Is AIP p.Phe288fs (c.864del) pathogenic?

AIP p.Phe288fs (c.864del) is classified Likely pathogenic in AIP (ClinVar, Single submitter, 1 submitter; last evaluated 2025-05-21). Associated with hereditary neoplastic syndrome.

What condition is associated with AIP p.Phe288fs (c.864del)?

AIP p.Phe288fs (c.864del) is associated with hereditary neoplastic syndrome (ClinVar).

AIP p.Phe288fs

c.864del · VCV4029838

Likely pathogenic Single submitter

Classification

Likely pathogenic

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

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
NMD	escapes	premature termination codon in the last exon (6 of 6) — the truncated protein is likely expressed. PVS1 input, not an applied code
Splicing
SpliceAI	—	not assessed · substitutions only
Constraint at this position
Conservation	phyloP 3.3	GERP 0.9, phastCons 1

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

Variant & gene context

Gene: AIP
Protein: p.Phe288fs
Coding: c.864del
MANE Select: NM_003977
Type: Deletion
Location: chr11:67490862 (GRCh38)
Gene constraint: LOEUF 0.626 · pLI 0.28 (gnomAD)
Structure: AlphaFold pLDDT 91.09 · 5 PDB
Residue 288: an α-helix

Full AIP 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

AIP p.Phe288= Likely benign ★★ same residue
AIP p.Gln239fs Pathogenic ★★ same condition
AIP p.Lys273fs Pathogenic ★★ same condition
AIP p.Arg325fs Uncertain significance ★★ same condition
AIP p.Asn264del Uncertain significance ★★ same condition
AIP p.Gly47_Arg54del Uncertain significance ★★ same condition
AIP p.Lys316del Uncertain significance ★★ same condition
AIP c.100-4del Likely benign ★★ 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/aip-p-phe288fs (accessed [today's date]).

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