CTSF

Summary

CTSF (cathepsin F, HGNC:2531) is a protein-coding gene on chromosome 11q13.2, encoding Cathepsin F (Q9UBX1). Thiol protease which is believed to participate in intracellular degradation and turnover of proteins.

Cathepsins are papain family cysteine proteinases that represent a major component of the lysosomal proteolytic system. Cathepsins generally contain a signal sequence, followed by a propeptide and then a catalytically active mature region. The very long (251 amino acid residues) proregion of the cathepsin F precursor contains a C-terminal domain similar to the pro-segment of cathepsin L-like enzymes, a 50-residue flexible linker peptide, and an N-terminal domain predicted to adopt a cystatin-like fold. The cathepsin F proregion is unique within the papain family cysteine proteases in that it contains this additional N-terminal segment predicted to share structural similarities with cysteine protease inhibitors of the cystatin superfamily. This cystatin-like domain contains some of the elements known to be important for inhibitory activity. CTSF encodes a predicted protein of 484 amino acids which contains a 19 residue signal peptide. Cathepsin F contains five potential N-glycosylation sites, and it may be targeted to the endosomal/lysosomal compartment via the mannose 6-phosphate receptor pathway. The cathepsin F gene is ubiquitously expressed, and it maps to chromosome 11q13, close to the gene encoding cathepsin W.

Source: NCBI Gene 8722 — RefSeq curated summary.

At a glance

• Gene–disease (curated): adult neuronal ceroid lipofuscinosis (Definitive, ClinGen) — +1 more curated relationship
• GWAS associations: 4
• Clinical variants (ClinVar): 321 total — 18 pathogenic, 18 likely-pathogenic
• Phenotypes (HPO): 25
• Druggable target: yes — 3 molecules with ChEMBL bioactivity
• MANE Select transcript: NM_003793

Identifiers

Gene identifiers

Field	Value
HGNC ID	HGNC:2531
Approved symbol	CTSF
Name	cathepsin F
Location	11q13.2
Locus type	gene with protein product
Status	Approved
Aliases	CATSF, CLN13
Ensembl gene	ENSG00000174080
Ensembl biotype	protein_coding
OMIM	603539
Entrez	8722

Gene structure

Transcript identifiers

Ensembl transcripts: 46 — 19 protein_coding, 15 retained_intron, 10 nonsense_mediated_decay, 2 protein_coding_CDS_not_defined

ENST00000310325, ENST00000524994, ENST00000525733, ENST00000526010, ENST00000527141, ENST00000529199, ENST00000529561, ENST00000530565, ENST00000533168, ENST00000676860, ENST00000676924, ENST00000677005, ENST00000677020, ENST00000677186, ENST00000677298, ENST00000677365, ENST00000677526, ENST00000677587, ENST00000677678, ENST00000677779, ENST00000677896, ENST00000677920, ENST00000678154, ENST00000678294, ENST00000678305, ENST00000678383, ENST00000678413, ENST00000678471, ENST00000678614, ENST00000678710, ENST00000678872, ENST00000678946, ENST00000678953, ENST00000679011, ENST00000679024, ENST00000679160, ENST00000679225, ENST00000679314, ENST00000679347, ENST00000878093, ENST00000878094, ENST00000878095, ENST00000878096, ENST00000878097, ENST00000942856, ENST00000942857

RefSeq mRNA: 1 — MANE Select: NM_003793 NM_003793

CCDS: CCDS8144

Canonical transcript exons

ENST00000310325 — 13 exons

Exon	Start	End
ENSE00001188333	66564088	66564146
ENSE00001188372	66567444	66567662
ENSE00001188380	66568274	66568606
ENSE00001233018	66564558	66564648
ENSE00002162432	66563464	66564007
ENSE00003503975	66567984	66568082
ENSE00003508471	66566291	66566404
ENSE00003518332	66564887	66565006
ENSE00003588637	66565671	66565751
ENSE00003628383	66566022	66566167
ENSE00003634039	66565831	66565927
ENSE00003668465	66567246	66567321
ENSE00003674781	66564742	66564806

Expression profiles

Bgee: expression breadth ubiquitous, 293 present calls, max score 98.56.

FANTOM5 (CAGE): breadth ubiquitous, TPM avg 23.8863 / max 216.7242, expressed in 1525 samples.

FANTOM5 promoters (3 alternative TSS)

Promoter ID	TPM avg	Samples expressed
120815	16.5766	1469
120816	7.0760	1342
120814	0.2336	120

Top tissues by expression

302 total, by Bgee expression score (0-100, higher = more expressed):

Tissue	Anatomy ID	Expression score	Quality
right hemisphere of cerebellum	UBERON:0014890	98.56	gold quality
cerebellar hemisphere	UBERON:0002245	98.41	gold quality
cerebellar cortex	UBERON:0002129	98.36	gold quality
left testis	UBERON:0004533	98.21	gold quality
right testis	UBERON:0004534	98.16	gold quality
right coronary artery	UBERON:0001625	97.94	gold quality
left ovary	UBERON:0002119	97.91	gold quality
cerebellum	UBERON:0002037	97.75	gold quality
right frontal lobe	UBERON:0002810	97.58	gold quality
right ovary	UBERON:0002118	97.27	gold quality
peripheral nervous system	UBERON:0000010	97.21	gold quality
nerve	UBERON:0001021	97.21	gold quality
tibial nerve	UBERON:0001323	97.21	gold quality
mucosa of stomach	UBERON:0001199	97.18	gold quality
ascending aorta	UBERON:0001496	97.03	gold quality
thoracic aorta	UBERON:0001515	97.01	gold quality
descending thoracic aorta	UBERON:0002345	96.98	gold quality
prefrontal cortex	UBERON:0000451	96.96	gold quality
endocervix	UBERON:0000458	96.91	gold quality
right atrium auricular region	UBERON:0006631	96.90	gold quality
Brodmann (1909) area 9	UBERON:0013540	96.79	gold quality
putamen	UBERON:0001874	96.71	gold quality
nucleus accumbens	UBERON:0001882	96.69	gold quality
right adrenal gland cortex	UBERON:0035827	96.69	gold quality
cardiac atrium	UBERON:0002081	96.63	gold quality
gall bladder	UBERON:0002110	96.57	gold quality
coronary artery	UBERON:0001621	96.53	gold quality
apex of heart	UBERON:0002098	96.53	gold quality
body of uterus	UBERON:0009853	96.49	gold quality
left coronary artery	UBERON:0001626	96.44	gold quality

Single-cell (SCXA)

Detected in 3 experiment(s), a significant marker in 2.

Experiment	Marker?	Max mean expression
E-GEOD-135922	yes	23.41
E-ENAD-20	no	710.48
E-ANND-3	no	0.00

Regulation

Is transcription factor: no

Upstream regulators (CollecTRI, top): IRF6, MYC

miRNA regulators (miRDB)

22 targeting CTSF, top 30 by miRDB confidence (max_score; target_count = how many genes the miRNA targets in total — lower means more specific):

miRNA	Max score	Avg score	miRNA target_count
HSA-MIR-4282	99.99	75.36	6408
HSA-MIR-3065-5P	99.97	71.56	3281
HSA-MIR-9902	99.89	69.15	2250
HSA-MIR-137-3P	99.87	74.74	2401
HSA-MIR-3065-3P	99.87	70.25	1407
HSA-MIR-6756-5P	99.82	67.97	2466
HSA-MIR-378G	99.71	64.90	1106
HSA-MIR-6766-5P	99.68	67.70	2325
HSA-MIR-7159-5P	99.53	72.12	2472
HSA-MIR-18A-5P	99.29	71.05	806
HSA-MIR-18B-5P	99.29	71.05	806
HSA-MIR-3074-5P	98.82	66.56	1414
HSA-MIR-4272	98.76	68.74	1810
HSA-MIR-4664-5P	98.17	65.07	1020
HSA-MIR-4483	98.09	64.12	1642
HSA-MIR-6847-5P	97.93	66.74	1808
HSA-MIR-3620-3P	97.78	64.88	772
HSA-MIR-342-5P	97.25	64.10	817
HSA-MIR-27A-5P	97.01	65.63	528
HSA-MIR-383-5P	96.86	67.55	820
HSA-MIR-3690	96.44	65.18	737
HSA-MIR-1293	96.16	64.69	916

Literature-anchored findings (GeneRIF, showing 11)

• cathepsin F has a role in modifying low density lipoprotein particles (PMID:15184381)
• cathepsin F, matrix metalloproteinases 11 and 12 are upregulated in cervical cancer (PMID:15989693)
• data demonstrate a novel proatherogenic role for AngII, namely its ability to enhance secretion of lysosomal cathepsin F by monocyte-derived macrophages (PMID:16963053)
• Homozygous and compound heterozygous missense mutations in CTSF are associated with adult-onset neuronal ceroid lipofuscinosis. (PMID:23297359)
• Small hairpin RNA silencing of proteinases overexpressed in diabetic corneas enhanced corneal epithelial and stem cell marker staining and accelerated wound healing. (PMID:24255036)
• Disease-causing cathepsin-F mutants fail to cleave LIMP-2. Our findings provide evidence that LIMP-2 represents an in vivo substrate of cathepsin-F with relevance for understanding the pathophysiology of type-B-Kufs-disease. (PMID:25576872)
• Biallelic mutations in this gene have been shown to cause Type B Kufs disease, an adult-onset neuronal ceroid lipofuscinosis with some cases resembling the impairment seen in AD. (PMID:27524508)
• The CTSF gene may function as a tumor suppressor in gastric cancer (PMID:28474574)
• Clinical distinction of type A (progressive myoclonus epilepsy) and type B (dementia with motor disturbance) Kufs disease was supported by molecular diagnoses. Type A is usually caused by recessive pathogenic variants in CLN6 or dominant variants in DNAJC5. Type B Kufs is usually associated with recessive CTSF pathogenic variants. (PMID:30561534)
• Long noncoding RNA LINC00982 upregulates CTSF expression to inhibit gastric cancer progression via the transcription factor HEY1. (PMID:33236952)
• Cathepsin F genetic mutation is associated with familial papillary thyroid cancer. (PMID:35447134)

Cross-species orthologs

29 orthologs

Organism	Symbol	Gene ID
danio_rerio	ctsl.1	ENSDARG00000003902
danio_rerio	ctss1	ENSDARG00000036940
danio_rerio	tinagl1	ENSDARG00000061231
danio_rerio	ctsf	ENSDARG00000063095
danio_rerio	ctsbb	ENSDARG00000101051
mus_musculus	Ctsf	ENSMUSG00000083282
rattus_norvegicus	Ctsf	ENSRNOG00000019708
drosophila_melanogaster	CtsB	FBGN0030521
drosophila_melanogaster	CtsL4	FBGN0032228
drosophila_melanogaster	CtsL2	FBGN0033874
drosophila_melanogaster	Swim	FBGN0034709
drosophila_melanogaster	CtsL3	FBGN0037396
drosophila_melanogaster	CtsF	FBGN0260462
caenorhabditis_elegans		WBGENE00000781
caenorhabditis_elegans		WBGENE00000782
caenorhabditis_elegans		WBGENE00000784
caenorhabditis_elegans		WBGENE00000785
caenorhabditis_elegans	cpz-1	WBGENE00000788
caenorhabditis_elegans		WBGENE00007055
caenorhabditis_elegans	F26E4.3	WBGENE00009158
caenorhabditis_elegans		WBGENE00013072
caenorhabditis_elegans		WBGENE00013076
caenorhabditis_elegans		WBGENE00013764
caenorhabditis_elegans		WBGENE00016300
caenorhabditis_elegans		WBGENE00016306
caenorhabditis_elegans		WBGENE00019314
caenorhabditis_elegans		WBGENE00019986
caenorhabditis_elegans		WBGENE00022189
caenorhabditis_elegans		WBGENE00044760

Paralogs (12): CTSZ (ENSG00000101160), CTSH (ENSG00000103811), CTSC (ENSG00000109861), CTSL (ENSG00000135047), CTSV (ENSG00000136943), TINAG (ENSG00000137251), TINAGL1 (ENSG00000142910), CTSK (ENSG00000143387), CTSS (ENSG00000163131), CTSB (ENSG00000164733), CTSW (ENSG00000172543), CTSO (ENSG00000256043)

Protein

Protein identifiers

Cathepsin F — Q9UBX1 (reviewed: Q9UBX1)

All UniProt accessions (21): Q9UBX1, A0A024R5G9, A0A7I2V2K3, A0A7I2V313, A0A7I2V3E7, A0A7I2V3L9, A0A7I2V3M3, A0A7I2V3V9, A0A7I2V3X1, A0A7I2V411, A0A7I2V4A8, A0A7I2V4V5, A0A7I2V5B9, A0A7I2V5F8, A0A7I2V5Q1, A0A7I2YQ73, A0A7I2YQB3, A0A7I2YQH8, A0A7I2YQW3, H0YD65, H0YE42

UniProt curated annotations — full annotation on UniProt →

Function. Thiol protease which is believed to participate in intracellular degradation and turnover of proteins. Has also been implicated in tumor invasion and metastasis.

Subcellular location. Lysosome.

Tissue specificity. High expression levels in heart, skeletal muscle, brain, testis and ovary; moderate levels in prostate, placenta, liver and colon; and no detectable expression in peripheral leukocytes and thymus.

Disease relevance. Ceroid lipofuscinosis, neuronal, 13 (Kufs type) (CLN13) [MIM:615362] A form of neuronal ceroid lipofuscinosis characterized by adult onset of progressive cognitive decline and motor dysfunction leading to dementia and often early death. Some patients develop seizures. Neuronal ceroid lipofuscinoses are progressive neurodegenerative, lysosomal storage diseases characterized by intracellular accumulation of autofluorescent liposomal material. CLN13 inheritance is autosomal recessive. The disease is caused by variants affecting the gene represented in this entry.

Similarity. Belongs to the peptidase C1 family.

RefSeq proteins (1): NP_003784* (*=MANE)

Domains & families (InterPro)

ID	Name	Type
IPR000169	Pept_cys_AS	Active_site
IPR000668	Peptidase_C1A_C	Domain
IPR013128	Peptidase_C1A	Family
IPR013201	Prot_inhib_I29	Domain
IPR025660	Pept_his_AS	Active_site
IPR038765	Papain-like_cys_pep_sf	Homologous_superfamily
IPR039417	Peptidase_C1A_papain-like	Domain

Pfam: PF00112, PF08246

Enzyme classification (BRENDA):

• EC 3.4.22.41 — cathepsin F (BRENDA: 12 organisms, 46 substrates, 30 inhibitors, 6 Km, 6 kcat entries)

Substrate kinetics (BRENDA)

6 substrates with measured Km, best-characterized 6. Km ranges are aggregated across organisms/conditions.

Substrate	Km (mM)	Measurements
BENZYLOXYCARBONYL-PHE-ARG-4-METHYLCOUMARIN 7-AMI	0.043	1
BENZYLOXYCARBONYL-PHE-ARG-4-METHYLCOUMARYL-7-AMI	0.017	1
N-BENZYLOXYCARBONYL-L-ARG-L-ARG-4-METHYLCOUMARIN	0.0029	1
N-BENZYLOXYCARBONYL-L-LEU-L-ARG-4-METHYLCOUMARIN	0.0002	1
N-BENZYLOXYCARBONYL-L-PHE-L-ARG-4-METHYLCOUMARIN	0.0004	1
N-BENZYLOXYCARBONYL-L-VAL-L-ARG-4-METHYLCOUMARIN	0.0012	1

UniProt features (41 total): helix 9, strand 9, glycosylation site 5, sequence variant 5, disulfide bond 3, active site 3, sequence conflict 2, turn 2, signal peptide 1, propeptide 1, chain 1

Structure

Experimental structures (PDB)

1 structures.

PDB	Method	Resolution (Å)
1M6D	X-RAY DIFFRACTION	1.7

Predicted structure (AlphaFold)

Model	pLDDT	Fraction very-high
AF-Q9UBX1-F1	82.78	0.57

Functional residue map

Curated UniProt residues grouped by drug-discovery relevance — catalytic, ligand-binding, modification, and mutation-validated positions. Source: UniProtKB sequence features.

Catalytic / active sites (3): 295; 431; 451

Disulfide bonds (3): 292–333, 326–366, 424–472

Glycosylation sites (5): 440, 160, 195, 367, 378

Function

Pathways and Gene Ontology

Reactome pathways

3 pathways

ID	Pathway
R-HSA-2132295	MHC class II antigen presentation
R-HSA-1280218	Adaptive Immune System
R-HSA-168256	Immune System

MSigDB gene sets: 218 (showing top): GSE45365_HEALTHY_VS_MCMV_INFECTION_CD8_TCELL_IFNAR_KO_DN, GSE37336_LY6C_POS_VS_NEG_NAIVE_CD4_TCELL_DN, GOBP_ANTIGEN_PROCESSING_AND_PRESENTATION_OF_PEPTIDE_OR_POLYSACCHARIDE_ANTIGEN_VIA_MHC_CLASS_II, REACTOME_ADAPTIVE_IMMUNE_SYSTEM, KAAB_HEART_ATRIUM_VS_VENTRICLE_UP, GOZGIT_ESR1_TARGETS_DN, GOBP_MACROMOLECULE_CATABOLIC_PROCESS, GAUSSMANN_MLL_AF4_FUSION_TARGETS_C_UP, KEGG_LYSOSOME, GOBP_ANTIGEN_PROCESSING_AND_PRESENTATION_OF_PEPTIDE_ANTIGEN, USF_C, chr11q13, MODULE_66, CAIRO_HEPATOBLASTOMA_CLASSES_DN, GOBP_ANTIGEN_PROCESSING_AND_PRESENTATION

GO Biological Process (4): proteolysis (GO:0006508), antigen processing and presentation of exogenous peptide antigen via MHC class II (GO:0019886), obsolete proteolysis involved in protein catabolic process (GO:0051603), immune system process (GO:0002376)

GO Molecular Function (5): cysteine-type endopeptidase activity (GO:0004197), cysteine-type peptidase activity (GO:0008234), protein binding (GO:0005515), peptidase activity (GO:0008233), hydrolase activity (GO:0016787)

GO Cellular Component (11): obsolete extracellular space (GO:0005615), lysosome (GO:0005764), endoplasmic reticulum (GO:0005783), plasma membrane (GO:0005886), extracellular matrix (GO:0031012), lysosomal lumen (GO:0043202), extracellular exosome (GO:0070062), extracellular vesicle (GO:1903561), cytoplasm (GO:0005737), endomembrane system (GO:0012505), intracellular organelle lumen (GO:0070013)

Reactome top-level categories

Rollup of top-2 pathways:

Category	Pathways
Adaptive Immune System	1
Immune System	1

GO top-level categories

Rollup of top GO terms by namespace:

Category	Terms
cellular anatomical structure	2
protein metabolic process	1
antigen processing and presentation of exogenous peptide antigen	1
antigen processing and presentation of peptide antigen via MHC class II	1
biological_process	1
endopeptidase activity	1
cysteine-type peptidase activity	1
peptidase activity	1
binding	1
hydrolase activity	1
catalytic activity, acting on a protein	1
catalytic activity	1
lytic vacuole	1
cytoplasm	1
endomembrane system	1
intracellular membrane-bounded organelle	1
membrane	1
cell periphery	1
external encapsulating structure	1
lysosome	1
vacuolar lumen	1
extracellular vesicle	1
extracellular region	1
vesicle	1
extracellular membrane-bounded organelle	1
intracellular anatomical structure	1
vacuole	1
plasma membrane	1
intracellular organelle	1
organelle lumen	1

Protein interactions and networks

STRING

1301 interactions, top by confidence (×1000):

Protein A	Protein B	Partner UniProt	Score
CTSF	ATG4B	Q9Y4P1	711
CTSF	MFSD8	Q8NHS3	708
CTSF	CTSD	P07339	693
CTSF	CLN5	O75503	692
CTSF	F5GZY7	F5GZY7	687
CTSF	CLN6	Q9NWW5	686
CTSF	GABARAPL2	P60520	673
CTSF	CLN3	Q13286	673
CTSF	KCTD7	Q96MP8	665
CTSF	CLN8	Q9UBY8	630
CTSF	LGMN	Q99538	617
CTSF	PPT1	P50897	607
CTSF	DNAJC5	Q9H3Z4	596
CTSF	TPP1	O14773	593
CTSF	MC3R	P41968	583

IntAct

47 interactions, top by confidence:

A	B	Type	Score
DEFA1	MANBA	psi-mi:“MI:0914”(association)	0.530
HSD3B2	NARS1	psi-mi:“MI:0914”(association)	0.530
DEFA6	EXTL3	psi-mi:“MI:0914”(association)	0.530
CRISP2	TUBA4A	psi-mi:“MI:0914”(association)	0.530
FBXO2	TMEM131L	psi-mi:“MI:0914”(association)	0.530
ISLR	BCKDK	psi-mi:“MI:0914”(association)	0.530
INSL5	COCH	psi-mi:“MI:0914”(association)	0.530
C1QTNF9B	PLOD3	psi-mi:“MI:0914”(association)	0.530
PTPRK	MANBA	psi-mi:“MI:0914”(association)	0.350
INSL5	LAMA5	psi-mi:“MI:0914”(association)	0.350
SIAE	COCH	psi-mi:“MI:0914”(association)	0.350
PON2	ENTPD6	psi-mi:“MI:0914”(association)	0.350
PDGFRA	GXYLT2	psi-mi:“MI:0914”(association)	0.350
CLEC12B	GXYLT2	psi-mi:“MI:0914”(association)	0.350
RAMP2	GXYLT2	psi-mi:“MI:0914”(association)	0.350
CGREF1	PLEKHG3	psi-mi:“MI:0914”(association)	0.350
LLCFC1	POTEF	psi-mi:“MI:0914”(association)	0.350
SUSD4	CCDC85C	psi-mi:“MI:0914”(association)	0.350
RLN1	RTL8C	psi-mi:“MI:0914”(association)	0.350
SCGB2A2	RTL8C	psi-mi:“MI:0914”(association)	0.350
NRSN1	FAM171A2	psi-mi:“MI:0914”(association)	0.350
CCL3L1	QSOX1	psi-mi:“MI:0914”(association)	0.350
PATE1	MANBA	psi-mi:“MI:0914”(association)	0.350
IGF2R	MANBA	psi-mi:“MI:0914”(association)	0.350
DEFB135	MANBA	psi-mi:“MI:0914”(association)	0.350
SLURP1	MANBA	psi-mi:“MI:0914”(association)	0.350
C1orf54	AGRN	psi-mi:“MI:0914”(association)	0.350

BioGRID (54): CTSF (Affinity Capture-MS), CTSF (Affinity Capture-MS), CTSF (Affinity Capture-MS), CTSF (Affinity Capture-MS), CTSF (Affinity Capture-MS), CTSF (Affinity Capture-MS), CTSF (Affinity Capture-MS), CTSF (Affinity Capture-MS), CTSF (Affinity Capture-MS), CTSF (Affinity Capture-MS), CTSF (Affinity Capture-MS), CTSF (Affinity Capture-MS), CTSF (Proximity Label-MS), CTSF (Two-hybrid), CTSF (Affinity Capture-MS)

ESM2 similar proteins: A0JPF9, A2VE29, A6QPN6, A8T658, B3SP85, E7E2N8, F1QVU0, H2N4I1, O00391, O08841, O95479, P06802, P07911, P13284, P20062, P23276, P48733, P55104, P56201, P59996, Q13219, Q16549, Q499T2, Q4R7M2, Q5R5C1, Q5REL7, Q5RER0, Q5RJG7, Q5U2X4, Q5XWD5, Q62849, Q6IUU3, Q6P6S4, Q80W65, Q86UX2, Q8BND5, Q8CFX1, Q8NCG5, Q92179, Q924C3

Diamond homologs: A0A068CNX1, A0A072UTP9, A0A0F7G352, A0A1S4F2V5, A2XQE8, A5HII1, B2LSD2, F4JNL3, O35186, O45734, O46427, O60911, O65039, O65493, O70370, O97397, P00785, P00786, P04989, P05167, P06797, P07154, P07711, P09648, P09668, P0DO76, P12412, P13277, P15242, P25251, P25326, P25773, P25774, P25776, P25777, P25778, P25782, P25784, P25803, P25804

SIGNOR signaling

2 interactions.

A	Effect	B	Mechanism
TFEB	“up-regulates quantity by expression”	CTSF	“transcriptional regulation”
TFE3	“up-regulates quantity by expression”	CTSF	“transcriptional regulation”

Disease & clinical

Clinical variants and AI predictions

ClinVar

321 variants total. Per-class counts are floors (≥ shown; pagination cap):

Classification	Count (floor)
Pathogenic	18
Likely pathogenic	18
Uncertain significance	132
Likely benign	94
Benign	23

Top pathogenic / likely-pathogenic (30)

Variant ID	HGVS	Classification
208844	NM_003793.4(CTSF):c.213+1G>C	Pathogenic
2417211	NM_003793.4(CTSF):c.594T>A (p.Tyr198Ter)	Pathogenic
2691546	NM_003793.4(CTSF):c.1119dup (p.Lys374fs)	Pathogenic
2857442	NM_003793.4(CTSF):c.992del (p.Lys331fs)	Pathogenic
3018158	NM_003793.4(CTSF):c.664C>T (p.Gln222Ter)	Pathogenic
3366554	NM_003793.4(CTSF):c.593_594del (p.Thr197_Tyr198insTer)	Pathogenic
3711871	NM_003793.4(CTSF):c.329_347del (p.Val110fs)	Pathogenic
4293328	NM_003793.4(CTSF):c.416C>A (p.Ser139Ter)	Pathogenic
434869	NM_003793.4(CTSF):c.843_844del (p.Ala282fs)	Pathogenic
4724736	NM_003793.4(CTSF):c.375_382del (p.Pro126fs)	Pathogenic
4765938	NM_003793.4(CTSF):c.871_872del (p.Met291fs)	Pathogenic
588283	NM_003793.4(CTSF):c.649C>T (p.Arg217Ter)	Pathogenic
60675	NM_003793.4(CTSF):c.962A>G (p.Gln321Arg)	Pathogenic
60676	NM_003793.4(CTSF):c.1373G>C (p.Gly458Ala)	Pathogenic
60679	NM_003793.4(CTSF):c.954del (p.Ser319fs)	Pathogenic
807589	NM_003793.4(CTSF):c.1247T>C (p.Ile416Thr)	Pathogenic
987064	NM_003793.4(CTSF):c.219_220insG (p.Gln74fs)	Pathogenic
987065	NM_003793.4(CTSF):c.218_219insCCC (p.Gly73_Gln74insPro)	Pathogenic
1064841	NM_003793.4(CTSF):c.600_603del (p.Glu202fs)	Likely pathogenic
1324192	NM_003793.4(CTSF):c.1045+1G>T	Likely pathogenic
1324193	NM_003793.4(CTSF):c.530_531+11del	Likely pathogenic
1690935	NM_003793.4(CTSF):c.1272C>A (p.Cys424Ter)	Likely pathogenic
1698527	NM_003793.4(CTSF):c.130del (p.Arg44fs)	Likely pathogenic
1704534	NM_003793.4(CTSF):c.264del (p.Cys89fs)	Likely pathogenic
1723409	NM_003793.4(CTSF):c.167_186del (p.Ala56fs)	Likely pathogenic
1804750	NM_003793.4(CTSF):c.105_129del (p.Ser36fs)	Likely pathogenic
2572494	NM_003793.4(CTSF):c.965-1G>A	Likely pathogenic
2631005	NM_003793.4(CTSF):c.693T>A (p.Tyr231Ter)	Likely pathogenic
2641996	NM_003793.4(CTSF):c.888G>A (p.Trp296Ter)	Likely pathogenic
3373769	NM_003793.4(CTSF):c.971T>C (p.Leu324Ser)	Likely pathogenic

SpliceAI

2177 predictions. Top by Δscore:

Variant	Effect	Δscore
11:66564006:CC:C	acceptor_gain	1.0000
11:66564007:CC:C	acceptor_gain	1.0000
11:66564802:CAGCT:C	acceptor_gain	1.0000
11:66564805:CT:C	acceptor_gain	1.0000
11:66564807:C:CC	acceptor_gain	1.0000
11:66564807:CTGAG:C	acceptor_loss	1.0000
11:66564881:A:AC	donor_gain	1.0000
11:66564882:C:CC	donor_gain	1.0000
11:66564882:CTCA:C	donor_gain	1.0000
11:66564883:TCACT:T	donor_loss	1.0000
11:66564885:A:AC	donor_gain	1.0000
11:66564885:ACT:A	donor_gain	1.0000
11:66564886:C:CT	donor_gain	1.0000
11:66564886:CT:C	donor_gain	1.0000
11:66564886:CTC:C	donor_gain	1.0000
11:66564886:CTCT:C	donor_gain	1.0000
11:66564886:CTCTG:C	donor_gain	1.0000
11:66564905:G:C	donor_gain	1.0000
11:66565002:CCCTC:C	acceptor_gain	1.0000
11:66565003:CCTCC:C	acceptor_gain	1.0000
11:66565004:CTC:C	acceptor_gain	1.0000
11:66565007:C:CC	acceptor_gain	1.0000
11:66565007:CT:C	acceptor_loss	1.0000
11:66565008:T:G	acceptor_loss	1.0000
11:66565015:C:CT	acceptor_gain	1.0000
11:66565016:G:T	acceptor_gain	1.0000
11:66566008:T:TA	donor_gain	1.0000
11:66566052:A:AC	donor_gain	1.0000
11:66566052:ACT:A	donor_gain	1.0000
11:66566053:C:CC	donor_gain	1.0000

AlphaMissense

3140 scored. Top likely-pathogenic:

Variant	Protein change	am_pathogenicity
11:66565907:C:A	W296C	0.996
11:66565907:C:G	W296C	0.996
11:66564109:C:A	W453C	0.995
11:66564109:C:G	W453C	0.995
11:66565901:G:C	F298L	0.995
11:66565901:G:T	F298L	0.995
11:66565903:A:G	F298L	0.995
11:66566301:A:C	S237R	0.995
11:66566301:A:T	S237R	0.995
11:66566303:T:G	S237R	0.995
11:66564111:A:G	W453R	0.994
11:66564111:A:T	W453R	0.994
11:66564115:G:C	N451K	0.994
11:66564115:G:T	N451K	0.994
11:66565909:A:G	W296R	0.994
11:66565909:A:T	W296R	0.994
11:66566304:G:C	F236L	0.994
11:66566304:G:T	F236L	0.994
11:66566306:A:G	F236L	0.994
11:66565886:A:C	N303K	0.993
11:66565886:A:T	N303K	0.993
11:66564112:G:C	S452R	0.992
11:66564112:G:T	S452R	0.992
11:66564114:T:G	S452R	0.992
11:66564118:C:A	K450N	0.992
11:66564118:C:G	K450N	0.992
11:66565839:G:A	S319F	0.992
11:66566157:G:C	F244L	0.992
11:66566157:G:T	F244L	0.992
11:66566159:A:G	F244L	0.992

dbSNP variants (sampled 300 via entrez): RS1000329619 (11:66570467 C>G,T), RS1000792424 (11:66564362 T>G), RS1000880959 (11:66568574 T>C), RS1001199791 (11:66564511 C>T), RS1002179439 (11:66563512 G>A), RS1002212039 (11:66563199 A>G), RS1002286441 (11:66566898 CT>C,CTT), RS1002330586 (11:66569285 T>G), RS1002770408 (11:66569013 C>A,G), RS1004267060 (11:66563961 G>C), RS1004369809 (11:66569555 G>A,T), RS1004430441 (11:66569328 T>C), RS1004505098 (11:66569100 A>G), RS1004729070 (11:66563590 G>A,C,T), RS1005336445 (11:66563989 G>A)

Disease associations

OMIM: gene MIM:603539 | disease phenotypes: MIM:615362, MIM:256730

GenCC curated gene-disease

Disease	Classification	Inheritance
neuronal ceroid lipofuscinosis 13	Definitive	Autosomal recessive

ClinGen Gene-Disease Validity (1)

Expert-panel classifications — Definitive > Strong > Moderate > Limited > Disputed > Refuted.

Disease	Classification	Inheritance
adult neuronal ceroid lipofuscinosis	Definitive	AR

Mondo (3): neurodevelopmental disorder (MONDO:0700092), neuronal ceroid lipofuscinosis 13 (MONDO:0014147), neuronal ceroid lipofuscinosis (MONDO:0016295)

Orphanet (4): CLN13 disease (Orphanet:352709), OBSOLETE: Adult neuronal ceroid lipofuscinosis (Orphanet:79262), Neuronal ceroid lipofuscinosis (Orphanet:216), OBSOLETE: Infantile neuronal ceroid lipofuscinosis (Orphanet:79263)

HPO phenotypes

25 total (25 of 25 shown, HPO-id order):

HPO	Term
HP:0000007	Autosomal recessive inheritance
HP:0000712	Emotional lability
HP:0000716	Depression
HP:0000726	Dementia
HP:0001250	Seizure
HP:0001251	Ataxia
HP:0001260	Dysarthria
HP:0001268	Mental deterioration
HP:0001272	Cerebellar atrophy
HP:0001289	Confusion
HP:0001336	Myoclonus
HP:0001337	Tremor
HP:0001347	Hyperreflexia
HP:0002066	Gait ataxia
HP:0002069	Bilateral tonic-clonic seizure
HP:0002071	Abnormality of extrapyramidal motor function
HP:0002119	Ventriculomegaly
HP:0002120	Cerebral cortical atrophy
HP:0002476	Primitive reflex
HP:0002506	Diffuse cerebral atrophy
HP:0002529	Neuronal loss in central nervous system
HP:0003487	Babinski sign
HP:0003676	Progressive
HP:0007359	Focal-onset seizure
HP:0011462	Young adult onset

GWAS associations

4 associations (top):

Study	Trait	p-value
GCST001241_12	Bipolar disorder	2.000000e-07
GCST002941_8	Airway imaging phenotypes	9.000000e-07
GCST006585_1817	Blood protein levels	2.000000e-11
GCST007576_250	Chronotype	5.000000e-13

EFO canonical traits (2, from GWAS)

EFO ID	Trait name
EFO:0007627	airway imaging measurement
EFO:0008328	chronotype measurement

MeSH disease descriptors (1)

Descriptor	Name	Tree numbers
D065886	Neurodevelopmental Disorders	F03.625

Drugs & pharmacology

Drug and pharmacology data

Is drug target: yes

ChEMBL targets (1): CHEMBL2517 (SINGLE PROTEIN)

Molecules with ChEMBL bioactivity

3 molecules (phase ≥1), by development phase (incl. off-target/promiscuous compounds). Patent mentions across the top 20 by phase: 3,636 (via chembl_molecule»patent_compound — counts attach to the compound, not the gene–compound relationship, so off-target/promiscuous molecules can dominate).

Molecule	Name	Phase	Patents
CHEMBL218394	BOCEPREVIR	4	2,760
CHEMBL481611	ODANACATIB	3	804
CHEMBL5095230	ATUZAGINSTAT	2	72

PharmGKB: 1 entry (VIP=true, CPIC=false)

GtoPdb / IUPHAR curated pharmacology

(IUPHAR/BPS Guide to Pharmacology — expert-curated)

Target class: enzyme — C1: Papain

Most potent curated ligand interactions (2 total), top 2:

Ligand	Action	Affinity	Parameter
VBY-825	Inhibition	8.33	pKi
compound (R)-26 [PMID: 22686657]	Inhibition	7.68	pKi

ChEMBL bioactivities

35 potent at pChembl≥5 of 37 total, top 33 by pChembl (potency: 10 = 0.1 nM, 6 = 1 µM).

pChembl	Type	Value	Unit	Molecule
9.52	IC50	0.3	nM	CHEMBL399361
8.40	IC50	4	nM	CHEMBL1288523
8.40	IC50	4	nM	CHEMBL1290084
7.92	IC50	12	nM	CHEMBL1289660
7.80	IC50	16	nM	CHEMBL1288531
7.68	Ki	21	nM	CHEMBL2153161
7.66	IC50	22	nM	CHEMBL1288526
7.64	IC50	23	nM	CHEMBL1288530
7.62	IC50	24	nM	CHEMBL1289764
7.43	IC50	37	nM	CHEMBL1288525
7.29	IC50	51	nM	CHEMBL1288528
7.25	IC50	56	nM	CHEMBL1288532
7.19	IC50	64	nM	CHEMBL1288527
7.17	IC50	67	nM	CHEMBL1289440
7.13	IC50	74	nM	CHEMBL3427166
7.12	IC50	76	nM	CHEMBL1288524
7.10	IC50	80	nM	CHEMBL1290303
6.83	IC50	147	nM	CHEMBL1289988
6.76	IC50	174	nM	CHEMBL1290191
6.48	IC50	331	nM	CHEMBL390474
6.31	IC50	487	nM	CHEMBL230474
6.30	IC50	500	nM	CHEMBL5848986
6.26	IC50	547	nM	CHEMBL1289441
6.18	IC50	654	nM	CHEMBL1289553
6.11	IC50	769	nM	CHEMBL1288529
6.10	IC50	795	nM	ODANACATIB
5.96	IC50	1100	nM	BOCEPREVIR
5.74	IC50	1826	nM	CHEMBL230478
5.50	Ki	3200	nM	CHEMBL2153169
5.49	IC50	3242	nM	CHEMBL1288521
5.42	IC50	3760	nM	CHEMBL390475
5.23	IC50	5908	nM	CHEMBL230473
5.21	IC50	6100	nM	ATUZAGINSTAT

PubChem BioAssay actives

31 with measured affinity, of 68 total; 31 most potent distinct compounds. Largely complementary to BindingDB; screening values are coarse (µM, 4 dp), so sub-nM hits tie at the floor.

Compound	Assay	Type	Value	Unit
(2S)-N-[(1S)-1-cyano-2-phenylethyl]-4-methyl-2-[[(1S)-2,2,2-trifluoro-1-[4-(4-methylsulfonylphenyl)phenyl]ethyl]amino]pentanamide	538812: Inhibition of human Cat F expressed in rabbit HIG82 cells	ic50	0.0003	uM
(2S)-N-[(1S)-1-cyano-2-(4-cyano-2-fluorophenyl)ethyl]-4-fluoro-4-methyl-2-[[(1S)-2,2,2-trifluoro-1-[4-(4-methylsulfonylphenyl)phenyl]ethyl]amino]pentanamide	538812: Inhibition of human Cat F expressed in rabbit HIG82 cells	ic50	0.0040	uM
(2S)-4,4-dichloro-N-[(1S)-1-cyano-2-phenylethyl]-2-[[(1S)-2,2,2-trifluoro-1-[4-(4-methylsulfonylphenyl)phenyl]ethyl]amino]butanamide	538812: Inhibition of human Cat F expressed in rabbit HIG82 cells	ic50	0.0040	uM
(2S)-N-[(1S)-1-cyano-2-pyridin-4-ylethyl]-4-fluoro-4-methyl-2-[[(1S)-2,2,2-trifluoro-1-[4-(4-methylsulfonylphenyl)phenyl]ethyl]amino]pentanamide	538812: Inhibition of human Cat F expressed in rabbit HIG82 cells	ic50	0.0120	uM
1-[4-[4-[(1S)-1-[[(2S)-1-[[(1S)-1-cyano-2-(4-cyano-2-fluorophenyl)ethyl]amino]-3-methyl-1-oxobutan-2-yl]amino]-2,2,2-trifluoroethyl]phenyl]phenyl]cyclopropane-1-carboxamide	538812: Inhibition of human Cat F expressed in rabbit HIG82 cells	ic50	0.0160	uM
N-[(2R)-1-[[cyano(methyl)amino]-methylamino]-3-(2-methylpropylsulfonyl)-1-oxopropan-2-yl]benzamide	691906: Inhibition of human recombinant cathepsin F using Z-Phe-Arg-AMC as substrate by fluorimetric analysis	ki	0.0210	uM
(2S)-N-[(1S)-1-cyano-2-phenylethyl]-4-fluoro-4-methyl-2-[[(1S)-2,2,2-trifluoro-1-[4-[4-[1-(morpholine-4-carbonyl)cyclopropyl]phenyl]phenyl]ethyl]amino]pentanamide	538812: Inhibition of human Cat F expressed in rabbit HIG82 cells	ic50	0.0220	uM
(2S)-N-[(1S)-1-cyano-2-(4-cyano-2-fluorophenyl)ethyl]-3-methyl-2-[[(1S)-2,2,2-trifluoro-1-[4-(4-methylsulfonylphenyl)phenyl]ethyl]amino]butanamide	538812: Inhibition of human Cat F expressed in rabbit HIG82 cells	ic50	0.0230	uM
(2S)-N-[(1S)-1-cyano-2-phenylethyl]-4-fluoro-4-methyl-2-[[(1S)-2,2,2-trifluoro-1-[4-(1H-pyrazol-4-yl)phenyl]ethyl]amino]pentanamide	538812: Inhibition of human Cat F expressed in rabbit HIG82 cells	ic50	0.0240	uM
1-[4-[4-[(1S)-1-[[(2S)-1-[[(1S)-1-cyano-2-phenylethyl]amino]-4-fluoro-4-methyl-1-oxopentan-2-yl]amino]-2,2,2-trifluoroethyl]phenyl]phenyl]cyclopropane-1-carboxamide	538812: Inhibition of human Cat F expressed in rabbit HIG82 cells	ic50	0.0370	uM
(2S)-N-[(1S)-1-cyano-2-phenylethyl]-4-fluoro-4-methyl-2-[[(1S)-2,2,2-trifluoro-1-[4-(4-pyridin-4-ylphenyl)phenyl]ethyl]amino]pentanamide	538812: Inhibition of human Cat F expressed in rabbit HIG82 cells	ic50	0.0510	uM
(2S)-N-[(1S)-1-cyano-2-(4-cyano-2-fluorophenyl)ethyl]-2-[[(1S)-1-[4-[4-[(1R)-2,2-difluoro-1-hydroxyethyl]phenyl]phenyl]-2,2,2-trifluoroethyl]amino]-3-methylbutanamide	538812: Inhibition of human Cat F expressed in rabbit HIG82 cells	ic50	0.0560	uM
(2S)-N-[(1S)-1-cyano-2-phenylethyl]-2-[[(1S)-1-[4-[4-[(1R)-2,2-difluoro-1-hydroxyethyl]phenyl]phenyl]-2,2,2-trifluoroethyl]amino]-4-fluoro-4-methylpentanamide	538812: Inhibition of human Cat F expressed in rabbit HIG82 cells	ic50	0.0640	uM
(2S)-N-[(1S)-1-cyano-2-phenylethyl]-4-fluoro-4-methyl-2-[[(1S)-2,2,2-trifluoro-1-[4-(4-methylsulfonylphenyl)phenyl]ethyl]amino]pentanamide	538812: Inhibition of human Cat F expressed in rabbit HIG82 cells	ic50	0.0670	uM
sodium (2S)-1-hydroxy-2-[[(2S)-4-methyl-2-(phenylmethoxycarbonylamino)pentanoyl]amino]-3-[(3S)-2-oxopyrrolidin-3-yl]propane-1-sulfonate	1851891: Inhibition of human Cathepsin F using Z-Phe-Arg-AMC as fluorogenic substrate incubated for 60 mins by FRET assay	ic50	0.0740	uM
(2S)-N-[(1R)-1-cyano-2-(4-cyano-2-fluorophenyl)ethyl]-4-fluoro-4-methyl-2-[[(1S)-2,2,2-trifluoro-1-[4-(4-methylsulfonylphenyl)phenyl]ethyl]amino]pentanamide	538812: Inhibition of human Cat F expressed in rabbit HIG82 cells	ic50	0.0760	uM
(2S)-N-[(1S)-1-cyano-2-phenylethyl]-2-cyclopropyl-2-[[(1S)-2,2,2-trifluoro-1-[4-(4-methylsulfonylphenyl)phenyl]ethyl]amino]acetamide	538812: Inhibition of human Cat F expressed in rabbit HIG82 cells	ic50	0.0800	uM
(2S)-N-[(1S)-1-cyano-2-phenylethyl]-3-cyclopropyl-2-[[(1S)-2,2,2-trifluoro-1-[4-(4-methylsulfonylphenyl)phenyl]ethyl]amino]propanamide	538812: Inhibition of human Cat F expressed in rabbit HIG82 cells	ic50	0.1470	uM
(2S)-N-[(1S)-1-cyano-2-phenylethyl]-3-methyl-2-[[(1S)-2,2,2-trifluoro-1-[4-(4-methylsulfonylphenyl)phenyl]ethyl]amino]butanamide	538812: Inhibition of human Cat F expressed in rabbit HIG82 cells	ic50	0.1740	uM
(4S,5R)-4-(2,3-dimethylphenoxy)-6-oxa-1-azabicyclo[3.2.1]octan-7-one	290158: Inhibition of human recombinant cathepsin F	ic50	0.3310	uM
(4S,5R)-4-phenoxy-6-oxa-1-azabicyclo[3.2.1]octan-7-one	290158: Inhibition of human recombinant cathepsin F	ic50	0.4870	uM
(2S)-N-(cyanomethyl)-4-fluoro-4-methyl-2-[[(1S)-2,2,2-trifluoro-1-[4-(4-methylsulfonylphenyl)phenyl]ethyl]amino]pentanamide	538812: Inhibition of human Cat F expressed in rabbit HIG82 cells	ic50	0.5470	uM
(2S)-N-[(1S)-1-cyano-3,3,3-trifluoropropyl]-4-fluoro-4-methyl-2-[[(1S)-2,2,2-trifluoro-1-[4-(4-methylsulfonylphenyl)phenyl]ethyl]amino]pentanamide	538812: Inhibition of human Cat F expressed in rabbit HIG82 cells	ic50	0.6540	uM
(2S)-N-[(1S)-1-cyano-2-phenylethyl]-3-phenyl-2-[[(1S)-2,2,2-trifluoro-1-[4-(4-methylsulfonylphenyl)phenyl]ethyl]amino]propanamide	538812: Inhibition of human Cat F expressed in rabbit HIG82 cells	ic50	0.7690	uM
(2S)-N-(1-cyanocyclopropyl)-4-fluoro-4-methyl-2-[[(1S)-2,2,2-trifluoro-1-[4-(4-methylsulfonylphenyl)phenyl]ethyl]amino]pentanamide	314223: Inhibition of cathepsin F	ic50	0.7950	uM
(1R,2S,5S)-N-(4-amino-1-cyclobutyl-3,4-dioxobutan-2-yl)-3-[(2S)-2-(tert-butylcarbamoylamino)-3,3-dimethylbutanoyl]-6,6-dimethyl-3-azabicyclo[3.1.0]hexane-2-carboxamide	508173: Inhibition of human Cathepsin F	ic50	1.1000	uM
(4S,5R)-4-(2-methylpropoxy)-6-oxa-1-azabicyclo[3.2.1]octan-7-one	290158: Inhibition of human recombinant cathepsin F	ic50	1.8260	uM
N-[1-(cyanomethylamino)-3-(2-methylpropylsulfonyl)-1-oxopropan-2-yl]-5-thiophen-2-ylthiophene-2-carboxamide	691901: Inhibition of human recombinant cathepsin F using Z-Phe-Arg-AMC as substrate after 8 min by fluorimetric analysis	ki	3.2000	uM
(2S)-N-[(1S)-1-cyano-3-phenylpropyl]-4-fluoro-4-methyl-2-[[(1S)-2,2,2-trifluoro-1-[4-(4-methylsulfonylphenyl)phenyl]ethyl]amino]pentanamide	538812: Inhibition of human Cat F expressed in rabbit HIG82 cells	ic50	3.2420	uM
(4S,5R)-4-phenylmethoxy-6-oxa-1-azabicyclo[3.2.1]octan-7-one	290158: Inhibition of human recombinant cathepsin F	ic50	3.7600	uM
(4S,5S)-4-(2,3-dimethylphenoxy)-6-oxa-1-azabicyclo[3.2.1]octan-7-one	290158: Inhibition of human recombinant cathepsin F	ic50	5.9080	uM

CTD chemical–gene interactions

34 total (human), top 30 by PubMed support.

Chemical	Actions (top 5)	PubMed papers
Estradiol	affects cotreatment, increases expression, decreases expression	3
bisphenol A	increases expression, affects cotreatment	2
Aflatoxin B1	decreases expression, decreases methylation	2
Particulate Matter	decreases expression, increases abundance	2
afuresertib	increases expression	1
sodium arsenite	decreases expression	1
nickel sulfate	decreases expression	1
beta-methylcholine	affects expression	1
yessotoxin	increases expression	1
CGP 52608	increases reaction, affects binding	1
jinfukang	increases expression, affects cotreatment	1
PP242	increases expression	1
Temozolomide	decreases expression	1
Air Pollutants	decreases expression, increases abundance	1
Benzo(a)pyrene	increases methylation	1
Chelating Agents	affects binding, decreases expression	1
Cisplatin	affects cotreatment, increases expression	1
Copper	affects binding, decreases expression	1
Dexamethasone	affects cotreatment, increases expression	1
Diethylhexyl Phthalate	decreases expression	1
Doxorubicin	decreases expression	1
Indomethacin	affects cotreatment, increases expression	1
Nickel	decreases expression	1
Rotenone	decreases expression	1
Silicon Dioxide	decreases expression	1
Smoke	decreases expression	1
Testosterone	decreases expression	1
Thiram	decreases expression	1
Tobacco Smoke Pollution	decreases expression	1
Tretinoin	increases expression	1

ChEMBL screening assays

18 unique, capped per target: 17 binding, 1 toxicity

Representative assays (with source publication via chembl_document):

Assay ID	Type	Description	Source paper
CHEMBL1042340	Binding	Inhibition of human cathepsin F	Pyrazole-based cathepsin S inhibitors with arylalkynes as P1 binding elements. — Bioorg Med Chem Lett
CHEMBL5154225	Toxicity	Inhibition of human cathepsin F using Z-Phe-Arg-AMC as substrate by FRET assay	Discovery and Crystallographic Studies of Nonpeptidic Piperazine Derivatives as Covalent SARS-CoV-2 Main Protease Inhibitors. — J Med Chem

Cellosaurus cell lines

2 cell lines: 1 cancer cell line, 1 embryonic stem cell

First 10 cell lines (id-ordered, not curated):

Cellosaurus	Name	Category	Sex
CVCL_D5F8	HeLa::TMEM192-3xHA CTSF partial KO	Cancer cell line	Female
CVCL_F0PS	H9 AAVS1-TRE3G-NGN2 TMEM192-3xHA (heterozygous) CTSF-/-	Embryonic stem cell	Female

Clinical trials (associated diseases)

202 trials via MONDO — disease-level, not drug-specific.

Trial	Phase	Status	Title
NCT04586348	PHASE4	UNKNOWN	Prenatal Iodine Supplementation and Early Childhood Neurodevelopment
NCT04873115	PHASE4	UNKNOWN	Double-blind, Placebo-controlled, Randomized Clinical Trial Comparing the Efficacy and Safety of Sialanar Plus orAl rehabiLitation Against Placebo Plus Oral Rehabilitation for chIldren and Adolescents With seVere Sialorrhoea and Neurodisabilties,
NCT02559102	PHASE3	COMPLETED	Dexmedetomidine Sedation Versus General Anaesthesia for Inguinal Hernia Surgery in Infants
NCT02757079	PHASE3	COMPLETED	Study of the Efficacy and Safety of NPC-15 for Sleep Disorders of Children With Neurodevelopmental Disorders
NCT06915480	PHASE3	RECRUITING	Reducing Missed Appointments
NCT07377032	PHASE3	RECRUITING	TAP-GRIN: Interventional Study on Patients With GRIN-related Neurodevelopmental Disorders
NCT02909959	PHASE2	COMPLETED	Sulforaphane for the Treatment of Young Men With Autism Spectrum Disorder
NCT06081348	PHASE2	RECRUITING	Sertraline vs. Placebo in the Treatment of Anxiety in Children and AdoLescents With NeurodevelopMental Disorders
NCT06352372	PHASE2	COMPLETED	Safety and Efficacy of tPBM for Epileptiform Activity in Autism
NCT00503191	PHASE1	COMPLETED	NeuroModulation Technique Treatment of Autism
NCT04475848	PHASE1	COMPLETED	A Study to Investigate the Safety, Tolerability, Pharmacokinetics, Pharmacodynamics and Food Effect of RO6953958 in Healthy Participants
NCT06300398	PHASE1	COMPLETED	IAMA-6 Oral Dose Study in Healthy Adults
NCT01783041	PHASE2/PHASE3	COMPLETED	Effect of Early L-Carnitine Supplementation on Neurodevelopmental Outcomes in Very Preterm Infants
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NCT05675098	EARLY_PHASE1	NOT_YET_RECRUITING	Central Nervous System Stimulants and Physical Function in Children With Cerebral Palsy
NCT00783783	Not specified	COMPLETED	CYP2D6 Pharmacogenetics in Risperidone-Treated Children
NCT01778504	Not specified	RECRUITING	Studying Childhood-onset Behavioral, Psychiatric, and Developmental Disorders
NCT01850784	Not specified	UNKNOWN	High Energy Formula Feeding in Infants With Congenital Heart Disease
NCT01922791	Not specified	COMPLETED	Nutrition and Pregnancy Intervention Study
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NCT02003170	Not specified	COMPLETED	Etiology and Early Diagnosis of Neurodevelopmental Disorders
NCT02118649	Not specified	ACTIVE_NOT_RECRUITING	Enhancing Behavior and Brain Response to Visual Targets Using a Computer Game
NCT02557191	Not specified	TERMINATED	Biomarkers, Neurodevelopment and Preterm Infants
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NCT02694003	Not specified	COMPLETED	Better Nights, Better Days for Children With Neurodevelopment Disorders
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NCT02871674	Not specified	UNKNOWN	Good Night Project: Behavioural Sleep Interventions for Children With ADHD: A Randomised Controlled Trial
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NCT02912780	Not specified	UNKNOWN	Introduction of Microsystems in a Level 3 Neonatal Intensive Care Unit
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NCT03023644	Not specified	COMPLETED	Improving Neurodevelopmental Outcomes in Children With Congenital Heart Disease: An Intervention Study
NCT03032991	Not specified	UNKNOWN	Early Biomarkers of Neurodevelopment in Offspring of Diabetic Mothers
NCT03088189	Not specified	TERMINATED	Effect of Parental Peri-conceptional Vitamin B12 Supplementation on Infant Neurocognitive Development in Offspring
NCT03096028	Not specified	COMPLETED	Developmental Origins of Mental Health Disorders
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NCT03172104	Not specified	COMPLETED	Neurobehavioural Development of Infants Born <30 Weeks Gestational Age Between Birth and Five Years of Age
NCT03222375	Not specified	RECRUITING	SQUED™ Series 28.1 Home-use and Treatment of Autowave Reverberator of Autism
NCT03229928	Not specified	COMPLETED	Clinical Testing of a Real-Time Behavior Measurement Tool: Measuring Outcomes for CHAnge
NCT03232489	Not specified	UNKNOWN	Study for the Evaluation of the Feasibility of Applying Advanced MRI Scanning in Pediatric Clinical Practice