CTSE

cathepsin E, the group of Peptidase family A1|Cathepsins

Basic information

Region (hg38): 1:206008534-206023909

Links

ENSG00000196188 ∙ NCBI:1510 ∙ OMIM:116890 ∙ HGNC:2530 ∙ Uniprot:P14091 ∙ 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 CTSE gene.

• Inborn genetic diseases (24 variants)
• not provided (1 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the CTSE 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			24			24
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	24	1	0

Variants in CTSE

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

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

Position	Type	Phenotype	Significance	ClinVar
1-206010211-C-T		not specified	Uncertain significance (May 10, 2023)
1-206010322-C-G		not specified	Uncertain significance (Apr 27, 2023)
1-206010347-C-G			Uncertain significance (Oct 21, 2022)
1-206012317-G-A		not specified	Likely benign (Sep 20, 2023)
1-206012337-T-A		not specified	Uncertain significance (May 26, 2022)
1-206012349-C-T		not specified	Uncertain significance (Mar 24, 2023)
1-206012350-G-A		not specified	Likely benign (Sep 13, 2023)
1-206012372-G-A		not specified	Uncertain significance (Feb 01, 2023)
1-206012534-T-G		not specified	Uncertain significance (Mar 01, 2023)
1-206012579-G-A		not specified	Uncertain significance (May 26, 2023)
1-206012638-C-T		not specified	Uncertain significance (Feb 27, 2024)
1-206013782-C-G		not specified	Uncertain significance (Sep 22, 2022)
1-206013812-G-T		not specified	Uncertain significance (Jan 10, 2023)
1-206013869-C-T		not specified	Uncertain significance (May 03, 2023)
1-206015977-C-T		not specified	Uncertain significance (Dec 19, 2022)
1-206015984-G-T		not specified	Uncertain significance (Jul 09, 2021)
1-206016031-C-T		not specified	Uncertain significance (Aug 04, 2023)
1-206016115-C-T		not specified	Uncertain significance (Sep 01, 2021)
1-206021060-C-T		not specified	Uncertain significance (Sep 29, 2022)
1-206021146-G-A		not specified	Uncertain significance (Jan 04, 2022)
1-206022174-C-T		Malignant tumor of prostate	Uncertain significance (-)
1-206022190-G-T		not specified	Uncertain significance (Jan 23, 2023)
1-206022254-C-T		not specified	Uncertain significance (Dec 19, 2022)
1-206022267-T-C		not specified	Uncertain significance (Sep 14, 2022)
1-206022939-C-A		not specified	Uncertain significance (Jun 16, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
CTSE	protein_coding	protein_coding	ENST00000358184	9	14646

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
1.44e-14	0.00679	125328	6	406	125740	0.00164

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	-0.296	241	228	1.06	0.0000123	2594
Missense in Polyphen		96	93.712	1.0244		1101
Synonymous	-0.981	107	94.8	1.13	0.00000590	801
Loss of Function	-0.469	20	17.9	1.12	7.60e-7	208

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.00623	0.00625
Ashkenazi Jewish	0.00	0.00
East Asian	0.000109	0.000109
Finnish	0.0000925	0.0000924
European (Non-Finnish)	0.000486	0.000484
Middle Eastern	0.000109	0.000109
South Asian	0.00790	0.00767
Other	0.000491	0.000489

dbNSFP

Source: dbNSFP

• Function: FUNCTION: May have a role in immune function. Probably involved in the processing of antigenic peptides during MHC class II-mediated antigen presentation. May play a role in activation-induced lymphocyte depletion in the thymus, and in neuronal degeneration and glial cell activation in the brain. {ECO:0000269|PubMed:8765029}.
• Pathway: Lysosome - Homo sapiens (human);MHC class II antigen presentation;Immune System;Adaptive Immune System (Consensus)

Recessive Scores

• pRec: 0.242

Intolerance Scores

• loftool: 0.859
• rvis_EVS: 0.85
• rvis_percentile_EVS: 88.42

Haploinsufficiency Scores

• pHI: 0.282
• hipred: N
• hipred_score: 0.350
• ghis: 0.416

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.866

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Ctse
• Phenotype: homeostasis/metabolism 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); immune system phenotype; hematopoietic system phenotype

Gene ontology

• Biological process: proteolysis;protein autoprocessing;antigen processing and presentation of exogenous peptide antigen via MHC class II;protein catabolic process
• Cellular component: endosome
• Molecular function: aspartic-type endopeptidase activity;protein homodimerization activity