PRSS58

protein-coding

serine protease 58, the group of Serine proteases

Gene summary

This gene encodes a member of the trypsin family of serine proteases. This gene and several related trypsinogen genes are localized to the T cell receptor beta locus on chromosome 7. This gene was previously described as a trypsinogen-like pseudogene, but it is now thought to be a protein-coding gene. [provided by RefSeq, Jul 2008]

MANE transcript

NM_001001317.5

Inheritance

—

ClinVar variants

U:41B:2

Top phenotype

—

gnomAD constraint

pLI —, LoF o/e 1.18

Max pathogenic AF

—

Genomic locus

chr7:142,252,143-142,258,058

External References & Databases

Ensembl (ENSG00000258223)

Transcript & Mutation Effects

hg38 • Region Span ~5.9 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 PRSS58 variants in ClinVar

1 Conditions Cataloged

not specifiedTotal: 42

ClinVar Variants & Pathogenicity by Type

Statistics based on transcript NM_001001317.5. 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			40 clinvar	2 clinvar		42
nonsense						0
start loss						0
frameshift						0
splice donor/acceptor (+/-2bp)						0
Total	0	0	41	2	0	43

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Transcript Catalog

Annotated transcript isoforms across RefSeq and Ensembl databases

Showing 4 of 5 transcripts

Transcript ID	Source	Protein ID	Coding Exons	MANE Status
NM_001001317.5	RefSeq	NP_001001317.1	5	MANE Select
ENST00000547058.6	Ensembl	ENSP00000447588.2	5	MANE Select
ENST00000552471.1	Ensembl	ENSP00000446916.1	5	Standard
ENST00000552471.2	Ensembl	ENSP00000446916.1	5	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
secretory granule

gnomAD Constraint

Source: gnomAD

Gene type: protein_coding
Transcript type: protein_coding
Transcript: ENST00000552471
Coding exons: 5
Length: 5916
Individuals with no LoFs: 125683
Homozygous LoFs: 0
Heterozygous LoFs: 49
Defined: 125732
p: 0.000195

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible
Missense	-0.537	146	129	1.13	0.00000623	1575
Missense (PolyPhen)		45	50.342	0.89389		612
Synonymous	-1.11	60	50.0	1.20	0.00000268	463
Loss of Function	-0.543	12	10.1	1.18	5.25e-7	123

Population LoF Frequency

Population	CAF	p-value	Status
African	0.00012	0.00012	rare
Latino/Admixed American	0.00052	0.00052	rare
Ashkenazi Jewish	0	0.0	absent
East Asian	0.00011	0.00011	rare
Finnish	0	0.0	absent
European (Non-Finnish)	0.00015	0.00015	rare
South Asian	0.00020	0.00020	rare
Other	0.00066	0.00065	rare

dbNSFP Gene Annotations

Source: dbNSFP

Intolerance Scores

RVIS EVS: 0.24
RVIS percentile EVS: 69.37

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	Medium	Medium	Medium
Cancer	Medium	Medium	Medium