CTSO

cathepsin O, the group of Cathepsins

Basic information

Region (hg38): 4:155921579-155953912

Previous symbols: [ "CTSO1" ]

Links

ENSG00000256043 ∙ NCBI:1519 ∙ OMIM:600550 ∙ HGNC:2542 ∙ Uniprot:P43234 ∙ 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 CTSO gene.

• Inborn genetic diseases (18 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the CTSO 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						0
missense			18			18
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	18	0	0

Variants in CTSO

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

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

Position	Type	Phenotype	Significance	ClinVar
4-155926056-C-T		not specified	Uncertain significance (Apr 01, 2022)
4-155928344-T-C		not specified	Uncertain significance (Dec 21, 2023)
4-155928399-A-C		not specified	Uncertain significance (Sep 15, 2021)
4-155928404-C-T		not specified	Uncertain significance (Aug 21, 2023)
4-155928405-G-A		not specified	Uncertain significance (Nov 12, 2021)
4-155929565-A-G		not specified	Uncertain significance (Dec 01, 2022)
4-155929640-G-C		not specified	Uncertain significance (Dec 18, 2023)
4-155929695-C-T		not specified	Uncertain significance (Dec 27, 2022)
4-155937390-T-C		not specified	Uncertain significance (Jun 11, 2021)
4-155939400-T-C		not specified	Uncertain significance (Oct 20, 2023)
4-155939405-C-A		not specified	Uncertain significance (Jan 23, 2024)
4-155939433-A-G		not specified	Uncertain significance (Apr 12, 2022)
4-155942342-A-G		not specified	Uncertain significance (Dec 06, 2022)
4-155942355-C-T		not specified	Uncertain significance (Jan 03, 2022)
4-155942400-T-C		not specified	Uncertain significance (Jan 04, 2022)
4-155943179-T-C		not specified	Uncertain significance (Feb 15, 2023)
4-155943210-T-C		not specified	Uncertain significance (Feb 13, 2023)
4-155943243-A-G		not specified	Uncertain significance (Jul 13, 2022)
4-155953720-G-A		not specified	Uncertain significance (Jul 14, 2021)
4-155953735-T-C		not specified	Uncertain significance (Feb 28, 2024)
4-155953756-G-C		not specified	Uncertain significance (May 04, 2022)
4-155953793-C-T		not specified	Uncertain significance (Jul 12, 2023)
4-155953841-C-T		not specified	Uncertain significance (Oct 12, 2021)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
CTSO	protein_coding	protein_coding	ENST00000433477	8	29800

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
5.95e-9	0.243	125671	0	77	125748	0.000306

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	-0.102	149	146	1.02	0.00000679	2077
Missense in 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

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000923	0.000922
Ashkenazi Jewish	0.00	0.00
East Asian	0.000164	0.000163
Finnish	0.00	0.00
European (Non-Finnish)	0.000219	0.000211
Middle Eastern	0.000164	0.000163
South Asian	0.000645	0.000588
Other	0.000869	0.000815

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Proteolytic enzyme possibly involved in normal cellular protein degradation and turnover.
• Pathway: Lysosome - Homo sapiens (human);Apoptosis - Homo sapiens (human);MHC class II antigen presentation;Immune System;Adaptive Immune System (Consensus)

Recessive Scores

• pRec: 0.126

Intolerance Scores

• loftool: 0.553
• rvis_EVS: -0.01
• rvis_percentile_EVS: 53.51

Haploinsufficiency Scores

• pHI: 0.200
• hipred: N
• hipred_score: 0.170
• ghis: 0.536

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.260

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Ctso
• Phenotype: integument phenotype (the observable morphological and physiological characteristics of the skin and its associated structures, such as the hair, nails, sweat glands, sebaceous glands and other secretory glands that are manifested through development and lifespan); homeostasis/metabolism phenotype

Gene ontology

• Biological process: proteolysis;proteolysis involved in cellular protein catabolic process
• Cellular component: extracellular space;lysosome
• Molecular function: cysteine-type endopeptidase activity