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PRKD1
Final classification
VUS
PRKD1 c.2130A>T · p.Glu710Asp
PRKD1

NM_002742.3:c.2130A>T (p.Glu710Asp) is a missense variant in exon 15 of PRKD1.

Gene
PRKD1
Transcript
NM_002742.3
HGVS · transcript:coding
NM_002742.3:c.2130A>T
Consequence
N/A
GRCh38
chr14:29599063 T>A
GRCh37
chr14:30068269 T>A
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: PM2 moderate; combination = 1 moderate, 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: PM2 moderate; combination = 1 moderate, which maps to VUS.
Classification rationale
PM2 VUS
PRKD1 c.2130A>T

NM_002742.3:c.2130A>T (p.Glu710Asp) is a missense variant in exon 15 of PRKD1. This variant is absent from gnomAD v2.1, gnomAD v4.1, and gnomAD-Canada v1.0, meeting PM2 at moderate strength.1 Missense variants in PRKD1 are an established germline disease mechanism (PMID:32817298 reports de novo p.Gly592Arg and p.Arg603His causing syndromic congenital heart disease with ectodermal dysplasia); BP1 does not apply. In silico predictors yield mixed results — REVEL 0.744 (damaging), BayesDel 0.117 (benign-leaning), SpliceAI 0.00 (neutral) — and do not meet the threshold for either PP3 or BP4.2 No variant-specific functional data, de novo reports, cosegregation data, ClinVar classification, or case-control evidence are available for this variant.3 With only one moderate criterion (PM2) met and no supporting or pathogenic moderate criteria, the variant is classified as a Variant of Uncertain Significance (VUS) under generic ACMG/AMP 2015 combination rules.4

PM2 VUS
2 revelbayesdelspliceai ↗
4 generic_acmg_combination_rules
Gene diagram · NM_002742.3 · variants mapped to exon structure
PRKD1 NM_002742.3
Fetching transcript structure from UCSC…
Applied criteria · 1 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 = 0.00). REVEL score = 0.744. BayesDel score = 0.117429.
      Functional / OncoKB screenshot
      Functional Unknown Oncogenic Effect
      OncoKB did not identify variant-specific reviewed functional evidence for this variant; gene-level curated context is available for reviewer follow-up. PRKD1, a serine/threonine kinase, is mutated in salivary gland carcinomas.
      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