CTSL

cathepsin L, the group of Cathepsins

Basic information

Region (hg38): 9:87724050-87731469

Previous symbols: [ "CTSL1" ]

Links

ENSG00000135047 ∙ NCBI:1514 ∙ OMIM:116880 ∙ HGNC:2537 ∙ Uniprot:P07711 ∙ 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 CTSL gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the CTSL 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			19	1	1	21
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	19	2	1

Variants in CTSL

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

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

Position	Type	Phenotype	Significance	ClinVar
9-87727608-A-C			Likely benign (Oct 01, 2023)
9-87727613-A-G		not specified	Uncertain significance (Apr 12, 2023)
9-87727621-C-G		not specified	Uncertain significance (Jan 23, 2023)
9-87727672-C-A		not specified	Uncertain significance (Dec 06, 2022)
9-87728124-T-C		not specified	Uncertain significance (Sep 29, 2022)
9-87728259-G-A		not specified	Uncertain significance (Feb 17, 2022)
9-87728328-C-A		not specified	Uncertain significance (Aug 26, 2022)
9-87728350-C-A			Benign (Jun 14, 2018)
9-87728352-G-C		not specified	Uncertain significance (Oct 04, 2022)
9-87728373-T-C		not specified	Uncertain significance (Oct 03, 2022)
9-87728589-A-G		not specified	Uncertain significance (Jan 23, 2023)
9-87728645-C-T		not specified	Uncertain significance (Jul 12, 2023)
9-87728646-G-A		not specified	Uncertain significance (Nov 07, 2022)
9-87728650-A-C		not specified	Uncertain significance (Aug 20, 2023)
9-87728687-G-A		not specified	Uncertain significance (Jan 26, 2023)
9-87728724-A-G		not specified	Uncertain significance (Nov 20, 2023)
9-87728764-T-A		not specified	Likely benign (Mar 30, 2024)
9-87728808-C-T		not specified	Uncertain significance (Aug 04, 2023)
9-87729577-A-G		not specified	Uncertain significance (Feb 07, 2023)
9-87729730-A-G		not specified	Uncertain significance (Mar 19, 2024)
9-87730437-G-A		not specified	Uncertain significance (Nov 05, 2021)
9-87730448-A-C			Likely benign (Jul 27, 2018)
9-87731057-C-T		not specified	Uncertain significance (Nov 03, 2023)
9-87731093-T-C		not specified	Uncertain significance (Oct 02, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
CTSL	protein_coding	protein_coding	ENST00000343150	7	5875

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.00805	0.979	125678	0	70	125748	0.000278

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.361	167	181	0.924	0.00000891	2222
Missense in Polyphen		44	65.928	0.66739		865
Synonymous	0.514	59	64.2	0.918	0.00000343	592
Loss of Function	2.18	6	15.2	0.396	6.45e-7	190

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.0000291	0.0000291
Ashkenazi Jewish	0.00	0.00
East Asian	0.0000544	0.0000544
Finnish	0.00	0.00
European (Non-Finnish)	0.0000441	0.0000439
Middle Eastern	0.0000544	0.0000544
South Asian	0.00207	0.00206
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Important for the overall degradation of proteins in lysosomes.
• Pathway: Antigen processing and presentation - Homo sapiens (human);Phagosome - Homo sapiens (human);Autophagy - animal - Homo sapiens (human);Lysosome - Homo sapiens (human);Fluid shear stress and atherosclerosis - Homo sapiens (human);Proteoglycans in cancer - Homo sapiens (human);Rheumatoid arthritis - Homo sapiens (human);Apoptosis - Homo sapiens (human);Primary Focal Segmental Glomerulosclerosis FSGS;Ebola Virus Pathway on Host;Ebola Virus Pathway on Host;Assembly of collagen fibrils and other multimeric structures;Gene expression (Transcription);Generic Transcription Pathway;Trafficking and processing of endosomal TLR;Toll-Like Receptors Cascades;Collagen degradation;RNA Polymerase II Transcription;Collagen formation;Extracellular matrix organization;MHC class II antigen presentation;Innate Immune System;Immune System;Adaptive Immune System;Endosomal/Vacuolar pathway;Antigen processing-Cross presentation;Class I MHC mediated antigen processing & presentation;Degradation of the extracellular matrix;RUNX1 regulates transcription of genes involved in differentiation of keratinocytes;Transcriptional regulation by RUNX1 (Consensus)

Recessive Scores

• pRec: 0.763

Intolerance Scores

• rvis_EVS: 0.13
• rvis_percentile_EVS: 63.2

Haploinsufficiency Scores

• pHI: 0.0992
• hipred: N
• hipred_score: 0.432
• ghis: 0.440

Essentials

• essential_gene_CRISPR: N
• essential_gene_gene_trap: N

Gene Damage Prediction

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

Gene ontology

• Biological process: adaptive immune response;proteolysis;antigen processing and presentation;antigen processing and presentation of exogenous peptide antigen via MHC class II;extracellular matrix disassembly;collagen catabolic process;regulation of keratinocyte differentiation;proteolysis involved in cellular protein catabolic process;macrophage apoptotic process;cellular response to thyroid hormone stimulus
• Cellular component: extracellular region;extracellular space;nucleus;lysosome;endolysosome lumen;lysosomal lumen;extracellular exosome
• Molecular function: fibronectin binding;cysteine-type endopeptidase activity;serine-type endopeptidase activity;protein binding;collagen binding;cysteine-type peptidase activity;histone binding;proteoglycan binding;serpin family protein binding