Is PEX1 p.Arg827fs (c.2480del) pathogenic?

PEX1 p.Arg827fs (c.2480del) is classified Pathogenic in PEX1 (ClinVar, Multiple submitters, 3 submitters; last evaluated 2024-05-15). Very rare (popmax 6.84e-05%); Associated with peroxisome biogenesis disorder 1B.

What condition is associated with PEX1 p.Arg827fs (c.2480del)?

PEX1 p.Arg827fs (c.2480del) is associated with peroxisome biogenesis disorder 1B, peroxisome biogenesis disorder 1A (Zellweger), Zellweger spectrum disorders (ClinVar).

How common is PEX1 p.Arg827fs (c.2480del) in the general population?

PEX1 p.Arg827fs (c.2480del) is very rare (popmax 6.84e-05%) (gnomAD).

PEX1 p.Arg827fs

c.2480del · rs2484660252 · VCV2735053

Pathogenic Multiple submitters

Classification

Pathogenic

ClinVar

Review

Multiple submitters ★★☆☆

ClinVar · 3 submitters

Consequence

frameshift

predicted LoF

gnomAD v4.1

Rare

very rare (popmax 6.84e-05%)

Conditions

peroxisome biogenesis disorder 1B

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 15 of 24
Splicing
SpliceAI	—	not assessed · substitutions only
Constraint at this position
Conservation	phyloP 0.5	GERP 1.7, phastCons 1

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

Population frequency

gnomAD v4.1 · exomes + genomes

Grpmax group 6.84e-05%

Overall 6.84e-05% 1/1,461,684 alleles · very rare

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: PEX1
Protein: p.Arg827fs
Coding: c.2480del
MANE Select: NM_000466
dbSNP: rs2484660252
Type: Deletion
Location: chr7:92501610 (GRCh38)
Gene constraint: LOEUF 0.746 · pLI <0.01 (gnomAD)
Structure: AlphaFold pLDDT 67.19
Residue 827: a UniProt-annotated variant site (in pbd1a)

Full PEX1 gene report on Sugi Atlas → Gene function, pathways, protein structure, interactions & more

Disease context

peroxisome biogenesis disorder 1B — disease report on Sugi Atlas → Associated genes, phenotypes, clinical trials & treatments

Also linked: peroxisome biogenesis disorder 1A (Zellweger)Zellweger spectrum disorders

Similar variants

PEX1 p.Arg827Ter Pathogenic ★★ same residue
PEX1 p.Arg827Gln Uncertain significance ★ ⚠ same residue
PEX1 p.Arg827Pro Uncertain significance ★ ⚠ same residue
PEX1 p.Arg827= Likely benign ★ same residue
PEX1 c.2072-42_2085del Likely pathogenic ★★ same condition
PEX1 p.Ala15fs Pathogenic/Likely pathogenic ★★ same condition
PEX1 p.Ala921fs Pathogenic/Likely pathogenic ★★ same condition
PEX1 p.Arg1208fs 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/pex1-p-arg827fs (accessed [today's date]).

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