Is TP53 p.Pro58= (c.174A>T) pathogenic?

TP53 p.Pro58= (c.174A>T) is classified Likely benign in TP53 (ClinVar, Single submitter, 1 submitter; last evaluated 2024-10-12). Absent from gnomAD v4.1; Associated with hereditary neoplastic syndrome.

What condition is associated with TP53 p.Pro58= (c.174A>T)?

TP53 p.Pro58= (c.174A>T) is associated with hereditary neoplastic syndrome (ClinVar).

How common is TP53 p.Pro58= (c.174A>T) in the general population?

TP53 p.Pro58= (c.174A>T) is absent from gnomAD v4.1 (gnomAD).

TP53 p.Pro58=

c.174A>T · VCV3460326

Likely benign Single submitter

Classification

Likely benign

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

gnomAD v4.1

Absent

absent from gnomAD v4.1

Conditions

hereditary neoplastic syndrome

Computational evidence

Protein change
Missense predictors do not apply to this variant type; conservation/SpliceAI carries the signal.
Splicing
SpliceAI	Δ0.32	donor loss, 1 bp away · masked 0 · deltas
Constraint at this position
Conservation	phyloP -1.7	GERP -2.6
Overall
CADD	2.063	PHRED · no single calibrated threshold — expert panels disagree

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.Pro58=
Coding: c.174A>T
MANE Select: NM_000546
Type: single nucleotide variant
Location: chr17:7676195 (GRCh38)
Gene constraint: LOEUF 0.449 · pLI 1.00 · ClinGen HI 3/3 (gnomAD)
Structure: AlphaFold pLDDT 75.83 · 321 PDB
Residue 58: a UniProt-annotated variant site (in a sporadic cancer; somatic mutation); the 'interaction with ccar2' region; the 'interaction with hrmt1l2' region; the 'disordered' region

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

Disease context

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

Similar variants

TP53 p.Pro58Arg Conflicting classifications of pathogenicity ★ ⚠ same residue
TP53 p.Pro58Thr Conflicting classifications of pathogenicity ★ ⚠ same residue
TP53 p.Pro58Ala Likely benign ★ same residue
TP53 p.Pro58fs Pathogenic ★★ 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
TP53 p.Ala138Pro 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-pro58 (accessed [today's date]).

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