is >5.0 and the confidence interval around the estimate of RR or OR does not include 1.0.

Evidence considered

• PMID:24976289 abstract: the review discusses pediatric chronic myeloid leukemia management but does not mention this ABL1 variant or report variant-specific affected/control frequencies.
• The literature_pass.json packet indexed PMID:24976289 as a PS4 candidate, but verification did not confirm case-control evidence.

Still missing

• Variant-specific case and control counts or frequencies and a corresponding 95% confidence interval are unavailable.

Sources

Reasoning

The variant is a missense substitution, so the generic rule requires the missense REVEL path only; SpliceAI and BayesDel are not used for PP3. REVEL is 0.587, which is below the generic ClinGen SVI PP3 supporting threshold of >=0.644, the moderate threshold of >=0.773, and the strong threshold of >=0.932. Therefore PP3 is not met.

Rule

Multiple lines of computational evidence support a deleterious effect on the gene or gene product (conservation, evolutionary, splicing impact, etc.).

Evidence considered

• The normalized consequence is missense: NM_005157.6:c.944C>T, NP_005148.2:p.(Thr315Ile), in exon 6.
• The local REVEL lookup reports a score of 0.587 for chr9:130872896 C>T.
• Under the supplied generic ClinGen SVI calibration, REVEL PP3 supporting requires >=0.644, moderate >=0.773, and strong >=0.932; these thresholds are from Pejaver et al. 2022, PMID:36413997.
• SpliceAI max delta 0.002 and BayesDel 0.236673 were not counted because the generic missense path is REVEL only and BayesDel has no established generic ACMG-strength calibration.

Sources

Reasoning

PP5 is not met under the supplied generic rule because the exact-variant ClinVar record has zero expert-panel submissions. It contains ordinary laboratory and literature-only assertions, including Pathogenic and Likely pathogenic classifications, but these are not expert-panel classifications and therefore cannot trigger PP5.

Rule

Reputable source recently reports variant as pathogenic, but the evidence is not available to the laboratory to perform an independent evaluation.

Evidence considered

• ClinVar exact match NM_005157.6(ABL1):c.944C>T (p.Thr315Ile) reports zero expert-panel submissions; the available Pathogenic and Likely pathogenic assertions are non-expert submissions.

Still missing

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

Sources

Reasoning

BA1 is not met. NM_005157.6:c.944C>T (ABL1 p.Thr315Ile) was absent from gnomAD v2.1 and gnomAD v4.1, including the reported non-cancer subsets, so no filtering allele frequency is available and the generic BA1 threshold of >=0.05 is not reached. No popmax point estimate is available to override this conclusion.

Rule

BA1: Allele frequency is above 5% in Exome Sequencing Project, 1000 Genomes or Exome Aggregation Consortium. ... BA1 (stand-alone): >= 0.05 — ACMG/AMP 2015 stand-alone benign allele frequency (PMID:25741868)

Evidence considered

• gnomAD v2.1 all-comers: variant absent.
• gnomAD v4.1 all-comers: variant absent.
• The case evidence also reports the variant absent from the gnomAD v2.1 non-cancer and gnomAD v3.1 non-cancer datasets; no allele count, popmax point estimate, or grpmax FAF is available.
• Generic calibration threshold supplied for BA1: >= 0.05, attributed to ACMG/AMP 2015 (PMID:25741868).

Sources

Reasoning

BS1 is not met on the available population data. The variant was absent from gnomAD v2.1 and gnomAD v4.1, including the reported non-cancer subsets, so its filtering allele frequency is not greater than expected for the disorder and does not reach the generic default threshold of >=0.01. Because no elevated frequency is observed, a maximum-credible-allele-frequency calculation is not triggered.

Rule

BS1: Allele frequency is greater than expected for the disorder. ... BS1 (strong): >= 0.01 — Generic SVI default; per-gene derivation preferred (Whiffin et al. 2017) (PMID:28518168)

Evidence considered

• gnomAD v2.1 all-comers: variant absent.
• gnomAD v4.1 all-comers: variant absent.
• The case evidence also reports absence from the gnomAD v2.1 non-cancer and gnomAD v3.1 non-cancer datasets; no filtering allele frequency, grpmax FAF, or ancestry-specific frequency is available.
• Generic BS1 default supplied in the governing prompt: >=0.01; the prompt directs that BS1 uses filtering allele frequency (grpmax FAF), not a popmax point estimate, and cites Whiffin et al. 2017 (PMID:28518168) for maximum-credible-frequency assessment.

Sources

Reasoning

No reviewed functional study shows that ABL1 p.Thr315Ile has no damaging effect on protein function or splicing. Instead, the available direct functional evidence demonstrates increased kinase activity, cellular transformation-associated phenotypes, and an in vivo leukemia phenotype, which is inconsistent with BS3.

Rule

Well-established in vitro or in vivo functional studies show no damaging effect on protein function or splicing.

Evidence considered

• Activation of tyrosine kinases by mutation of the gatekeeper threonine, PMID:18794843: functional assays demonstrated increased activity and transformation-associated cellular and in vivo phenotypes for the corresponding ABL1 T315I substitution, providing evidence against a no-damaging-effect conclusion.

Sources

Reasoning

The variant is a missense substitution, so the generic rule requires the missense REVEL path only; SpliceAI is not applicable to BP4 for this missense interpretation. REVEL is 0.587, which exceeds the generic ClinGen SVI BP4 supporting threshold of <=0.29, moderate threshold of <=0.183, and strong threshold of <=0.016. The result is therefore indeterminate rather than evidence of no impact, so BP4 is not met.

Rule

Multiple lines of computational evidence suggest no impact on gene or gene product (conservation, evolutionary, splicing impact, etc)

Evidence considered

• The normalized consequence is missense: NM_005157.6:c.944C>T, NP_005148.2:p.(Thr315Ile), in exon 6.
• The local REVEL lookup reports a score of 0.587 for chr9:130872896 C>T.
• Under the supplied generic ClinGen SVI calibration, REVEL BP4 supporting requires <=0.29, moderate <=0.183, and strong <=0.016; these thresholds are from Pejaver et al. 2022, PMID:36413997.
• The available SpliceAI max delta of 0.002 was not used because a missense variant must be evaluated through the REVEL path only; the gray-zone REVEL result does not permit substituting SpliceAI.

Sources

Reasoning

BP6 is not met under the supplied generic rule because the exact-variant ClinVar record has zero expert-panel submissions and no exact-variant expert-panel benign or likely benign classification. The available ClinVar assertions are Pathogenic, Likely pathogenic, and association, not expert-panel Benign or Likely benign.

Rule

Reputable source recently reports variant as benign, but the evidence is not available to the laboratory to perform an independent evaluation.

Evidence considered

• ClinVar exact match reports zero expert-panel submissions and no Benign or Likely benign expert-panel classification.

Still missing

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

Sources

Reasoning

The variant is p.Thr315Ile, but the available evidence does not document a previously established pathogenic variant causing the same amino-acid change through a different nucleotide change. The exact variant's pathogenic or likely pathogenic submissions cannot themselves establish PS1, and no alternate-codon comparator is provided.

Rule

Same amino acid change as a previously established pathogenic variant regardless of nucleotide change.

Evidence considered

• ClinVar variation 12624 confirms the observed variant as NM_005157.6:c.944C>T (p.Thr315Ile), but the record supplied no distinct nucleotide-change comparator encoding the same amino-acid substitution.

Still missing

• A verified pathogenic ABL1 nucleotide change other than NM_005157.6:c.944C>T that produces p.Thr315Ile is needed.

Sources

Reasoning

PS2 cannot be assessed because the available evidence does not document a proband with the relevant disease phenotype, absence of family history, or confirmed maternity and paternity. ClinVar records germline origin for submissions but do not establish de novo status or parental testing.

Rule

De novo (both maternity and paternity confirmed) in a patient with the disease and no family history.

Evidence considered

• ClinVar variation 12624 records germline origin for two submissions, but provides no documented de novo assertion, parental genotypes, maternity confirmation, paternity confirmation, or family-history assessment.
• The available case evidence contains no documented segregation or parental-testing result for NM_005157.6:c.944C>T (p.Thr315Ile).

Still missing

• Clinical phenotype and disease diagnosis for the proband
• Family history status
• Variant testing results in the biological mother and father
• Confirmation of both maternity and paternity

Sources

Reasoning

p.Thr315Ile lies at the ABL1 kinase-domain gatekeeper threonine, and the reviewed study describes the gatekeeper as part of the active site and demonstrates functional effects of the T315I/T334I substitution. However, no VCEP domain table is available and the supplied evidence does not establish absence of benign variation throughout the relevant domain, as required by the generic PM1 wording. The variant is also not reported in the supplied Cancer Hotspots result.

Rule

Located in a mutational hot spot and/or critical and well-established functional domain (e.g. active site of an enzyme) without benign variation.

Evidence considered

• Activation of tyrosine kinases by mutation of the gatekeeper threonine, Results: the ABL1 gatekeeper substitution is evaluated as T315I in BCR-ABL and T334I in c-ABL isoform 1b; the paper describes the gatekeeper as part of the active site and reports increased kinase activity, BaF3 transformation, and leukemia in mice.
• Cancer Hotspots returned no statistically significant hotspot result for ABL1 T315.
• The observed variant was absent from gnomAD v2.1 and v4.1, which does not by itself establish absence of benign variation across the entire functional domain.

Still missing

• Evidence that the relevant ABL1 functional domain lacks benign variation, using an appropriate population or curated domain-level dataset, is needed.

Sources

Reasoning

PM3 cannot be assessed from the available evidence. The rule requires a recessive disorder and demonstration that NM_005157.6:c.944C>T (p.Thr315Ile) is in trans with a pathogenic variant, with parental or offspring testing to establish phase. The case evidence contains no affected-proband allelic observations, pathogenic partner variant, parent/offspring testing, or phase result. ABL1 has reported germline disorders with differing inheritance mechanisms, but no inheritance assignment or phase evidence specific to this variant is documented here.

Rule

For recessive disorders, detected in trans with a pathogenic variant ... Note: This requires testing of parents (or offspring) to determine phase.

Evidence considered

• The available case evidence identifies ABL1 NM_005157.6:c.944C>T (p.Thr315Ile) but provides no affected-proband observation, partner pathogenic variant, parental or offspring testing, or phase assignment.
• No VCEP or gene-specific allelic rule is available; the case is governed by generic ACMG/AMP rules.

Still missing

• Determine the relevant ABL1 disorder and inheritance mode for this variant.
• Identify any pathogenic or likely pathogenic partner variant in the same affected proband.
• Obtain parental or offspring testing establishing that the variants are in trans.

Reasoning

The supplied evidence identifies the observed p.Thr315Ile substitution but does not document a different missense substitution at ABL1 residue 315 that was determined to be pathogenic. The PM5 candidate artifact contains no same-residue candidates, and the exact variant's own classification cannot serve as the required comparator.

Rule

Novel missense change at an amino acid residue where a different missense change determined to be pathogenic has been seen before.

Evidence considered

• The PM5 candidate collection reported zero same-residue candidates and no comparator variant.
• ClinVar variation 12624 documents the observed p.Thr315Ile variant but no different pathogenic missense change at residue 315.

Still missing

• A verified pathogenic ABL1 missense variant at residue 315, different from p.Thr315Ile, is needed.

Sources

Reasoning

PM6 cannot be assessed because the available evidence does not document an assumed de novo occurrence in an affected patient. No parental testing, maternity status, paternity status, or de novo observation is reported for this variant; germline origin alone is insufficient.

Rule

Assumed de novo, but without confirmation of paternity and maternity.

Evidence considered

• ClinVar variation 12624 records germline origin for two submissions, but does not report an assumed de novo event or parental-testing results.
• The available case evidence contains no documented de novo observation for NM_005157.6:c.944C>T (p.Thr315Ile).

Still missing

• Affected-patient clinical context
• A documented de novo observation
• Parental testing or explicit statement that maternity and paternity were not confirmed

Sources

Reasoning

PP1 cannot be assessed because no affected family members, variant-positive relatives, variant-negative relatives, or meioses are documented for this variant. The available evidence does not provide family segregation data sufficient to evaluate co-segregation.

Rule

Co-segregation with disease in multiple affected family members in a gene definitively known to cause the disease.

Evidence considered

• No family pedigree, affected-relative genotypes, unaffected-relative genotypes, or informative meioses are documented in the available case evidence for NM_005157.6:c.944C>T (p.Thr315Ile).
• The available variant-specific literature concerns somatic or functional ABL1 studies and does not provide family co-segregation data for this variant.

Still missing

• Pedigree and number of affected relatives
• Phenotype status of each family member
• Variant genotypes of affected and unaffected relatives
• Number of informative meioses

Sources

Reasoning

The supplied evidence does not establish both required gene-level conditions: a low rate of benign missense variation and missense variants as a common mechanism of disease. ABL1 literature in the bundle describes both activating missense disease mechanisms and loss-of-function disease context, but it does not provide the required benign-missense rate or a defensible gene-level predominance assessment.

Rule

Missense variant in a gene that has a low rate of benign missense variation and where missense variants are a common mechanism of disease.

Still missing

• A gene-level assessment of benign missense constraint is needed.
• A gene-level assessment showing missense variants are a common disease mechanism is needed.

Reasoning

PP4 cannot be assessed from the available evidence because no patient-specific phenotype or family-history description is provided for this variant. A ClinVar condition label of chronic myeloid leukemia and imatinib resistance is not sufficient to establish that the patient's phenotype is highly specific for a disease with a single genetic etiology.

Rule

Patient’s phenotype or family history is highly specific for a disease with a single genetic etiology.

Evidence considered

• ClinVar lists chronic myeloid leukemia and Philadelphia-chromosome-positive leukemia resistant to imatinib, but supplies no patient-specific phenotype or family-history assessment.

Still missing

• Patient-specific phenotype, diagnostic findings, and family history are needed to assess phenotypic specificity.

Sources

Reasoning

BS2 is not assessed. The available evidence contains population-level absence statements but no documented healthy adult individual carrying ABL1 p.Thr315Ile in the heterozygous, homozygous, or hemizygous state. Therefore the required healthy-adult observation cannot be evaluated, and no conclusion about early-age full penetrance can be made from the supplied data.

Rule

BS2: Observed in a healthy adult individual for a recessive (homozygous), dominant (heterozygous), or X-linked (hemizygous) disorder, with full penetrance expected at an early age.

Evidence considered

• The available gnomAD evidence reports absence of the variant and does not document any individual-level heterozygous, homozygous, or hemizygous carrier observation.
• No healthy-adult case or cohort record with genotype, age, phenotype, and inheritance context was supplied.

Still missing

• A documented healthy adult carrier genotype and relevant age/phenotype information are unavailable.

Sources

Reasoning

BS4 cannot be assessed because no affected family members with known variant status are documented. There is therefore no demonstrated lack of segregation, and the available evidence does not permit evaluation of phenocopy or multiple-variant explanations.

Rule

Lack of segregation in affected members of a family.

Evidence considered

• No affected relatives with documented NM_005157.6:c.944C>T (p.Thr315Ile) status are identified in the available case evidence.
• Without affected-relative genotypes and phenotype review, lack of segregation cannot be distinguished from incomplete assessment, phenocopy, or contribution from another pathogenic variant.

Still missing

• Affected-family-member pedigree
• Variant status of affected relatives
• Phenotype confirmation and assessment for phenocopies
• Assessment for additional pathogenic variants in the family

Sources

Reasoning

The supplied evidence does not establish that ABL1 disease is caused primarily by truncating variants. The available gene context instead documents both germline gain-of-function missense disease and germline loss-of-function disease, without a quantitative or curated predominance of truncating pathogenic variants.

Rule

Missense variant in a gene for which primarily truncating variants are known to cause disease.

Still missing

• A curated gene-level variant-spectrum assessment demonstrating that pathogenic ABL1 disease is primarily truncating is needed.

Reasoning

BP2 cannot be assessed from the available evidence. The rule requires observation of NM_005157.6:c.944C>T (p.Thr315Ile) in trans with a pathogenic variant for a fully penetrant dominant gene/disorder, or in cis with a pathogenic variant in any inheritance pattern. The case evidence documents neither an allelic partner, phase, affected-proband observation, nor a sufficiently established inheritance context for this variant.

Rule

Observed in trans with a pathogenic variant for a fully penetrant dominant gene/disorder or observed in cis with a pathogenic variant in any inheritance pattern.

Evidence considered

• The available case evidence identifies ABL1 NM_005157.6:c.944C>T (p.Thr315Ile) but provides no pathogenic partner variant, phase result, affected-proband allelic observation, or inheritance evidence relevant to BP2.
• No VCEP or gene-specific allelic rule is available; the case is governed by generic ACMG/AMP rules.

Still missing

• Identify any pathogenic partner variant observed with this variant.
• Obtain parental, offspring, or haplotyping data establishing cis or trans phase.
• Establish whether the applicable ABL1 disorder is a fully penetrant dominant disorder.

Reasoning

BP5 cannot be assessed because the available COSMIC record reports this variant once in a somatic cancer but does not identify a specific case in which an alternate molecular basis for disease was established. A somatic occurrence alone does not document the BP5 case context.

Rule

Variant found in a case with an alternate molecular basis for disease.

Evidence considered

• COSMIC record COSV59339341 reports the variant once in somatic cancer, without patient-level evidence of an alternate molecular basis for disease.

Still missing

• A patient-level case report must document the alternate molecular basis and the disease context.

Sources