Is PEX1 p.Lys359= (c.1077G>A) pathogenic?

PEX1 p.Lys359= (c.1077G>A) is classified Benign/Likely benign in PEX1 (ClinVar, Multiple submitters, 4 submitters; last evaluated 2026-01-31). Rare (popmax 0.461%, afr); Associated with Zellweger spectrum disorders.

What condition is associated with PEX1 p.Lys359= (c.1077G>A)?

PEX1 p.Lys359= (c.1077G>A) is associated with Zellweger spectrum disorders (ClinVar).

How common is PEX1 p.Lys359= (c.1077G>A) in the general population?

PEX1 p.Lys359= (c.1077G>A) is rare (popmax 0.461%, afr) (gnomAD).

How is Zellweger syndrome inherited?

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

PEX1 p.Lys359=

c.1077G>A · rs138905930 · VCV497945

Benign/Likely benign Multiple submitters

Classification

Benign/Likely benign

ClinVar

Review

Multiple submitters ★★☆☆

ClinVar · 4 submitters

gnomAD v4.1

Rare

rare (popmax 0.461%, afr)

Conditions

Zellweger spectrum disorders

Computational evidence

Protein change
Missense predictors do not apply to this variant type; conservation carries the signal.
Splicing
SpliceAI	—	not assessed · no allele here is in the release
Constraint at this position
Conservation	phyloP 0.12	GERP 0.65, phastCons 0.92
Overall
CADD	6.122	PHRED · no single calibrated threshold — expert panels disagree

Population frequency

gnomAD v4.1 · exomes + genomes

Grpmax group 0.461% African / African-American · 346/74,980 alleles

Filtering AF 0.421% ClinGen BA1/BS1 input FAF95, joint · FAF99 0.406%

Overall 0.0258% 416/1,613,888 alleles · rare

Ancestry group	Frequency	1 in
African / African-Americangrpmax	0.461%	217
Admixed American	0.075%	1,333
Remaining individualsnot grpmax-eligible	0.0256%	3,907
Middle Eastern	0.0165%	6,060
European (non-Finnish)	0.000678%	147,499

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.Lys359=
Coding: c.1077G>A
MANE Select: NM_000466
dbSNP: rs138905930
Type: single nucleotide variant
Location: chr7:92517438 (GRCh38)
Gene constraint: LOEUF 0.746 · pLI <0.01 (gnomAD)
Structure: AlphaFold pLDDT 67.19
Residue 359: the 'disordered' region

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 p.Lys359Asn Conflicting classifications of pathogenicity ★ ⚠ same residue
PEX1 p.Lys359fs Pathogenic/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
PEX1 c.1587+1G>A 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-lys359 (accessed [today's date]).

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