Is TP53 p.Ser106fs (c.315del) pathogenic?

TP53 p.Ser106fs (c.315del) is classified Pathogenic in TP53 (ClinVar, Multiple submitters, 2 submitters; last evaluated 2025-05-29). Associated with hereditary neoplastic syndrome.

What condition is associated with TP53 p.Ser106fs (c.315del)?

TP53 p.Ser106fs (c.315del) is associated with hereditary neoplastic syndrome, Li-Fraumeni syndrome (ClinVar).

TP53 p.Ser106fs

c.315del · VCV3972454

Pathogenic Multiple submitters

Classification

Pathogenic

ClinVar

Review

Multiple submitters ★★☆☆

ClinVar · 2 submitters

Consequence

frameshift

predicted LoF

gnomAD v4.1

Rare

Conditions

hereditary neoplastic 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 -0.35	GERP -4.4

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

Variant & gene context

Gene: TP53
Protein: p.Ser106fs
Coding: c.315del
MANE Select: NM_000546
Type: Deletion
Location: chr17:7676054 (GRCh38)
Gene constraint: LOEUF 0.449 · pLI 1.00 · ClinGen HI 3/3 (gnomAD)
Structure: AlphaFold pLDDT 75.83 · 321 PDB
Residue 106: a DNA-binding region; a turn; the 'interaction with ccar2' region; a UniProt-annotated variant site (in a sporadic cancer; somatic mutation); a UniProt-annotated variant site (in a familial cancer not matching lfs; germline mutation and in sporadic cancers; somatic mutation); the 'interaction with wwox' region; the 'interaction with hipk1' region; the 'required for interaction with znf385a' 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

Also linked: Li-Fraumeni syndrome

Similar variants

TP53 p.Ser106Arg Pathogenic ★★★ ⚠ same residue
TP53 p.Ser106Cys Uncertain significance ★ ⚠ same residue
TP53 p.Ser106Ile Conflicting classifications of pathogenicity ★ ⚠ same residue
TP53 p.Ser106_Gly112del Likely pathogenic ★ same residue
TP53 c.993+1del Likely pathogenic ★★★ same condition
TP53 p.Ala161_Tyr163delinsAsp Likely pathogenic ★★★ same condition
TP53 p.Arg213fs Pathogenic ★★★ same condition
TP53 p.Leu252_Ile254del 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-ser106fs (accessed [today's date]).

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