PRX
protein-codingperiaxin, the group of PDZ domain containing
Gene summary
This gene encodes a protein involved in peripheral nerve myelin upkeep. The encoded protein contains 2 PDZ domains which were named after PSD95 (post synaptic density protein), DlgA (Drosophila disc large tumor suppressor), and ZO1 (a mammalian tight junction protein). Two alternatively spliced transcript variants have been described for this gene which encode different protein isoforms and which are targeted differently in the Schwann cell. Mutations in this gene cause Charcot-Marie-Tooth neuoropathy, type 4F and Dejerine-Sottas neuropathy. [provided by RefSeq, Jul 2008]
MANE transcript
Inheritance
ClinVar variants
Top phenotype
gnomAD constraint
Max pathogenic AF
Genomic locus
External References & Databases
Transcript & Mutation Effects
hg38 • Region Span ~21.0 kbGenCC Phenotypes & Disease Associations
Curated gene-disease validity assertions and inheritance patterns
Inheritance Pattern: AR
Disease ID:MONDO:0013959
Submitter: Orphanet
Inheritance Pattern: AR
Disease ID:MONDO:0018995
Submitter: PanelApp Australia
Inheritance Pattern: AR
Disease ID:MONDO:0013959
Submitter: Labcorp Genetics (formerly Invitae)
Inheritance Pattern: AD
Disease ID:MONDO:0007790
Submitter: Orphanet
Inheritance Pattern: AR
Disease ID:MONDO:0013959
Submitter: Ambry Genetics
Inheritance Pattern: AR
Disease ID:MONDO:0018995
Submitter: ClinGen
PRX was first reported in relation to autosomal Charcot-Marie-Tooth disease type 4 in 2001 in a large consanguineous Lebanese family (Guilbot et al., PMID: 11157804). Patients had severe and slowly progressive demyelinating CMT with onset in early childhood. A homozygous stop-gain variant, Arg196X, segregated in the affected individuals. Linkage analysis revealed a LOD score of 5.3. PRX mutations have also been frequently reported in patients diagnosed with Dejerine Sottas neuropathy (Boerkoel et al., PMID: 11133365). Both phenotypes are part of the same disease spectrum consisting of early-onset severe demyelinating motor and sensory neuropathy. Per criteria outlined by the ClinGen Lumping and Splitting Working Group, we found no difference in molecular mechanism, inheritance pattern, and phenotypic variability. Therefore, the following disease entities have been lumped into one disease entity, autosomal recessive CMT type 4. Ten families with biallelic loss-of-function variants (nonsense and frameshift) from different publications have been included in this curation. Most variants are localized to the last exon and escape nonsense mediated mRNA decay. Expression of a truncated protein was detected in patient nerve biopsies (PMID: 12112076). More evidence is available in the literature, but the maximum score for genetic evidence (12 pts.) has been reached. The mechanism of pathogenicity is not known. This gene-disease association is also supported by a PRX knockout mouse model, which developed an unsteady gait phenotype and demyelinating motor and sensory neuropathy (PMID: 10839370). In summary, the final classification for PRX is definitive. This has been repeatedly demonstrated in both the research and clinical diagnostic settings and has been upheld over time.
Inheritance Pattern: AR
Disease ID:MONDO:0007790
Submitter: Ambry Genetics
Clinical Genomic Database (CGD)
Manifestation: Neurologic
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
ClinVar Associated Diseases & Phenotypes
Reported disease conditions connected to PRX variants in ClinVar
ClinVar Variants & Pathogenicity by Type
Statistics based on transcript NM_181882.3. 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.
| Effect | PathogenicP | Likely pathogenicLP | VUS | Likely benignLB | BenignB | Sum |
|---|---|---|---|---|---|---|
| synonymous | 7 | 413 | 7 | 427 | ||
| missense | 1 | 797 | 59 | 6 | 863 | |
| nonsense | 12 | 19 | 10 | 41 | ||
| start loss | 1 | 1 | ||||
| frameshift | 33 | 32 | 16 | 81 | ||
| splice donor/acceptor (+/-2bp) | 1 | 2 | 1 | 4 | ||
| Total | 46 | 55 | 831 | 472 | 13 | 1417 |
Highest pathogenic variant AF is 0.000023544018
Transcript Catalog
Annotated transcript isoforms across RefSeq and Ensembl databases
| Transcript ID | Source | Protein ID | Coding Exons | MANE Status |
|---|---|---|---|---|
| RefSeq | NP_870998.2 | 4 | MANE Select | |
| Ensembl | ENSP00000326018.6 | 4 | MANE Select | |
| RefSeq | NP_001398056.1 | 7 | Standard | |
| RefSeq | NP_066007.1 | 3 | Standard |
Gene Ontology (GO) Annotations & Pathways
Biological processes, molecular functions, cellular components and pathways
Biological Process
- axon ensheathment
- regulation of RNA splicing
Molecular Function
- molecular_function
- protein binding
Cellular Component
- nucleus
- cytoplasm
- plasma membrane
- cell junction
- T-tubule
gnomAD Constraint
Source:
- Gene type
- protein_coding
- Transcript type
- protein_coding
- Transcript
- ENST00000324001
- Coding exons
- 4
- Length
- 19599
- Individuals with no LoFs
- 125629
- Homozygous LoFs
- 0
- Heterozygous LoFs
- 119
- Defined
- 125748
- p
- 0.000473
| Z-Score | Observed | Expected | Observed/Expected | Mutation Rate | Total Possible | |
|---|---|---|---|---|---|---|
| Missense | -0.131 | 862 | 851 | 1.01 | 0.0000542 | 9100 |
| Missense (PolyPhen) | 99 | 87.276 | 1.1343 | 844 | ||
| Synonymous | -0.0113 | 376 | 376 | 1.00 | 0.0000250 | 3363 |
| Loss of Function | 1.63 | 27 | 37.9 | 0.713 | 0.00000253 | 467 |
Population LoF Frequency
| Population | CAF | p-value | Status |
|---|---|---|---|
| African | 0.00070 | 0.00068 | rare |
| Latino/Admixed American | 0.00099 | 0.00098 | rare |
| Ashkenazi Jewish | 0.00030 | 0.00030 | rare |
| East Asian | 0.00071 | 0.00071 | rare |
| Finnish | 0.00043 | 0.00042 | rare |
| European (Non-Finnish) | 0.00030 | 0.00029 | rare |
| South Asian | 0.00030 | 0.00029 | rare |
| Other | 0.0011 | 0.0011 | notable |
dbNSFP Gene Annotations
Source:
- Function
- FUNCTION: Scaffolding protein that functions as part of a dystroglycan complex in Schwann cells, and as part of EZR and AHNAK-containing complexes in eye lens fiber cells. Required for the maintenance of the peripheral myelin sheath that is essential for normal transmission of nerve impulses and normal perception of sensory stimuli. Required for normal transport of MBP mRNA from the perinuclear to the paranodal regions. Required for normal remyelination after nerve injury. Required for normal elongation of Schwann cells and normal length of the internodes between the nodes of Ranvier. The demyelinated nodes of Ranvier permit saltatory transmission of nerve impulses; shorter internodes cause slower transmission of nerve impulses. Required for the formation of appositions between the abaxonal surface of the myelin sheath and the Schwann cell plasma membrane; the Schwann cell cytoplasm is restricted to regions between these appositions. Required for the formation of Cajal bands and of Schmidt-Lanterman incisures that correspond to short, cytoplasm-filled regions on myelinated nerves. Recruits DRP2 to the Schwann cell plasma membrane. Required for normal protein composition of the eye lens fiber cell plasma membrane and normal eye lens fiber cell morphology. {ECO:0000250|UniProtKB:O55103}.;
- Disease
- DISEASE: Dejerine-Sottas syndrome (DSS) [MIM:145900]: A severe degenerating neuropathy of the demyelinating Charcot-Marie-Tooth disease category, with onset by age 2 years. Characterized by motor and sensory neuropathy with very slow nerve conduction velocities, increased cerebrospinal fluid protein concentrations, hypertrophic nerve changes, delayed age of walking as well as areflexia. There are both autosomal dominant and autosomal recessive forms of Dejerine-Sottas syndrome. {ECO:0000269|PubMed:11133365}. Note=The disease is caused by mutations affecting the gene represented in this entry.; DISEASE: Charcot-Marie-Tooth disease 4F (CMT4F) [MIM:614895]: A recessive demyelinating form of Charcot-Marie-Tooth disease, a disorder of the peripheral nervous system, characterized by progressive weakness and atrophy, initially of the peroneal muscles and later of the distal muscles of the arms. Charcot- Marie-Tooth disease is classified in two main groups on the basis of electrophysiologic properties and histopathology: primary peripheral demyelinating neuropathies (designated CMT1 when they are dominantly inherited) and primary peripheral axonal neuropathies (CMT2). Demyelinating neuropathies are characterized by severely reduced nerve conduction velocities (less than 38 m/sec), segmental demyelination and remyelination with onion bulb formations on nerve biopsy, slowly progressive distal muscle atrophy and weakness, absent deep tendon reflexes, and hollow feet. By convention autosomal recessive forms of demyelinating Charcot-Marie-Tooth disease are designated CMT4. CMT4F is characterized by distal sensory impairment and distal muscle weakness and atrophy affecting the lower more than the upper limbs. The age at onset is variable and can range from childhood to adult years. When the onset is in infancy, the phenotype is characterized as Dejerine-Sottas syndrome. {ECO:0000269|PubMed:22847150}. Note=The disease is caused by mutations affecting the gene represented in this entry.;
Recessive Scores
- pRec
- 0.170
Intolerance Scores
- LoFtool
- 0.749
- RVIS EVS
- -0.18
- RVIS percentile EVS
- 40.17
Essentials
- Essential (CRISPR)
- N
- Essential (CRISPR2)
- N
- Essential (gene trap)
- N
- Indispensability pred.
- E
- Indispensability score
- 0.659
Gene Damage Prediction
| All | Recessive | Dominant | |
|---|---|---|---|
| Mendelian | Medium | Medium | Medium |
| Primary Immunodeficiency | Medium | Medium | Medium |
| Cancer | Medium | Medium | Medium |