PEX16

protein-coding

peroxisomal biogenesis factor 16, the group of Peroxins

Gene summary

The protein encoded by this gene is an integral peroxisomal membrane protein. An inactivating nonsense mutation localized to this gene was observed in a patient with Zellweger syndrome of the complementation group CGD/CG9. Expression of this gene product morphologically and biochemically restores the formation of new peroxisomes, suggesting a role in peroxisome organization and biogenesis. Alternative splicing has been observed for this gene and two variants have been described. [provided by RefSeq, Jul 2008]

MANE transcript

NM_004813.4

Inheritance

AR

ClinVar variants

P:47U:192B:190

Top phenotype

Peroxisome biogenesis factor disorder 8A (Zellweger syndrome); Peroxisome biogenesis disorder 8B

gnomAD constraint

pLI —, LoF o/e 0.49

Max pathogenic AF

—

Genomic locus

chr11:45,909,663-45,918,812

External References & Databases

Transcript & Mutation Effects

hg38 • Region Span ~9.1 kb
Loading mutation effect viewer...

GenCC Phenotypes & Disease Associations

Curated gene-disease validity assertions and inheritance patterns

peroxisome biogenesis disorderDEFINITIVE

Inheritance Pattern: AR

Disease ID:MONDO:0019234

Submitter: ClinGen

The relationship between PEX16 and peroxisome biogenesis disorder (types 8A and 8B included), an autosomal recessive disorder, was evaluated using the ClinGen Clinical Validity Framework as of July 19, 2019. PEX16 encodes a peroxisome membrane protein involved in early peroxisome membrane biosynthesis prior to matrix protein import. Peroxisomal biogenesis disorders are caused by defects in various stages of peroxisomal protein import and/or peroxisome biogenesis, involving at least 14 PEX genes. PEX3 belongs to complementation group D and mutations in the gene result in cells devoid of peroxisomal remnants (Waterham and Ebberink 2012, PMID 22871920) or with a small number of enlarged peroxisomes (Ebberink et al, 2010, PMID 20647552). PEX16 was first reported in relation to autosomal recessive Peroxisome biogenesis disorder in 1998. (Honsho et al, PMID: 9837814). At least 10 nonsense, splice site, frameshift, deletion/duplication and missense variants have been reported in humans. Evidence supporting this gene-disease relationship includes case-level data and experimental data. Summary of Case Level Data (12 points): Variants in this gene have been reported in at least 11 probands in 9 publications (PMID: 20681997, 30078639, 26644994, 30094183, 20647552, 24091540, 11890679, 9837814, 21031596). The mechanism for disease is expected to be homozygous loss of function. Summary of experimental data (3.5 points): This gene-disease association is supported by in vitro functional assays and a fly model (PMIDs 12096124, 25002403, 21826223). PEX16 interacts with PEX19 and may have a role in the trafficking of PEX3. In summary, PEX16 is definitively associated with autosomal recessive Peroxisome biogenesis disorder. This has been repeatedly demonstrated in both the research and clinical diagnostic settings, and has been upheld over time. This classification was approved by the Peroxisomal Disorders GCEP on January 13, 2020.

peroxisome biogenesis disorderSTRONG

Inheritance Pattern: AR

Disease ID:MONDO:0019234

Submitter: PanelApp Australia

peroxisome biogenesis disorder 8BSTRONG

Inheritance Pattern: AR

Disease ID:MONDO:0013943

Submitter: Labcorp Genetics (formerly Invitae)

peroxisome biogenesis disorder 8A (Zellweger)DEFINITIVE

Inheritance Pattern: AR

Disease ID:MONDO:0013942

Submitter: G2P

peroxisome biogenesis disorder 8BDEFINITIVE

Inheritance Pattern: AR

Disease ID:MONDO:0013943

Submitter: G2P

peroxisome biogenesis disorder 8A (Zellweger)MODERATE

Inheritance Pattern: AR

Disease ID:MONDO:0013942

Submitter: Ambry Genetics

Zellweger spectrum disordersSUPPORTIVE

Inheritance Pattern: AR

Disease ID:MONDO:0019609

Submitter: Orphanet

peroxisome biogenesis disorder 8BMODERATE

Inheritance Pattern: AR

Disease ID:MONDO:0013943

Submitter: Ambry Genetics

Clinical Genomic Database (CGD)

Peroxisome biogenesis factor disorder 8A (Zellweger syndrome); Peroxisome biogenesis disorder 8BAR

Manifestation: Biochemical; Craniofacial; Gastrointestinal; Genitourinary; Musculoskeletal; Neurologic; Renal

Intervention: General

Rationale: Genetic knowledge may be beneficial related to issues such as selection of optimal supportive care, informed medical decision-making, prognostic considerations, and avoidance of unnecessary testing

Refs: 9837814; 11890679; 20647552Source: CGD (NHGRI)

ClinVar Associated Diseases & Phenotypes

Reported disease conditions connected to PEX16 variants in ClinVar

10 Conditions Cataloged
Peroxisome biogenesis disorderTotal: 553
PEX16-related disorderTotal: 77
not providedTotal: 75
not specifiedTotal: 67
Inborn genetic diseasesTotal: 50
Peroxisome biogenesis disorder 8A (Zellweger)Total: 34
Peroxisome biogenesis disorder 8BTotal: 20
Methylmalonic aciduria due to methylmalonyl-CoA mutase deficiencyTotal: 1

ClinVar Variants & Pathogenicity by Type

Statistics based on transcript NM_004813.4. Only rare variants are included.

We include only reliable ClinVar variants with their consequences to MANE Select, MANE Plus Clinical transcripts, or transcripts with TSL equal to 1. Click a count to filter the variants table below.

Slight differences between displayed counts and ClinVar may occur due to a different transcript/consequence chosen by our variant effect predictor, or because we classify Benign/Likely benign as Likely benign and Pathogenic/Likely pathogenic as Likely pathogenic.

EffectPLPVUSLBBSum
synonymous
4
clinvar
181
clinvar
1
clinvar
186
missense
1
clinvar
6
clinvar
181
clinvar
8
clinvar
196
nonsense
15
clinvar
1
clinvar
2
clinvar
18
start loss
0
frameshift
8
clinvar
3
clinvar
2
clinvar
13
splice donor/acceptor (+/-2bp)
2
clinvar
11
clinvar
3
clinvar
16
Total26211921891429

Highest pathogenic variant AF is 0.000013050676

Loading ClinVar variants...

Transcript Catalog

Annotated transcript isoforms across RefSeq and Ensembl databases

Showing 4 of 36 transcripts
Transcript IDSourceProtein IDCoding ExonsMANE Status
NM_004813.4RefSeqNP_004804.211MANE Select
ENST00000378750.10EnsemblENSP00000368024.511MANE Select
NM_057174.3RefSeqNP_476515.211Standard
ENST00000241041.7EnsemblENSP00000241041.311Standard

Gene Ontology (GO) Annotations & Pathways

Biological processes, molecular functions, cellular components and pathways

Pathways ConsensusPathDB

  • Peroxisome - Homo sapiens (human)

Biological Process

  • protein targeting to peroxisome
  • peroxisome organization
  • peroxisome membrane biogenesis
  • protein import into peroxisome matrix
  • protein to membrane docking

Molecular Function

  • protein binding
  • protein C-terminus binding

Cellular Component

  • peroxisome
  • peroxisomal membrane
  • integral component of peroxisomal membrane
  • endoplasmic reticulum
  • endoplasmic reticulum membrane

gnomAD Constraint

Source: gnomAD

Gene type
protein_coding
Transcript type
protein_coding
Transcript
ENST00000241041
Coding exons
11
Length
9144
Individuals with no LoFs
125728
Homozygous LoFs
0
Heterozygous LoFs
20
Defined
125748
p
0.0000795
Z-ScoreObservedExpectedObserved/ExpectedMutation RateTotal Possible
Missense0.4521952140.9130.00001502132
Missense (PolyPhen)5370.7380.74925680
Synonymous-0.1219593.51.020.00000607765
Loss of Function2.161020.60.4869.89e-7219

Population LoF Frequency

PopulationCAFp-valueStatus
African0.000130.00012rare
Latino/Admixed American0.0000870.000087rare
Ashkenazi Jewish00.0absent
East Asian0.000160.00016rare
Finnish0.0000540.000046rare
European (Non-Finnish)0.0000440.000044rare
South Asian0.000160.00016rare
Other0.000160.00016rare

dbNSFP Gene Annotations

Source: dbNSFP

Function
FUNCTION: Required for peroxisome membrane biogenesis. May play a role in early stages of peroxisome assembly. Can recruit other peroxisomal proteins, such as PEX3 and PMP34, to de novo peroxisomes derived from the endoplasmic reticulum (ER). May function as receptor for PEX3. {ECO:0000269|PubMed:10704444, ECO:0000269|PubMed:12223482, ECO:0000269|PubMed:16717127}.;
Disease
DISEASE: Peroxisome biogenesis disorder complementation group 9 (PBD-CG9) [MIM:614876]: A peroxisomal disorder arising from a failure of protein import into the peroxisomal membrane or matrix. The peroxisome biogenesis disorders (PBD group) are genetically heterogeneous with at least 14 distinct genetic groups as concluded from complementation studies. Include disorders are: Zellweger syndrome (ZWS), neonatal adrenoleukodystrophy (NALD), infantile Refsum disease (IRD), and classical rhizomelic chondrodysplasia punctata (RCDP). ZWS, NALD and IRD are distinct from RCDP and constitute a clinical continuum of overlapping phenotypes known as the Zellweger spectrum (PBD-ZSS). {ECO:0000269|PubMed:9837814}. Note=The disease is caused by mutations affecting the gene represented in this entry.; DISEASE: Peroxisome biogenesis disorder 8A (PBD8A) [MIM:614876]: A fatal peroxisome biogenesis disorder belonging to the Zellweger disease spectrum and clinically characterized by severe neurologic dysfunction with profound psychomotor retardation, severe hypotonia and neonatal seizures, craniofacial abnormalities, liver dysfunction, and biochemically by the absence of peroxisomes. Additional features include cardiovascular and skeletal defects, renal cysts, ocular abnormalities, and hearing impairment. Most severely affected individuals with the classic form of the disease (classic Zellweger syndrome) die within the first year of life. {ECO:0000269|PubMed:9837814}. Note=The disease is caused by mutations affecting the gene represented in this entry.; DISEASE: Peroxisome biogenesis disorder 8B (PBD8B) [MIM:614877]: A relatively mild peroxisome biogenesis disorder. Affected individuals manifest lower limb spasticity and ataxia resulting in wheelchair dependence. Other features include optic atrophy, cataracts, dysarthria, dysphagia, constipation, and a peripheral demyelinating motor and sensory neuropathy. Cognition is relatively preserved. Biochemical abnormalities are mild and include increased very-long-chain fatty acids (VLCFA), increased bile acid intermediates, and increased branched chain fatty acids. Phytanic acid alpha-oxidation, pristanic acid beta-oxidation, and red cell plasmalogen are normal. {ECO:0000269|PubMed:20647552}. Note=The disease is caused by mutations affecting the gene represented in this entry.;

Recessive Scores

pRec
0.194

Intolerance Scores

LoFtool
0.678
RVIS EVS
0.26
RVIS percentile EVS
70.44

Essentials

Essential (CRISPR)
N
Essential (CRISPR2)
E
Essential (gene trap)
N
Indispensability pred.
E
Indispensability score
0.719

Gene Damage Prediction

AllRecessiveDominant
MendelianMediumMediumMedium
Primary ImmunodeficiencyMediumMediumMedium
CancerMediumMediumMedium
For research and educational, non-commercial use only. Not for clinical or diagnostic use. GeneBe does not provide medical advice. Data use for AI modeling is prohibited: if used, the cost is $0.001 per byte of downloaded uncompressed data.