Is PEX1 p.Arg135Ter (c.403C>T) pathogenic?

PEX1 p.Arg135Ter (c.403C>T) is classified Pathogenic/Likely pathogenic in PEX1 (ClinVar, Multiple submitters, 7 submitters; last evaluated 2025-03-24). Very rare (popmax 0.00223%, eas); Associated with peroxisome biogenesis disorder 1A (Zellweger).

What condition is associated with PEX1 p.Arg135Ter (c.403C>T)?

PEX1 p.Arg135Ter (c.403C>T) is associated with peroxisome biogenesis disorder 1A (Zellweger), peroxisome biogenesis disorder 1B, Zellweger spectrum disorders (ClinVar).

How common is PEX1 p.Arg135Ter (c.403C>T) in the general population?

PEX1 p.Arg135Ter (c.403C>T) is very rare (popmax 0.00223%, eas) (gnomAD).

PEX1 p.Arg135Ter

c.403C>T · rs201415996 · VCV810635

Pathogenic/Likely pathogenic Multiple submitters

Classification

Pathogenic/Likely pathogenic

ClinVar

Review

Multiple submitters ★★☆☆

ClinVar · 7 submitters

Consequence

nonsense (stop-gain)

predicted LoF

gnomAD v4.1

Rare

very rare (popmax 0.00223%, eas)

Conditions

peroxisome biogenesis disorder 1A (Zellweger)

Computational evidence

Protein change
Missense predictors do not apply to this variant type; conservation carries the signal.
Consequence	nonsense (stop-gain)	predicted loss-of-function
NMD	predicted	premature termination codon in exon 4 of 24
Splicing
SpliceAI	—	not assessed · no allele here is in the release
Pangolin	Δ0.37	loss · gain 0.00 · not in the SpliceAI release · independent
Constraint at this position
Conservation	phyloP 12	GERP 2.3, phastCons 1
Overall
CADD	39.0	PHRED · no single calibrated threshold — expert panels disagree

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

Population frequency

gnomAD v4.1 · exomes + genomes

Grpmax group 0.00223% East Asian · 1/44,860 alleles

Filtering AF 0.000124% ClinGen BA1/BS1 input FAF95, joint · FAF99 9e-05%

Overall 0.000411% 6/1,461,188 alleles · very rare

Ancestry group	Frequency	1 in
East Asiangrpmax	0.00223%	44,860
European (non-Finnish)	0.000424%	235,889

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.Arg135Ter
Coding: c.403C>T
MANE Select: NM_000466
dbSNP: rs201415996
Type: single nucleotide variant
Location: chr7:92518210 (GRCh38)
Gene constraint: LOEUF 0.746 · pLI <0.01 (gnomAD)
Structure: AlphaFold pLDDT 67.19

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

Disease context

peroxisome biogenesis disorder 1A (Zellweger) — disease report on Sugi Atlas → Associated genes, phenotypes, clinical trials & treatments

Also linked: peroxisome biogenesis disorder 1B Zellweger spectrum disorders

Similar variants

PEX1 p.Arg135Gln Uncertain significance ★ ⚠ same residue
PEX1 p.Arg135= Likely benign ★ same residue
PEX1 p.Arg135fs Likely pathogenic ★ same residue
PEX1 c.1239+1G>T Pathogenic ★★ same condition
PEX1 c.130-1G>T Pathogenic/Likely pathogenic ★★ same condition
PEX1 c.130-2A>G Pathogenic/Likely pathogenic ★★ same condition
PEX1 c.130-2A>T Pathogenic/Likely pathogenic ★★ same condition
PEX1 c.1483+1G>A 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-arg135ter (accessed [today's date]).

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