Is PEX10 p.Pro207= (c.621C>T) pathogenic?

PEX10 p.Pro207= (c.621C>T) is classified Conflicting classifications of pathogenicity in PEX10 (ClinVar, Conflicting submitters, 2 submitters; last evaluated 2024-08-27). Very rare (popmax 0.00401%, afr); Associated with Peroxisome biogenesis disorder, complementation group 7.

What condition is associated with PEX10 p.Pro207= (c.621C>T)?

PEX10 p.Pro207= (c.621C>T) is associated with Peroxisome biogenesis disorder, complementation group 7 (ClinVar).

How common is PEX10 p.Pro207= (c.621C>T) in the general population?

PEX10 p.Pro207= (c.621C>T) is very rare (popmax 0.00401%, afr) (gnomAD).

PEX10 p.Pro207=

c.621C>T · rs140107510 · VCV1662204

Conflicting classifications of pathogenicity Conflicting submitters

Classification

Conflicting classifications of pathogenicity

ClinVar

Review

Conflicting submitters ★☆☆☆

ClinVar · 2 submitters

gnomAD v4.1

Rare

very rare (popmax 0.00401%, afr)

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	<0.2	no splice effect predicted · four deltas, not one · how we know
Constraint at this position
Conservation	phyloP -5.2	GERP -4
Overall
CADD	0.184	PHRED · no single calibrated threshold — expert panels disagree

Population frequency

gnomAD v4.1 · exomes + genomes

Grpmax group 0.00401% African / African-American · 3/74,838 alleles

Filtering AF 0.00106% ClinGen BA1/BS1 input FAF95, joint · FAF99 0.000495%

Overall 0.000435% 7/1,609,122 alleles · very rare exomes 6/1,456,928 · genomes 1/152,194 · joint denominator

Ancestry group	Frequency	1 in
African / African-Americangrpmax	0.00401%	24,946
Remaining individualsnot grpmax-eligible	0.00161%	62,294
European (non-Finnish)	0.000255%	392,722

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.Pro207=
Coding: c.621C>T
MANE Select: NM_002617
dbSNP: rs140107510
Type: single nucleotide variant
Location: chr1:2406875 (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.Pro207Ser Uncertain significance ★ ⚠ 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
PEX10 c.776+5G>A Uncertain significance ★★ same condition
PEX10 p.Ala150Val Uncertain significance ★★ ⚠ same condition
PEX10 p.Ala163Val Uncertain significance ★★ ⚠ 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-pro207 (accessed [today's date]).

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