PRSS56

serine protease 56, the group of Serine proteases

Basic information

Region (hg38): 2:232520388-232525716

Links

ENSG00000237412

∙ NCBI:646960 ∙ OMIM:613858 ∙ HGNC:39433 ∙ Uniprot:P0CW18 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

Phenotypes

GenCC

Source: genCC

nanophthalmia (Supportive), mode of inheritance: AD
isolated microphthalmia 6 (Definitive), mode of inheritance: AR
isolated microphthalmia 6 (Strong), mode of inheritance: AR
isolated microphthalmia 6 (Strong), mode of inheritance: AR

Clinical Genomic Database

Source: CGD

Condition	Inheritance	Intervention Categories	Intervention/Rationale	Manifestation Categories	References
Microphthalmia, isolated 6	AR	Ophthalmologic; Pharmacogenomic	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	Ophthalmologic	15823920; 19526372; 21397065; 21532570; 21850159; 23127749

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the PRSS56 gene.

Inborn_genetic_diseases (103 variants)
Isolated_microphthalmia_6 (96 variants)
not_provided (28 variants)
PRSS56-related_disorder (7 variants)
Nanophthalmia (1 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the PRSS56 gene is commonly pathogenic or not. These statistics are base on transcript: NM_001195129.2. Only rare variants are included in the table.

In the table, we include only reliable ClinVar variants with their consequences to MANE Select, Mane Plus Clinical transcripts, or transcripts with TSL equals 1. Click the count to view the source variants.

Warning: slight differences between displayed counts and the number of variants in ClinVar may occur, primarily due to (1) the application of a different transcript and/or consequence by our variant effect predictor or (2) differences in clinical significance: we classify Benign/Likely benign variants as Likely benign and Pathogenic/Likely pathogenic variants as Likely pathogenic.

Effect	PathogenicP	Likely pathogenicLP	VUSVUS	Likely benignLB	BenignB	Sum
synonymous				20 clinvar	4 clinvar	24
missense	5 clinvar	5 clinvar	120 clinvar	8 clinvar	4 clinvar	142
nonsense	2 clinvar					2
start loss						0
frameshift	5 clinvar	2 clinvar				7
splice donor/acceptor (+/-2bp)	2 clinvar					2
Total	14	7	120	28	8

Highest pathogenic variant AF is 0.000389409

Loading clinvar variants...

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
PRSS56	protein_coding	protein_coding	ENST00000449534	13	5250

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.000341	0.998	0	0	0	0	0.00

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	1.05	241	292	0.826	0.0000159	3693
Missense in 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

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.00	0.00
Ashkenazi Jewish	0.00	0.00
East Asian	0.00	0.00
Finnish	0.00	0.00
European (Non-Finnish)	0.00	0.00
Middle Eastern	0.00	0.00
South Asian	0.00	0.00
Other	0.00	0.00

dbNSFP

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_gene_CRISPR
essential_gene_CRISPR2: N
essential_gene_gene_trap
gene_indispensability_pred
gene_indispensability_score

Gene Damage Prediction

	All	Recessive	Dominant
Mendelian	Medium	Medium	Medium
Primary Immunodeficiency	Medium	Medium	Medium
Cancer	Medium	Medium	Medium

Mouse Genome Informatics

Gene name: Prss56
Phenotype: hematopoietic system phenotype; nervous system phenotype (the observable morphological and physiological characteristics of the extensive, intricate network of electochemical structures in the body that is comprised of the brain, spinal cord, nerves, ganglia and parts of the receptor organs that are manifested through development and lifespan); vision/eye phenotype; immune system phenotype;

Gene ontology

Biological process: proteolysis;camera-type eye development
Cellular component: extracellular space;endoplasmic reticulum
Molecular function: serine-type endopeptidase activity