Is TP53 p.Asn239del (c.716_718del) pathogenic?

TP53 p.Asn239del (c.716718del) is classified Uncertain significance in TP53 (ClinVar, Single submitter, 1 submitter; last evaluated 2019-06-07). Absent from gnomAD; Associated with hereditary neoplastic syndrome.

What condition is associated with TP53 p.Asn239del (c.716_718del)?

TP53 p.Asn239del (c.716_718del) is associated with hereditary neoplastic syndrome (ClinVar).

How common is TP53 p.Asn239del (c.716_718del) in the general population?

TP53 p.Asn239del (c.716_718del) is absent from gnomAD (gnomAD).

TP53 p.Asn239del

c.716_718del · rs1597364916 · VCV826874

Uncertain significance Single submitter

Classification

Uncertain significance

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

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 4.9	GERP 2.4, 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.Asn239del
Coding: c.716_718del
MANE Select: NM_000546
dbSNP: rs1597364916
Type: Deletion
Location: chr17:7674245 (GRCh38)
Gene constraint: LOEUF 0.449 · pLI 1.00 · ClinGen HI 3/3 (gnomAD)
Structure: AlphaFold pLDDT 75.83 · 321 PDB
Residue 239: a DNA-binding region; the 'interaction with axin1' region; the 'interaction with ccar2' region; the 'interaction with hipk1' region; the 'required for interaction with znf385a' region; a UniProt-annotated variant site (in sporadic cancers; somatic mutation); a UniProt-annotated variant site (in a sporadic cancer; somatic mutation)

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.Asn239_Gly245del Likely pathogenic ★ same residue
TP53 p.Asn239Ser Pathogenic/Likely pathogenic ★★ same residue
TP53 p.Asn239dup Uncertain significance ★★ same residue
TP53 p.Asn239= Benign/Likely benign ★★ same residue
TP53 p.Asn239fs Pathogenic ★ same residue
TP53 p.Asn239Asp Conflicting classifications of pathogenicity ★ ⚠ same residue
TP53 p.Asn239Ile Conflicting classifications of pathogenicity ★ ⚠ same residue
TP53 p.Asn239Lys Conflicting classifications of pathogenicity ★ ⚠ same residue

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-asn239del (accessed [today's date]).

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