PRSS56
protein-codingserine protease 56, the group of Serine proteases
Gene summary
This gene encodes a protein that contains a peptidase S1 domain and possesses trypsin-like serine protease activity. The encoded protein may play a role in eye development, and mutations in this gene are a cause of autosomal recessive posterior microphthalmos. [provided by RefSeq, Dec 2011]
MANE transcript
Inheritance
ClinVar variants
Top phenotype
gnomAD constraint
Max pathogenic AF
Genomic locus
External References & Databases
Transcript & Mutation Effects
hg38 • Region Span ~5.3 kbGenCC Phenotypes & Disease Associations
Curated gene-disease validity assertions and inheritance patterns
Inheritance Pattern: AR
Disease ID:MONDO:0013293
Submitter: G2P
Inheritance Pattern: AR
Disease ID:MONDO:0013293
Submitter: Labcorp Genetics (formerly Invitae)
Inheritance Pattern: AR
Disease ID:MONDO:0013293
Submitter: ClinGen
The *PRSS56* gene was first reported in relation to microphthalmia in 2011, with the identification of homozygous or compound heterozygous *PRSS56* variants in a number of affected individuals including multiple large families (Gal et al., PMID: 21397065, Nair et al., PMID: 21532570, and Orr et al., PMID: 21850159). Affected individuals are generally reported with a diagnosis of posterior microphthalmia or nanophthalmia and exhibit clinical features including short axial length, high hypermetropia, reduced visual acuity, high intraocular pressure, angle closure glaucoma, crowded optic discs, and/or papillomacular fold. Per criteria outlined by the ClinGen Lumping & Splitting Working Group, the molecular mechanism (biallelic loss of function) and mode of inheritance (autosomal recessive) were found to be consistent among patients regardless of diagnosis, while the phenotypic variability between them appeared to represent a spectrum of disease rather than separate disease entities. Therefore, cases caused by inherited *PRSS56* variants have been lumped for curation as a single disease entity, referred to as PRSS56-related nanophthalmos. This curation has scored eight suspected disease-causing variants (three frameshift, four missense, and one canonical splice site disruption), which have collectively been reported in eight probands from six publications (PMID: 21397065, PMID: 21532570, PMID: 21850159, PMID: 23127749, PMID: 31992737, PMID: 33203948). Two of the variants are predicted to trigger nonsense-mediated decay, consistent with a biallelic loss-of-function mechanism of pathogenicity. Co-segregation of the homozygous genotype with affected status in the proband’s family was also incorporated into the genetic evidence component of this curation (PMID: 23127749). Additional genetic evidence was available but not included in this curation. This gene-disease association is also supported by evidence that *PRSS56* is highly expressed in retina, as well as in the testis, muscle and brain (PMID: 30239781). The specific areas of the retina with highest expression are the inner nuclear layer and the ganglion cell layer (PMID: 21532570). Biochemical studies indicate that *PRSS56* encodes a secreted serine protease (PMID: 21532570, PMID: 37400936). This is consistent with electron microscopy results from mice indicating that homozygous *Prss56* loss-of-function results in focal hypoplasia of the trabecular meshwork, reduced collagen fibrils in the trabecular beams, increased occurrence of open spaces lacking extracellular matrix, and foci of collagen fibril crowding in the sclera (PMID: 21532570). Mouse models additionally show short axial eye length, reduced vitreous chamber depth and equatorial diameter, and reduced distance between the retina and Schlemm's canal leading to angle closure, as well as choroidal expansion, anterior chamber enlargement, hyperopia, high intraocular pressure with reduced outflow facility, and glaucomatous nerve damage with optic nerve excavation and nerve fiber layer thinning (PMID: 21532570, PMID: 32152063). In summary, *PRSS56* has definitive evidence of association with PRSS56-related nanophthalmos. This has been repeatedly demonstrated in both research and diagnostic settings, and has been upheld over time without the emergence of contradictory evidence, leading to a Definitive classification. This classification was approved by the ClinGen Glaucoma and Neuro-Ophthalmology Gene Curation Expert Panel on May 15th, 2025 (SOP Version 11).
Inheritance Pattern: AD
Disease ID:MONDO:0005514
Submitter: Orphanet
Inheritance Pattern: AR
Disease ID:MONDO:0013293
Submitter: PanelApp Australia
Clinical Genomic Database (CGD)
Manifestation: Ophthalmologic
Intervention: Ophthalmologic; Pharmacogenomic
Rationale: Some individuals with angle-closure glaucoma have been described, and awareness of disease risk and surveillance may allow early treatment; Agents that may contribute to glaucoma should be avoided
ClinVar Associated Diseases & Phenotypes
Reported disease conditions connected to PRSS56 variants in ClinVar
ClinVar Variants & Pathogenicity by Type
Statistics based on transcript NM_001195129.2. 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 | 27 | 2 | 29 | |||
| missense | 5 | 7 | 135 | 8 | 4 | 159 |
| nonsense | 3 | 3 | ||||
| start loss | 0 | |||||
| frameshift | 4 | 4 | 8 | |||
| splice donor/acceptor (+/-2bp) | 2 | 5 | 7 | |||
| Total | 14 | 11 | 140 | 35 | 6 | 206 |
Highest pathogenic variant AF is 0.0003894091
Transcript Catalog
Annotated transcript isoforms across RefSeq and Ensembl databases
| Transcript ID | Source | Protein ID | Coding Exons | MANE Status |
|---|---|---|---|---|
| RefSeq | NP_001182058.1 | 13 | MANE Select | |
| Ensembl | ENSP00000479745.1 | 13 | MANE Select | |
| RefSeq | NP_001356777.1 | 13 | Standard | |
| RefSeq | XP_047301387.1 | 12 | Standard |
Gene Ontology (GO) Annotations & Pathways
Biological processes, molecular functions, cellular components and pathways
Biological Process
- proteolysis
- camera-type eye development
Molecular Function
- serine-type endopeptidase activity
Cellular Component
- extracellular space
- endoplasmic reticulum
gnomAD Constraint
Source:
- Gene type
- protein_coding
- Transcript type
- protein_coding
- Transcript
- ENST00000449534
- Coding exons
- 13
- Length
- 5250
- Individuals with no LoFs
- 0
- Homozygous LoFs
- 0
- Heterozygous LoFs
- 0
- Defined
- 0
- p
- 0.00
| Z-Score | Observed | Expected | Observed/Expected | Mutation Rate | Total Possible | |
|---|---|---|---|---|---|---|
| Missense | 1.05 | 241 | 292 | 0.826 | 0.0000159 | 3693 |
| Missense (PolyPhen) | 61 | 88.623 | 0.68831 | 1211 | ||
| Synonymous | 0.536 | 129 | 137 | 0.942 | 0.00000790 | 1379 |
| Loss of Function | 2.69 | 10 | 24.3 | 0.411 | 0.00000129 | 281 |
Population LoF Frequency
| Population | CAF | p-value | Status |
|---|---|---|---|
| African | 0 | 0.0 | absent |
| Latino/Admixed American | 0 | 0.0 | absent |
| Ashkenazi Jewish | 0 | 0.0 | absent |
| East Asian | 0 | 0.0 | absent |
| Finnish | 0 | 0.0 | absent |
| European (Non-Finnish) | 0 | 0.0 | absent |
| South Asian | 0 | 0.0 | absent |
| Other | 0 | 0.0 | absent |
dbNSFP Gene Annotations
Source:
- Function
- FUNCTION: Serine protease required during eye development. {ECO:0000269|PubMed:21397065}.;
- Disease
- DISEASE: Microphthalmia, isolated, 6 (MCOP6) [MIM:613517]: A developmental ocular disorder characterized by small malformed eyes. Clinical features are extreme hyperopia due to short axial length with essentially normal anterior segment, steep corneal curvatures, shallow anterior chamber, thick lenses, and thickened scleral wall. Palpebral fissures appear narrow because of relatively deep-set eyes, visual acuity is mildly to moderately reduced, and anisometropic or strabismic amblyopia is common. The fundus of the eye shows crowded optical disks, tortuous vessels, and an abnormal foveal avascular zone. {ECO:0000269|PubMed:21397065, ECO:0000269|PubMed:21532570, ECO:0000269|PubMed:21850159}. Note=The disease is caused by mutations affecting the gene represented in this entry.;
Essentials
- Essential (CRISPR2)
- N
Gene Damage Prediction
| All | Recessive | Dominant | |
|---|---|---|---|
| Mendelian | Medium | Medium | Medium |
| Primary Immunodeficiency | Medium | Medium | Medium |
| Cancer | Medium | Medium | Medium |