Is PEX6 p.Ile604= (c.1812C>A) pathogenic?

PEX6 p.Ile604= (c.1812C>A) is classified Likely benign in PEX6 (ClinVar, Single submitter, 1 submitter; last evaluated 2022-12-08). No allele count reported in gnomAD v4.1 (AN 1,613,140); Associated with peroxisome biogenesis disorder.

What condition is associated with PEX6 p.Ile604= (c.1812C>A)?

PEX6 p.Ile604= (c.1812C>A) is associated with peroxisome biogenesis disorder (ClinVar).

How common is PEX6 p.Ile604= (c.1812C>A) in the general population?

PEX6 p.Ile604= (c.1812C>A) is no allele count reported in gnomAD v4.1 (AN 1,613,140) (gnomAD).

PEX6 p.Ile604=

c.1812C>A · rs2114242525 · VCV1463535

Likely benign Single submitter

Classification

Likely benign

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

gnomAD v4.1

Not reported

no allele count reported in gnomAD v4.1 (AN 1,613,140)

Conditions

peroxisome biogenesis disorder

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 1.8	GERP -0.74, phastCons 1
Overall
CADD	7.653	PHRED · no single calibrated threshold — expert panels disagree

Population frequency

gnomAD v4.1 · exomes + genomes

No allele count reported in gnomAD v4.1 (AN 1,613,140). This is missing data, not an absence: the variant may or may not be present in gnomAD. Rarity (ACMG PM2) and BA1/BS1 cannot be assessed for it.

Variant & gene context

Gene: PEX6
Protein: p.Ile604=
Coding: c.1812C>A
MANE Select: NM_000287
dbSNP: rs2114242525
Type: single nucleotide variant
Location: chr6:42967440 (GRCh38)
Gene constraint: LOEUF 0.799 · pLI <0.01 (gnomAD)
Structure: AlphaFold pLDDT 69.87

Full PEX6 gene report on Sugi Atlas → Gene function, pathways, protein structure, interactions & more

Disease context

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

Similar variants

PEX6 p.Ile604Val Uncertain significance ★ ⚠ same residue
PEX6 c.1130+1G>A Likely pathogenic ★★ same condition
PEX6 c.1233+1G>A Likely pathogenic ★★ same condition
PEX6 c.1688+1G>A Pathogenic ★★ same condition
PEX6 c.1689-1G>A Likely pathogenic ★★ same condition
PEX6 c.1885-1G>A Likely pathogenic ★★ same condition
PEX6 c.1962-1G>A Pathogenic/Likely pathogenic ★★ same condition
PEX6 c.2094+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/pex6-p-ile604 (accessed [today's date]).

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