PRSS53

protein-coding

serine protease 53, the group of Serine proteases

Gene summary

Predicted to enable serine-type endopeptidase activity. Predicted to be involved in proteolysis. Predicted to be located in extracellular region. [provided by Alliance of Genome Resources, Jul 2025]

MANE transcript

NM_001039503.3

Inheritance

—

ClinVar variants

U:105B:7

Top phenotype

—

gnomAD constraint

pLI —, LoF o/e 0.98

Max pathogenic AF

—

Genomic locus

chr16:31,083,437-31,089,628

External References & Databases

Ensembl (ENSG00000151006)

Transcript & Mutation Effects

hg38 • Region Span ~6.2 kb

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GenCC 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 PRSS53 variants in ClinVar

2 Conditions Cataloged

not specifiedTotal: 101

not providedTotal: 5

ClinVar Variants & Pathogenicity by Type

Statistics based on transcript NM_001039503.3. 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				1 clinvar		1
missense			99 clinvar	6 clinvar		105
nonsense			1 clinvar			1
start loss						0
frameshift			2 clinvar			2
splice donor/acceptor (+/-2bp)			3 clinvar			3
Total	0	0	105	7	0	112

Loading ClinVar variants...

Transcript Catalog

Annotated transcript isoforms across RefSeq and Ensembl databases

Showing 4 of 7 transcripts

Transcript ID	Source	Protein ID	Coding Exons	MANE Status
NM_001039503.3	RefSeq	NP_001034592.1	11	MANE Select
ENST00000280606.7	Ensembl	ENSP00000280606.6	11	MANE Select
XM_011545816.3	RefSeq	XP_011544118.1	9	Standard
XM_011545817.3	RefSeq	XP_011544119.1	9	Standard

Gene Ontology (GO) Annotations & Pathways

Biological processes, molecular functions, cellular components and pathways

Biological Process

proteolysis

Molecular Function

serine-type endopeptidase activity

Cellular Component

extracellular region
cytoplasm

gnomAD Constraint

Source: gnomAD

Gene type: protein_coding
Transcript type: protein_coding
Transcript: ENST00000280606
Coding exons: 11
Length: 6204
Individuals with no LoFs: 124655
Homozygous LoFs: 0
Heterozygous LoFs: 163
Defined: 124818
p: 0.000653

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible
Missense	0.485	294	318	0.923	0.0000185	3463
Missense (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

Population LoF Frequency

Population	CAF	p-value	Status
African	0.0041	0.0041	notable
Latino/Admixed American	0.00061	0.00061	rare
Ashkenazi Jewish	0.0022	0.0022	notable
East Asian	0.00017	0.00017	rare
Finnish	0	0.0	absent
European (Non-Finnish)	0.00040	0.00039	rare
South Asian	0.00023	0.00023	rare
Other	0.00050	0.00049	rare

dbNSFP Gene Annotations

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

Essentials

Essential (CRISPR): N
Essential (CRISPR2): N
Essential (gene trap): N
Indispensability pred.: N
Indispensability score: 0.114

Gene Damage Prediction

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