Is PEX10 p.Arg202Pro (c.605G>C) pathogenic?

PEX10 p.Arg202Pro (c.605G>C) is classified Uncertain significance in PEX10 (ClinVar, Single submitter, 1 submitter; last evaluated 2023-05-23). AlphaMissense: likely benign (0.199); Absent from gnomAD v4.1; Associated with Peroxisome biogenesis disorder, complementation group 7.

What condition is associated with PEX10 p.Arg202Pro (c.605G>C)?

PEX10 p.Arg202Pro (c.605G>C) is associated with Peroxisome biogenesis disorder, complementation group 7 (ClinVar).

How common is PEX10 p.Arg202Pro (c.605G>C) in the general population?

PEX10 p.Arg202Pro (c.605G>C) is absent from gnomAD v4.1 (gnomAD).

What do computational predictors say about PEX10 p.Arg202Pro (c.605G>C)?

AlphaMissense predicts likely benign (score 0.199) — an in-silico prediction, not a clinical call.

PEX10 p.Arg202Pro

c.605G>C · rs371979619 · VCV2007338

Uncertain significance Single submitter

Classification

Uncertain significance

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

AlphaMissense

likely benign

0.199 · ACMG-weighted

gnomAD v4.1

Absent

absent from gnomAD v4.1

Missense predictors

1/3 damaging

AlphaMissense, REVEL, SaProt

Conditions

Peroxisome biogenesis disorder, complementation group 7

Computational evidence

Protein change
AlphaMissense	0.199	likely benign
REVEL	0.655	pathogenic-leaning
SaProt	LLR -9.09	tolerated
⇒ REVEL calls this damaging; AlphaMissense and SaProt do not.
Splicing
SpliceAI	<0.2	no splice effect predicted · four deltas, not one · how we know
Constraint at this position
Conservation	phyloP -0.014	GERP -2.7, phastCons 0.001
Regional constraint	o/e 1.06	unconstrained · MANE · 6,733 bp · p 0.24 · regional, not allelic
Overall
CADD	20.1	PHRED · no single calibrated threshold — expert panels disagree

AlphaMissense carries the ACMG weight for missense; REVEL and SaProt are independent agreement signals.

Population frequency

gnomAD v4.1 · exomes + genomes

Absent from gnomAD v4.1. Not observed in any sequenced alleles — a rarity signal (ACMG PM2-supporting), not evidence of pathogenicity on its own.

Variant & gene context

Gene: PEX10
Protein: p.Arg202Pro
Coding: c.605G>C
MANE Select: NM_002617
dbSNP: rs371979619
Type: single nucleotide variant
Location: chr1:2406891 (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

Similar variants

PEX10 p.Arg202His Uncertain significance ★★ ⚠ same residue
PEX10 p.Arg202Ser Uncertain significance ★★ ⚠ same residue
PEX10 p.Arg202Cys Uncertain significance ★ ⚠ same residue
PEX10 p.Arg202= Likely benign ★ same residue
PEX10 c.113-1G>A Likely pathogenic ★★ same condition
PEX10 c.776+1G>A Likely pathogenic ★★ same condition
PEX10 p.Arg125Ter Pathogenic/Likely pathogenic ★★ same condition
PEX10 p.Met1Ile Pathogenic/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-arg202pro (accessed [today's date]).

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