PRB4
protein-codingproline rich protein BstNI subfamily 4, the group of Proline rich proteins
Gene summary
This gene encodes a member of the heterogeneous family of basic, proline-rich, human salivary glycoproteins. The encoded preproprotein undergoes proteolytic processing to generate one or more mature peptides before secretion from the parotid glands. Multiple alleles of this gene exhibiting variations in the length of the tandem repeats have been identified. The reference genome encodes the "Small" allele. This gene is located in a cluster of closely related salivary proline-rich proteins on chromosome 12. Alternative splicing results in multiple transcript variants encoding different isoforms that may undergo similar proteolytic processing. [provided by RefSeq, Nov 2015]
MANE transcript
Inheritance
ClinVar variants
Top phenotype
gnomAD constraint
Max pathogenic AF
Genomic locus
External References & Databases
Transcript & Mutation Effects
hg38 • Region Span ~3.4 kbGenCC Phenotypes & Disease Associations
Curated gene-disease validity assertions and inheritance patterns
No GenCC data available for this gene.
ClinVar Associated Diseases & Phenotypes
Reported disease conditions connected to PRB4 variants in ClinVar
ClinVar Variants & Pathogenicity by Type
Statistics based on transcript NM_002723.6. 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 | 7 | 7 | ||||
| missense | 48 | 5 | 1 | 54 | ||
| nonsense | 0 | |||||
| start loss | 0 | |||||
| frameshift | 0 | |||||
| splice donor/acceptor (+/-2bp) | 1 | 1 | ||||
| Total | 0 | 0 | 49 | 12 | 1 | 62 |
Transcript Catalog
Annotated transcript isoforms across RefSeq and Ensembl databases
| Transcript ID | Source | Protein ID | Coding Exons | MANE Status |
|---|---|---|---|---|
| RefSeq | NP_002714.2 | 3 | MANE Select | |
| Ensembl | ENSP00000279575.1 | 3 | MANE Select | |
| RefSeq | NP_001248328.1 | 4 | Standard | |
| Ensembl | ENSP00000412740.2 | 4 | Standard |
Gene Ontology (GO) Annotations & Pathways
Biological processes, molecular functions, cellular components and pathways
Biological Process
- biological_process
Molecular Function
- molecular_function
Cellular Component
- extracellular region
gnomAD Constraint
Source:
- Gene type
- protein_coding
- Transcript type
- protein_coding
- Transcript
- ENST00000279575
- Coding exons
- 3
- Length
- 3353
- Individuals with no LoFs
- 91945
- Homozygous LoFs
- 351
- Heterozygous LoFs
- 33452
- Defined
- 125748
- p
- 0.145
| Z-Score | Observed | Expected | Observed/Expected | Mutation Rate | Total Possible | |
|---|---|---|---|---|---|---|
| Missense | -3.21 | 234 | 131 | 1.79 | 0.00000645 | 1472 |
| Missense (PolyPhen) | ||||||
| Synonymous | -1.69 | 60 | 45.5 | 1.32 | 0.00000196 | 560 |
| Loss of Function | -2.93 | 10 | 3.82 | 2.62 | 1.63e-7 | 48 |
Population LoF Frequency
| Population | CAF | p-value | Status |
|---|---|---|---|
| African | 0.036 | 0.034 | notable |
| Latino/Admixed American | 0.16 | 0.17 | notable |
| Ashkenazi Jewish | 0.11 | 0.12 | notable |
| East Asian | 0.0012 | 0.0011 | notable |
| Finnish | 0.18 | 0.20 | notable |
| European (Non-Finnish) | 0.18 | 0.20 | notable |
| South Asian | 0.066 | 0.067 | notable |
| Other | 0.15 | 0.16 | notable |
dbNSFP Gene Annotations
Source:
Intolerance Scores
- LoFtool
- 0.976
- RVIS EVS
- 1.35
- RVIS percentile EVS
- 94.37
Essentials
- Essential (CRISPR)
- N
- Indispensability pred.
- N
- Indispensability score
- 0.00223
Gene Damage Prediction
| All | Recessive | Dominant | |
|---|---|---|---|
| Mendelian | Medium | Medium | Medium |
| Primary Immunodeficiency | Medium | Medium | Medium |
| Cancer | Medium | Medium | Medium |