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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 applied · 18 assessed
Applied · 2
Strength Supporting Moderate Strong Very strong
PM2 supporting Pathogenic
Variant is absent from gnomAD v2.1, v4.1, and gnomAD-Canada v1.0, representing large population cohorts (combined >250,000 alleles). Allele frequency is 0.0, meeting the generic ACMG PM2 threshold (<0.1%).
Absent from gnomAD v2.1 (0 alleles). Absent from gnomAD v4.1 (0 alleles). Absent from gnomAD-Canada v1.0 (0 alleles).
PP3 supporting Pathogenic
Multiple in silico tools predict a deleterious effect: REVEL score 0.502 (threshold ≥0.5 for damaging) and BayesDel score 0.217 (threshold >0.07 for damaging, noAF model). SpliceAI predicts no significant splicing impact (max delta 0.07). Two of three computational lines support pathogenicity.
REVEL: 0.502 (damaging). BayesDel (noAF): 0.217 (damaging). SpliceAI max delta: 0.07 (no splicing impact).
Assessed · not applied
Pathogenic
PS2 No de novo occurrence data identified for NM_002393.4:c.1091G>T.
PS3 No variant-specific functional assay data identified for p.Arg364Ile.
PS4 Variant is absent from ClinVar with no patient observations documented.
PM1 Variant lies in the MDM4 RING finger domain (residues 290–490) which is functionally important for MDM2 heterodimerization and E3 ubiquitin ligase activity.
PM6 No assumed de novo evidence (without confirmed parentage) available for NM_002393.4:c.1091G>T.
PP1 No family-based cosegregation data available.
PP2 MDM4 does not meet PP2 criteria: the gene does not have an established low rate of benign missense variation and a high proportion of pathogenic missense variants.
PP4 No patient phenotype or family history data available for the proband harboring this variant.
Benign
BA1 Variant is absent from all gnomAD population cohorts (allele frequency 0.0), far below the BA1 threshold of >1% allele frequency in any population.
BS1 Variant is absent from all gnomAD population cohorts (allele frequency 0.0), below the BS1 threshold of >0.3% allele frequency.
BS2 Variant has not been observed in any healthy adult individual in population databases.
BS3 No well-established in vitro or in vivo functional studies demonstrate a neutral or benign effect for p.Arg364Ile.
BS4 No family segregation data available.
BP1 While MDM4 loss of function is supported as a germline disease mechanism (PVS1 gene context eligible), there is insufficient evidence that only truncating variants cause MDM4-related disease to apply BP1 to this missense variant under generic ACMG/AMP.
BP2 No observation of NM_002393.4:c.1091G>T in trans with a known pathogenic MDM4 variant.
BP4 Computational evidence does not suggest a benign impact.
BP5 No alternate molecular basis for disease has been identified in any individual harboring this variant.
BP6 No reputable source (e.g., clinical diagnostic laboratory) has reported this variant as benign or likely benign.
N/A · 6 PVS1 · PS1 · PM5 · PP5 · BP3 · BP7
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