Is AIP p.Lys273fs (c.816del) pathogenic?

AIP p.Lys273fs (c.816del) is classified Pathogenic in AIP (ClinVar, Multiple submitters, 2 submitters; last evaluated 2026-03-27). Absent from gnomAD; Associated with hereditary neoplastic syndrome.

What condition is associated with AIP p.Lys273fs (c.816del)?

AIP p.Lys273fs (c.816del) is associated with hereditary neoplastic syndrome (ClinVar).

How common is AIP p.Lys273fs (c.816del) in the general population?

AIP p.Lys273fs (c.816del) is absent from gnomAD (gnomAD).

AIP p.Lys273fs

c.816del · rs2495409667 · VCV2735676

Pathogenic Multiple submitters

Classification

Pathogenic

ClinVar

Review

Multiple submitters ★★☆☆

ClinVar · 2 submitters

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; NMD-escape possible for C-terminal truncations
Splicing
SpliceAI	—	not assessed · substitutions only
Constraint at this position
Conservation	phyloP 12	GERP 0.76, 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: AIP
Protein: p.Lys273fs
Coding: c.816del
MANE Select: NM_017900 · reported on NM_003977
dbSNP: rs2495409667
Type: Deletion
Location: chr11:67490816 (GRCh38)
Structure: AlphaFold pLDDT 70.14 · 81 PDB

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.Lys273Thr Uncertain significance ★ ⚠ same residue
AIP p.Lys273= Likely benign ★ same residue
AIP p.Gln239fs 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-lys273fs (accessed [today's date]).

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