Starting
Initialising…
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MDM4
Final classification
VUS
MDM4 c.1091G>T · p.Arg364Ile
MDM4

NM_002393.4:c.1091G>T (p.Arg364Ile) is a missense variant in exon 11 of MDM4 encoding the RING finger domain.

Gene
MDM4
Transcript
NM_002393.4
HGVS · transcript:coding
NM_002393.4:c.1091G>T
Consequence
N/A
GRCh38
chr1:204549300 G>T
GRCh37
chr1:204518428 G>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: PM2 supporting, PP3 supporting; combination = 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: PM2 supporting, PP3 supporting; combination = 2 supporting, which maps to VUS.
Classification rationale
PM2PP3 VUS
MDM4 c.1091G>T

NM_002393.4:c.1091G>T (p.Arg364Ile) is a missense variant in exon 11 of MDM4 encoding the RING finger domain. This variant is absent from large population cohorts including gnomAD v2.1, v4.1, and gnomAD-Canada, meeting PM2 at supporting strength.1 Multiple in silico tools predict a deleterious effect: REVEL score 0.502 and BayesDel score 0.217 both exceed damaging thresholds, meeting PP3 at supporting strength. SpliceAI predicts no splicing impact (max delta 0.07).2 No variant-specific functional studies, de novo observations, cosegregation data, case-control data, or ClinVar submissions were identified for this variant.3 The variant lies in the MDM4 RING finger domain (residues 290–490) which is critical for MDM2 heterodimerization and p53 regulation, but no formal mutational hotspot has been established for PM1. PVS1 is not applicable as this is a missense variant that does not fall into null variant categories under generic ClinGen SVI PVS1 framework.4 With PM2_Supporting and PP3_Supporting, the variant receives two supporting-level pathogenic criteria. No benign criteria are met. By generic ACMG/AMP 2015 combination rules (PMID:25741868), two supporting criteria are insufficient to reach Likely Pathogenic (which requires at least one strong criterion + two supporting, or two moderate). The variant is classified as a Variant of Uncertain Significance (VUS).5

PM2 + PP3 VUS
Gene diagram · NM_002393.4 · variants mapped to exon structure
MDM4 NM_002393.4
Fetching transcript structure from UCSC…
Applied criteria · 2 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). REVEL score = 0.502. BayesDel score = 0.216576.
      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. MDM4, a negative regulator of the p53 tumor suppressor, is altered by amplification and overexpression in various cancer types including breast cancer
      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