Is MDM2 p.Ser122= (c.366G>A) pathogenic?

MDM2 p.Ser122= (c.366G>A) is classified Likely benign in MDM2 (ClinVar, Single submitter, 2 submitters; last evaluated 2025-12-22). Ultra-rare (popmax 0.0146%, nfe); Associated with Accelerated tumor formation, susceptibility to.

What condition is associated with MDM2 p.Ser122= (c.366G>A)?

MDM2 p.Ser122= (c.366G>A) is associated with Accelerated tumor formation, susceptibility to (ClinVar).

How common is MDM2 p.Ser122= (c.366G>A) in the general population?

MDM2 p.Ser122= (c.366G>A) is ultra-rare (popmax 0.0146%, nfe) (gnomAD).

MDM2 p.Ser122=

c.366G>A · rs376611439 · VCV1139277

Likely benign Single submitter

Classification

Likely benign

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 2 submitters

gnomAD v4.1

Rare

ultra-rare (popmax 0.0146%, nfe)

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 2.8	GERP -3, phastCons 1
Overall
CADD	14.85	PHRED · no single calibrated threshold — expert panels disagree

Population frequency

gnomAD v4.1 · exomes + genomes

Grpmax group 0.0146% European (non-Finnish) · 172/1,179,256 alleles

Filtering AF 0.0128% ClinGen BA1/BS1 input FAF95, joint · FAF99 0.0121%

Overall 0.011% 178/1,612,070 alleles · ultra-rare

Ancestry group	Frequency	1 in
European (non-Finnish)grpmax	0.0146%	6,856
Remaining individualsnot grpmax-eligible	0.0032%	31,204
African / African-American	0.00268%	37,341
East Asian	0.00223%	44,832
Admixed American	0.00168%	59,682

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.Ser122=
Coding: c.366G>A
MANE Select: NM_002392
dbSNP: rs376611439
Type: single nucleotide variant
Location: chr12:68824370 (GRCh38)
Gene constraint: LOEUF 0.325 · pLI 1.00 (gnomAD)
Structure: AlphaFold pLDDT 63.24 · 148 PDB

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.Ser122Leu 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-ser122 (accessed [today's date]).

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