Is TP53 p.Pro82fs (c.245del) pathogenic?

TP53 p.Pro82fs (c.245del) is classified Pathogenic in TP53 (ClinVar, Single submitter, 1 submitter; last evaluated 2020-04-03). Absent from gnomAD; Associated with Li-Fraumeni syndrome.

What condition is associated with TP53 p.Pro82fs (c.245del)?

TP53 p.Pro82fs (c.245del) is associated with Li-Fraumeni syndrome (ClinVar).

How common is TP53 p.Pro82fs (c.245del) in the general population?

TP53 p.Pro82fs (c.245del) is absent from gnomAD (gnomAD).

How is Li-Fraumeni syndrome inherited?

Typically Autosomal dominant (Orphanet). A genetic counselor can assess individual risk for a family.

TP53 p.Pro82fs

c.245del · rs2151041085 · VCV1071800

Pathogenic Single submitter

Classification

Pathogenic

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

Consequence

frameshift

predicted LoF

gnomAD v4.1

Not reported

no gnomAD frequency available for this variant

Conditions

Li-Fraumeni syndrome

Computational evidence

Protein change
Missense predictors do not apply to this variant type; conservation carries the signal.
Consequence	frameshift	predicted loss-of-function in a haploinsufficient gene (ClinGen)
NMD	predicted	premature termination codon in exon 4 of 11
Splicing
SpliceAI	—	not assessed · substitutions only
Constraint at this position
Conservation	phyloP -11	GERP -3.7

Predicted loss-of-function is descriptive, not an applied PVS1 code.

Population frequency

dbSNP / gnomAD

No gnomAD frequency available for this variant. This is missing data, not an absence: the variant may or may not be present in gnomAD. Rarity (ACMG PM2) and BA1/BS1 cannot be assessed for it.

Variant & gene context

Gene: TP53
Protein: p.Pro82fs
Coding: c.245del
MANE Select: NM_000546
dbSNP: rs2151041085
Type: Deletion
Location: chr17:7676124 (GRCh38)
Gene constraint: LOEUF 0.449 · pLI 1.00 · ClinGen HI 3/3 (gnomAD)
Structure: AlphaFold pLDDT 75.83 · 321 PDB
Residue 82: a UniProt-annotated variant site (in lfs; germline mutation and in sporadic cancers; somatic mutation); a UniProt-annotated variant site (in sporadic cancers; somatic mutation); the 'interaction with ccar2' region; the 'interaction with hrmt1l2' region; the 'disordered' region; the 'interaction with wwox' region

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

Disease context

Li-Fraumeni syndrome — disease report on Sugi Atlas → Associated genes, phenotypes, clinical trials & treatments

For Li-Fraumeni syndrome (Orphanet):

Inheritance: Autosomal dominant
Onset: All ages
Prevalence: 1-9 / 100 000 (United Kingdom)

Similar variants

TP53 p.Pro82Leu Likely benign ★★★ ⚠ same residue
TP53 p.Pro82_Ala83insThrPro Uncertain significance ★ same residue
TP53 p.Pro82Ala Conflicting classifications of pathogenicity ★ ⚠ same residue
TP53 p.Pro82Arg Uncertain significance ★ ⚠ same residue
TP53 p.Pro82Ser Conflicting classifications of pathogenicity ★ ⚠ same residue
TP53 c.993+1del Likely pathogenic ★★★ same condition
TP53 p.Ala161_Tyr163delinsAsp Likely pathogenic ★★★ same condition
TP53 p.Arg213fs 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-pro82fs (accessed [today's date]).

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