Is PEX1 p.Val1003= (c.3009A>G) pathogenic?

PEX1 p.Val1003= (c.3009A>G) is classified Likely benign in PEX1 (ClinVar, Multiple submitters, 2 submitters; last evaluated 2024-05-27). Ultra-rare (popmax 0.0373%, sas); Associated with Zellweger spectrum disorders.

What condition is associated with PEX1 p.Val1003= (c.3009A>G)?

PEX1 p.Val1003= (c.3009A>G) is associated with Zellweger spectrum disorders (ClinVar).

How common is PEX1 p.Val1003= (c.3009A>G) in the general population?

PEX1 p.Val1003= (c.3009A>G) is ultra-rare (popmax 0.0373%, sas) (gnomAD).

How is Zellweger syndrome inherited?

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

PEX1 p.Val1003=

c.3009A>G · rs560095065 · VCV1097349

Likely benign Multiple submitters

Classification

Likely benign

ClinVar

Review

Multiple submitters ★★☆☆

ClinVar · 2 submitters

gnomAD v4.1

Rare

ultra-rare (popmax 0.0373%, sas)

Conditions

Zellweger spectrum disorders

⚠ Built without this gene's context — gene constraint and dosage, protein structure, pathways, panels and related-variant links were not looked up for this page. why

Computational evidence

Protein change
Missense predictors do not apply to this variant type; conservation carries the signal.
Splicing
SpliceAI	—	not looked up on this page · why
Constraint at this position
Conservation	phyloP -2.5	GERP -1.5
Overall
CADD	11.14	PHRED · no single calibrated threshold — expert panels disagree

Population frequency

gnomAD v4.1 · exomes + genomes

Grpmax group 0.0373% South Asian · 34/91,050 alleles

Filtering AF 0.0274% ClinGen BA1/BS1 input FAF95, joint · FAF99 0.024%

Overall 0.00217% 35/1,613,740 alleles · ultra-rare exomes 33/1,461,426 · genomes 2/152,314 · joint denominator

Ancestry group	Frequency	1 in
South Asiangrpmax	0.0373%	2,678
Remaining individualsnot grpmax-eligible	0.0016%	62,494

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.Val1003=
Coding: c.3009A>G
MANE Select: NM_000466
dbSNP: rs560095065
Type: single nucleotide variant
Location: chr7:92494314 (GRCh38)

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

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-val1003 (accessed [today's date]).

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