PRSS56

protein-coding

serine 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

NM_001195129.2

Inheritance

AR, AD

ClinVar variants

P:25U:140B:41

Top phenotype

Microphthalmia, isolated 6

gnomAD constraint

pLI —, LoF o/e 0.41

Max pathogenic AF

—

Genomic locus

chr2:232,520,388-232,525,716

External References & Databases

Transcript & Mutation Effects

hg38 • Region Span ~5.3 kb
Loading mutation effect viewer...

GenCC Phenotypes & Disease Associations

Curated gene-disease validity assertions and inheritance patterns

isolated microphthalmia 6DEFINITIVE

Inheritance Pattern: AR

Disease ID:MONDO:0013293

Submitter: G2P

isolated microphthalmia 6STRONG

Inheritance Pattern: AR

Disease ID:MONDO:0013293

Submitter: Labcorp Genetics (formerly Invitae)

isolated microphthalmia 6DEFINITIVE

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).

nanophthalmiaSUPPORTIVE

Inheritance Pattern: AD

Disease ID:MONDO:0005514

Submitter: Orphanet

isolated microphthalmia 6STRONG

Inheritance Pattern: AR

Disease ID:MONDO:0013293

Submitter: PanelApp Australia

Clinical Genomic Database (CGD)

Microphthalmia, isolated 6AR

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

Refs: 15823920; 19526372; 21397065; 21532570; 21850159; 23127749Source: CGD (NHGRI)

ClinVar Associated Diseases & Phenotypes

Reported disease conditions connected to PRSS56 variants in ClinVar

6 Conditions Cataloged
Inborn genetic diseasesTotal: 116
Isolated microphthalmia 6Total: 106
not providedTotal: 34
PRSS56-related disorderTotal: 10
not specifiedTotal: 9
NanophthalmiaTotal: 2

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.

EffectPLPVUSLBBSum
synonymous
27
clinvar
2
clinvar
29
missense
5
clinvar
7
clinvar
135
clinvar
8
clinvar
4
clinvar
159
nonsense
3
clinvar
3
start loss
0
frameshift
4
clinvar
4
clinvar
8
splice donor/acceptor (+/-2bp)
2
clinvar
5
clinvar
7
Total1411140356206

Highest pathogenic variant AF is 0.0003894091

Loading ClinVar variants...

Transcript Catalog

Annotated transcript isoforms across RefSeq and Ensembl databases

Showing 4 of 4 transcripts
Transcript IDSourceProtein IDCoding ExonsMANE Status
NM_001195129.2RefSeqNP_001182058.113MANE Select
ENST00000617714.2EnsemblENSP00000479745.113MANE Select
NM_001369848.1RefSeqNP_001356777.113Standard
XM_047445431.1RefSeqXP_047301387.112Standard

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: gnomAD

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-ScoreObservedExpectedObserved/ExpectedMutation RateTotal Possible
Missense1.052412920.8260.00001593693
Missense (PolyPhen)6188.6230.688311211
Synonymous0.5361291370.9420.000007901379
Loss of Function2.691024.30.4110.00000129281

Population LoF Frequency

PopulationCAFp-valueStatus
African00.0absent
Latino/Admixed American00.0absent
Ashkenazi Jewish00.0absent
East Asian00.0absent
Finnish00.0absent
European (Non-Finnish)00.0absent
South Asian00.0absent
Other00.0absent

dbNSFP Gene Annotations

Source: dbNSFP

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

AllRecessiveDominant
MendelianMediumMediumMedium
Primary ImmunodeficiencyMediumMediumMedium
CancerMediumMediumMedium
For research and educational, non-commercial use only. Not for clinical or diagnostic use. GeneBe does not provide medical advice. Data use for AI modeling is prohibited: if used, the cost is $0.001 per byte of downloaded uncompressed data.