Is TP53 p.Ala159fs (c.475_476del) pathogenic?

TP53 p.Ala159fs (c.475476del) is classified Pathogenic in TP53 (ClinVar, Single submitter, 2 submitters; last evaluated 2023-08-14). Absent from gnomAD; Associated with Li-Fraumeni syndrome.

What condition is associated with TP53 p.Ala159fs (c.475_476del)?

TP53 p.Ala159fs (c.475_476del) is associated with Li-Fraumeni syndrome (ClinVar).

How common is TP53 p.Ala159fs (c.475_476del) in the general population?

TP53 p.Ala159fs (c.475_476del) 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.Ala159fs

c.475_476del · rs1443098123 · VCV2752474

Pathogenic Single submitter

Classification

Pathogenic

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 2 submitters

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 5 of 11
Splicing
SpliceAI	—	not assessed · substitutions only
Constraint at this position
Conservation	phyloP 2.7	GERP 1.5, phastCons 1

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.Ala159fs
Coding: c.475_476del
MANE Select: NM_000546
dbSNP: rs1443098123
Type: Microsatellite
Location: chr17:7675136 (GRCh38)
Gene constraint: LOEUF 0.449 · pLI 1.00 · ClinGen HI 3/3 (gnomAD)
Structure: AlphaFold pLDDT 75.83 · 321 PDB
Residue 159: a DNA-binding region; the 'interaction with axin1' region; a β-strand; the 'interaction with ccar2' region; a UniProt-annotated variant site (in sporadic cancers; somatic mutation); a UniProt-annotated variant site (in a sporadic cancer; somatic mutation; requires 2 nucleotide substitutions); the 'interaction with hipk1' region; the 'required for interaction with znf385a' region; the 'required for interaction with fbxo42' 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.Ala159Asp Pathogenic/Likely pathogenic ★★ same residue
TP53 p.Ala159Val Pathogenic/Likely pathogenic ★★ same residue
TP53 p.Ala159_Met160insArgAla Uncertain significance ★★ same residue
TP53 p.Ala159Pro Conflicting classifications of pathogenicity ★ ⚠ same residue
TP53 p.Ala159Thr Conflicting classifications of pathogenicity ★ ⚠ same residue
TP53 p.Asn30del Likely benign ★★★ same condition
TP53 p.Gln317fs Pathogenic ★★ same condition
TP53 p.Ile255del Pathogenic/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-ala159fs (accessed [today's date]).

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