CTSO

protein-coding

cathepsin O, the group of Cathepsins

Gene summary

The protein encoded by the gene is a cysteine proteinase and a member of the papain superfamily. This proteolytic enzyme is involved in cellular protein degradation and turnover. The recombinant form of this enzyme was shown to degrade synthetic peptides typically used as substrates for cysteine proteinases and its proteolytic activity was abolished by an inhibitor of cyteine proteinase. [provided by RefSeq, Jul 2008]

Previous symbols:

CTSO1

MANE transcript

NM_001334.3

Inheritance

—

ClinVar variants

U:50B:2

Top phenotype

—

gnomAD constraint

pLI —, LoF o/e 0.85

Max pathogenic AF

—

Genomic locus

chr4:155,921,580-155,953,912

External References & Databases

Ensembl (ENSG00000256043)

Transcript & Mutation Effects

hg38 • Region Span ~32.3 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 CTSO variants in ClinVar

1 Conditions Cataloged

not specifiedTotal: 46

ClinVar Variants & Pathogenicity by Type

Statistics based on transcript NM_001334.3. 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			46 clinvar	2 clinvar		48
nonsense						0
start loss						0
frameshift						0
splice donor/acceptor (+/-2bp)			3 clinvar			3
Total	0	0	50	2	0	52

Loading ClinVar variants...

Transcript Catalog

Annotated transcript isoforms across RefSeq and Ensembl databases

Showing 4 of 25 transcripts

Transcript ID	Source	Protein ID	Coding Exons	MANE Status
NM_001334.3	RefSeq	NP_001325.1	8	MANE Select
ENST00000433477.4	Ensembl	ENSP00000414904.3	8	MANE Select
ENST00000676791.2	Ensembl	ENSP00000504976.1	8	Standard
ENST00000678374.1	Ensembl	ENSP00000504174.1	2	Standard

Gene Ontology (GO) Annotations & Pathways

Biological processes, molecular functions, cellular components and pathways

Pathways ConsensusPathDB

Lysosome - Homo sapiens (human)
Apoptosis - Homo sapiens (human)
MHC class II antigen presentation
Immune System
Adaptive Immune System

Biological Process

proteolysis
proteolysis involved in cellular protein catabolic process

Molecular Function

cysteine-type endopeptidase activity

Cellular Component

extracellular space
lysosome

gnomAD Constraint

Source: gnomAD

Gene type: protein_coding
Transcript type: protein_coding
Transcript: ENST00000433477
Coding exons: 8
Length: 29800
Individuals with no LoFs: 125671
Homozygous LoFs: 0
Heterozygous LoFs: 77
Defined: 125748
p: 0.000306

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible
Missense	-0.102	149	146	1.02	0.00000679	2077
Missense (PolyPhen)		70	62.354	1.1226		783
Synonymous	0.499	48	52.6	0.912	0.00000272	601
Loss of Function	0.554	14	16.4	0.852	7.64e-7	211

Population LoF Frequency

Population	CAF	p-value	Status
African	0.00025	0.00025	rare
Latino/Admixed American	0.00068	0.00067	rare
Ashkenazi Jewish	0	0.0	absent
East Asian	0.00016	0.00016	rare
Finnish	0	0.0	absent
European (Non-Finnish)	0.00022	0.00021	rare
South Asian	0.00065	0.00059	rare
Other	0.00087	0.00081	rare

dbNSFP Gene Annotations

Source: dbNSFP

Function: FUNCTION: Proteolytic enzyme possibly involved in normal cellular protein degradation and turnover.;

Recessive Scores

pRec: 0.126

Intolerance Scores

LoFtool: 0.553
RVIS EVS: -0.01
RVIS percentile EVS: 53.51

Essentials

Essential (CRISPR): N
Essential (CRISPR2): N
Essential (gene trap): N
Indispensability pred.: N
Indispensability score: 0.260

Gene Damage Prediction

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