FLT3 c.2503G>T, p.Asp835Tyr

Reasoning

PS3 is met at Strong strength under generic ACMG/AMP. Multiple variant-specific functional studies provide concordant evidence across independent experimental systems: FLT3-D835Y was constitutively tyrosine-phosphorylated and transformed IL-3-dependent 32D cells without IL-3 or FLT3 ligand (PMID:11290608); retrovirally transduced Ba/F3 cells expressing D835Y showed constitutive FLT3 phosphorylation, STAT5/ERK activation, IL-3-independent proliferation, and a measured MLN518 IC50 greater than 10 µM (PMID:15256420); D835Y was evaluated in technical triplicates and at least three independent experiments in Ba/F3 inhibitor assays (PMID:26108694); and a homologous Flt3/D838Y knock-in mouse model showed constitutive activation, altered downstream signaling, and a reproducible myeloproliferative phenotype relative to wild-type controls (PMID:24255108). The in vivo study also showed that D835Y alone was insufficient to cause leukemia, which refines disease severity but does not negate the demonstrated abnormal gain-of-function effect. OncoKB independently provides exact-variant support, labeling FLT3 D835Y Oncogenic with Gain-of-function. The two governing VCEP files were searched for c.2503G>T, p.Asp835Tyr, and p.D835Y; neither contains an exact-variant table entry, and the local notes are restricted to ITD/activating length-mutation classes, so this assessment uses generic ACMG/AMP rather than local FLT3 criterion logic.

Rule

Well-established in vitro or in vivo functional studies supportive of a damaging effect on the gene or gene product.

Evidence considered

• Yamamoto et al. 2001, PMID:11290608: FLT3 D835Y was the most frequent D835 mutation (22 of 32); all D835-mutant FLT3 proteins were constitutively tyrosine-phosphorylated and transformed 32D cells, supporting constitutive activation. The exact variant is reported as D835Y, corresponding to NP_004110.2:p.(D835Y).
• Griffith et al. 2004, PMID:15256420: in retrovirally transduced Ba/F3 cells, FLT3-D835Y produced constitutive FLT3 tyrosine phosphorylation, downstream STAT5 and ERK activation, and IL-3-independent proliferation; D835Y had an MLN518 cellular IC50 greater than 10 µM.
• Li et al. 2013, PMID:24255108: a homologous Flt3/D838Y knock-in mouse model corresponding to human FLT3/D835Y showed constitutive activation, altered STAT5 signaling, and a distinct myeloproliferative phenotype compared with wild-type controls; median survival was 678 days versus 430 days for FLT3/ITD mice, with P<0.0001.
• Kiyoi et al. 2015, PMID:26108694: Ba/F3 assays of FLT3-ITD D835 mutants used technical triplicates and at least three independent experiments; D835Y caused high resistance to type II FLT3 inhibitors while retaining sensitivity to crenolanib, demonstrating a reproducible variant-associated functional phenotype.
• OncoKB exact FLT3 D835Y page: variant-specific curated evidence reports Oncogenic classification together with Gain-of-function biological effect.
• flt3_itd_hotspot_and_function.md.txt: searched for c.2503G>T, p.Asp835Tyr, and p.D835Y; no exact entry was found. Its stated scope is in-frame ITD/insertion/duplication/delins/length-mutation events, not missense substitutions.
• flt3_oncokb_guidance.md.txt: searched for c.2503G>T, p.Asp835Tyr, and p.D835Y; no exact entry was found. Its stated scope is FLT3 ITDs and activating length mutations, not missense substitutions.

Still missing

• No exact c.2503G>T, p.Asp835Tyr, or p.D835Y entry was found in flt3_itd_hotspot_and_function.md.txt.
• No exact c.2503G>T, p.Asp835Tyr, or p.D835Y entry was found in flt3_oncokb_guidance.md.txt.
• The governing local FLT3 notes do not provide a missense-specific PS3 strength rule for this variant; generic ACMG/AMP was therefore applied.

Sources

Reasoning

FLT3 p.D835Y is in the activation loop of the tyrosine kinase domain, a recurrent critical functional region. PMID:11290608 reports D835Y as the most frequent D835 mutation and states that D835-mutant FLT3 proteins were constitutively phosphorylated and transformed 32D cells; PMID:24255108 describes D835Y as the most frequent kinase-domain mutation; and PMID:26108694 identifies D835 as a recurrent activation-loop residue. The variant is absent from gnomAD v2.1, gnomAD v4.1, and gnomAD-Canada, providing no observed benign population variation in the reviewed datasets. The local FLT3 VCEP notes were searched but are restricted to ITD/activating length-mutation classes and do not govern this missense substitution, so generic PM1 is applied.

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

• Yamamoto et al. (PMID:11290608), Results/Table 1: D835Y was the most frequent D835 mutation (22 of 32), and all D835-mutant FLT3 proteins were constitutively tyrosine-phosphorylated and transformed 32D cells.
• Lee et al. (PMID:24255108): FLT3/D835Y is described as the most frequent kinase-domain mutation and is modeled as a constitutively activating mutation in the tyrosine kinase domain.
• Smith et al. (PMID:26108694): activating FLT3 mutations commonly involve the activation-loop residue D835, and D835Y is specifically studied.
• The variant is absent from gnomAD v2.1, gnomAD v4.1, and gnomAD-Canada v1.0.

Still missing

• No matching entry for c.2503G>T, p.Asp835Tyr, or p.D835Y was found in flt3_itd_hotspot_and_function.md.txt.
• No matching entry for c.2503G>T, p.Asp835Tyr, or p.D835Y was found in flt3_oncokb_guidance.md.txt.

Sources

Reasoning

PM2 is met at Supporting strength under the supplied generic threshold. The exact variant NM_004119.3:c.2503G>T (p.Asp835Tyr) is absent from gnomAD v2.1 and gnomAD v4.1, and is also reported absent from the gnomAD v2.1 non-cancer and gnomAD v3.1 non-cancer subsets. Thus the observed allele frequency is 0 in the available population datasets, satisfying the supplied PM2 threshold of <=0.0001. No variant-specific frequency, ancestry, or homozygote signal was observed. This is population evidence only and should not be interpreted as proof of a germline disorder association, particularly because the case's clinical records describe a somatic leukemia-associated variant.

Rule

PM2 (supporting): <= 0.0001 — SVI recommendation to downgrade PM2 to Supporting (ClinGen SVI 2020) (PMID:25741868)

Evidence considered

• gnomAD v2.1 all-comers: absent; gnomAD v4.1 all-comers: absent.
• gnomAD v2.1 non-cancer exomes: absent; gnomAD v3.1 non-cancer genomes: absent.
• Generic PM2 calibration supplied for this case: <=0.0001, described as the SVI recommendation to downgrade PM2 to Supporting (ClinGen SVI 2020; PMID:25741868).
• The available ClinVar record is an exact-match Pathogenic somatic leukemia record with no assertion criteria; it was not used to establish PM2.

Sources

Reasoning

The variant is an exonic missense substitution, NM_004119.3:c.2503G>T (p.Asp835Tyr), so the governing computational path is REVEL only; SpliceAI and BayesDel are not used for PP3/BP4 in this situation. The exact REVEL score is 0.875, which meets the supplied generic PP3 moderate threshold of >= 0.773 (ClinGen SVI REVEL calibration, Pejaver et al. 2022, PMID:36413997). The score does not meet the stronger PP3 threshold of >= 0.932, so PP3 is applied at moderate strength.

Rule

Multiple lines of computational evidence support a deleterious effect on the gene or gene product (conservation, evolutionary, splicing impact, etc.). ... Missense variant -> REVEL only. ... PP3 (moderate): >= 0.773 — ClinGen SVI REVEL calibration (Pejaver et al. 2022, Am J Hum Genet) (PMID:36413997)

Evidence considered

• Local REVEL predictor lookup for NM_004119.3:c.2503G>T (p.Asp835Tyr): REVEL = 0.875.
• Supplied generic calibration: REVEL PP3 moderate >= 0.773 and strong >= 0.932, from ClinGen SVI REVEL calibration (Pejaver et al. 2022, PMID:36413997).
• Consequence and location: exonic missense substitution in exon 20; therefore the generic missense REVEL path applies and the SpliceAI score is not counted for PP3.

Sources

Reasoning

Abu-Duhier et al. (PMID:11442493) reported the exact FLT3 p.Asp835Tyr variant in 5 of 97 adult de novo AML cases and no Asp835 alterations in 80 normal controls, so this is a case-control comparison. Using a 0.5 continuity correction for the zero control cell, the odds ratio is 9.68 with an approximate 95% CI of 0.53-177.75. The governing PS4 requirement is OR >5.0 and a confidence interval that does not include 1.0; the explicit comparison is OR 9.68 > 5.0 (yes), but CI 0.53-177.75 includes 1.0 (no), so PS4 is not met.

Rule

The prevalence of the variant in affected individuals is significantly increased compared to the prevalence in controls. ... 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

• Abu-Duhier et al. 2001 abstract, adult de novo AML cohort: 5 D835Y cases among 97 AML cases and no Asp835 alterations among 80 normal controls.
• Computed case-control OR from 5/97 versus 0/80 using a 0.5 continuity correction for the zero control cell: OR = 9.68; approximate Wald 95% CI = 0.53-177.75.
• The comparison was written explicitly as OR 9.68 > 5.0? yes; 95% CI 0.53-177.75 excludes 1.0? no.

Sources

Reasoning

The reviewed evidence supports that missense activating variants are a recognized FLT3 disease mechanism, including recurrent D835 substitutions, but it does not establish the required low rate of benign missense variation for FLT3 under a validated gene-level framework. Because both elements of the PP2 definition are required and the benign-missense component is not demonstrated, PP2 is not met.

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.

Evidence considered

• PMID:11290608 and PMID:24255108 support recurrent activating FLT3 missense variation as a disease mechanism, but neither supplies a validated gene-level benign-missense-rate assessment.

Still missing

• A validated gene-level assessment of benign missense variation for FLT3 is not available in the reviewed evidence.

Sources

Reasoning

The reviewed clinical evidence concerns acute myeloid leukemia, and the exact variant is also associated in ClinVar with acute lymphoid leukemia, but neither leukemia phenotype is highly specific to a single genetic etiology. FLT3 D835Y is one recurrent molecular alteration among multiple genetic causes of these malignancies; the available evidence does not establish a phenotype-specific single-gene presentation sufficient for PP4.

Rule

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

Evidence considered

• Abu-Duhier et al. 2001 studied adult de novo AML and reported the exact D835Y variant in that disease cohort.
• ClinVar exact-variant record lists acute myeloid leukemia and acute lymphoid leukemia, demonstrating disease association but not a phenotype highly specific to one genetic etiology.

Sources

Reasoning

The exact ClinVar record is classified Pathogenic, but it has no assertion criteria, no expert-panel submission, and only laboratory or literature-only submissions. Under the required generic PP5 restriction, this does not qualify as an exact-variant ClinVar expert-panel classification; therefore PP5 is not met.

Rule

Apply them only for an exact-variant ClinVar expert-panel classification: Pathogenic/Likely pathogenic supports PP5; Benign/Likely benign supports BP6. Ordinary laboratory submissions, aggregate ClinVar labels, and non-expert assertions must never trigger either criterion.

Evidence considered

• ClinVar exact variant NM_004119.3:c.2503G>T (p.Asp835Tyr): Pathogenic, review status ‘no assertion criteria provided,’ expert-panel submissions = 0.
• The available submissions are OMIM literature-only submissions and one clinical-testing submission, not an exact-variant expert-panel assertion.

Sources

Reasoning

BA1 is not met. The variant is absent from gnomAD v2.1 and gnomAD v4.1, including the reported non-cancer subsets, so no allele frequency meets or exceeds the generic stand-alone benign threshold of 0.05. No population frequency above 5% is available from the specified population datasets. The exact variant has a documented somatic disease association and pathogenic ClinVar submissions, but those records do not establish a benign high-frequency allele; therefore there is no basis to apply BA1 as a stand-alone benign call.

Rule

BA1 (stand-alone): >= 0.05 — ACMG/AMP 2015 stand-alone benign allele frequency (PMID:25741868)

Evidence considered

• gnomAD v2.1 all-comers: absent; gnomAD v4.1 all-comers: absent.
• gnomAD v2.1 non-cancer: absent; gnomAD v3.1 non-cancer genomes: absent.
• Generic BA1 calibration supplied for this case: >=0.05, attributed to ACMG/AMP 2015 stand-alone benign allele frequency (PMID:25741868).
• ClinVar exact record NM_004119.3:c.2503G>T (p.Asp835Tyr) is Pathogenic but has no assertion criteria and represents somatic leukemia submissions; this conflicts with using a default high-frequency benign call rather than supporting BA1.

Sources

Reasoning

BS1 is not met. The variant is absent from gnomAD v2.1 and gnomAD v4.1, including the reported non-cancer subsets, so the observed filtering allele frequency is not greater than expected for the disorder and does not reach the generic default threshold of 0.01. No ancestry-specific frequency, grpmax FAF, or population count is available to support a frequency-based BS1 call. Because the variant is absent rather than elevated, the reduced-penetrance/founder-allele caveat does not alter this conclusion.

Rule

BS1 (strong): >= 0.01 — Generic SVI default; per-gene derivation preferred (Whiffin et al. 2017) (PMID:28518168)

Evidence considered

• gnomAD v2.1 all-comers: absent; gnomAD v4.1 all-comers: absent.
• gnomAD v2.1 non-cancer: absent; gnomAD v3.1 non-cancer genomes: absent.
• No grpmax FAF, popmax point estimate, ancestry-specific allele count, or observed allele count is reported for this variant; therefore no frequency-based BS1 threshold is reached.
• Generic BS1 calibration supplied for this case: >=0.01; the generic rule is that allele frequency must be greater than expected for the disorder, with per-gene derivation preferred (Whiffin et al. 2017, PMID:28518168).

Sources

Reasoning

BS3 is not met. The available variant-specific functional evidence is directionally opposite to a benign functional interpretation: FLT3-D835Y shows constitutive phosphorylation, downstream signaling activation, factor-independent cellular proliferation or transformation, inhibitor-resistance phenotypes, and an abnormal knock-in mouse phenotype. None of the reviewed studies establishes that D835Y has no damaging effect on FLT3 function or splicing. The two governing VCEP files were searched for c.2503G>T, p.Asp835Tyr, and p.D835Y; neither contains an exact-variant table entry, and their restricted ITD/length-mutation scope does not govern this missense substitution.

Rule

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

Evidence considered

• Yamamoto et al. 2001, PMID:11290608: exact D835Y showed constitutive tyrosine phosphorylation and transformed 32D cells, providing evidence against a no-damaging-effect interpretation.
• Griffith et al. 2004, PMID:15256420: exact D835Y activated FLT3, STAT5, and ERK and supported IL-3-independent Ba/F3 proliferation; the measured MLN518 IC50 was greater than 10 µM.
• Li et al. 2013, PMID:24255108: homologous D835Y knock-in mice showed constitutive activation and an abnormal myeloproliferative phenotype, although D835Y alone was insufficient to cause leukemia.
• Kiyoi et al. 2015, PMID:26108694: D835Y produced a reproducible inhibitor-resistance phenotype in Ba/F3 assays performed in technical triplicates and at least three independent experiments.
• flt3_itd_hotspot_and_function.md.txt: searched for c.2503G>T, p.Asp835Tyr, and p.D835Y; no exact entry was found.
• flt3_oncokb_guidance.md.txt: searched for c.2503G>T, p.Asp835Tyr, and p.D835Y; no exact entry was found.

Still missing

• No exact c.2503G>T, p.Asp835Tyr, or p.D835Y entry was found in flt3_itd_hotspot_and_function.md.txt.
• No exact c.2503G>T, p.Asp835Tyr, or p.D835Y entry was found in flt3_oncokb_guidance.md.txt.
• No variant-specific assay demonstrating absence of a damaging effect on FLT3 protein function or splicing was identified.

Sources

Reasoning

The available FLT3 evidence does not support a gene in which disease is primarily caused by truncating variants. Instead, the reviewed literature describes recurrent activating missense substitutions in the kinase-domain activation loop, including D835Y, and identifies kinase-domain point mutations as a common FLT3 mutation class. Therefore the premise of BP1 is contradicted for this variant context.

Rule

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

Evidence considered

• PMID:11290608 reports recurrent activating D835 missense mutations and constitutive activity of D835-mutant FLT3.
• PMID:24255108 states that FLT3 point mutations in the tyrosine kinase domain are a major mutation class and studies D835Y.
• PMID:26108694 describes activating FLT3 point mutations at the D835 activation-loop residue.

Still missing

• No comprehensive gene-wide variant-spectrum reference was available, although the reviewed FLT3 literature documents a prominent activating missense mechanism.

Sources

Reasoning

The variant is an exonic missense substitution, so BP4 must be assessed through the REVEL-only missense path; the SpliceAI score cannot substitute for an indeterminate REVEL result, and BayesDel has no generic ACMG-strength calibration. REVEL is 0.875, which is above the supplied BP4 supporting cutoff of <= 0.29 and does not meet any benign REVEL threshold. Therefore BP4 is not met.

Rule

Multiple lines of computational evidence suggest no impact on gene or gene product (conservation, evolutionary, splicing impact, etc). ... Missense variant -> REVEL only. ... BP4 (supporting): <= 0.29 — ClinGen SVI REVEL calibration (Pejaver et al. 2022, Am J Hum Genet) (PMID:36413997)

Evidence considered

• Local REVEL predictor lookup for NM_004119.3:c.2503G>T (p.Asp835Tyr): REVEL = 0.875.
• Supplied generic calibration: REVEL BP4 supporting <= 0.29, moderate <= 0.183, and strong <= 0.016, from ClinGen SVI REVEL calibration (Pejaver et al. 2022, PMID:36413997).
• SpliceAI max delta = 0.149 was not used because this is a missense variant and the governing rule selects REVEL only for the missense path; BayesDel = 0.338586 was not used because no generic ACMG-strength calibration is established.

Sources

Reasoning

The exact ClinVar record is classified Pathogenic, not Benign or Likely benign, and has no expert-panel submission. No exact-variant ClinVar expert-panel benign classification is available to trigger BP6; therefore BP6 is not met.

Rule

Apply them only for an exact-variant ClinVar expert-panel classification: Pathogenic/Likely pathogenic supports PP5; Benign/Likely benign supports BP6. Ordinary laboratory submissions, aggregate ClinVar labels, and non-expert assertions must never trigger either criterion.

Evidence considered

• ClinVar exact variant NM_004119.3:c.2503G>T (p.Asp835Tyr): Pathogenic, review status ‘no assertion criteria provided,’ expert-panel submissions = 0.
• The available ClinVar submissions are not expert-panel benign assertions and therefore cannot trigger BP6.

Sources

Reasoning

The variant is reported as p.D835Y / p.Asp835Tyr, but the reviewed evidence establishes the same c.2503G>T nucleotide change rather than an independently established pathogenic nucleotide substitution producing the same amino-acid change. The two governing FLT3 VCEP files were searched for c.2503G>T, p.Asp835Tyr, and p.D835Y and contained no variant entry. A different-nucleotide same-amino-acid comparator is therefore not available for applying PS1.

Rule

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

Evidence considered

• The normalized case variant is NM_004119.3:c.2503G>T, NP_004110.2:p.(Asp835Tyr) / p.(D835Y).
• The exact variant is reported in the reviewed literature, but no different nucleotide change producing p.D835Y was established in the available evidence.

Still missing

• No matching entry for c.2503G>T, p.Asp835Tyr, or p.D835Y was found in flt3_itd_hotspot_and_function.md.txt.
• No matching entry for c.2503G>T, p.Asp835Tyr, or p.D835Y was found in flt3_oncokb_guidance.md.txt.
• An independently established pathogenic alternate nucleotide change encoding p.D835Y is still needed for PS1.

Reasoning

The available case evidence does not document a proband-level de novo finding, confirmed maternity, confirmed paternity, absence of family history, or the clinical disease context required to evaluate PS2. The variant is reported in somatic AML/ALL literature, but those reports do not establish germline de novo status for this case.

Rule

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

Evidence considered

• The available case evidence contains no proband-specific parental testing or family-history data establishing a de novo germline event.
• The relevant literature reports FLT3 D835Y as a somatic leukemia-associated variant, which does not establish de novo status in this proband.

Still missing

• Proband-level variant result and disease phenotype documentation
• Parental testing confirming maternity and paternity
• Family-history assessment

Reasoning

The reviewed literature reports alternate missense substitutions at FLT3 residue D835, including D835V, D835H, D835E, D835N, and D835A, and shows activating activity for several of them. However, the available evidence does not establish any of those alternate substitutions as a previously determined pathogenic variant under the governing evidence record; the PM5 candidate artifact also identified no eligible same-residue comparator. The local FLT3 VCEP notes do not govern this missense SNV and cannot supply the custom ITD PM5 extension.

Rule

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

Evidence considered

• PMID:11290608 reports D835V, D835H, D835E, and D835N in addition to D835Y and shows constitutive activation for D835-mutant FLT3, but does not provide an independent pathogenic classification for an alternate D835 missense variant.
• PMID:15256420 functionally studies D835A, D835E, D835H, D835N, and D835V alongside D835Y, but functional activation alone does not establish the required prior pathogenic determination for PM5.

Still missing

• No matching entry for c.2503G>T, p.Asp835Tyr, or p.D835Y was found in flt3_itd_hotspot_and_function.md.txt.
• No matching entry for c.2503G>T, p.Asp835Tyr, or p.D835Y was found in flt3_oncokb_guidance.md.txt.
• A separately established pathogenic alternate missense substitution at residue D835 is needed for classic PM5.

Sources

Reasoning

The available case evidence does not document an assumed de novo occurrence in the proband, nor does it provide parental testing or a family-history assessment. Therefore, the evidence is insufficient to distinguish PM6 from an unassessed familial or somatic finding.

Rule

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

Evidence considered

• No proband-specific de novo statement or parental testing result is present in the available case evidence.
• Published D835Y reports describe somatic hematologic malignancy findings and cannot substitute for case-specific de novo evidence.

Still missing

• Proband-level variant and phenotype documentation
• Evidence supporting an assumed de novo occurrence
• Parental testing status and family-history assessment

Reasoning

No affected relatives, informative meioses, segregation results, or family-level phenotype data are documented. The available D835Y publications describe unrelated somatic disease cohorts and do not provide family segregation evidence for this case.

Rule

Co-segregation with disease in multiple affected family members in a gene definitively known to cause the disease. ... Note: May be used as stronger evidence with increasing segregation data.

Evidence considered

• The available case evidence contains no family pedigree, affected-relative testing, or segregation analysis.
• The reviewed D835Y literature reports somatic leukemia cohorts rather than co-segregation with disease in affected family members.

Still missing

• Affected relatives and their molecular test results
• Family phenotype and disease-status documentation
• Informative meioses and segregation analysis

Reasoning

BS2 cannot be assessed from the available evidence. The case contains no documented observation of this variant in a healthy adult individual as a homozygote, heterozygote, or hemizygote, and no phenotype, inheritance, penetrance, or age-of-onset information that would establish the required healthy-adult observation for a fully penetrant early-onset disorder. Absence from population databases is not evidence that a specific healthy adult carried the variant.

Rule

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 case evidence reports absence from gnomAD v2.1, v4.1, gnomAD v2.1 non-cancer, and gnomAD v3.1 non-cancer, but does not identify any individual carrier or homozygote.
• No healthy-adult case, zygosity, inheritance model, penetrance estimate, or early-onset disease assessment was provided.

Still missing

• A documented healthy adult observation with genotype, zygosity, phenotype, age, inheritance model, and penetrance context is required to assess BS2.

Reasoning

No affected family members have been identified and tested in the available evidence, so there is no documented non-segregation result. Absence of family data cannot be interpreted as lack of segregation.

Rule

Lack of segregation in affected members of a family.

Evidence considered

• No pedigree or affected-relative genotype/phenotype information is documented in the available case evidence.
• The absence of family data is insufficient to demonstrate lack of segregation.

Still missing

• Identification of affected family members
• Variant testing results for affected relatives
• Phenotype assessment and evaluation for phenocopies or multiple pathogenic variants

Reasoning

BP2 cannot be assessed from the available evidence. No affected-proband or inherited-family observation documents this variant in trans with a pathogenic variant in a fully penetrant dominant disorder, and no observation documents it in cis with a pathogenic variant. The available tumor literature establishes somatic FLT3 p.Asp835Tyr occurrence and functional activity, but does not provide parental testing, offspring testing, haplotyping, or phase-resolved allelic observations.

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

• No phase-resolved cis/trans observation, parental testing, offspring testing, or affected-proband inheritance record is present in the case evidence.
• The available exact-variant literature concerns somatic FLT3-mutant leukemia and does not establish the BP2 allelic configurations required by the rule.

Still missing

• Phase-resolved data are needed: parental or offspring testing, haplotyping, or direct cis/trans characterization.
• A qualifying fully penetrant dominant disorder or inherited affected-proband observation is not documented.

Reasoning

The available materials document FLT3 D835Y in AML and functional models but do not provide a sufficiently characterized individual case showing an alternate molecular basis for that patient's disease. The BP5 rule therefore cannot be assessed from the available case-level evidence.

Rule

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

Evidence considered

• The reviewed literature reports cohort observations and experimental models, not a documented alternate molecular cause in the evaluated patient.
• ClinVar submissions identify the variant and disease labels but do not provide the required case-level alternate molecular basis.

Still missing

• A case-level report identifying an alternate molecular basis for the disease in the evaluated patient is needed.