Is PEX12 p.Asp96fs (c.286del) pathogenic?

PEX12 p.Asp96fs (c.286del) is classified Pathogenic in PEX12 (ClinVar, Single submitter, 1 submitter; last evaluated 2022-02-03). No gnomAD frequency available for this variant; Associated with peroxisome biogenesis disorder 3A (Zellweger).

What condition is associated with PEX12 p.Asp96fs (c.286del)?

PEX12 p.Asp96fs (c.286del) is associated with peroxisome biogenesis disorder 3A (Zellweger) (ClinVar).

How common is PEX12 p.Asp96fs (c.286del) in the general population?

PEX12 p.Asp96fs (c.286del) is no gnomAD frequency available for this variant (gnomAD).

PEX12 p.Asp96fs

c.286del · rs2509170297 · VCV2092385

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

peroxisome biogenesis disorder 3A (Zellweger)

Computational evidence

Protein change
Missense predictors do not apply to this variant type; conservation carries the signal.
Consequence	frameshift	predicted loss-of-function
NMD	predicted	premature termination codon in exon 2 of 3
Splicing
SpliceAI	—	not assessed · substitutions only
Constraint at this position
Conservation	phyloP 4.1	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: PEX12
Protein: p.Asp96fs
Coding: c.286del
MANE Select: NM_000286
dbSNP: rs2509170297
Type: Deletion
Location: chr17:35577432 (GRCh38)
Gene constraint: LOEUF 1.218 · pLI <0.01 (gnomAD)
Structure: AlphaFold pLDDT 81.58

Full PEX12 gene report on Sugi Atlas → Gene function, pathways, protein structure, interactions & more

Disease context

peroxisome biogenesis disorder 3A (Zellweger) — disease report on Sugi Atlas → Associated genes, phenotypes, clinical trials & treatments

Similar variants

PEX12 p.Asp96= Likely benign ★ same residue
PEX12 p.Gln17fs Pathogenic/Likely pathogenic ★★ same condition
PEX12 p.Gln270fs Pathogenic/Likely pathogenic ★★ same condition
PEX12 p.Glu171fs Pathogenic/Likely pathogenic ★★ same condition
PEX12 p.Gly321fs Pathogenic/Likely pathogenic ★★ same condition
PEX12 p.Leu296fs Pathogenic ★★ same condition
PEX12 p.Lys299_Met300insTer Pathogenic/Likely pathogenic ★★ same condition
PEX12 p.Ser229fs Pathogenic/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/pex12-p-asp96fs (accessed [today's date]).

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