Is AP3B2 p.Asp1094fs (c.3280del) pathogenic?

AP3B2 p.Asp1094fs (c.3280del) is classified Uncertain significance in AP3B2 (ClinVar, Single submitter, 1 submitter; last evaluated 2021-03-26). Absent from gnomAD.

How common is AP3B2 p.Asp1094fs (c.3280del) in the general population?

AP3B2 p.Asp1094fs (c.3280del) is absent from gnomAD (gnomAD).

AP3B2 p.Asp1094fs

c.3280del · rs2151425004 · VCV1411518

Uncertain significance Single submitter

Classification

Uncertain significance

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

Consequence

frameshift

predicted LoF

gnomAD v4.1

Not reported

no gnomAD frequency available for this variant

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 (27 of 27) — the truncated protein is likely expressed. PVS1 input, not an applied code
Splicing
SpliceAI	—	not assessed · substitutions only
Constraint at this position
Conservation	phyloP 6.1	GERP 1.6, 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: AP3B2
Protein: p.Asp1094fs
Coding: c.3280del
MANE Select: NM_001278512
dbSNP: rs2151425004
Type: Deletion
Location: chr15:82659586 (GRCh38)
Gene constraint: LOEUF 0.52 · pLI 0.22 (gnomAD)
Structure: AlphaFold pLDDT 75.73

Full AP3B2 gene report on Sugi Atlas → Gene function, pathways, protein structure, interactions & more

Similar variants

AP3B2 p.Pro993fs Pathogenic/Likely pathogenic ★★ same type
AP3B2 p.Tyr94fs Pathogenic/Likely pathogenic ★★ same type
AP3B2 c.1489-5_1489-3del Benign/Likely benign ★★ same type
AP3B2 c.2262-34_2268del Likely pathogenic ★ same type
AP3B2 p.Ala6fs Pathogenic ★ same type
AP3B2 p.Asn220fs Pathogenic ★ same type
AP3B2 p.Glu152fs Likely pathogenic ★ same type
AP3B2 p.Glu613fs Pathogenic ★ same type

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/ap3b2-p-asp1094fs (accessed [today's date]).

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