Is TP53 p.Pro250Ala (c.748C>G) pathogenic?

TP53 p.Pro250Ala (c.748C>G) is classified Uncertain significance in TP53 (ClinVar, Multiple submitters, 3 submitters; last evaluated 2026-05-18). AlphaMissense: ambiguous (0.4876); Absent from gnomAD v4.1; Associated with adrenocortical carcinoma, hereditary.

What condition is associated with TP53 p.Pro250Ala (c.748C>G)?

TP53 p.Pro250Ala (c.748C>G) is associated with adrenocortical carcinoma, hereditary, hereditary neoplastic syndrome, Li-Fraumeni syndrome (ClinVar).

How common is TP53 p.Pro250Ala (c.748C>G) in the general population?

TP53 p.Pro250Ala (c.748C>G) is absent from gnomAD v4.1 (gnomAD).

How is Adrenocortical carcinoma inherited?

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

What do computational predictors say about TP53 p.Pro250Ala (c.748C>G)?

AlphaMissense predicts ambiguous (score 0.4876) — an in-silico prediction, not a clinical call.

TP53 p.Pro250Ala

c.748C>G · rs2151020578 · VCV1759142

Uncertain significance Multiple submitters

Classification

Uncertain significance

ClinVar

Review

Multiple submitters ★★☆☆

ClinVar · 3 submitters

AlphaMissense

ambiguous

0.4876 · ACMG-weighted

gnomAD v4.1

Absent

absent from gnomAD v4.1

Missense predictors

1/2 damaging

REVEL, SaProt · AlphaMissense no call

Conditions

adrenocortical carcinoma, hereditary

Computational evidence

Protein change
AlphaMissense	0.4876	ambiguous
REVEL	0.892	moderately pathogenic-leaning
SaProt	LLR -8.38	tolerated
⇒ REVEL calls this damaging; SaProt does not; AlphaMissense makes no call.
Splicing
SpliceAI	—	not assessed · no allele here is in the release
Constraint at this position
Conservation	phyloP 12	GERP 2.5, phastCons 1
Regional constraint	o/e 0.89	unconstrained · MANE · 6,982 bp · p 0.0085 · regional, not allelic
Overall
CADD	23.5	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.Pro250Ala
Coding: c.748C>G
MANE Select: NM_000546
dbSNP: rs2151020578
Type: single nucleotide variant
Location: chr17:7674215 (GRCh38)
Gene constraint: LOEUF 0.449 · pLI 1.00 · ClinGen HI 3/3 (gnomAD)
Structure: AlphaFold pLDDT 75.83 · 321 PDB
Residue 250: a DNA-binding region; the 'interaction with axin1' region; a UniProt-annotated variant site (in sporadic cancers; somatic mutation); a UniProt-annotated variant site (in sporadic cancers; somatic mutation; requires 2 nucleotide substitutions); the 'interaction with ccar2' region; the 'interaction with hipk1' region; the 'required for interaction with znf385a' region; a UniProt-annotated variant site (in a sporadic cancer; somatic mutation)

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

Disease context

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

Also linked: hereditary neoplastic syndrome Li-Fraumeni syndrome

For Adrenocortical carcinoma (Orphanet):

Inheritance: Not applicable
Onset: Childhood
Prevalence: 1-9 / 1 000 000 (Europe)

Similar variants

TP53 p.Pro250Leu Pathogenic/Likely pathogenic ★★ ⚠ same residue
TP53 p.Pro250Ser Uncertain significance ★★ ⚠ same residue
TP53 p.Pro250Thr Uncertain significance ★★ ⚠ same residue
TP53 p.Pro250Arg Uncertain significance ★ ⚠ same residue
TP53 p.Pro250= Likely benign ★ same residue
TP53 c.375+5G>A Likely pathogenic ★★★ same condition
TP53 c.919+1G>A Pathogenic ★★★ same condition
TP53 c.97-1G>A 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-pro250ala (accessed [today's date]).

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