PHF6 c.903delinsGTTTCCT, p.(Tyr301Ter)

Reasoning

No PHF6-specific ClinGen VCEP or CSPEC specification was available, so the generic ClinGen SVI PVS1 framework (PMC6185798) applies. NM_001015877.1:c.903delinsGTTTCCT is a validated nonsense variant in the clinically relevant RefSeq transcript, producing NP_001015877.1:p.(Tyr301Ter). The variant lies in exon 9 of 10, with the premature termination approximately 66 coding nucleotides upstream of the exon 9/exon 10 junction, supporting escape from the last-exon exception and expected nonsense-mediated decay under the generic framework. The predicted product would terminate at 301 amino acids rather than the 366-amino-acid reference protein, removing approximately 65 residues, and the truncation occurs within the structured coding region rather than a documented low-importance distal tail or repeat region. PHF6 loss of function is supported as the relevant germline disease mechanism in the supplied gene-level context. No named SVI or VCEP downgrade rule is triggered; therefore PVS1 remains at full strength.

Rule

ClinGen SVI generic PVS1 framework (PMC6185798): nonsense variant predicted to undergo NMD; no last-exon, non-critical-region, transcript-relevance, or repeat-region downgrade applies.

Evidence considered

• VariantValidator confirms NM_001015877.1:c.903delinsGTTTCCT as a nonsense variant producing NP_001015877.1:p.(Tyr301Ter) in PHF6 and places it in exon 9.
• The transcript structure in the case evidence places exon 9 at coding positions c.835-c.968 and exon 10 at c.969-c.1098; the premature termination at c.903 is therefore approximately 66 coding nucleotides upstream of the final exon junction, supporting NMD rather than the last-exon escape exception.
• The normalized protein consequence predicts a 301-amino-acid product versus the 366-amino-acid reference protein, a loss of approximately 65 C-terminal residues.
• The supplied gene-level context marks PHF6 loss of function as an eligible germline disease mechanism, allowing generic PVS1 assessment.
• No PHF6-specific VCEP/CSPEC specification or named downgrade rule was available; PMC6185798 therefore governs and supports full-strength PVS1 for this NMD-predicted nonsense variant.

Sources

Reasoning

No applicable PHF6-specific VCEP framework was available, so the supplied generic PM2 threshold of allele frequency <=0.0001 was used. The variant is absent from gnomAD v2.1 and gnomAD v4.1, corresponding to an observed allele frequency of 0 and meeting PM2 at supporting strength.

Rule

Generic ClinGen SVI PM2: supporting evidence when allele frequency is <=0.0001; governing PHF6-specific framework not available.

Evidence considered

• gnomAD v2.1 and gnomAD v4.1 both report the variant as absent, giving an observed allele frequency of 0 in each queried dataset.
• The supplied ClinGen SVI recommendation uses PM2 at supporting strength for allele frequency <=0.0001 (PMID:25741868); no PHF6-specific VCEP framework was available.

Sources

Reasoning

PP5 was restricted to an exact-variant ClinVar expert-panel classification of Pathogenic or Likely pathogenic. The exact variant has no ClinVar result, no ClinVar variation ID, and no expert-panel assertion in the available ClinVar evidence. OncoKB's variant-specific Likely Oncogenic label is not a ClinVar expert-panel classification and cannot trigger PP5. Therefore PP5 is not met.

Rule

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

Evidence considered

• ClinVar returned no exact match for NM_001015877.1:c.903delinsGTTTCCT, with no variation ID or expert-panel review status.
• OncoKB reported a variant-specific Likely Oncogenic label, but this is not a ClinVar expert-panel classification and was excluded from PP5 by rule.

Sources

Reasoning

No applicable PHF6-specific VCEP framework was available, so the generic ACMG/AMP BA1 threshold of allele frequency >=0.05 was used. The variant was absent from gnomAD v2.1 and gnomAD v4.1, with no observed allele frequency approaching 0.05; therefore BA1 is not met.

Rule

Generic ACMG/AMP BA1: stand-alone benign when allele frequency is >=0.05; governing PHF6-specific framework not available.

Evidence considered

• gnomAD v2.1 and gnomAD v4.1 both report the variant as absent, so no population allele frequency supports BA1.
• The supplied generic ACMG/AMP BA1 stand-alone threshold is allele frequency >=0.05 (ACMG/AMP 2015, PMID:25741868); no applicable PHF6-specific threshold was available.

Sources

Reasoning

No applicable PHF6-specific VCEP framework was available, so the supplied generic BS1 threshold of allele frequency >=0.01 was used. The variant was absent from gnomAD v2.1 and gnomAD v4.1, with no elevated population frequency; therefore BS1 is not met.

Rule

Generic SVI BS1: strong benign evidence when allele frequency is >=0.01; governing PHF6-specific framework not available.

Evidence considered

• gnomAD v2.1 and gnomAD v4.1 both report the variant as absent, providing no evidence of an allele frequency at or above 0.01.
• The supplied generic SVI BS1 threshold is allele frequency >=0.01; no PHF6-specific population-frequency derivation was available.

Sources

Reasoning

BS2 requires the variant to be observed in healthy adults, typically including appropriate homozygotes or hemizygotes for the disease mechanism. The variant is absent from gnomAD v2.1 and v4.1, and no unaffected carrier or hemizygote observation is documented; absence of such observations does not satisfy BS2.

Rule

Generic ACMG/AMP BS2: benign evidence requires observation of the variant in healthy adults in an appropriate zygosity or hemizygosity context; absence alone is insufficient.

Evidence considered

• gnomAD v2.1 and gnomAD v4.1 report the variant as absent, so they provide no observation of an unaffected adult carrying the variant.
• Generic ACMG/AMP BS2 requires observation in healthy adults in a manner relevant to the inheritance model; non-observation cannot be converted into BS2 evidence.

Sources

Reasoning

BP6 was restricted to an exact-variant ClinVar expert-panel classification of Benign or Likely benign. The exact variant has no ClinVar result, no ClinVar variation ID, and no expert-panel assertion in the available ClinVar evidence. No ordinary laboratory submission, aggregate ClinVar label, non-expert assertion, or external database label can trigger BP6. Therefore BP6 is not met.

Rule

BP6 is met only when an exact-variant ClinVar expert panel classifies the variant as Benign or Likely benign; ordinary submissions, aggregate labels, non-expert assertions, and external database labels do not qualify.

Evidence considered

• ClinVar returned no exact match for NM_001015877.1:c.903delinsGTTTCCT, with no variation ID or expert-panel review status.
• Because no exact-variant ClinVar expert-panel Benign or Likely benign classification exists in the available evidence, BP6 cannot be applied.

Sources

Reasoning

No proband-level parental testing, maternity/paternity confirmation, or de novo observation is documented for NM_001015877.1:c.903delinsGTTTCCT (PHF6 p.(Y301*)). The available literature does not report this variant. Therefore, the de novo criterion cannot be assessed.

Rule

Generic ACMG/AMP PS2: de novo occurrence in a patient with the disease and no family history, with confirmed maternity and paternity; strength depends on supporting clinical and family evidence.

Evidence considered

• The case records contain no documented parental testing, maternity or paternity confirmation, or de novo result for NM_001015877.1:c.903delinsGTTTCCT.
• The reviewed extracted publications do not mention the current PHF6 c.903delinsGTTTCCT or p.(Y301*) variant.

Still missing

• Documented parental genotypes and maternity/paternity confirmation are unavailable.
• A proband-level clinical report linking this exact variant to the phenotype is unavailable.

Reasoning

No validated functional assay directly evaluated NM_001015877.1:c.903delinsGTTTCCT or p.(Tyr301Ter). PMID:23791194 reports PHF6 knockdown and rescue experiments in neuronal models, but does not test this variant; PMID:27479181 reports a somatic PHF6 mutation cohort without a variant-specific functional assay; and PMID:12676923 reports segregation of a different p.D333del variant without functional testing. Gene-level loss-of-function observations and evidence from other PHF6 variants cannot establish PS3 for this variant, so no PS3 strength is assigned.

Evidence considered

• PMID:23791194 describes PHF6 knockdown and rescue experiments affecting neuronal migration, but the tested construct or perturbation was not NM_001015877.1:c.903delinsGTTTCCT and p.(Tyr301Ter) was not mentioned.
• PMID:27479181 describes 62 somatic PHF6 mutations in 1,760 myeloid-neoplasm cases, including truncating variants, but provides no validated functional assay for this variant.
• PMID:12676923 reports family segregation of the different PHF6 variant p.D333del and does not provide functional assay evidence for p.(Tyr301Ter).

Still missing

• A validated assay directly testing p.(Tyr301Ter) is needed, with appropriate wild-type and assay controls and biologically relevant readouts.

Sources

Reasoning

No applicable PHF6-specific VCEP framework was available, so the generic ACMG/AMP PS4 definition was used. PS4 requires a statistically significant increase of the variant in affected individuals compared with controls, typically supported by case-control enrichment or an adequately documented affected-case series. The available evidence contains no exact-variant affected-case count, control count, odds ratio, or other enrichment statistic for NM_001015877.1:c.903delinsGTTTCCT (p.(Y301*)). PMID:12676923 reports a different PHF6 variant, p.D333del; PMID:23791194 is a PHF6 functional study without this variant; and PMID:27479181 reports other somatic PHF6 mutations without this variant. Therefore PS4 cannot be assessed from the available evidence; no PS4 numeric threshold is applicable because no enrichment statistic is available.

Rule

PS4 requires a statistically significant increase of the variant in affected individuals compared with controls; no exact-variant enrichment statistic is available.

Evidence considered

• No PHF6-specific VCEP specification was available; the generic ACMG/AMP PS4 definition was therefore used.
• PMID:12676923 describes a three-generation BFLS family with a different PHF6 variant, p.D333del, and does not mention c.903delinsGTTTCCT or p.(Y301*).
• PMID:23791194 describes PHF6 functional studies and does not mention c.903delinsGTTTCCT or p.(Y301*).
• PMID:27479181 reports 62 somatic PHF6 mutations in 1,760 myeloid-neoplasm cases but does not report this exact variant or provide an exact-variant PS4 enrichment comparison.

Still missing

• Exact-variant affected-case count and phenotype ascertainment
• Appropriate control count and comparison dataset
• Case-control enrichment statistic and its significance

Sources

Reasoning

No affected-proband observation, second pathogenic allele, phase result, or compound-heterozygous/hemizygous segregation evidence is provided for NM_001015877.1:c.903delinsGTTTCCT (p.Tyr301Ter). PHF6 is associated with an X-linked disorder, and the available case materials do not establish a recessive allelic configuration to which generic PM3 could be applied. Therefore PM3 cannot be assessed from the available evidence.

Rule

Generic ACMG/AMP PM3 requires the variant to be observed in trans with a pathogenic variant in an affected individual with a recessive disease; no such allelic observation is documented.

Evidence considered

• The governing materials report no ClinGen/VCEP specification for PHF6, so generic ACMG/AMP guidance was used.
• The case evidence contains no affected-proband, compound-allele, phase, or segregation observation for this variant.
• The available gene context identifies PHF6-related Börjeson-Forssman-Lehmann syndrome as X-linked; no recessive configuration supporting PM3 is documented.

Still missing

• Affected-proband observations with a documented second pathogenic PHF6 allele are unavailable.
• Phase information and inheritance testing are unavailable.
• The applicable disease model does not establish a recessive PM3 configuration for this X-linked gene.

Sources

Reasoning

No unconfirmed de novo observation is documented for NM_001015877.1:c.903delinsGTTTCCT (PHF6 p.(Y301*)). There is no available proband report, parental testing result, or family-history documentation from which PM6 could be evaluated.

Rule

Generic ACMG/AMP PM6: assumed de novo occurrence in a patient with the disease, without confirmation of maternity and paternity; use only when the de novo observation itself is documented but parental confirmation is incomplete.

Evidence considered

• The case records provide no unconfirmed de novo finding, parental genotype data, or family-history information for the current variant.
• The reviewed extracted publications do not report the current PHF6 c.903delinsGTTTCCT or p.(Y301*) variant.

Still missing

• A clinical proband report with family history is unavailable.
• Parental genotype results and confirmation status are unavailable.

Reasoning

No relatives carrying or lacking NM_001015877.1:c.903delinsGTTTCCT (PHF6 p.(Y301*)) are documented, and no phenotype-segregation data or meioses are available. PMID:12676923 describes segregation of a different PHF6 p.D333del variant and cannot establish segregation for this variant.

Rule

Generic ACMG/AMP PP1: cosegregation with disease in multiple affected family members; strength increases with the number and informativeness of meioses and requires phenotype and genotype data for the evaluated variant.

Evidence considered

• No case-specific relatives, informative meioses, or phenotype-segregation observations are documented for NM_001015877.1:c.903delinsGTTTCCT.
• PMID:12676923 reports segregation of a different PHF6 p.D333del variant in a three-generation BFLS family; it does not provide segregation evidence for the current variant.

Still missing

• Variant genotypes and phenotypes of informative relatives are unavailable.
• The number of informative meioses and segregation phase are unavailable.

Sources

Reasoning

No applicable PHF6-specific VCEP framework was available, so the generic ACMG/AMP PP4 definition was used. PP4 requires a highly specific phenotype or family history consistent with a disease for which the gene is known to cause disease. The case evidence provides the variant and predicted p.(Y301*) consequence but no patient phenotype, clinical diagnosis, family history, or phenotype-to-disease match. The reviewed papers do not report this exact variant and cannot supply the missing case phenotype. PP4 is therefore not assessable rather than met or not met.

Rule

PP4 requires a highly specific phenotype or family history consistent with a disease for which the gene is known to cause disease; patient-specific phenotype evidence is absent.

Evidence considered

• No PHF6-specific VCEP specification was available; the generic ACMG/AMP PP4 definition was therefore used.
• The case evidence contains no patient phenotype, clinical diagnosis, or family history for this variant.
• The reviewed publications describe PHF6-related disease or somatic PHF6 mutation cohorts but do not report this exact variant and do not provide the missing patient-specific phenotype.

Still missing

• Patient clinical phenotype and formal diagnosis
• Family history or segregation-compatible phenotype
• Assessment of phenotype specificity for a PHF6-associated disorder

Sources

Reasoning

No validated functional assay demonstrated preserved function for NM_001015877.1:c.903delinsGTTTCCT or p.(Tyr301Ter). PMID:23791194 provides gene-level neuronal knockdown and rescue experiments rather than a benign assay result for this variant, while PMID:27479181 and PMID:12676923 concern variant sets or a different PHF6 variant and do not establish preserved function for p.(Tyr301Ter). Therefore BS3 cannot be assigned at any strength.

Evidence considered

• PMID:23791194 reports PHF6 knockdown and rescue effects in neuronal models but does not test p.(Tyr301Ter) or provide evidence that this variant preserves function.
• PMID:27479181 reports somatic PHF6 mutation patterns without a benign functional result for this variant.
• PMID:12676923 reports segregation of p.D333del, a different PHF6 variant, without a functional assay establishing preserved activity.

Still missing

• A validated assay directly testing p.(Tyr301Ter) is needed to demonstrate preserved function relative to wild type with suitable controls.

Sources

Reasoning

No tested unaffected relatives, non-segregating carriers, or informative family members are documented for NM_001015877.1:c.903delinsGTTTCCT (PHF6 p.(Y301*)). Consequently, non-segregation cannot be evaluated.

Rule

Generic ACMG/AMP BS4: lack of segregation in affected family members or presence in unaffected family members when the phenotype is expected to be highly penetrant, with adequate phenotype ascertainment and informative testing.

Evidence considered

• The case records contain no unaffected relatives tested for the current variant and no non-segregation observations.
• The reviewed extracted publications do not report the current PHF6 c.903delinsGTTTCCT or p.(Y301*) variant.

Still missing

• Genotypes and phenotypes of unaffected relatives are unavailable.
• Family structure, age-related penetrance information, and test methodology are unavailable.

Reasoning

No reliable observation places NM_001015877.1:c.903delinsGTTTCCT (p.Tyr301Ter) in trans or in cis with another pathogenic or likely pathogenic variant in an informative individual. The available materials provide no affected-proband genotyping, parental testing, phase result, or segregation data. Consequently, the allelic configuration required to evaluate generic BP2 is unavailable, and BP2 cannot be assessed.

Rule

Generic ACMG/AMP BP2 requires a documented cis/trans relationship with another pathogenic or likely pathogenic variant in the relevant disease-model context; no such relationship is documented.

Evidence considered

• The governing materials report no ClinGen/VCEP specification for PHF6, so generic ACMG/AMP guidance was used.
• The case evidence contains no documented cis/trans phase observation involving this variant and another pathogenic or likely pathogenic variant.
• The available literature extracts concern other PHF6 variants or gene-level function and do not provide an allelic observation for this variant.

Still missing

• No informative individual with a second pathogenic or likely pathogenic variant is documented.
• No parental testing, haplotyping, or other phase determination is available.
• No segregation data are available to establish the relevant allelic configuration.

Sources

Reasoning

No applicable PHF6-specific VCEP framework was available, so the generic ACMG/AMP BP5 concept was considered. BP5 requires a variant observed in an affected individual who has an alternative molecular explanation for the phenotype, or equivalent evidence that the variant is not responsible for the phenotype. The case evidence supplies no affected individual phenotype, no alternative pathogenic molecular diagnosis, and no exact-variant case report establishing such a relationship. The available literature either concerns a different PHF6 variant or does not mention this variant. BP5 therefore cannot be assessed.

Rule

BP5 requires an affected individual with an alternative molecular explanation for the phenotype; no such exact-variant evidence is available.

Evidence considered

• No PHF6-specific VCEP specification was available; the generic ACMG/AMP BP5 concept was considered.
• No exact-variant affected individual with an alternative molecular explanation is documented in the case evidence.
• PMID:12676923 reports a different PHF6 variant, while PMID:23791194 and PMID:27479181 do not report c.903delinsGTTTCCT or p.(Y301*) and do not establish BP5 evidence for it.

Still missing

• Affected individual and phenotype documentation
• Alternative molecular diagnosis in that individual
• Evidence linking both findings to the same clinical presentation

Sources