Is MDM2 p.Glu360= (c.1080A>G) pathogenic?

MDM2 p.Glu360= (c.1080A>G) is classified Benign in MDM2 (ClinVar, Multiple submitters, 2 submitters; last evaluated 2026-02-03). Common (popmax 12.7%, afr) — too common for a highly-penetrant pathogenic allele; Associated with Accelerated tumor formation, susceptibility to.

What condition is associated with MDM2 p.Glu360= (c.1080A>G)?

MDM2 p.Glu360= (c.1080A>G) is associated with Accelerated tumor formation, susceptibility to (ClinVar).

MDM2 p.Glu360=

Q: How common is MDM2 p.Glu360= (c.1080A>G) in the general population?

MDM2 p.Glu360= (c.1080A>G) is common (popmax 12.7%, afr) — too common for a highly-penetrant pathogenic allele (gnomAD).

c.1080A>G · rs769412 · VCV1167676

Benign Multiple submitters

Classification

Benign

ClinVar

Review

Multiple submitters ★★☆☆

ClinVar · 2 submitters

gnomAD v4.1

Common

common (popmax 12.7%, afr) — too common for a highly-penetrant pathogenic allele

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	—	not assessed · no allele here is in the release
Constraint at this position
Conservation	phyloP 0.64	GERP 0.7, phastCons 0.94
Overall
CADD	6.896	PHRED · no single calibrated threshold — expert panels disagree

Population frequency

gnomAD v4.1 · exomes + genomes

Grpmax group 12.7% African / African-American · 9,507/74,906 alleles

Filtering AF 12.5% ClinGen BA1/BS1 input FAF95, joint · FAF99 12.4%

Overall 6.22% 100,365/1,613,782 alleles · common exomes 89,135/1,461,854 · genomes 11,230/151,928 · joint denominator

Ancestry group	Frequency	1 in
African / African-Americangrpmax	12.7%	8
Middle Eastern	6.96%	14
Remaining individualsnot grpmax-eligible	6.32%	16
European (non-Finnish)	6.29%	16
South Asian	5.87%	17
Admixed American	4.94%	20
Ashkenazi Jewishnot grpmax-eligible	4.16%	24
Finnishnot grpmax-eligible	2.99%	33
Amishnot grpmax-eligible	1.75%	57
East Asian	1.67%	60

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.Glu360=
Coding: c.1080A>G
MANE Select: NM_002392
dbSNP: rs769412
Type: single nucleotide variant
Location: chr12:68839435 (GRCh38)
Gene constraint: LOEUF 0.325 · pLI 1.00 (gnomAD)
Structure: AlphaFold pLDDT 63.24 · 148 PDB
Residue 360: the 'necessary for interaction with usp2' 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 p.Glu360Gly Uncertain significance ★ ⚠ same residue
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

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-glu360 (accessed [today's date]).

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