Is TP53 p.Arg379fs (c.1135del) pathogenic?

TP53 p.Arg379fs (c.1135del) is classified Uncertain significance in TP53 (ClinVar, Single submitter, 1 submitter; last evaluated 2020-03-24). No gnomAD frequency available for this variant; Associated with Li-Fraumeni syndrome.

What condition is associated with TP53 p.Arg379fs (c.1135del)?

TP53 p.Arg379fs (c.1135del) is associated with Li-Fraumeni syndrome (ClinVar).

How common is TP53 p.Arg379fs (c.1135del) in the general population?

TP53 p.Arg379fs (c.1135del) is no gnomAD frequency available for this variant (gnomAD).

How is Li-Fraumeni syndrome inherited?

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

TP53 p.Arg379fs

c.1135del · rs2072836882 · VCV1023676

Uncertain significance Single submitter

Classification

Uncertain significance

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	escapes	premature termination codon in the last exon (11 of 11) — the truncated protein is likely expressed. PVS1 input, not an applied code
Splicing
SpliceAI	—	not assessed · substitutions only
Constraint at this position
Conservation	phyloP 0.066	GERP 0.084, phastCons 0.068

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.Arg379fs
Coding: c.1135del
MANE Select: NM_000546
dbSNP: rs2072836882
Type: Deletion
Location: chr17:7669656 (GRCh38)
Gene constraint: LOEUF 0.449 · pLI 1.00 · ClinGen HI 3/3 (gnomAD)
Structure: AlphaFold pLDDT 75.83 · 321 PDB
Residue 379: a UniProt-annotated variant site (in sporadic cancers; somatic mutation); the 'interaction with carm1' region; an α-helix; the 'disordered' region; the 'basic (repression of dna-binding)' region; the 'interaction with morn3' 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.Arg379His Likely benign ★★★ same residue
TP53 p.Arg379Leu Likely benign ★★★ same residue
TP53 p.Arg379Ser Likely benign ★★★ same residue
TP53 p.Arg379= Benign/Likely benign ★★ same residue
TP53 p.Arg379Cys 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-arg379fs (accessed [today's date]).

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