Is PEX7 p.Glu23fs (c.57_67dup) pathogenic?

PEX7 p.Glu23fs (c.5767dup) is classified Pathogenic in PEX7 (ClinVar, Single submitter, 1 submitter; last evaluated 2023-03-12). Very rare (popmax 8.78e-05%, nfe); Associated with peroxisome biogenesis disorder 9B.

What condition is associated with PEX7 p.Glu23fs (c.57_67dup)?

PEX7 p.Glu23fs (c.57_67dup) is associated with peroxisome biogenesis disorder 9B (ClinVar).

How common is PEX7 p.Glu23fs (c.57_67dup) in the general population?

PEX7 p.Glu23fs (c.57_67dup) is very rare (popmax 8.78e-05%, nfe) (gnomAD).

PEX7 p.Glu23fs

c.57_67dup · rs2115122515 · VCV1384934

Pathogenic Single submitter

Classification

Pathogenic

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

Consequence

frameshift

predicted LoF

gnomAD v4.1

Rare

very rare (popmax 8.78e-05%, nfe)

Conditions

peroxisome biogenesis disorder 9B

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 1 of 10
Splicing
SpliceAI	—	not assessed · substitutions only
Constraint at this position
Conservation	phyloP 11	GERP 1.6, phastCons 1

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

Population frequency

gnomAD v4.1 · exomes + genomes

Grpmax group 8.78e-05% European (non-Finnish) · 1/1,138,382 alleles

Overall 6.6e-05% 1/1,514,946 alleles · very rare exomes 1/1,362,842 · genomes 0/152,104 · joint denominator

Rarity supports pathogenicity (ACMG PM2); frequency above a disease-specific BA1/BS1 threshold argues against it. A variant frequent in one ancestry group can be near-absent in others, so a single global figure can mislead.

Variant & gene context

Gene: PEX7
Protein: p.Glu23fs
Coding: c.57_67dup
MANE Select: NM_000288
dbSNP: rs2115122515
Type: Duplication
Location: chr6:136822720 (GRCh38)
Gene constraint: LOEUF 0.941 · pLI <0.01 (gnomAD)
Structure: AlphaFold pLDDT 95.54

Full PEX7 gene report on Sugi Atlas → Gene function, pathways, protein structure, interactions & more

Disease context

peroxisome biogenesis disorder 9B — disease report on Sugi Atlas → Associated genes, phenotypes, clinical trials & treatments

Similar variants

PEX7 p.Glu23Gln Uncertain significance ★ ⚠ same residue
PEX7 p.Glu23= Likely benign ★ same residue
PEX7 p.Gly176fs Pathogenic ★★ same condition
PEX7 p.Ile158fs Likely pathogenic ★★ same condition
PEX7 p.Leu70fs Likely pathogenic ★★ same condition
PEX7 c.130+48_130+53dup Benign ★★ same condition
PEX7 c.748-5dup Benign/Likely benign ★★ same condition
PEX7 c.748-6_748-5dup 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/pex7-p-glu23fs (accessed [today's date]).

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