PEX7
Basic information
Region (hg38): 6:136822564-136913934
Links
Phenotypes
GenCC
Source:
- rhizomelic chondrodysplasia punctata type 1 (Definitive), mode of inheritance: AR
- peroxisome biogenesis disorder 9B (Moderate), mode of inheritance: AR
- rhizomelic chondrodysplasia punctata type 1 (Definitive), mode of inheritance: AR
- peroxisome biogenesis disorder 9B (Definitive), mode of inheritance: AR
- adult Refsum disease (Supportive), mode of inheritance: AR
- rhizomelic chondrodysplasia punctata type 1 (Definitive), mode of inheritance: AR
- rhizomelic chondrodysplasia punctata type 1 (Strong), mode of inheritance: AR
- peroxisome biogenesis disorder 9B (Strong), mode of inheritance: AR
- peroxisome biogenesis disorder (Definitive), mode of inheritance: AR
Clinical Genomic Database
Source:
Condition | Inheritance | Intervention Categories | Intervention/Rationale | Manifestation Categories | References |
---|---|---|---|---|---|
Refsum disease | AR | Biochemical | Dietary measures (eg, phytanic acid restriction, high calorie diet) can help with dermatologic and neurologic manifestations; Surveillance and medical carefor cardiac arrhythmias and cardiomyopathy can reduce morbidity/mortality; Plasmapheresis/lipid apheresis may be used; Fasting and ibuprofen should be avoided | Audiologic/Otolaryngologic; Biochemical; Cardiovascular; Craniofacial; Dermatologic; Gastrointestinal; Musculoskeletal; Neurologic; Ophthalmologic | 18140089; 13045168; 4159604; 85164; 6160883; 2452736; 7541833; 9090381; 9090382; 9090383; 12325024; 11781871; 12522768; 14974078; 17325280; 20301527; 23352163 |
ClinVar
This is a list of variants' phenotypes submitted to
- Peroxisome biogenesis disorder 9B (35 variants)
- Rhizomelic chondrodysplasia punctata type 1 (9 variants)
- not provided (5 variants)
- Rhizomelic chondrodysplasia punctata (3 variants)
- PEX7-related disorder (3 variants)
- Peroxisome biogenesis disorder 9B;Rhizomelic chondrodysplasia punctata type 1;Phytanic acid storage disease (3 variants)
- Peroxisome biogenesis disorder 9B;Rhizomelic chondrodysplasia punctata type 1 (1 variants)
- Inborn genetic diseases (1 variants)
Variants pathogenicity by type
Statistics on ClinVar variants can assist in determining whether a specific variant type in the PEX7 gene is commonly pathogenic or not.
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.
Variant type | Pathogenic | Likely pathogenic | VUS | Likely benign | Benign | Sum |
---|---|---|---|---|---|---|
synonymous | 148 | 149 | ||||
missense | 137 | 149 | ||||
nonsense | 19 | 26 | ||||
start loss | 0 | |||||
frameshift | 24 | 26 | 53 | |||
inframe indel | 5 | |||||
splice donor/acceptor (+/-2bp) | 21 | 27 | ||||
splice region | 10 | 33 | 5 | 48 | ||
non coding | 13 | 101 | 24 | 139 | ||
Total | 37 | 77 | 159 | 251 | 24 |
Highest pathogenic variant AF is 0.000447
Variants in PEX7
This is a list of pathogenic ClinVar variants found in the PEX7 region.
You can filter this list by clicking the number of variants in the Variants pathogenicity by type table.
Position | Type | Phenotype | Significance | ClinVar |
---|---|---|---|---|
6-136822571-T-C | Peroxisome biogenesis disorder 9B • Rhizomelic chondrodysplasia punctata type 1 | Benign (Jul 10, 2021) | ||
6-136822575-G-A | Phytanic acid storage disease • Rhizomelic chondrodysplasia punctata | Uncertain significance (Jun 14, 2016) | ||
6-136822578-T-C | Phytanic acid storage disease • Rhizomelic chondrodysplasia punctata | Uncertain significance (Jun 14, 2016) | ||
6-136822589-T-C | Phytanic acid storage disease • Rhizomelic chondrodysplasia punctata | Uncertain significance (Jun 14, 2016) | ||
6-136822597-C-A | Rhizomelic chondrodysplasia punctata type 1 • Peroxisome biogenesis disorder 9B | Uncertain significance (Apr 27, 2017) | ||
6-136822601-A-T | Rhizomelic chondrodysplasia punctata type 1 • Peroxisome biogenesis disorder 9B | Benign/Likely benign (Aug 14, 2018) | ||
6-136822610-C-T | Rhizomelic chondrodysplasia punctata type 1 • Peroxisome biogenesis disorder 9B • Rhizomelic chondrodysplasia punctata | Benign (Jun 14, 2018) | ||
6-136822619-A-AACGGCTTCC | Rhizomelic chondrodysplasia punctata type 1 | Uncertain significance (Apr 30, 2018) | ||
6-136822621-C-T | Phytanic acid storage disease • Peroxisome biogenesis disorder 9B | Likely pathogenic (Jan 24, 2024) | ||
6-136822622-G-A | not specified | Likely benign (Sep 08, 2017) | ||
6-136822631-G-A | Peroxisome biogenesis disorder 9B • Rhizomelic chondrodysplasia punctata type 1 | Uncertain significance (Jan 13, 2018) | ||
6-136822635-G-A | not specified • Peroxisome biogenesis disorder 9B • Rhizomelic chondrodysplasia punctata type 1 • Rhizomelic chondrodysplasia punctata | Benign/Likely benign (Apr 27, 2017) | ||
6-136822638-G-A | Rhizomelic chondrodysplasia punctata type 1 • Peroxisome biogenesis disorder 9B | Uncertain significance (Jan 13, 2018) | ||
6-136822648-C-T | Peroxisome biogenesis disorder 9B • Rhizomelic chondrodysplasia punctata type 1 | Uncertain significance (Jan 13, 2018) | ||
6-136822656-G-T | PEX7-related disorder | Likely benign (Jul 22, 2019) | ||
6-136822663-G-A | Peroxisome biogenesis disorder 9B • Rhizomelic chondrodysplasia punctata type 1 | Uncertain significance (Jan 12, 2018) | ||
6-136822665-G-A | not specified | Uncertain significance (Aug 02, 2023) | ||
6-136822669-A-AGTGCGGT | Peroxisome biogenesis disorder 9B • Rhizomelic chondrodysplasia punctata type 1 • Rhizomelic chondrodysplasia punctata | Pathogenic/Likely pathogenic (Mar 26, 2024) | ||
6-136822673-CG-C | Peroxisome biogenesis disorder 9B | Pathogenic (Jul 25, 2023) | ||
6-136822674-G-A | Peroxisome biogenesis disorder 9B | Likely benign (Dec 14, 2023) | ||
6-136822674-G-C | Peroxisome biogenesis disorder 9B | Likely benign (Jan 31, 2024) | ||
6-136822676-TG-T | Peroxisome biogenesis disorder 9B | Pathogenic (Dec 14, 2023) | ||
6-136822677-G-A | Peroxisome biogenesis disorder 9B | Likely benign (Jul 03, 2023) | ||
6-136822680-C-T | Peroxisome biogenesis disorder 9B | Likely benign (Jul 10, 2022) | ||
6-136822682-G-C | Peroxisome biogenesis disorder 9B | Uncertain significance (Nov 27, 2023) |
GnomAD
Source:
Gene | Type | Bio Type | Transcript | Coding Exons | Length |
---|---|---|---|---|---|
PEX7 | protein_coding | protein_coding | ENST00000318471 | 10 | 91359 |
pLI Probability LOF Intolerant | pRec Probability LOF Recessive | Individuals with no LOFs | Individuals with Homozygous LOFs | Individuals with Heterozygous LOFs | Defined | p |
---|---|---|---|---|---|---|
8.18e-13 | 0.0377 | 125601 | 0 | 147 | 125748 | 0.000585 |
Z-Score | Observed | Expected | Observed/Expected | Mutation Rate | Total Possible in Transcript | |
---|---|---|---|---|---|---|
Missense | 0.497 | 145 | 163 | 0.890 | 0.00000774 | 2096 |
Missense in Polyphen | 50 | 50.659 | 0.98699 | 674 | ||
Synonymous | -0.747 | 71 | 63.4 | 1.12 | 0.00000351 | 621 |
Loss of Function | 0.142 | 19 | 19.7 | 0.966 | 9.40e-7 | 226 |
LoF frequencies by population
Ethnicity | Sum of pLOFs | p |
---|---|---|
African & African-American | 0.000810 | 0.000810 |
Ashkenazi Jewish | 0.00 | 0.00 |
East Asian | 0.000761 | 0.000761 |
Finnish | 0.0000925 | 0.0000924 |
European (Non-Finnish) | 0.000933 | 0.000932 |
Middle Eastern | 0.000761 | 0.000761 |
South Asian | 0.000131 | 0.000131 |
Other | 0.000326 | 0.000326 |
dbNSFP
Source:
- Function
- FUNCTION: Binds to the N-terminal PTS2-type peroxisomal targeting signal and plays an essential role in peroxisomal protein import.;
- Disease
- DISEASE: Rhizomelic chondrodysplasia punctata 1 (RCDP1) [MIM:215100]: A peroxisome biogenesis disorder. It is characterized by severely disturbed endochondral bone formation, rhizomelic shortening of femur and humerus, vertebral disorders, dwarfism, cataract, cutaneous lesions, facial dysmorphism, and severe mental retardation with spasticity. {ECO:0000269|PubMed:9090381}. Note=The disease is caused by mutations affecting the gene represented in this entry.; DISEASE: Peroxisome biogenesis disorder 9B (PBD9B) [MIM:614879]: A peroxisome biogenesis disorder with unusually mild clinical and biochemical manifestations. Affected individuals manifest a variable phenotype similar to, and in some cases indistinguishable from, classic Refsum disease. Variable features include ocular abnormalities, sensorimotor neuropathy, ichthyosis, deafness, chondrodysplasia punctata without rhizomelia or growth failure. {ECO:0000269|PubMed:12522768}. Note=The disease is caused by mutations affecting the gene represented in this entry.;
- Pathway
- Peroxisome - Homo sapiens (human);Metabolism of proteins;Peroxisomal protein import
(Consensus)
Recessive Scores
- pRec
- 0.200
Intolerance Scores
- loftool
- 0.616
- rvis_EVS
- 0.01
- rvis_percentile_EVS
- 54.95
Haploinsufficiency Scores
- pHI
- 0.113
- hipred
- N
- hipred_score
- 0.335
- ghis
- 0.519
Essentials
- essential_gene_CRISPR
- E
- essential_gene_CRISPR2
- N
- essential_gene_gene_trap
- N
- gene_indispensability_pred
- E
- gene_indispensability_score
- 0.584
Gene Damage Prediction
All | Recessive | Dominant | |
---|---|---|---|
Mendelian | Medium | Medium | Medium |
Primary Immunodeficiency | Medium | Medium | Medium |
Cancer | Medium | Medium | Medium |
Mouse Genome Informatics
- Gene name
- Pex7
- Phenotype
- nervous system phenotype (the observable morphological and physiological characteristics of the extensive, intricate network of electochemical structures in the body that is comprised of the brain, spinal cord, nerves, ganglia and parts of the receptor organs that are manifested through development and lifespan); vision/eye phenotype; immune system phenotype; skeleton phenotype; liver/biliary system phenotype; behavior/neurological phenotype (the observable actions or reactions of mammalian organisms that are manifested through development and lifespan); reproductive system phenotype; mortality/aging (the observable characteristics related to the ability of a mammalian organism to live and age that are manifested throughout development and life span); cardiovascular system phenotype (the observable morphological and physiological characteristics of the mammalian heart, blood vessels, or circulatory system that are manifested through development and lifespan); hematopoietic system phenotype; growth/size/body region phenotype; endocrine/exocrine gland phenotype; muscle phenotype; cellular phenotype; homeostasis/metabolism phenotype;
Gene ontology
- Biological process
- neuron migration;endochondral ossification;protein targeting to peroxisome;fatty acid beta-oxidation;peroxisome organization;ether lipid biosynthetic process;protein import into peroxisome matrix
- Cellular component
- peroxisome;peroxisomal membrane;peroxisomal matrix;cytosol
- Molecular function
- peroxisome matrix targeting signal-2 binding;protein binding;enzyme binding;protein homodimerization activity