Is TP53 p.Ser96del (c.283TCT[1]) pathogenic?

TP53 p.Ser96del (c.283TCT[1]) is classified Uncertain significance in TP53 (ClinVar, Multiple submitters, 7 submitters; last evaluated 2025-12-30). Absent from gnomAD; Associated with hereditary neoplastic syndrome.

What condition is associated with TP53 p.Ser96del (c.283TCT[1])?

TP53 p.Ser96del (c.283TCT[1]) is associated with hereditary neoplastic syndrome, hereditary breast ovarian cancer syndrome, Li-Fraumeni syndrome (ClinVar).

How common is TP53 p.Ser96del (c.283TCT[1]) in the general population?

TP53 p.Ser96del (c.283TCT[1]) is absent from gnomAD (gnomAD).

TP53 p.Ser96del

c.283TCT[1] · rs878854068 · VCV237946

Uncertain significance Multiple submitters

Classification

Uncertain significance

ClinVar

Review

Multiple submitters ★★☆☆

ClinVar · 7 submitters

gnomAD v4.1

Not reported

no gnomAD frequency available for this variant

Conditions

hereditary neoplastic syndrome

Computational evidence

Protein change
Missense predictors do not apply to this variant type; conservation carries the signal.
Splicing
SpliceAI	—	not assessed · substitutions only
Constraint at this position
Conservation	phyloP 6	GERP 1.2, phastCons 1

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.Ser96del
Coding: c.283TCT[1]
MANE Select: NM_000546
dbSNP: rs878854068
Type: Microsatellite
Location: chr17:7676081 (GRCh38)
Gene constraint: LOEUF 0.449 · pLI 1.00 · ClinGen HI 3/3 (gnomAD)
Structure: AlphaFold pLDDT 75.83 · 321 PDB
Residue 96: a UniProt-annotated variant site (in a sporadic cancer; somatic mutation); a UniProt-annotated variant site (in sporadic cancers; somatic mutation); the 'interaction with ccar2' 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

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

Also linked: hereditary breast ovarian cancer syndrome Li-Fraumeni syndrome

Similar variants

TP53 p.Ser96fs Pathogenic ★★ same residue
TP53 p.Ser96= Likely benign ★★ same residue
TP53 p.Asn30del Likely benign ★★★ same condition
TP53 p.Gln317fs Pathogenic ★★ same condition
TP53 p.Ile255del Pathogenic/Likely pathogenic ★★ same condition
TP53 p.Leu257fs Pathogenic ★★ same condition
TP53 p.Pro191del Pathogenic/Likely pathogenic ★★ same condition
TP53 p.Thr211fs 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-ser96del (accessed [today's date]).

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