Is PEX1 p.Asp545= (c.1635C>T) pathogenic?

PEX1 p.Asp545= (c.1635C>T) is classified Likely benign in PEX1 (ClinVar, Single submitter, 1 submitter; last evaluated 2026-02-04). Very rare (popmax 0.00671%, eas); Associated with Zellweger spectrum disorders.

What condition is associated with PEX1 p.Asp545= (c.1635C>T)?

PEX1 p.Asp545= (c.1635C>T) is associated with Zellweger spectrum disorders (ClinVar).

How common is PEX1 p.Asp545= (c.1635C>T) in the general population?

PEX1 p.Asp545= (c.1635C>T) is very rare (popmax 0.00671%, eas) (gnomAD).

How is Zellweger syndrome inherited?

Typically Autosomal recessive (Orphanet). A genetic counselor can assess individual risk for a family.

PEX1 p.Asp545=

c.1635C>T · rs759202828 · VCV1547866

Likely benign Single submitter

Classification

Likely benign

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

gnomAD v4.1

Rare

very rare (popmax 0.00671%, eas)

Conditions

Zellweger spectrum disorders

Computational evidence

Protein change
Missense predictors do not apply to this variant type; conservation/SpliceAI carries the signal.
Splicing
SpliceAI	Δ0.20	donor loss, 35 bp away · masked 0 · deltas
Constraint at this position
Conservation	phyloP 6.7	GERP 4.4, phastCons 1
Overall
CADD	9.255	PHRED · no single calibrated threshold — expert panels disagree

Population frequency

gnomAD v4.1 · exomes + genomes

Grpmax group 0.00671% East Asian · 3/44,740 alleles

Filtering AF 0.00178% ClinGen BA1/BS1 input FAF95, joint · FAF99 0.000893%

Overall 0.00031% 5/1,612,858 alleles · very rare exomes 5/1,460,670 · genomes 0/152,188 · joint denominator

Ancestry group	Frequency	1 in
East Asiangrpmax	0.00671%	14,913
South Asian	0.0011%	91,058
European (non-Finnish)	8.48e-05%	1,179,244

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.Asp545=
Coding: c.1635C>T
MANE Select: NM_000466
dbSNP: rs759202828
Type: single nucleotide variant
Location: chr7:92509364 (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

Zellweger spectrum disorders — disease report on Sugi Atlas → Associated genes, phenotypes, clinical trials & treatments

For Zellweger syndrome (Orphanet):

Inheritance: Autosomal recessive
Onset: Neonatal

Similar variants

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
PEX1 c.1587+1G>A Likely pathogenic ★★ same condition
PEX1 c.1670+1G>A Pathogenic/Likely pathogenic ★★ same condition
PEX1 c.1670+1G>T 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-asp545 (accessed [today's date]).

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