PRX

protein-coding

periaxin, 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

NM_181882.3

Inheritance

AR, AD

ClinVar variants

P:101U:831B:485

Top phenotype

Dejerine-Sottas disease; Charcot-Marie-Tooth disease, type 4F

gnomAD constraint

pLI —, LoF o/e 0.71

Max pathogenic AF

—

Genomic locus

chr19:40,393,766-40,414,793

External References & Databases

Transcript & Mutation Effects

hg38 • Region Span ~21.0 kb
Loading mutation effect viewer...

GenCC Phenotypes & Disease Associations

Curated gene-disease validity assertions and inheritance patterns

Charcot-Marie-Tooth disease type 4FSUPPORTIVE

Inheritance Pattern: AR

Disease ID:MONDO:0013959

Submitter: Orphanet

Charcot-Marie-Tooth disease type 4STRONG

Inheritance Pattern: AR

Disease ID:MONDO:0018995

Submitter: PanelApp Australia

Charcot-Marie-Tooth disease type 4FSTRONG

Inheritance Pattern: AR

Disease ID:MONDO:0013959

Submitter: Labcorp Genetics (formerly Invitae)

Charcot-Marie-Tooth disease type 3SUPPORTIVE

Inheritance Pattern: AD

Disease ID:MONDO:0007790

Submitter: Orphanet

Charcot-Marie-Tooth disease type 4FSTRONG

Inheritance Pattern: AR

Disease ID:MONDO:0013959

Submitter: Ambry Genetics

Charcot-Marie-Tooth disease type 4DEFINITIVE

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.

Charcot-Marie-Tooth disease type 3MODERATE

Inheritance Pattern: AR

Disease ID:MONDO:0007790

Submitter: Ambry Genetics

Clinical Genomic Database (CGD)

Dejerine-Sottas disease; Charcot-Marie-Tooth disease, type 4FAR

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

Refs: 10848494; 11523566; 11157804; 12112076; 16534116; 21079185; 22847150Source: CGD (NHGRI)

ClinVar Associated Diseases & Phenotypes

Reported disease conditions connected to PRX variants in ClinVar

19 Conditions Cataloged
Charcot-Marie-Tooth disease type 4Total: 1125
Inborn genetic diseasesTotal: 448
not providedTotal: 375
PRX-related disorderTotal: 206
Charcot-Marie-Tooth diseaseTotal: 205
Charcot-Marie-Tooth disease type 4FTotal: 169
not specifiedTotal: 142
Dejerine-Sottas diseaseTotal: 33

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.

EffectPLPVUSLBBSum
synonymous
7
clinvar
413
clinvar
7
clinvar
427
missense
1
clinvar
797
clinvar
59
clinvar
6
clinvar
863
nonsense
12
clinvar
19
clinvar
10
clinvar
41
start loss
1
clinvar
1
frameshift
33
clinvar
32
clinvar
16
clinvar
81
splice donor/acceptor (+/-2bp)
1
clinvar
2
clinvar
1
clinvar
4
Total4655831472131417

Highest pathogenic variant AF is 0.000023544018

Loading ClinVar variants...

Transcript Catalog

Annotated transcript isoforms across RefSeq and Ensembl databases

Showing 4 of 25 transcripts
Transcript IDSourceProtein IDCoding ExonsMANE Status
NM_181882.3RefSeqNP_870998.24MANE Select
ENST00000324001.8EnsemblENSP00000326018.64MANE Select
NM_001411127.1RefSeqNP_001398056.17Standard
NM_020956.2RefSeqNP_066007.13Standard

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: gnomAD

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-ScoreObservedExpectedObserved/ExpectedMutation RateTotal Possible
Missense-0.1318628511.010.00005429100
Missense (PolyPhen)9987.2761.1343844
Synonymous-0.01133763761.000.00002503363
Loss of Function1.632737.90.7130.00000253467

Population LoF Frequency

PopulationCAFp-valueStatus
African0.000700.00068rare
Latino/Admixed American0.000990.00098rare
Ashkenazi Jewish0.000300.00030rare
East Asian0.000710.00071rare
Finnish0.000430.00042rare
European (Non-Finnish)0.000300.00029rare
South Asian0.000300.00029rare
Other0.00110.0011notable

dbNSFP Gene Annotations

Source: dbNSFP

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

AllRecessiveDominant
MendelianMediumMediumMedium
Primary ImmunodeficiencyMediumMediumMedium
CancerMediumMediumMedium
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