PRG4
protein-codingproteoglycan 4
Gene summary
The protein encoded by this gene is a large proteoglycan that is synthesized by chondrocytes located at the surface of articular cartilage and by some synovial lining cells. This protein contains both chondroitin sulfate and keratan sulfate glycosaminoglycans. It functions as a boundary lubricant at the cartilage surface and contributes to the elastic absorption and energy dissipation of synovial fluid. Mutations in this gene result in camptodactyly-arthropathy-coxa vara-pericarditis syndrome. Alternative splicing results in multiple transcript variants. [provided by RefSeq, Dec 2014]
- CACP
MANE transcript
Inheritance
ClinVar variants
Top phenotype
gnomAD constraint
Max pathogenic AF
Genomic locus
External References & Databases
Transcript & Mutation Effects
hg38 • Region Span ~18.3 kbGenCC Phenotypes & Disease Associations
Curated gene-disease validity assertions and inheritance patterns
Inheritance Pattern: AR
Disease ID:MONDO:0008828
Submitter: Illumina
The PRG4 gene is located on chromosome 1 at 1q31.1 and encodes the proteoglycan 4 protein, which is lubricating component of the synovial fluid and acts as a boundary lubricant at the cartilage surface. It also has a chondroprotective feature and acts by preventing protein deposition from the synovial fluid onto the cartilage surface. PRG4 was first reported in relation to autosomal recessive, camptodactyly-arthropathy-coxa vara-pericarditis syndrome in 1999 (10545950: Marcelino et al. 1999). At least seven unique loss of function variants have been reported in literature. Evidence supporting this gene-disease relationship includes case-level data, segregation data, experimental data. Variants in this gene have been reported in at least six probands from three publications (10545950: Marcelino et al. 1999; 27224999: Peters et al. 2016; 29397575: Yilmaz et al. 2018). Variants in this gene segregated with disease in three families. One of the families reported 12 affected family members, five of whom were genotyped. More evidence is available in the literature, but the maximum score for genetic evidence (12 pts.) has been reached. Homozygous loss of function is implicated as the mechanism of disease. This gene-disease association is supported by expression studies and two independent Prg4 -/- mouse modes that recapitulate the human disease (10545950: Marcelino et al. 1999; 15719068: Rhee et al. 2005; 20191580: Coles et al. 2010). In summary, PRG4 is definitively associated with autosomal recessive, camptodactyly-arthropathy-coxa vara-pericarditis syndrome.
Inheritance Pattern: AR
Disease ID:MONDO:0008828
Submitter: Labcorp Genetics (formerly Invitae)
Inheritance Pattern: AR
Disease ID:MONDO:0008828
Submitter: ClinGen
The PRG4 gene is located on chromosome 1 at 1q31.1 and encodes the proteoglycan 4 protein, which is a lubricating component of synovial fluid and acts as a boundary lubricant at the cartilage surface. It also has a chondroprotective feature and acts by preventing protein deposition from the synovial fluid onto the cartilage surface. PRG4 was first reported in relation to autosomal recessive, camptodactyly-arthropathy-coxa vara-pericarditis syndrome in 1999 (Marcelino et al., 1999 PMID 10545950). This is a rare disorder characterized by early onset camptodactyly, non-inflammatory arthropathy with synovial hyperplasia, and progressive coxa vara deformity. Pericardial or pleural effusions have also been reported in some patients. Camptodactyly is usually the first finding in the majority of patients, followed by swellings of the wrists, knees, and elbows around the age of 4 years. Large joint involvement and age of onset of pain varies among patients. Severe hip and vertebral involvement developed after 20 years of age. At least 7 unique loss of function variants have been reported in literature. Evidence supporting this gene-disease relationship includes case-level data, segregation data, and experimental data. Variants in this gene have been reported in at least 6 probands from 3 publications (Marcelino et al., 1999 PMID 10545950; Peters et al., 2016 PMID 27224999; Yilmaz et al., 2018 PMID 29397575). Variants in this gene segregated with disease in three families. One clan comprising five families reported 12 affected family members, five of whom were homozygous for the same variant (PMID 29397575). More evidence is available in the literature, but the maximum score for genetic evidence (12 pts.) has been reached. The mechanism for disease is biallelic loss of function. This gene-disease relationship is supported by two independent Prg4 KO mouse modes that recapitulate the human disease (Rhee et al., 2005 PMID 15719068; Coles et al., 2010 PMID 20191580). In summary, there is definitive evidence to support the relationship between PRG4 and autosomal recessive camptodactyly-arthropathy-coxa vara-pericarditis syndrome. 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 ClinGen Syndromic Disorders Gene Curation Expert Panel on the meeting date April 27th, 2021 (SOP Version 8).
Inheritance Pattern: AR
Disease ID:MONDO:0008828
Submitter: PanelApp Australia
Clinical Genomic Database (CGD)
Manifestation: Cardiovascular; Musculoskeletal
Intervention: Cardiovascular
Rationale: The disorder may be recognizable by noncardiac manifestations, but individuals frequently develop pericarditis refractory to other treatments and requiring pericardiectomy, and awareness may allow early detection and efficient targeted medical management
ClinVar Associated Diseases & Phenotypes
Reported disease conditions connected to PRG4 variants in ClinVar
ClinVar Variants & Pathogenicity by Type
Statistics based on transcript NM_005807.6. 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 | 58 | 1 | 59 | |||
| missense | 215 | 38 | 1 | 254 | ||
| nonsense | 4 | 6 | 10 | |||
| start loss | 0 | |||||
| frameshift | 25 | 18 | 43 | |||
| splice donor/acceptor (+/-2bp) | 3 | 1 | 1 | 5 | ||
| Total | 29 | 27 | 216 | 97 | 2 | 371 |
Highest pathogenic variant AF is 0.00014262486
Transcript Catalog
Annotated transcript isoforms across RefSeq and Ensembl databases
| Transcript ID | Source | Protein ID | Coding Exons | MANE Status |
|---|---|---|---|---|
| RefSeq | NP_005798.3 | 12 | MANE Select | |
| Ensembl | ENSP00000399679.3 | 12 | MANE Select | |
| RefSeq | NP_001121180.2 | 11 | Standard | |
| RefSeq | NP_001121181.2 | 10 | Standard |
Gene Ontology (GO) Annotations & Pathways
Biological processes, molecular functions, cellular components and pathways
Biological Process
- receptor-mediated endocytosis
- immune response
- cell population proliferation
Molecular Function
- scavenger receptor activity
- extracellular matrix structural constituent conferring compression resistance
- polysaccharide binding
Cellular Component
- collagen-containing extracellular matrix
gnomAD Constraint
Source:
- Gene type
- protein_coding
- Transcript type
- protein_coding
- Transcript
- ENST00000445192
- Coding exons
- 12
- Length
- 18290
- Individuals with no LoFs
- 125644
- Homozygous LoFs
- 0
- Heterozygous LoFs
- 104
- Defined
- 125748
- p
- 0.000414
| Z-Score | Observed | Expected | Observed/Expected | Mutation Rate | Total Possible | |
|---|---|---|---|---|---|---|
| Missense | -0.296 | 758 | 735 | 1.03 | 0.0000365 | 8930 |
| Missense (PolyPhen) | 77 | 93.497 | 0.82356 | 1313 | ||
| Synonymous | -0.698 | 278 | 264 | 1.05 | 0.0000138 | 3066 |
| Loss of Function | 2.80 | 19 | 37.5 | 0.507 | 0.00000170 | 605 |
Population LoF Frequency
| Population | CAF | p-value | Status |
|---|---|---|---|
| African | 0.0037 | 0.0036 | notable |
| Latino/Admixed American | 0.00029 | 0.00029 | rare |
| Ashkenazi Jewish | 0 | 0.0 | absent |
| East Asian | 0.00027 | 0.00027 | rare |
| Finnish | 0.000046 | 0.000046 | rare |
| European (Non-Finnish) | 0.00014 | 0.00014 | rare |
| South Asian | 0.00049 | 0.00046 | rare |
| Other | 0 | 0.0 | absent |
dbNSFP Gene Annotations
Source:
- Function
- FUNCTION: Plays a role in boundary lubrication within articulating joints. Prevents protein deposition onto cartilage from synovial fluid by controlling adhesion-dependent synovial growth and inhibiting the adhesion of synovial cells to the cartilage surface.;
- Disease
- DISEASE: Camptodactyly-arthropathy-coxa vara-pericarditis syndrome (CACP) [MIM:208250]: An autosomal recessive disorder characterized by the association of congenital or early-onset camptodactyly and non-inflammatory arthropathy with synovial hyperplasia. Individuals with CACP have normal appearing joints at birth but with advancing age develop joint failure, non-inflammatory synoviocyte hyperplasia and subintimal fibrosis of the synovial capsule. Some patients also manifest progressive coxa vara deformity and/or non-inflammatory pericardial or pleural effusions. {ECO:0000269|PubMed:10545950}. Note=The disease is caused by mutations affecting the gene represented in this entry.;
Intolerance Scores
- LoFtool
- 0.905
- RVIS EVS
- 1.5
- RVIS percentile EVS
- 95.39
Essentials
- Essential (CRISPR)
- N
- Essential (CRISPR2)
- N
- Essential (gene trap)
- N
- Indispensability pred.
- N
- Indispensability score
- 0.145
Gene Damage Prediction
| All | Recessive | Dominant | |
|---|---|---|---|
| Mendelian | Medium | Medium | Medium |
| Primary Immunodeficiency | Medium | Medium | High |
| Cancer | Medium | Medium | Medium |