CTSZ

cathepsin Z, the group of Cathepsins

Basic information

Region (hg38): 20:58985685-59008238

Links

ENSG00000101160 ∙ NCBI:1522 ∙ OMIM:603169 ∙ HGNC:2547 ∙ Uniprot:Q9UBR2 ∙ 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 CTSZ gene.

• Inborn genetic diseases (21 variants)
• not provided (5 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the CTSZ 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			11	2	3	16
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding			8		1	9
Total	0	0	19	3	4

Variants in CTSZ

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

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

Position	Type	Phenotype	Significance	ClinVar
20-58986131-G-T		not specified	Uncertain significance (Feb 03, 2022)
20-58987804-C-G		not specified	Uncertain significance (Apr 07, 2022)
20-58989901-C-T		not specified	Uncertain significance (Dec 22, 2023)
20-58989912-G-A		not specified	Uncertain significance (Jan 26, 2022)
20-58990918-A-G		not specified	Uncertain significance (Oct 14, 2023)
20-58991036-C-G		not specified	Uncertain significance (Jun 03, 2022)
20-58991046-A-G		not specified	Uncertain significance (May 30, 2023)
20-58991053-T-C		not specified	Uncertain significance (Feb 17, 2022)
20-58991378-C-A		not specified	Uncertain significance (Jul 30, 2023)
20-58991417-G-T		not specified	Uncertain significance (Aug 02, 2021)
20-58991423-A-G		not specified	Uncertain significance (Oct 13, 2023)
20-58993122-C-T			Benign (Jun 27, 2018)
20-58993452-A-G		not specified	Uncertain significance (Nov 08, 2022)
20-58993721-A-G		not specified	Uncertain significance (Feb 22, 2023)
20-58993760-C-T		not specified	Uncertain significance (Dec 20, 2023)
20-58994221-C-T		not specified	Uncertain significance (May 30, 2023)
20-58995735-C-T		not specified	Uncertain significance (Dec 04, 2023)
20-58995756-C-T		not specified	Uncertain significance (Nov 22, 2021)
20-58996649-C-T		not specified	Uncertain significance (Oct 27, 2021)
20-58996734-T-C		not specified	Uncertain significance (Feb 12, 2024)
20-58996738-C-G		not specified	Likely benign (Aug 19, 2023)
20-58996763-G-C			Benign (May 09, 2018)
20-58997654-A-G			Benign (Jul 17, 2018)
20-58997670-C-T			Benign (May 20, 2018)
20-58997674-C-T			Likely benign (Jul 01, 2022)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
CTSZ	protein_coding	protein_coding	ENST00000217131	6	12063

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
2.26e-16	0.000589	125678	0	70	125748	0.000278

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.600	150	172	0.871	0.0000102	1953
Missense in Polyphen		50	62.318	0.80234		660
Synonymous	-0.178	75	73.1	1.03	0.00000503	585
Loss of Function	-1.70	20	13.3	1.50	5.68e-7	154

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000913	0.000912
Ashkenazi Jewish	0.000100	0.0000992
East Asian	0.000113	0.000109
Finnish	0.0000463	0.0000462
European (Non-Finnish)	0.000277	0.000273
Middle Eastern	0.000113	0.000109
South Asian	0.000464	0.000457
Other	0.000491	0.000489

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Exhibits carboxy-monopeptidase as well as carboxy- dipeptidase activity.
• Pathway: Lysosome - Homo sapiens (human);Apoptosis - Homo sapiens (human);Lysosome Vesicle Biogenesis;Clathrin derived vesicle budding;Neutrophil degranulation;trans-Golgi Network Vesicle Budding;Peptide hormone metabolism;Vesicle-mediated transport;Membrane Trafficking;Post-translational protein modification;Metabolism of proteins;Metabolism of Angiotensinogen to Angiotensins;Innate Immune System;Immune System;Cargo concentration in the ER;Transport to the Golgi and subsequent modification;Asparagine N-linked glycosylation;COPII-mediated vesicle transport;ER to Golgi Anterograde Transport (Consensus)

Recessive Scores

• pRec: 0.149

Intolerance Scores

• loftool: 0.573
• rvis_EVS: 0.62
• rvis_percentile_EVS: 83.25

Haploinsufficiency Scores

• pHI: 0.0927
• hipred: N
• hipred_score: 0.197
• ghis: 0.434

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.713

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Ctsz
• Phenotype: normal phenotype; neoplasm; cellular phenotype

Gene ontology

• Biological process: angiotensin maturation;proteolysis;endoplasmic reticulum to Golgi vesicle-mediated transport;negative regulation of plasminogen activation;negative regulation of neuron projection development;negative regulation of protein binding;neutrophil degranulation;positive regulation of neuron apoptotic process;COPII vesicle coating;proteolysis involved in cellular protein catabolic process;epithelial tube branching involved in lung morphogenesis;regulation of neuron death;positive regulation of neural precursor cell proliferation
• Cellular component: Golgi membrane;extracellular region;extracellular space;lysosome;endoplasmic reticulum;endoplasmic reticulum lumen;plasma membrane;cell surface;COPII-coated ER to Golgi transport vesicle;growth cone;cytoplasmic vesicle;endoplasmic reticulum-Golgi intermediate compartment membrane;specific granule lumen;intracellular membrane-bounded organelle;collagen-containing extracellular matrix;extracellular exosome;cell cortex region;ficolin-1-rich granule lumen
• Molecular function: carboxypeptidase activity;cysteine-type endopeptidase activity;protein binding;cysteine-type peptidase activity