Is MDM2 p.Gly93= (c.279C>T) pathogenic?

MDM2 p.Gly93= (c.279C>T) is classified Likely benign in MDM2 (ClinVar, Single submitter, 2 submitters; last evaluated 2023-08-27). Very rare (popmax 0.00223%, eas); Associated with Accelerated tumor formation, susceptibility to.

What condition is associated with MDM2 p.Gly93= (c.279C>T)?

MDM2 p.Gly93= (c.279C>T) is associated with Accelerated tumor formation, susceptibility to (ClinVar).

How common is MDM2 p.Gly93= (c.279C>T) in the general population?

MDM2 p.Gly93= (c.279C>T) is very rare (popmax 0.00223%, eas) (gnomAD).

MDM2 p.Gly93=

c.279C>T · rs764994410 · VCV2851580

Likely benign Single submitter

Classification

Likely benign

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 2 submitters

gnomAD v4.1

Rare

very rare (popmax 0.00223%, eas)

Conditions

Accelerated tumor formation, susceptibility to

Computational evidence

Protein change
Missense predictors do not apply to this variant type; conservation carries the signal.
Splicing
SpliceAI	<0.2	all four deltas below 0.2 · C>G here scores Δ0.29 · evaluated, not missing
Constraint at this position
Conservation	phyloP 0.81	GERP -3.7, phastCons 0.98
Overall
CADD	10.06	PHRED · no single calibrated threshold — expert panels disagree

Population frequency

gnomAD v4.1 · exomes + genomes

Grpmax group 0.00223% East Asian · 1/44,792 alleles

Filtering AF 0.000359% ClinGen BA1/BS1 input FAF95, joint · FAF99 0.00026%

Overall 0.000753% 11/1,460,274 alleles · very rare

Ancestry group	Frequency	1 in
East Asiangrpmax	0.00223%	44,792
African / African-American	0.00133%	74,946
European (non-Finnish)	0.000763%	131,065

Rarity supports pathogenicity (ACMG PM2); frequency above a disease-specific BA1/BS1 threshold argues against it. A variant frequent in one ancestry group can be near-absent in others, so a single global figure can mislead.

Variant & gene context

Gene: MDM2
Protein: p.Gly93=
Coding: c.279C>T
MANE Select: NM_002392
dbSNP: rs764994410
Type: single nucleotide variant
Location: chr12:68816916 (GRCh38)
Gene constraint: LOEUF 0.325 · pLI 1.00 (gnomAD)
Structure: AlphaFold pLDDT 63.24 · 148 PDB
Residue 93: the swib/mdm2 domain; the 'necessary for interaction with usp2' region; the 'sufficient to promote the mitochondrial pathway of apoptosis' region

Full MDM2 gene report on Sugi Atlas → Gene function, pathways, protein structure, interactions & more

Disease context

Accelerated tumor formation, susceptibility to — disease report on Sugi Atlas → Associated genes, phenotypes, clinical trials & treatments

Similar variants

MDM2 c.523+5A>G Uncertain significance ★★ same condition
MDM2 p.Arg332His Uncertain significance ★★ ⚠ same condition
MDM2 p.Asn117Ser Uncertain significance ★★ ⚠ same condition
MDM2 p.Asn374Ser Uncertain significance ★★ ⚠ same condition
MDM2 p.Gln414Leu Uncertain significance ★★ ⚠ same condition
MDM2 p.Glu273Ala Uncertain significance ★★ ⚠ same condition
MDM2 p.Gly341Glu Uncertain significance ★★ ⚠ same condition
MDM2 p.Ser122Leu Uncertain significance ★★ ⚠ same condition

Built on 18 open, versioned datasets — ClinVar, gnomAD, AlphaMissense, REVEL, ClinGen & more — plus Sugi Variant's own cross-source analysis. Source data 2026-01–2026-10, ClinVar 2026-10. Full sources & versions →

Cite Sugi Variant

Gür T. Sugi Variant: A Deterministic Per-Variant Germline Reference from a Knowledge Graph for Humans and AI Agents. 2026. doi:10.5281/zenodo.21509445. This variant: https://sugi.bio/variant/mdm2-p-gly93 (accessed [today's date]).

Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown