Is MDM2 p.Arg103= (c.309G>A) pathogenic?

MDM2 p.Arg103= (c.309G>A) is classified Uncertain significance in MDM2 (ClinVar, Single submitter, 1 submitter; last evaluated 2019-10-23). Very rare (popmax 0.00591%, nfe); Associated with Accelerated tumor formation, susceptibility to.

What condition is associated with MDM2 p.Arg103= (c.309G>A)?

MDM2 p.Arg103= (c.309G>A) is associated with Accelerated tumor formation, susceptibility to (ClinVar).

How common is MDM2 p.Arg103= (c.309G>A) in the general population?

MDM2 p.Arg103= (c.309G>A) is very rare (popmax 0.00591%, nfe) (gnomAD).

MDM2 p.Arg103=

c.309G>A · rs766553126 · VCV971609

Uncertain significance Single submitter

Classification

Uncertain significance

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

gnomAD v4.1

Rare

very rare (popmax 0.00591%, nfe)

Conditions

Accelerated tumor formation, susceptibility to

Computational evidence

Protein change
Missense predictors do not apply to this variant type; conservation/SpliceAI carries the signal.
REVEL	0.095	moderately benign-leaning
Splicing
SpliceAI	Δ0.26	donor loss, 49 bp away · masked 0 · deltas
Constraint at this position
Conservation	phyloP 7.4	GERP 0.76, phastCons 1
Overall
CADD	21.1	PHRED · no single calibrated threshold — expert panels disagree

Population frequency

gnomAD v4.1 · exomes + genomes

Grpmax group 0.00591% European (non-Finnish) · 69/1,168,338 alleles

Filtering AF 0.00475% ClinGen BA1/BS1 input FAF95, joint · FAF99 0.00435%

Overall 0.00453% 72/1,587,952 alleles · very rare

Ancestry group	Frequency	1 in
European (non-Finnish)grpmax	0.00591%	16,932
Remaining individualsnot grpmax-eligible	0.00489%	20,471

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.Arg103=
Coding: c.309G>A
MANE Select: NM_002392
dbSNP: rs766553126
Type: single nucleotide variant
Location: chr12:68820325 (GRCh38)
Gene constraint: LOEUF 0.325 · pLI 1.00 (gnomAD)
Structure: AlphaFold pLDDT 63.24 · 148 PDB
Residue 103: the swib/mdm2 domain; the 'necessary for interaction with usp2' region; an α-helix

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-arg103 (accessed [today's date]).

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