GeneBe

PEX16

peroxisomal biogenesis factor 16, the group of Peroxins

Basic information

Region (hg38): 11:45909663-45918812

Links

ENSG00000121680 ∙ NCBI:9409 ∙ OMIM:603360 ∙ HGNC:8857 ∙ Uniprot:Q9Y5Y5 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

Phenotypes

GenCC

Source: genCC

  • peroxisome biogenesis disorder 8A (Zellweger) (Definitive), mode of inheritance: AR
  • Zellweger spectrum disorders (Supportive), mode of inheritance: AR
  • peroxisome biogenesis disorder 8B (Definitive), mode of inheritance: AR
  • peroxisome biogenesis disorder 8B (Strong), mode of inheritance: AR
  • peroxisome biogenesis disorder (Definitive), mode of inheritance: AR
  • peroxisome biogenesis disorder 8B (Moderate), mode of inheritance: AR
  • peroxisome biogenesis disorder 8A (Zellweger) (Moderate), mode of inheritance: AR

Clinical Genomic Database

Source: CGD

ConditionInheritanceIntervention CategoriesIntervention/Rationale Manifestation CategoriesReferences
Peroxisome biogenesis factor disorder 8A (Zellweger syndrome); Peroxisome biogenesis disorder 8BARGeneralGenetic knowledge may be beneficial related to issues such as selection of optimal supportive care, informed medical decision-making, prognostic considerations, and avoidance of unnecessary testingBiochemical; Craniofacial; Gastrointestinal; Genitourinary; Musculoskeletal; Neurologic; Renal9837814; 11890679; 20647552

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the PEX16 gene.

  • Peroxisome_biogenesis_disorder (529 variants)
  • not_provided (59 variants)
  • Inborn_genetic_diseases (47 variants)
  • PEX16-related_disorder (43 variants)
  • Peroxisome_biogenesis_disorder_8A_(Zellweger) (33 variants)
  • Peroxisome_biogenesis_disorder_8B (17 variants)
  • not_specified (7 variants)
  • Methylmalonic_aciduria_due_to_methylmalonyl-CoA_mutase_deficiency (1 variants)
  • Peroxisome_biogenesis_disorder_due_to_PEX16_defect (1 variants)
  • Peroxisome_biogenesis_disorder_1A_(Zellweger) (1 variants)
  • Microcephaly (1 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the PEX16 gene is commonly pathogenic or not. These statistics are base on transcript: NM_000004813.4. Only rare variants are included in the table.

In the table, we include only reliable ClinVar variants with their consequences to MANE Select, Mane Plus Clinical transcripts, or transcripts with TSL equals 1. Click the count to view the source variants.

Warning: slight differences between displayed counts and the number of variants in ClinVar may occur, primarily due to (1) the application of a different transcript and/or consequence by our variant effect predictor or (2) differences in clinical significance: we classify Benign/Likely benign variants as Likely benign and Pathogenic/Likely pathogenic variants as Likely pathogenic.

EffectPLPVUSLBBSum
synonymous
4
clinvar
171
clinvar
2
clinvar
 177
missense
1
clinvar
6
clinvar
177
clinvar
6
clinvar
 190
nonsense
14
clinvar
2
clinvar
 16
start loss
0
frameshift
5
clinvar
2
clinvar
1
clinvar
 8
splice donor/acceptor (+/-2bp)
1
clinvar
9
clinvar
2
clinvar
 12
Total 21 17 186 177 2

Highest pathogenic variant AF is 0.000013050676

Loading clinvar variants...

GnomAD

Source: gnomAD

GeneTypeBio TypeTranscript Coding Exons Length
PEX16protein_codingprotein_codingENST00000241041 119144
pLI Probability
LOF Intolerant 		pRec Probability
LOF Recessive 		Individuals with
no LOFs 		Individuals with
Homozygous LOFs 		Individuals with
Heterozygous LOFs 		Defined p
0.00008290.9851257280201257480.0000795
Z-Score Observed Expected Observed/Expected Mutation Rate Total Possible in Transcript
Missense0.4521952140.9130.00001502132
Missense in Polyphen5370.7380.74925680
Synonymous-0.1219593.51.020.00000607765
Loss of Function2.161020.60.4869.89e-7219

LoF frequencies by population

EthnicitySum of pLOFs p
African & African-American0.0002130.000210
Ashkenazi Jewish0.000.00
East Asian0.0001630.000163
Finnish0.00005430.0000462
European (Non-Finnish)0.00004440.0000439
Middle Eastern0.0001630.000163
South Asian0.0001630.000163
Other0.0001630.000163

dbNSFP

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.;
Pathway
Peroxisome - Homo sapiens (human) (Consensus)

Recessive Scores

pRec
0.194

Intolerance Scores

loftool
0.678
rvis_EVS
0.26
rvis_percentile_EVS
70.44

Haploinsufficiency Scores

pHI
0.0769
hipred
N
hipred_score
0.331
ghis
0.404

Essentials

essential_gene_CRISPR
N
essential_gene_CRISPR2
E
essential_gene_gene_trap
N
gene_indispensability_pred
E
gene_indispensability_score
0.719

Gene Damage Prediction

AllRecessiveDominant
MendelianMediumMediumMedium
Primary ImmunodeficiencyMediumMediumMedium
CancerMediumMediumMedium

Mouse Genome Informatics

Gene name
Pex16
Phenotype

Gene ontology

Biological process
protein targeting to peroxisome;peroxisome organization;peroxisome membrane biogenesis;protein import into peroxisome matrix;protein to membrane docking;ER-dependent peroxisome organization;protein import into peroxisome membrane;ER-dependent peroxisome localization
Cellular component
peroxisome;peroxisomal membrane;integral component of peroxisomal membrane;endoplasmic reticulum;endoplasmic reticulum membrane;membrane
Molecular function
protein binding;protein C-terminus binding