Is TP53 p.Arg282Pro (c.845G>C) pathogenic?

TP53 p.Arg282Pro (c.845G>C) is classified Pathogenic/Likely pathogenic in TP53 (ClinVar, Multiple submitters, 7 submitters; last evaluated 2025-09-15). AlphaMissense: likely pathogenic (0.9994); Absent from gnomAD v4.1; Associated with nasopharyngeal carcinoma.

What condition is associated with TP53 p.Arg282Pro (c.845G>C)?

TP53 p.Arg282Pro (c.845G>C) is associated with nasopharyngeal carcinoma, bone osteosarcoma, exocrine pancreatic carcinoma (ClinVar).

How common is TP53 p.Arg282Pro (c.845G>C) in the general population?

TP53 p.Arg282Pro (c.845G>C) is absent from gnomAD v4.1 (gnomAD).

How is Nasopharyngeal carcinoma inherited?

Typically Multigenic/multifactorial, Not applicable (Orphanet). A genetic counselor can assess individual risk for a family.

What do computational predictors say about TP53 p.Arg282Pro (c.845G>C)?

AlphaMissense predicts likely pathogenic (score 0.9994) — an in-silico prediction, not a clinical call.

TP53 p.Arg282Pro

c.845G>C · rs730882008 · VCV376659

Pathogenic/Likely pathogenic Multiple submitters

Classification

Pathogenic/Likely pathogenic

ClinVar

Review

Multiple submitters ★★☆☆

ClinVar · 7 submitters

AlphaMissense

likely pathogenic

0.9994 · ACMG-weighted

gnomAD v4.1

Absent

absent from gnomAD v4.1

Missense predictors

3/3 damaging

AlphaMissense, REVEL, SaProt

Conditions

nasopharyngeal carcinoma

Computational evidence

Protein change
AlphaMissense	0.9994	likely pathogenic ✓ concordant with ClinVar · top 1% in TP53
REVEL	0.911	moderately pathogenic-leaning
SaProt	LLR -16.62	damaging
⇒ AlphaMissense, REVEL and SaProt all call this damaging.
Splicing
SpliceAI	—	not assessed · no allele here is in the release
Constraint at this position
Conservation	phyloP 6	GERP 2.5, phastCons 1
Regional constraint	o/e 0.89	unconstrained · MANE · 6,982 bp · p 0.0085 · regional, not allelic
Overall
CADD	27.6	PHRED · no single calibrated threshold — expert panels disagree

AlphaMissense carries the ACMG weight for missense; REVEL and SaProt are independent agreement signals.

Population frequency

gnomAD v4.1 · exomes + genomes

Absent from gnomAD v4.1. Not observed in any sequenced alleles — a rarity signal (ACMG PM2-supporting), not evidence of pathogenicity on its own.

Variant & gene context

Gene: TP53
Protein: p.Arg282Pro
Coding: c.845G>C
MANE Select: NM_000546
dbSNP: rs730882008
Type: single nucleotide variant
Location: chr17:7673775 (GRCh38)
Gene constraint: LOEUF 0.449 · pLI 1.00 · ClinGen HI 3/3 (gnomAD)
Structure: AlphaFold pLDDT 75.83 · 321 PDB
Residue 282: a DNA-binding region; the 'interaction with axin1' region; a UniProt-annotated variant site (in sporadic cancers; somatic mutation); the 'interaction with e4f1' region; a UniProt-annotated variant site (in lfs; germline mutation and in sporadic cancers; somatic mutation); a UniProt-annotated variant site (in a sporadic cancer; somatic mutation); a UniProt-annotated variant site (in a familial cancer not matching lfs; germline mutation and in sporadic cancers; somatic mutation); a UniProt-annotated variant site (in lfs; germline mutation and in sporadic cancers; somatic mutation; does not induce snai1 degradation); the 'disordered' region; an α-helix; the 'interaction with ccar2' region; the 'interaction with hipk1' region; the 'required for interaction with znf385a' region

Full TP53 gene report on Sugi Atlas → Gene function, pathways, protein structure, interactions & more

Disease context

nasopharyngeal carcinoma — disease report on Sugi Atlas → Associated genes, phenotypes, clinical trials & treatments

Also linked: bone osteosarcoma exocrine pancreatic carcinoma colorectal cancer hepatocellular carcinoma adrenocortical carcinoma, hereditary choroid plexus papilloma head and neck squamous cell carcinoma basal cell carcinoma, susceptibility to, 7 hereditary neoplastic syndrome hereditary breast carcinoma Li-Fraumeni syndrome glioma susceptibility 1 bone marrow failure syndrome 5

For Nasopharyngeal carcinoma (Orphanet):

Inheritance: Multigenic/multifactorial, Not applicable
Onset: All ages
Prevalence: 1-9 / 1 000 000 (China)

Similar variants

TP53 p.Arg282Leu Uncertain significance ★★★ ⚠ same residue
TP53 p.Arg282Gly Pathogenic ★★ same residue
TP53 p.Arg282Trp Pathogenic/Likely pathogenic ★★ same residue
TP53 p.Arg282= Likely benign ★★ same residue
TP53 p.Arg282Gln Conflicting classifications of pathogenicity ★ ⚠ same residue
TP53 p.Arg282fs Pathogenic ★★ same residue
TP53 p.Arg282_Arg283insThr Uncertain significance ★ same residue
TP53 c.375+5G>A Likely pathogenic ★★★ 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/tp53-p-arg282pro (accessed [today's date]).

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