Is PEX5 p.Val75= (c.225G>C) pathogenic?

PEX5 p.Val75= (c.225G>C) is classified Likely benign in PEX5 (ClinVar, Single submitter, 1 submitter; last evaluated 2025-03-16). Very rare (popmax 0.00933%, afr); Associated with peroxisome biogenesis disorder 2B.

What condition is associated with PEX5 p.Val75= (c.225G>C)?

PEX5 p.Val75= (c.225G>C) is associated with peroxisome biogenesis disorder 2B (ClinVar).

How common is PEX5 p.Val75= (c.225G>C) in the general population?

PEX5 p.Val75= (c.225G>C) is very rare (popmax 0.00933%, afr) (gnomAD).

PEX5 p.Val75=

c.225G>C · rs1941054422 · VCV1578316

Likely benign Single submitter

Classification

Likely benign

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

gnomAD v4.1

Rare

very rare (popmax 0.00933%, afr)

Conditions

peroxisome biogenesis disorder 2B

Computational evidence

Protein change
Missense predictors do not apply to this variant type; conservation/SpliceAI carries the signal.
Splicing
SpliceAI	Δ0.22	acceptor gain · deltas
Constraint at this position
Conservation	phyloP -0.23	GERP -3.1, phastCons 0.014
Overall
CADD	7.552	PHRED · no single calibrated threshold — expert panels disagree

Population frequency

gnomAD v4.1 · exomes + genomes

Grpmax group 0.00933% African / African-American · 7/75,038 alleles

Filtering AF 0.00437% ClinGen BA1/BS1 input FAF95, joint · FAF99 0.00308%

Overall 0.00062% 10/1,614,144 alleles · very rare exomes 10/1,461,860 · genomes 0/152,284 · joint denominator

Ancestry group	Frequency	1 in
African / African-Americangrpmax	0.00933%	10,720
Remaining individualsnot grpmax-eligible	0.0048%	20,837

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: PEX5
Protein: p.Val75=
Coding: c.225G>C
MANE Select: NM_001351132
dbSNP: rs1941054422
Type: single nucleotide variant
Location: chr12:7191267 (GRCh38)
Gene constraint: LOEUF 0.768 · pLI <0.01 (gnomAD)
Structure: AlphaFold pLDDT 70.28 · 11 PDB

Full PEX5 gene report on Sugi Atlas → Gene function, pathways, protein structure, interactions & more

Disease context

peroxisome biogenesis disorder 2B — disease report on Sugi Atlas → Associated genes, phenotypes, clinical trials & treatments

Similar variants

PEX5 p.Val75Ala Uncertain significance ★ ⚠ same residue
PEX5 c.449-2A>G Pathogenic/Likely pathogenic ★★ same condition
PEX5 c.552-1G>A Pathogenic/Likely pathogenic ★★ same condition
PEX5 c.847-2A>G Likely pathogenic ★★ same condition
PEX5 c.967-1G>A Likely pathogenic ★★ same condition
PEX5 p.Arg237Ter Pathogenic/Likely pathogenic ★★ same condition
PEX5 p.Arg276Ter Pathogenic/Likely pathogenic ★★ same condition
PEX5 p.Arg420Ter 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/pex5-p-val75 (accessed [today's date]).

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