Is PEX10 p.Pro9= (c.27G>A) pathogenic?

PEX10 p.Pro9= (c.27G>A) is classified Benign/Likely benign in PEX10 (ClinVar, Multiple submitters, 5 submitters; last evaluated 2026-01-19). Rare (popmax 0.39%, eas); Associated with Peroxisome biogenesis disorder, complementation group 7.

What condition is associated with PEX10 p.Pro9= (c.27G>A)?

PEX10 p.Pro9= (c.27G>A) is associated with Peroxisome biogenesis disorder, complementation group 7, peroxisome biogenesis disorder 6A (Zellweger), Zellweger spectrum disorders (ClinVar).

How common is PEX10 p.Pro9= (c.27G>A) in the general population?

PEX10 p.Pro9= (c.27G>A) is rare (popmax 0.39%, eas) (gnomAD).

PEX10 p.Pro9=

c.27G>A · rs559431523 · VCV718967

Benign/Likely benign Multiple submitters

Classification

Benign/Likely benign

ClinVar

Review

Multiple submitters ★★☆☆

ClinVar · 5 submitters

gnomAD v4.1

Rare

rare (popmax 0.39%, eas)

Conditions

Peroxisome biogenesis disorder, complementation group 7

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 -3	GERP -4
Overall
CADD	15.06	PHRED · no single calibrated threshold — expert panels disagree

Population frequency

gnomAD v4.1 · exomes + genomes

Grpmax group 0.39% East Asian · 127/32,530 alleles

Filtering AF 0.335% ClinGen BA1/BS1 input FAF95, joint · FAF99 0.314%

Overall 0.0142% 198/1,392,842 alleles · rare exomes 156/1,240,702 · genomes 42/152,140 · joint denominator

Ancestry group	Frequency	1 in
East Asiangrpmax	0.39%	256
South Asian	0.0785%	1,273
Remaining individualsnot grpmax-eligible	0.0359%	2,783
Admixed American	0.00316%	31,630
African / African-American	0.0015%	66,448

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: PEX10
Protein: p.Pro9=
Coding: c.27G>A
MANE Select: NM_002617
dbSNP: rs559431523
Type: single nucleotide variant
Location: chr1:2412476 (GRCh38)
Gene constraint: LOEUF 1.234 · pLI <0.01 (gnomAD)
Structure: AlphaFold pLDDT 82.81

Full PEX10 gene report on Sugi Atlas → Gene function, pathways, protein structure, interactions & more

Disease context

Peroxisome biogenesis disorder, complementation group 7 — disease report on Sugi Atlas → Associated genes, phenotypes, clinical trials & treatments

Also linked: peroxisome biogenesis disorder 6A (Zellweger)Zellweger spectrum disorders

Similar variants

PEX10 p.Pro9Gln Uncertain significance ★ ⚠ same residue
PEX10 p.Pro9fs Pathogenic/Likely pathogenic ★★ same residue
PEX10 c.113-1G>A Likely pathogenic ★★ same condition
PEX10 c.600+1G>A Pathogenic/Likely pathogenic ★★ same condition
PEX10 c.776+1G>A Likely pathogenic ★★ same condition
PEX10 c.776+1G>C Pathogenic/Likely pathogenic ★★ same condition
PEX10 c.776+2T>C Likely pathogenic ★★ same condition
PEX10 c.777-1G>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/pex10-p-pro9 (accessed [today's date]).

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