PEX7

Chr 6AR

peroxisomal biogenesis factor 7

Also known as: PBD9B, PTS2R, RCDP1, RD

NCBI Gene: 5191 ENSG00000112357 OMIM: 601757

Encodes the cytosolic receptor for peroxisomal matrix enzymes that contain peroxisome targeting signal 2 (PTS2), facilitating their import into peroxisomes. Mutations cause autosomal recessive peroxisome biogenesis disorders including rhizomelic chondrodysplasia punctata type 1 and peroxisome biogenesis disorder 9B through impaired import of peroxisomal matrix proteins. The pathogenic mechanism involves defective peroxisomal protein targeting, leading to multiple peroxisomal functional defects.

GeneReviews OMIM ResearchSummary from RefSeq, OMIM, UniProt

This gene encodes the cytosolic receptor for the set of peroxisomal matrix enzymes targeted to the organelle by the peroxisome targeting signal 2 (PTS2). Defects in this gene cause peroxisome biogenesis disorders (PBDs), which are characterized by multiple defects in peroxisome function. There are at least 14 complementation groups for PBDs, with more than one phenotype being observed in cases falling into particular complementation groups. Although the clinical features of PBD patients vary, cells from all PBD patients exhibit a defect in the import of one or more classes of peroxisomal matrix proteins into the organelle. Defects in this gene have been associated with PBD complementation group 11 (PBD-CG11) disorders, rhizomelic chondrodysplasia punctata type 1 (RCDP1), and Refsum disease (RD). [provided by RefSeq, Oct 2008]

GeneReviews OMIM ResearchGenerating clinical summary…

LOFmechanismARLOEUF 1.422 OMIM phenotypes

Clinical Summary— PEX7

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Gene-Disease Validity (ClinGen)

peroxisome biogenesis disorder · ARDefinitive

Definitive — sufficient evidence for diagnostic panels

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Population Constraint (gnomAD)

Low constraint (pLI 0.00) — loss-of-function variants are relatively tolerated in the population.

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ClinVar Variants

153 unique Pathogenic / Likely Pathogenic· 222 VUS of 762 total submissions

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Clinical Trials

4 active or recruiting trials — potential therapeutic options may be available

Explore recent and relevant literature in Research Assistant →

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GeneReview available — PEX7

Authoritative clinical overview · Recommended first read

Open GeneReview ↗

Population Genetics & Constraint

gnomAD v4 — loss-of-function & missense intolerance

gnomAD

Tolerant — LoF & missense variants common in population

LoF Constraint?

1.42LOEUF

pLI 0.000

Z-score 0.14

OE 0.97 (0.67–1.42)

Tolerant

Highly tolerant — LoF variants common in population

Missense Constraint?

0.50Z-score

OE missense 0.89 (0.78–1.02)

145 obs / 162.9 exp

Tolerant

Mild missense constraint

Observed / Expected Ratios?

LoF OE?0.97 (0.67–1.42)

0≤0.351.4

Missense OE?0.89 (0.78–1.02)

0≤0.61.4

Synonymous OE?1.12

0≤1.21.6

LoF obs/exp: 19 / 19.7Missense obs/exp: 145 / 162.9Syn Z: -0.75

Curated Mechanism (G2P)Gene2Phenotype (DDG2P) ↗

definitivePEX7-related peroxisome biogenesis disorder complementation group 11LOFAR

definitivePEX7-related rhizomelic chondrodysplasia punctataLOFAR

This gene — mechanism propensity

Predictions shown for reference only — model trained on dominant genes, not applicable to AR conditions.

0.6452th %ile

GOF

0.5170th %ile

LOF

0.4331th %ile

The Badonyi & Marsh prediction model was trained exclusively on dominant disease genes. Predictions are not reliable for genes with autosomal recessive inheritance and are shown at reduced opacity for reference only.

Predictions from Badonyi M, Marsh JA. PLoS ONE. 2024;19(8):e0307312. Mechanism ranking also informed by gnomAD constraint, ClinVar, and ClinGen data.

ClinVar Variant Classifications

762 submitted variants in ClinVar

ClinVar

Classification Summary

Pathogenic54

Likely Pathogenic99

VUS222

Likely Benign313

Benign33

Conflicting32

Pathogenic

Likely Pathogenic

222

VUS

313

Likely Benign

Benign

Conflicting

Curated Variants Distribution

Classified variants from ClinVar · 5 ACMG categories

Classification	LoF	Missense + Inframe	Non-coding	Synonymous	Total
Pathogenic	43	2	9	0	54
Likely Pathogenic	85	9	5	0	99
VUS	9	174	29	10	222
Likely Benign	0	2	150	161	313
Benign	0	0	33	0	33
Conflicting	—				32
Total	137	187	226	171	753

LoF = frameshift, stop gained/lost, canonical splice · Counts from ClinVar esearch · Updated hourly

View in ClinVar →

19 pathogenic / likely-pathogenic (of 23) ClinVar copy-number / structural variants overlap PEX7 — these span large chromosomal regions, not the gene specifically, and are excluded from the counts above. Explore in CNV tools →