Is TP53 p.Ser20fs (c.58del) pathogenic?

TP53 p.Ser20fs (c.58del) is classified Pathogenic in TP53 (ClinVar, Single submitter, 1 submitter; last evaluated 2023-12-05). No gnomAD frequency available for this variant; Associated with hereditary neoplastic syndrome.

What condition is associated with TP53 p.Ser20fs (c.58del)?

TP53 p.Ser20fs (c.58del) is associated with hereditary neoplastic syndrome (ClinVar).

How common is TP53 p.Ser20fs (c.58del) in the general population?

TP53 p.Ser20fs (c.58del) is no gnomAD frequency available for this variant (gnomAD).

TP53 p.Ser20fs

c.58del · rs1131691018 · VCV428880

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

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 2 of 11
Splicing
SpliceAI	—	not assessed · substitutions only
Constraint at this position
Conservation	phyloP 4.5	GERP 2.3, 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.Ser20fs
Coding: c.58del
MANE Select: NM_000546
dbSNP: rs1131691018
Type: Deletion
Location: chr17:7676537 (GRCh38)
Gene constraint: LOEUF 0.449 · pLI 1.00 · ClinGen HI 3/3 (gnomAD)
Structure: AlphaFold pLDDT 75.83 · 321 PDB
Residue 20: an α-helix; the 'interaction with ccar2' region; the 'interaction with hrmt1l2' region; a modified residue (phosphoserine; by chek2, ck1 and plk3); the 'transcription activation (acidic)' 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

Similar variants

TP53 p.Ser20Leu Uncertain significance ★★ ⚠ same residue
TP53 p.Ser20Pro Uncertain significance ★★ ⚠ same residue
TP53 p.Ser20= Benign/Likely benign ★★ same residue
TP53 c.993+1del Likely pathogenic ★★★ same condition
TP53 p.Arg213fs Pathogenic ★★★ same condition
TP53 p.Leu252_Ile254del Pathogenic ★★★ same condition
TP53 p.Lys382fs Likely pathogenic ★★★ same condition
TP53 c.283_375+21del 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-ser20fs (accessed [today's date]).

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