MPL c.1544G>T, p.Trp515Leu

Reasoning

The queried variant is NP_005364.1:p.(Trp515Leu) (MPLW515L), an established pathogenic activating variant previously reported at the same amino-acid change. PMID:16834459 explicitly identifies c.1544G>T as producing W515L and reports cytokine-independent growth, constitutive signaling, and a lethal myeloproliferative phenotype in mice; ClinVar records a Pathogenic submission for this exact variant.

Rule

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

Evidence considered

• PMID:16834459 reports that MPL c.1544G>T produces the p.Trp515Leu substitution and demonstrates cytokine-independent growth, constitutive signaling, and lethal myeloproliferative disease in a mouse model.
• ClinVar variation 14164 contains a Pathogenic submission for NM_005373.3(MPL):c.1544G>T (p.Trp515Leu), although the overall record has conflicting classifications.

Sources

Reasoning

PS3 is met at strong strength. The exact MPL c.1544G>T (p.W515L) variant was evaluated in a well-established, biologically relevant functional program: it produced cytokine-independent growth, constitutive JAK-STAT, RAS/MAPK, and PI3K/AKT signaling, and thrombopoietin hypersensitivity in cellular assays, and caused a rapidly lethal myeloproliferative phenotype with thrombocytosis, organomegaly, extramedullary hematopoiesis, and myelofibrosis in a mouse bone-marrow-transplant model. The study included clinically characterized cohorts, matched buccal-DNA testing, HapMap controls, cytokine-dependence and thrombopoietin-response assays, signaling immunoblots, inhibitor studies, colony formation, and an in vivo disease model. These concordant cellular and in vivo results directly demonstrate a damaging gain-of-function effect on MPL, although the evidence is research-based rather than a validated clinical diagnostic laboratory assay.

Rule

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

• Pikman et al. 2006 (PMID:16834459), Results, functional analyses in Figures 1-7: exact MPL c.1544G>T/p.W515L produced cytokine-independent growth, constitutive JAK-STAT, RAS/MAPK, and PI3K/AKT signaling, and thrombopoietin hypersensitivity in cellular assays.
• Pikman et al. 2006 (PMID:16834459), mouse bone-marrow-transplant assays: MPLW515L induced rapidly developing lethal myeloproliferative disease with leukocytosis, marked thrombocytosis, splenomegaly, hepatomegaly, extramedullary hematopoiesis, and myelofibrosis.
• Pikman et al. 2006 (PMID:16834459), cohort and controls: matched granulocyte/buccal DNA sequencing and genotyping of 270 HapMap samples supported somatic variant identification; the study also used cytokine-dependence, thrombopoietin-response, Western blot, inhibitor, colony-forming, and murine assays.

Still missing

• The functional evidence is from research assays rather than a reproducible clinical diagnostic laboratory validation study.

Sources

Reasoning

MPL codon 515 is a recurrent mutational hotspot. PMID:21326037 found W515L in 46 of 68 MPL-mutated patients, representing 67.7% of all MPL mutations, and PMID:16868251 identified W515L in 17 affected patients and W515K in 5; the latter study also screened 64 healthy controls without reporting MPL515 mutations. No benign codon-515 variant is documented in the reviewed evidence.

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

• MPL mutation profile study: W515L was the most common substitution, occurring in 46 of 68 MPL mutations (67.7%).
• MPL515 cohort study: W515L occurred in 17 affected patients and W515K in 5; 64 healthy controls were also screened and MPL515 mutations were not reported in controls.

Sources

Reasoning

PM2 is met at supporting strength under the supplied generic SVI threshold of <=0.0001. In default all-comers gnomAD v4.1, the variant has AF=1.2398e-05 (20/1,613,182 alleles), and the required FILTERING grpmax FAF is 1.772e-05, both below 0.0001; no homozygotes were observed. The non-cancer v3.1 genome subset independently shows 0/147,926 alleles and grpmax FAF=0, while the v2.1 non-cancer query failed and cannot be used. Because no VCEP specifies a non-cancer source, the all-comers result is the governing default, with the non-cancer result as concordant supplementary evidence.

Rule

Absent from controls (or at extremely low frequency if recessive) in Exome Sequencing Project, 1000 Genomes or Exome Aggregation Consortium.

Evidence considered

• gnomAD v4.1 all-comers: AF=20/1,613,182=1.2398e-05; FILTERING grpmax FAF=1.772e-05; homozygotes=0.
• gnomAD v2.1 all-comers: AF=2/250,508=7.9838e-06; homozygotes=0; grpmax FAF was not reported.
• gnomAD v3.1 non-cancer genomes: AF=0/147,926=0; FILTERING grpmax FAF=0; homozygotes=0. The v2.1 non-cancer query failed, so it was not used as evidence of absence.
• No VCEP covers MPL in this case; therefore the supplied default is gnomAD v2.1/v4.1 all-comers, with non-cancer data used only as corroboration.
• Generic PM2 calibration supplied in the governing prompt: <=0.0001, described there as the ClinGen SVI recommendation to downgrade PM2 to Supporting.

Sources

Reasoning

A different missense substitution at the same residue, MPL p.Trp515Lys (W515K), was reported in five affected patients in PMID:16868251 alongside W515L. The study describes MPL515 changes as acquired gain-of-function mutations causing constitutive signaling, supporting pathogenicity of the alternate missense change, although the paper does not provide a W515K-specific functional assay.

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:16868251 reports MPL515 mutations consisting of W515L in 17 patients and a different missense change, W515K, in 5 patients, and describes MPL515 mutations as acquired gain-of-function mutations with constitutive JAK-STAT activation.
• The extracted paper evidence does not report a W515K-specific functional assay, so human confirmation is retained.

Still missing

• No W515K-specific functional assay was identified in the extracted evidence.

Sources

Reasoning

PS4 requires an affected-versus-control comparison with RR or OR >5.0 and a 95% confidence interval that does not include 1. PMID:16868251 reports MPLW515L in 17 of 1,182 affected patients and in 0 of 64 healthy controls, so this is a case-control comparison even though the paper does not print an odds ratio. The crude OR is infinite because the control cell is zero, and the substituted threshold comparison is 'infinite > 5.0? yes'; however, the available counts do not establish a 95% CI excluding 1 (the probability of observing zero carriers among 64 controls under the null, conditional on 17 total carriers among 1,246 subjects, is approximately 0.406). Because both PS4 conditions are required, the criterion 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

• Pardanani et al. 2006, PMID:16868251, reports MPLW515L in 17 of 1,182 patients with myeloproliferative or other myeloid disorders and in 0 of 64 healthy controls.
• The affected-versus-control counts were treated as a case-control comparison and the crude OR was computed from the 2x2 table; the zero control count produces an infinite point estimate, while the counts do not demonstrate a 95% CI excluding 1.
• Numeric threshold check from the governing rule: OR = infinite > 5.0? yes; the required confidence-interval condition is not established.

Sources

Reasoning

The variant is a missense substitution, NP_005364.1:p.(W515L), so PP3 must use the missense REVEL path only. REVEL is 0.328, below the generic ClinGen SVI supporting PP3 threshold of >= 0.644 (Pejaver et al. 2022, PMID:36413997); therefore PP3 is not met. The SpliceAI result and BayesDel score are not used for this missense PP3 assessment.

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 (supporting): >= 0.644 — ClinGen SVI REVEL calibration (Pejaver et al. 2022, Am J Hum Genet) (PMID:36413997)

Evidence considered

• NM_005373.3:c.1544G>T is a missense variant encoding NP_005364.1:p.(W515L).
• Local REVEL lookup reports score 0.328 for this variant.
• The supplied generic ClinGen SVI calibration sets supporting PP3 at REVEL >= 0.644; this value is attributed in the governing materials to Pejaver et al. 2022, Am J Hum Genet (PMID:36413997).
• Only the missense REVEL path was evaluated; SpliceAI and BayesDel were not counted for PP3.

Sources

Reasoning

PP5 applies only when a reputable source recently reports the exact variant as pathogenic and the evidence is unavailable for independent evaluation. The exact-variant ClinVar record has no expert-panel submission; it contains single-laboratory, OMIM/literature-only, and research submissions, none of which qualifies as an exact-variant ClinVar expert-panel classification. The literature and underlying evidence are available for independent evaluation, so PP5 is not met.

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 variation 14164 exact match for NM_005373.3:c.1544G>T reports zero expert-panel submissions; the listed submissions are single-laboratory, OMIM/literature-only, or research assertions.
• The relevant papers, including PMID:16868251, are available for independent evaluation rather than being unavailable evidence.

Sources

Reasoning

BA1 is not met. Under the generic default, BA1 requires an allele frequency of at least 0.05. The highest usable FILTERING frequency is the gnomAD v4.1 grpmax FAF of 1.772e-05 (0.001772%), far below 0.05; the corresponding East Asian point estimate of 6.683e-05 is not used because FAF is required, and its population has 44,890 observed alleles. The variant is also reported as MPL p.Trp515Leu, a known somatic activating mutation, and ClinVar contains conflicting pathogenic and uncertain-significance submissions; therefore no stand-alone benign conclusion is supported by population frequency.

Rule

Allele frequency is above 5% in Exome Sequencing Project, 1000 Genomes or Exome Aggregation Consortium.

Evidence considered

• gnomAD v4.1: total 20/1,613,182 alleles; FILTERING grpmax FAF=1.772e-05 (0.001772%).
• The highest observed East Asian point estimate was 3/44,890 alleles (6.683e-05), but point estimates are not used for BA1/BS1 under the supplied ClinGen SVI guidance; the population exceeds the 2,000-observed-allele minimum.
• Generic BA1 calibration supplied in the governing prompt: >=0.05, attributed there to ACMG/AMP 2015 (PMID:25741868).
• PMID:16834459 reports the exact MPL c.1544G>T/p.W515L variant as a somatic activating mutation; ClinVar (variation 14164) has conflicting pathogenic and uncertain-significance submissions.

Sources

Reasoning

BS1 is not met on population frequency. The governing generic default is >=0.01, but the required FILTERING allele frequency is gnomAD v4.1 grpmax FAF=1.772e-05 (0.001772%), well below 0.01. The highest point estimate, East Asian AF=6.683e-05 from 3/44,890 alleles, is not substituted for FAF. This is not an elevated ancestry-specific frequency requiring a maximum-credible-frequency exception; no BS1 evidence is present.

Rule

Allele frequency is greater than expected for the disorder.

Evidence considered

• gnomAD v4.1: FILTERING grpmax FAF=1.772e-05 (0.001772%); total AF=20/1,613,182=1.2398e-05.
• The highest observed East Asian point estimate was 6.683e-05 from 3/44,890 alleles, but the supplied ClinGen SVI instruction requires grpmax FAF rather than popmax point estimate and requires at least 2,000 observed alleles; both conditions are satisfied for use of the East Asian population, but the FAF remains far below 0.01.
• Generic BS1 default supplied in the governing prompt: >=0.01; Whiffin et al. 2017 (PMID:28518168) is the named source for maximum-credible-frequency assessment, and Ghosh et al. 2018 (PMID:30311383) is the named source for the FILTERING-frequency approach.

Sources

Reasoning

BS3 is not met. Glembotsky et al. reported normal MPL expression and no constitutive STAT3/STAT5 phosphorylation or enhanced thrombopoietin-induced phosphorylation in platelets from one MPLW515L-positive essential-thrombocythemia patient, but these observations do not establish that the variant has no damaging effect on MPL function or splicing. The platelet-context results are also outweighed and contradicted for the relevant biological effect by direct cellular and mouse studies showing MPLW515L gain of function, cytokine-independent growth, constitutive signaling, and myeloproliferative disease. Therefore this study cannot support a benign functional criterion.

Rule

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

Evidence considered

• Glembotsky et al. 2010 (PMID:20113333), Abstract and Results, genotyping and expression/phosphorylation studies: MPLW515L was detected in 1 of 100 essential-thrombocythemia patients and 1 of 11 primary-myelofibrosis patients; platelet MPL surface/total protein and transcript levels were normal, and constitutive STAT3/STAT5 phosphorylation and enhanced TPO-induced phosphorylation were not observed in the tested essential-thrombocythemia patient's platelets.
• The PMID:20113333 platelet assays tested expression and selected STAT/TPO responses in patient platelets, but did not establish absence of damaging MPL function or splicing and do not negate the variant's demonstrated gain-of-function phenotype in other biologically relevant systems.
• Pikman et al. 2006 (PMID:16834459), functional analyses in Figures 1-7 and mouse bone-marrow-transplant assays: the same exact variant caused cytokine-independent growth, constitutive signaling, thrombopoietin hypersensitivity, and lethal myeloproliferative disease.

Sources

Reasoning

The variant is a missense substitution, NP_005364.1:p.(W515L), so BP4 must use the missense REVEL path only. REVEL is 0.328, above the generic ClinGen SVI supporting BP4 threshold of <= 0.29 (Pejaver et al. 2022, PMID:36413997); it is therefore in the indeterminate range and BP4 is not met. The SpliceAI result cannot substitute for the applicable REVEL path, and BayesDel has no established generic calibration.

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

• NM_005373.3:c.1544G>T is a missense variant encoding NP_005364.1:p.(W515L).
• Local REVEL lookup reports score 0.328 for this variant.
• The supplied generic ClinGen SVI calibration sets supporting BP4 at REVEL <= 0.29; this value is attributed in the governing materials to Pejaver et al. 2022, Am J Hum Genet (PMID:36413997).
• The REVEL score is neither deleterious-supporting nor benign-supporting under the supplied cutoffs; the missense SpliceAI score and BayesDel score were not used for BP4.

Sources

Reasoning

BP6 applies only when a reputable source recently reports the exact variant as benign and the evidence is unavailable for independent evaluation. The exact-variant ClinVar record has zero expert-panel submissions and no exact-variant expert-panel benign or likely-benign classification. The available literature is independently reviewable and does not provide a qualifying reputable-source benign assertion. BP6 is not met.

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 variation 14164 exact match reports zero expert-panel submissions and no expert-panel benign or likely-benign classification.
• The available variant-specific literature is independently reviewable and does not supply a qualifying reputable-source benign assertion.

Sources

Reasoning

No evidence identifies a proband with a confirmed de novo NM_005373.3:c.1544G>T variant, confirms both maternity and paternity, establishes absence of a family history, or documents parental testing. The reviewed literature concerns somatic MPLW515L in myeloproliferative neoplasms; it does not provide the required germline trio evidence for this case. The report of absence from matched buccal DNA in somatic cases is not evidence about this proband's maternity or paternity.

Rule

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

Evidence considered

• Pikman et al. (PMID:16834459) reports MPLW515L as a somatic mutation and describes matched buccal-DNA testing in affected study subjects, but does not provide proband-specific maternity/paternity confirmation or a de novo trio assessment for this case.
• Pardanani et al. (PMID:16868251) reports MPLW515L in a myeloproliferative-neoplasm cohort as an acquired mutation, without proband-specific parental testing or a confirmed de novo germline event.
• Ma et al. (PMID:21326037) reports W515L in a patient cohort and provides no variant-specific segregation analysis.

Still missing

• Proband-specific parental genotypes for NM_005373.3:c.1544G>T are not available.
• Maternity and paternity have not both been confirmed.
• No proband-specific family-history documentation is available.

Sources

Reasoning

PM3 cannot be assessed because the available evidence does not document this variant in trans with a pathogenic variant in an affected proband, and no parental or offspring testing establishes phase. The main variant-specific reports describe MPL c.1544G>T (p.W515L) as a somatic activating mutation in myeloproliferative neoplasms; they do not establish a recessive inherited presentation or allelic phase. ClinVar lists both congenital amegakaryocytic thrombocytopenia and somatic myeloproliferative conditions for the record, but provides no phase-resolved affected-proband observation or pathogenic in-trans partner for this case.

Rule

For recessive disorders, detected in trans with a pathogenic variant

Evidence considered

• Pikman et al. 2006 (PMID:16834459): MPL c.1544G>T/p.W515L was reported as a somatic activating mutation in myelofibrosis; it was absent from matched buccal DNA, and the report supplies no pathogenic in-trans partner or parental phase.
• ClinVar variation 14164: the record includes congenital amegakaryocytic thrombocytopenia and somatic myeloproliferative conditions, but the case evidence provides no phase-resolved affected-proband observation or pathogenic opposite-allele result.

Still missing

• Documented affected-proband genotype and phenotype for a recessive MPL disorder.
• A confirmed pathogenic variant on the opposite allele.
• Parent or offspring testing establishing trans phase.

Sources

Reasoning

No evidence documents an assumed de novo occurrence of NM_005373.3:c.1544G>T in the proband. Neither parental testing, an unconfirmed de novo observation, nor a proband-specific family history is reported. The reviewed publications describe somatic MPLW515L observations rather than an assumed de novo germline event.

Rule

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

Evidence considered

• Pikman et al. (PMID:16834459) describes somatic MPLW515L in myelofibrosis and matched buccal-DNA findings, not an assumed de novo germline occurrence in a proband.
• Pardanani et al. (PMID:16868251) describes acquired MPLW515L in myeloid disorders without parental testing or assumed de novo germline interpretation.
• Ma et al. (PMID:21326037) explicitly provides no variant-specific segregation analysis.

Still missing

• No proband-specific report establishes the variant as de novo or assumed de novo.
• Parental testing results are unavailable.
• Family-history information is unavailable.

Sources

Reasoning

No affected family members, informative meioses, or cosegregation results for NM_005373.3:c.1544G>T are reported. The available publications are cohort studies of mostly somatic MPLW515L in myeloproliferative neoplasms and do not establish segregation of the variant with disease in a family. No strength upgrade can be assigned without segregation data.

Rule

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

Evidence considered

• Pikman et al. (PMID:16834459) reports affected patients and somatic functional studies but no familial cosegregation analysis.
• Pardanani et al. (PMID:16868251) reports a 1,182-patient cohort and MPLW515L observations, not affected-family segregation.
• Ma et al. (PMID:21326037) reports no variant-specific segregation analysis.

Still missing

• No pedigree or affected-relative genotypes are available.
• No informative meioses or cosegregation count is reported.
• The available cohort publications do not provide family segregation data.

Sources

Reasoning

The available evidence does not establish both requirements for PP2: a gene-wide low rate of benign missense variation and missense variants as a common disease mechanism. Variant-specific rarity and recurrent pathogenic MPL missense changes do not provide the required gene-wide metrics.

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

• Gene-wide benign missense variation rate for MPL.
• Gene-level evidence that missense variants are a common mechanism of disease for the relevant disorder.

Reasoning

The governing PP4 rule requires a patient phenotype or family history that is highly specific for a disease with a single genetic etiology. The available evidence identifies the variant mainly in somatic myeloproliferative neoplasms and does not provide the current patient's phenotype, family history, or a sufficiently specific phenotype-to-disease assessment for this germline interpretation. PP4 therefore cannot be assessed from the available case evidence.

Rule

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

Still missing

• Obtain the patient's clinical phenotype, diagnostic disease designation, and relevant family history, then assess phenotype specificity for a single genetic etiology.

Reasoning

BS2 is not assessed. gnomAD shows no homozygotes in v2.1 (0/250,508 alleles) or v4.1 (0/1,613,182 alleles), and the non-cancer v3.1 genome subset shows 0/147,926 alleles; these data do not establish the required healthy-adult observation for the applicable inheritance model. The exact variant is documented as a somatic activating MPL mutation, so a heterozygous population observation cannot be assumed to be a constitutional healthy adult carrier without genotype-origin and disease-model evidence. The gnomAD v2.1 non-cancer query failed and is not evidence of absence.

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

• gnomAD v2.1: 2/250,508 alleles, homozygotes=0; gnomAD v4.1: 20/1,613,182 alleles, homozygotes=0.
• gnomAD v3.1 non-cancer genomes: 0/147,926 alleles, homozygotes=0; the gnomAD v2.1 non-cancer query failed, so its frequency is unknown and was not treated as absence.
• PMID:16834459 explicitly reports MPL c.1544G>T/p.W515L as a somatic mutation, so population presence does not by itself prove a healthy constitutional carrier.
• No inheritance model, penetrance estimate, or verified constitutional healthy-adult carrier record was supplied for applying BS2.

Still missing

• A verified constitutional healthy-adult carrier observation and a defined inheritance/penetrance model for the condition being assessed are unavailable.

Sources

Reasoning

No affected family members carrying or lacking NM_005373.3:c.1544G>T are documented, so lack of segregation cannot be evaluated. The reviewed studies do not provide a family pedigree or non-segregation analysis, and their somatic case cohorts cannot establish BS4 for this proband or family.

Rule

Lack of segregation in affected members of a family.

Evidence considered

• Pikman et al. (PMID:16834459) reports somatic MPLW515L cases but no affected-family non-segregation data.
• Pardanani et al. (PMID:16868251) reports a disease cohort without a pedigree-based lack-of-segregation analysis.
• Ma et al. (PMID:21326037) provides no variant-specific segregation analysis.

Still missing

• No affected relatives with documented variant testing are available.
• No family pedigree or phenotype assessment is available.
• No non-segregation analysis distinguishing phenocopy or another pathogenic variant is available.

Sources

Reasoning

The available evidence does not establish that MPL disease is caused primarily by truncating variants. Evidence for MPL loss-of-function in inherited contexts and evidence for recurrent activating missense variants do not quantify the relative contribution of truncating versus missense variants required by BP1.

Rule

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

Still missing

• A gene-level disease-variant spectrum demonstrating that truncating variants are the primary known disease mechanism for MPL.

Reasoning

BP2 cannot be assessed because no source documents this variant in trans with a pathogenic variant in an affected proband with a fully penetrant dominant disorder, or in cis with a pathogenic variant in any inheritance pattern. The available reports describe MPL c.1544G>T (p.W515L) as a somatic activating mutation and do not provide parent/offspring testing, haplotype data, or a confirmed pathogenic cis/trans partner. Reports of co-occurring variants do not establish allelic phase.

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

• Pikman et al. 2006 (PMID:16834459): the exact MPL p.W515L variant was reported as a somatic activating mutation; the study does not establish cis/trans phase with a pathogenic variant.
• Pardanani et al. 2006 (PMID:16868251): six patients carried both MPLW515L and JAK2V617F, but the report does not establish whether the variants were in cis or trans and does not provide the required phase evidence for BP2.
• ClinVar variation 14164: the record contains germline and somatic condition labels but no phase-resolved pathogenic partner for this case.

Still missing

• A confirmed pathogenic partner variant in the same affected individual.
• Allelic phase showing cis or trans through parental, offspring, or haplotype testing.
• For the trans pathway, documentation of a fully penetrant dominant disorder.

Sources

Reasoning

BP5 requires that the variant be found in a case with an alternate molecular basis for disease. The available evidence does not document an alternate molecular diagnosis in the current case or a qualifying case report for this exact variant. Absence of such documentation is not evidence that an alternate molecular basis was excluded, so BP5 cannot be assessed.

Rule

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

Still missing

• Obtain the current case's complete molecular findings and disease diagnosis, including any confirmed alternate molecular basis.