Is PEX16 p.Phe332del (c.995_997del) pathogenic?

PEX16 p.Phe332del (c.995997del) is classified Likely pathogenic in PEX16 (ClinVar, Single submitter, 1 submitter; last evaluated 2012-10-19). Absent from gnomAD; Associated with peroxisome biogenesis disorder 8B.

What condition is associated with PEX16 p.Phe332del (c.995_997del)?

PEX16 p.Phe332del (c.995_997del) is associated with peroxisome biogenesis disorder 8B (ClinVar).

How common is PEX16 p.Phe332del (c.995_997del) in the general population?

PEX16 p.Phe332del (c.995_997del) is absent from gnomAD (gnomAD).

PEX16 p.Phe332del

c.995_997del · rs797045062 · VCV209181

Likely pathogenic Single submitter

Classification

Likely pathogenic

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

gnomAD v4.1

Not reported

no gnomAD frequency available for this variant

Conditions

peroxisome biogenesis disorder 8B

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 7.8	GERP 2.2, 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: PEX16
Protein: p.Phe332del
Coding: c.995_997del
MANE Select: NM_004813
dbSNP: rs797045062
Type: Deletion
Location: chr11:45910268 (GRCh38)
Gene constraint: LOEUF 0.957 · pLI <0.01 · ClinGen HI gene assoc. with recessive phenotype (gnomAD)
Structure: AlphaFold pLDDT 83.07
Residue 332: the 'interaction with pex19' region

Full PEX16 gene report on Sugi Atlas → Gene function, pathways, protein structure, interactions & more

Disease context

peroxisome biogenesis disorder 8B — disease report on Sugi Atlas → Associated genes, phenotypes, clinical trials & treatments

Similar variants

PEX16 p.Phe332_Tyr333del Uncertain significance ★ same residue
PEX16 p.Leu213fs Likely pathogenic ★ same condition
PEX16 p.Phe332= Conflicting classifications of pathogenicity ★ same residue
PEX16 c.952+118_*82del Pathogenic same condition
PEX16 p.Ile330fs Pathogenic same condition
PEX16 p.Arg287Cys Pathogenic/Likely pathogenic ★★ same condition
PEX16 p.Arg293Cys Uncertain significance ★★ ⚠ same condition
PEX16 c.542-16C>T Benign/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/pex16-p-phe332del (accessed [today's date]).

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