PRSS53

serine protease 53, the group of Serine proteases

Basic information

Region (hg38): 16:31083437-31089628

Links

ENSG00000151006 ∙ NCBI:339105 ∙ OMIM:610561 ∙ HGNC:34407 ∙ Uniprot:Q2L4Q9 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

Phenotypes

GenCC

Source: genCC

No genCC data.

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the PRSS53 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the PRSS53 gene is commonly pathogenic or not.

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.

Variant type	Pathogenic	Likely pathogenic	VUS	Likely benign	Benign	Sum
synonymous				1		1
missense			36	2	1	39
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	36	3	1

Variants in PRSS53

This is a list of pathogenic ClinVar variants found in the PRSS53 region.

You can filter this list by clicking the number of variants in the Variants pathogenicity by type table.

Position	Type	Phenotype	Significance	ClinVar
16-31084143-G-A		not specified	Uncertain significance (Feb 15, 2023)
16-31084167-C-T		not specified	Uncertain significance (Jul 19, 2022)
16-31084173-A-G		not specified	Uncertain significance (Jul 26, 2022)
16-31084223-G-A		not specified	Uncertain significance (Jun 22, 2024)
16-31084266-C-T		not specified	Uncertain significance (Aug 17, 2022)
16-31084281-C-T		not specified	Uncertain significance (Aug 13, 2021)
16-31084298-C-T		not specified	Uncertain significance (Dec 06, 2021)
16-31084322-G-T		not specified	Uncertain significance (Aug 11, 2022)
16-31084620-C-T		not specified	Uncertain significance (Dec 09, 2023)
16-31084638-C-T		not specified	Likely benign (May 05, 2023)
16-31084658-C-G		not specified	Uncertain significance (Oct 26, 2022)
16-31084797-C-T		not specified	Uncertain significance (Aug 26, 2022)
16-31084910-C-A		not specified	Uncertain significance (Sep 26, 2022)
16-31084924-C-G		not specified	Uncertain significance (Dec 31, 2023)
16-31084935-G-A		not specified	Uncertain significance (Apr 04, 2024)
16-31084980-G-A		not specified	Uncertain significance (Jun 16, 2023)
16-31084999-C-T		not specified	Uncertain significance (Mar 11, 2024)
16-31085022-C-T		not specified	Uncertain significance (Jan 10, 2022)
16-31085121-G-A			Likely benign (Jan 01, 2023)
16-31085168-A-G		not specified	Uncertain significance (Apr 11, 2023)
16-31085219-G-A		not specified	Uncertain significance (Apr 06, 2024)
16-31086004-G-C		not specified	Uncertain significance (Jul 14, 2021)
16-31086125-C-G		not specified	Uncertain significance (Oct 27, 2023)
16-31086145-G-C		not specified	Uncertain significance (Sep 20, 2023)
16-31086153-C-G		not specified	Uncertain significance (Aug 02, 2021)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
PRSS53	protein_coding	protein_coding	ENST00000280606	11	6204

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
9.35e-17	0.00927	124655	0	163	124818	0.000653

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.485	294	318	0.923	0.0000185	3463
Missense in Polyphen		109	133.02	0.81941		1515
Synonymous	-0.0345	131	131	1.00	0.00000804	1155
Loss of Function	0.113	25	25.6	0.976	0.00000117	275

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.00471	0.00468
Ashkenazi Jewish	0.00221	0.00219
East Asian	0.000171	0.000167
Finnish	0.00	0.00
European (Non-Finnish)	0.000396	0.000388
Middle Eastern	0.000171	0.000167
South Asian	0.000232	0.000229
Other	0.000499	0.000495

dbNSFP

Source: dbNSFP

• Function: FUNCTION: In vitro can degrade the fibrinogen alpha chain of as well as pro-urokinase-type plasminogen activator. {ECO:0000269|PubMed:16566820}.

Intolerance Scores

• rvis_EVS: -0.69
• rvis_percentile_EVS: 15.2

Haploinsufficiency Scores

• hipred: N
• hipred_score: 0.144
• ghis: 0.510

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.114

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Prss53

Gene ontology

• Biological process: proteolysis
• Cellular component: extracellular region;cytoplasm
• Molecular function: serine-type endopeptidase activity