Starting
Initialising…
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PHF6
Final classification
VUS
PHF6 c.1003A>T · p.Arg335Ter
PHF6

NM_001015877.1:c.1003A>T (p.Arg335Ter) introduces a premature termination codon in PHF6, a gene in which loss of function causes Börjeson-Forssman-Lehmann syndrome (X-linked intellectual disability).

Gene
PHF6
Transcript
NM_001015877.1
HGVS · transcript:coding
NM_001015877.1:c.1003A>T
Consequence
N/A
GRCh38
chrX:134425235 A>T
GRCh37
chrX:133559265 A>T
Basis gene-specific framework lacked a usable explicit final combination framework, so generic ACMG/AMP 2015 final-combination rules were applied as fallback; applied criteria: PVS1 moderate, PM2 supporting, PP3 supporting; combination = 1 moderate + 2 supporting, which maps to VUS.
gene-specific framework lacked a usable explicit final combination framework, so generic ACMG/AMP 2015 final-combination rules were applied as fallback; applied criteria: PVS1 moderate, PM2 supporting, PP3 supporting; combination = 1 moderate + 2 supporting, which maps to VUS.
Classification rationale
PVS1PM2PP3 VUS
PHF6 c.1003A>T

NM_001015877.1:c.1003A>T (p.Arg335Ter) introduces a premature termination codon in PHF6, a gene in which loss of function causes Börjeson-Forssman-Lehmann syndrome (X-linked intellectual disability).1 The nonsense variant lies in the terminal exon (exon 11/11) and removes only 31 C-terminal amino acids, consistent with predicted NMD escape; under PMC6185798, this is assigned PVS1 at Moderate strength.2 The variant is absent from gnomAD v2.1, gnomAD v4.1, and gnomAD-Canada v1.0, meeting PM2 at Supporting strength.3 BayesDel in silico prediction score of 0.83 supports a deleterious effect, meeting PP3 at Supporting strength.4 The combination of PVS1_Moderate, PM2_Supporting, and PP3_Supporting yields 1 Moderate and 2 Supporting criteria. Under generic ACMG/AMP 2015 final combination rules (PMID:25741868), this does not meet the threshold for Likely Pathogenic (which requires ≥3 Moderate, or 1 Moderate + ≥4 Supporting, or a Strong criterion). The evidence is indeterminate and the variant is classified as a Variant of Uncertain Significance.5

PVS1 + PM2 + PP3 VUS
Gene diagram · NM_001015877.1 · variants mapped to exon structure
PHF6 NM_001015877.1
Fetching transcript structure from UCSC…
Applied criteria · 3 met · select any tile
Met
Not met
Not assessed
N/A
Strength very strong supporting
Pathogenic evidence
PVS
PS
PM
PP
Benign evidence
BA
BS
BP
Rationale
Select a criterion.
Sources
Evidence used
    Gaps remaining
      Rule
      Research & evidence
      Population frequency
      gnomAD v4.1 screenshot
      gnomAD v4.1
      gnomAD v2.1 screenshot
      gnomAD v2.1
      v4.1
      Absent from gnomAD v4.1.
      v2.1
      Absent from gnomAD v2.1.
      🇨🇦 CA
      Absent from gnomAD-Canada v1.0.
      Allele frequency by ancestry
      three datasets · side by side
      gnomAD v4.1
      Absent · 0 / ?
      0 hom
      Not observed in any ancestry group.
      gnomAD v2.1
      Absent · 0 / ?
      0 hom
      Not observed in any ancestry group.
      gnomAD Canada 🇨🇦
      Absent · 0 / ?
      0 hom
      Not observed in any ancestry group.
      ClinVar screenshot
      ClinVar
      This variant is absent from ClinVar.
      SpliceAI screenshot
      In silico
      SpliceAI predicts no significant splice impact for this variant (max delta score = 0.07). BayesDel score = 0.83.
      Functional / OncoKB screenshot
      Functional Likely Oncogenic
      OncoKB identified variant-specific curated literature and context relevant to functional review; biological-effect context: Likely Loss-of-function; curated oncogenicity label: Likely Oncogenic.
      OncoKB ↗
      COSMIC screenshot
      COSMIC
      Cancer hotspots screenshot
      Cancer hotspots
      Somatic evidence Not in COSMIC / hotspots
      COSMIC
      This variant does not lie in a statistically significant hotspot. This variant has not previously been reported in somatic cancers (COSMIC).
      Hotspots
      This variant does not lie in a statistically significant hotspot.
      Sources & reference links
      8Sources
      ClinVar
      gnomAD v2.1
      gnomAD v4.1
      gnomAD-Canada
      SpliceAI
      OncoKB
      COSMIC
      Cancer hotspots
      Triaged references · 3 PMIDs not cited in assessment
      12676923 ↗ Novel PHF6 mutation p.D333del causes Börjeson-Forssman-Lehmann syndrome. ONCOKB
      23791194 ↗ The X-linked intellectual disability protein PHF6 associates with the PAF1 complex and regulates neuronal migration in the mammalian brain. ONCOKB
      27479181 ↗ Somatic PHF6 mutations in 1760 cases with various myeloid neoplasms. ONCOKB