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DICER1
Final classification
VUS
DICER1 c.5437G>C · p.Glu1813Gln
DICER1

PM1_Moderate is met: p.Glu1813Gln affects codon p.E1813, a metal ion-binding residue in the RNase IIIb domain explicitly listed in the DICER1 VCEP PM1 moderate rule. Crystal structure data confirm E1813 coordinates the catalytic Mg-1 ion.

Gene
DICER1
Transcript
NM_177438.3
HGVS · transcript:coding
NM_177438.3:c.5437G>C
Consequence
N/A
GRCh38
chr14:95091293 C>G
GRCh37
chr14:95557630 C>G
Basis ClinGen DICER1 and miRNA-Processing Gene Expert Panel Specifications to the ACMG/AMP Variant Interpretation Guidelines for DICER1 Version 1.4.0 v1.4.0 point-based framework: PM1 moderate (+2) + PM2 supporting (+1) + PP3 supporting (+1) = 4 points, which maps to VUS.
ClinGen DICER1 and miRNA-Processing Gene Expert Panel Specifications to the ACMG/AMP Variant Interpretation Guidelines for DICER1 Version 1.4.0 v1.4.0 point-based framework: PM1 moderate (+2) + PM2 supporting (+1) + PP3 supporting (+1) = 4 points, which maps to VUS.
Classification rationale
PM1PM2PP3 VUS
DICER1 c.5437G>C

PM1_Moderate is met: p.Glu1813Gln affects codon p.E1813, a metal ion-binding residue in the RNase IIIb domain explicitly listed in the DICER1 VCEP PM1 moderate rule. Crystal structure data confirm E1813 coordinates the catalytic Mg-1 ion.1 PM2_Supporting is met: NM_177438.3:c.5437G>C is absent from gnomAD v2.1, v4.1, and gnomAD-Canada (0 alleles across all populations), satisfying the VCEP threshold of AF < 0.000005.2 PP3_Supporting is met: REVEL score is 0.859, meeting the DICER1 VCEP threshold of ≥ 0.750 for missense variants.3 PVS1 is not applicable: this is a missense variant and does not fall into the VCEP-defined null-variant buckets (nonsense, frameshift, canonical splice).4 PS1 is not met: no comparator variant encoding p.Glu1813Gln has been classified as Pathogenic by the DICER1 VCEP.5 PS3 is not met: no variant-specific functional assay has been performed for p.Glu1813Gln. The cleavage assay in PMID:22187960 tested D1709N, D1709E, and E1705K but not E1813Q.6 PM5 is not applicable per VCEP rule: PM5 cannot be applied in combination with PM1, and PM1_Moderate is met.7 PP4 is not applicable per VCEP rule: the germline variant itself is a missense in one of the seven RNase IIIb hotspot codons (p.E1813).8 With PM1_Moderate (+2), PM2_Supporting (+1), and PP3_Supporting (+1), the total Tavtigian point score is +4, which falls in the DICER1 VCEP Uncertain Significance range (-1 to +5).9

PM1 + PM2 + PP3 VUS
Gene diagram · NM_177438.3 · variants mapped to exon structure
DICER1 NM_177438.3
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 has been reported in ClinVar as Uncertain significance (1 clinical laboratory). (ClinVarID = 933089)
      SpliceAI screenshot
      In silico
      SpliceAI predicts no significant splice impact for this variant (max delta score = 0.00). REVEL score = 0.859. BayesDel score = 0.370717.
      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 Hotspot
      COSMIC
      This variant lies in a statistically significant hotspot. This variant has previously been reported in somatic cancers (COSMIC; COSV58617855, n = 21 times).
      Hotspots
      This variant lies in a statistically significant hotspot.
      Literature · how each cited paper was used
      1papers cited
      Each card is an audit: what was searched, what was found, whether it names the variant, which criteria it fed, and why. 7 further PMIDs triaged but not cited — see Sources & References.
      Homodimeric structure and double-stranded RNA cleavage activity of the C-terminal RNase III domain of human dicer.
      Searched
      c.5437G>Cp.Glu1813GlnE1813QE1813
      Found
      Reports the crystal structure of the human DICER1 RNase IIIb domain at 2.0 Å resolution. Demonstrates that E1813 directly coordinates the Mg-1 ion at the catalytic active site, along with E1705 and D1810. Provides structural evidence for the functional importance of the metal ion-binding residues.
      Variant
      ◇ Residue / gene-level — variant not named
      Applied to
      PM1 supports · met
      Why
      Establishes E1813 as a metal ion-binding residue critical to RNase IIIb catalytic function; supports PM1_Moderate applicability.
      Mg-1 is coordinated directly by the carboxylate oxygen atoms of E1705, D1810, and E1813 and by three water molecules
      Location Results, Active site section; Figure 5b  ·  Context X-ray crystallography of purified recombinant Hs-Dicer RNase IIIb domain  ·  full text
      Sources & reference links
      9Sources
      CSpec VCEP
      ClinVar
      gnomAD v2.1
      gnomAD v4.1
      gnomAD-Canada
      SpliceAI
      OncoKB
      COSMIC
      Cancer hotspots
      Triaged references · 7 PMIDs not cited in assessment
      21205968 ↗ DICER1 mutations in familial multinodular goiter with and without ovarian Sertoli-Leydig cell tumors. CLINVAR
      22187960 ↗ Recurrent somatic DICER1 mutations in nonepithelial ovarian cancers. CLINVAR
      24136150 ↗ DICER1 hotspot mutations in non-epithelial gonadal tumours. CLINVAR
      25741868 ↗ Standards and guidelines for the interpretation of sequence variants: a joint consensus recommendation of the American College of Medical Genetics and Genomics and the Association for Molecular Pathology. CLINVAR
      26475046 ↗ High-sensitivity sequencing reveals multi-organ somatic mosaicism causing DICER1 syndrome. CLINVAR
      27459524 ↗ Deep Sequencing Reveals Spatially Distributed Distinct Hot Spot Mutations in DICER1-Related Multinodular Goiter. CLINVAR
      29037807 ↗ DICER1-related Sertoli-Leydig cell tumor and gynandroblastoma: Clinical and genetic findings from the International Ovarian and Testicular Stromal Tumor Registry. CLINVAR