CTSF (cathepsin F)

Gene

• Entrez ID: 8722
• Gene name: Cathepsin F
• Gene symbol: CTSF
• Synonyms (NCBI Gene): CATSF, CLN13
• Chromosome: 11
• Chromosome location: 11q13.2
• Summary: 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 (

SNPs

SNP ID	Visualize variation	Clinical significance	Consequence
rs141915593	T>C,G	Likely-pathogenic	Splice acceptor variant
rs143313688	G>A	Likely-benign, conflicting-interpretations-of-pathogenicity	Coding sequence variant, missense variant
rs143889283	T>C	Pathogenic	Coding sequence variant, missense variant
rs148611356	G>C	Uncertain-significance, conflicting-interpretations-of-pathogenicity	Missense variant, coding sequence variant
rs375562245	G>A,C	Pathogenic	Missense variant, stop gained, coding sequence variant
rs397514731	T>C	Pathogenic	Missense variant, coding sequence variant
rs397514732	C>G,T	Pathogenic	Missense variant, coding sequence variant
rs397514733	G>A	Pathogenic	Missense variant, coding sequence variant
rs753084727	G>-	Pathogenic	Frameshift variant, coding sequence variant
rs797045136	C>G	Pathogenic	Splice donor variant, upstream transcript variant, genic upstream transcript variant
rs1555058286	CC>-	Pathogenic	Coding sequence variant, frameshift variant
rs1565311875	A>G	Pathogenic	Coding sequence variant, missense variant

miRNA

miRTarBase ID	miRNA	Experiments	Reference
MIRT018210	hsa-miR-335-5p	Microarray	18185580
MIRT2207335	hsa-miR-383	CLIP-seq
MIRT2207336	hsa-miR-4691-3p	CLIP-seq
MIRT2207337	hsa-miR-4714-5p	CLIP-seq
MIRT2207338	hsa-miR-4772-5p	CLIP-seq
MIRT2207339	hsa-miR-486-3p	CLIP-seq
MIRT2510460	hsa-miR-140-3p	CLIP-seq
MIRT2510461	hsa-miR-18a	CLIP-seq
MIRT2510462	hsa-miR-18b	CLIP-seq
MIRT2510463	hsa-miR-298	CLIP-seq
MIRT2510464	hsa-miR-3065-5p	CLIP-seq
MIRT2510465	hsa-miR-3127-5p	CLIP-seq
MIRT2510466	hsa-miR-342-5p	CLIP-seq
MIRT2510467	hsa-miR-3665	CLIP-seq
MIRT2510468	hsa-miR-412	CLIP-seq
MIRT2510469	hsa-miR-421	CLIP-seq
MIRT2510470	hsa-miR-4272	CLIP-seq
MIRT2510471	hsa-miR-4480	CLIP-seq
MIRT2510472	hsa-miR-4651	CLIP-seq
MIRT2510473	hsa-miR-4664-5p	CLIP-seq
MIRT2510474	hsa-miR-4735-3p	CLIP-seq
MIRT2510475	hsa-miR-608	CLIP-seq
MIRT2510476	hsa-miR-657	CLIP-seq
MIRT2510477	hsa-miR-764	CLIP-seq
MIRT2510460	hsa-miR-140-3p	CLIP-seq
MIRT2510468	hsa-miR-412	CLIP-seq
MIRT2510471	hsa-miR-4480	CLIP-seq

Gene ontology (GO)

GO ID	Ontology	Definition	Evidence	Reference
GO:0002376	Process	Immune system process	IEA
GO:0004197	Function	Cysteine-type endopeptidase activity	IBA
GO:0004197	Function	Cysteine-type endopeptidase activity	IEA
GO:0004197	Function	Cysteine-type endopeptidase activity	TAS	9822672
GO:0005515	Function	Protein binding	IPI	15752368
GO:0005615	Component	Extracellular space	IBA
GO:0005737	Component	Cytoplasm	IEA
GO:0005764	Component	Lysosome	IBA
GO:0005764	Component	Lysosome	IEA
GO:0005764	Component	Lysosome	TAS	9822672
GO:0005783	Component	Endoplasmic reticulum	IDA
GO:0005886	Component	Plasma membrane	IDA
GO:0006508	Process	Proteolysis	IEA
GO:0006508	Process	Proteolysis	TAS	9822672
GO:0008233	Function	Peptidase activity	IEA
GO:0008234	Function	Cysteine-type peptidase activity	IDA	15752368
GO:0008234	Function	Cysteine-type peptidase activity	IEA
GO:0012505	Component	Endomembrane system	IEA
GO:0016787	Function	Hydrolase activity	IEA
GO:0019886	Process	Antigen processing and presentation of exogenous peptide antigen via MHC class II	TAS
GO:0031012	Component	Extracellular matrix	HDA	25037231
GO:0043202	Component	Lysosomal lumen	TAS
GO:0051603	Process	Proteolysis involved in protein catabolic process	IBA
GO:0070013	Component	Intracellular organelle lumen	IEA
GO:0070062	Component	Extracellular exosome	HDA	18570454
GO:1903561	Component	Extracellular vesicle	HDA	24769233

Other IDs

• MIM: 603539
• HGNC: 2531
• e!Ensembl: ENSG00000174080

Protein

• UniProt ID: Q9UBX1
• Protein name: Cathepsin F (CATSF) (EC 3.4.22.41)
• Protein function: Thiol protease which is believed to participate in intracellular degradation and turnover of proteins. Has also been implicated in tumor invasion and metastasis.
• PDB: 1M6D
• Family and domains:

  Pfam

  Accession	ID	Position in sequence	Description	Type
  PF08246	Inhibitor_I29	187 → 244	Cathepsin propeptide inhibitor domain (I29)	Domain
  PF00112	Peptidase_C1	271 → 482	Papain family cysteine protease	Domain

• Tissue specificity: 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.
• Sequence:

  MAPWLQLLSLLGLLPGAVAAPAQPRAASFQAWGPPSPELLAPTRFALEMFNRGRAAGTRA
  VLGLVRGRVRRAGQGSLYSLEATLEEPPCNDPMVCRLPVSKKTLLCSFQVLDELGRHVLL
  RKDCGPVDTKVPGAGEPKSAFTQGSAMISSLSQNHPDNRNETFSSVISLLNEDPLSQDLP
  VKMASIFKNFVITYNRTYESKEEARWRLSVFVNNMVRAQKIQALDRGTAQYGVTKFSDLT
  EEEFRTIYLNTLLRKEPGNKMKQAKSVGDLAPPEWDWRSKGAVTKVKDQGMCGSCWAFSV
  TGNVEGQWFLNQGTLLSLSEQELLDCDKMDKACMGGLPSNAYSAIKNLGGLETEDDYSYQ
  GHMQSCNFSAEKAKVYINDSVELSQNEQKLAAWLAKRGPISVAINAFGMQFYRHGISRPL
  RPLCSPWLIDHAVLLVGYGNRSDVPFWAIKNSWGTDWGEKGYYYLHRGSGACGVNTMASS
  AVVD

• Sequence length: 484

Pathways

KEGG:

Lysosome
Apoptosis

Reactome:

MHC class II antigen presentation

Associated diseases

Evidence Score:

• ★☆☆☆☆  Gene-disease association found in Text Mining only
• ★★☆☆☆  Found in Text Mining and Unknown/Other Associations
• ★★★☆☆  Reported in Unknown/Other Associations across ≥2 Sources
• ★★★★☆  ClinVar: Pathogenic/Likely Pathogenic (<5 Variants)
• ★★★★★  ClinVar: Pathogenic/Likely Pathogenic (≥5 Variants)

Causal
Phenotype Name	Clinical Significance	dbSNP ID	RCV Accession	Evidence Score
CTSF-related disorder	Likely pathogenic	rs929020615	RCV003404379	★★★★☆ ClinVar: Pathogenic / Likely Pathogenic (<5 Variants)
Neurodevelopmental disorder	Likely pathogenic	rs2134954582	RCV001375004	★★★★☆ ClinVar: Pathogenic / Likely Pathogenic (<5 Variants)
Neuronal ceroid lipofuscinosis	Likely pathogenic; Pathogenic	rs2134951897, rs1857984449, rs2495284476, rs1336749001, rs2495286249, rs2495273817	RCV002509766 RCV002271804 RCV002282861 RCV002308685 RCV002470047 RCV003487266	★★★★★ ClinVar: Pathogenic / Likely Pathogenic (≥5 Variants)
Neuronal ceroid lipofuscinosis 13	Pathogenic; Likely pathogenic	rs758004789, rs1456291681, rs2134954887, rs797045136, rs1051519244, rs2495276170, rs766762684, rs1555058286, rs397514731, rs397514732, rs753084727, rs1565311875	RCV003112039 RCV001780897 RCV001780898 RCV000190878 RCV003314379 RCV003742256 RCV003876821 RCV000504328 RCV000054490 RCV000054491 RCV000054494 RCV000995752	★★★★★ ClinVar: Pathogenic / Likely Pathogenic (≥5 Variants)

Unknown / Other Associations
Phenotype Name	Clinical Significance	Source	Evidence Score
ADULT NEURONAL CEROID LIPOFUSCINOSIS	—	GWAS catalog	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
BIPOLAR DISORDER	—	GWAS catalog	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
BREAST CANCER	—	GWAS catalog	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
BREAST CARCINOMA	—	GWAS catalog	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
CEROID LIPOFUSCINOSIS, NEURONAL, 13	—	CTD, Disgenet, HPO CTD, Disgenet, HPO CTD, Disgenet, HPO	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Cholangiocarcinoma	Uncertain significance	ClinVar	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
CLN13 DISEASE	—	Orphanet	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
DEVELOPMENTAL DISABILITIES	—	Disgenet	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Developmental disorder	Uncertain significance	ClinVar	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
JUVENILE NEURONAL CEROID LIPOFUSCINOSIS	—	Disgenet	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
LATE-INFANTILE NEURONAL CEROID LIPOFUSCINOSIS	—	Disgenet	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
NEURODEVELOPMENTAL DISORDERS	—	Disgenet	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
NEURONAL CEROID-LIPOFUSCINOSES	—	Disgenet	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Nonpapillary renal cell carcinoma	Likely benign	ClinVar	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Sarcoma	Uncertain significance	ClinVar	★★☆☆☆ Found in Text Mining + Unknown/Other Associations

Associations from Text Mining
Disease Name	Disease (Merged)	Source	PMID	Relationship Type	Evidence Score
Adult Neuronal Ceroid Lipofuscinosis	Neuronal Ceroid Lipofuscinosis	BEFREE	23297359, 25576872, 29120254		★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Agenesis of Corpus Callosum	Corpus callosum agenesis	Pubtator	26141065	Associate	★☆☆☆☆ Found in Text Mining only
Alzheimer Disease	Alzheimer disease	Pubtator	27524508, 31521194	Associate	★☆☆☆☆ Found in Text Mining only
Alzheimer Disease, Early Onset	Alzheimer disease	BEFREE	27524508		★☆☆☆☆ Found in Text Mining only
Behcet Syndrome	Behcet disease	Pubtator	39191728	Inhibit	★☆☆☆☆ Found in Text Mining only
Bipolar Disorder	Bipolar Disorder	GWASCAT_DG	19416921		★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Bipolar Disorder	Bipolar Disorder	GWASDB_DG	19416921		★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Breast Neoplasms	Breast neoplasm	Pubtator	34646403	Associate	★☆☆☆☆ Found in Text Mining only
Carcinoma Basal Cell	Basal cell carcinoma	Pubtator	39312365	Stimulate	★☆☆☆☆ Found in Text Mining only
Cerebellar atrophy	Cerebellar atrophy	HPO_DG			★☆☆☆☆ Found in Text Mining only
CEROID LIPOFUSCINOSIS, NEURONAL, 13	Ceroid Lipofuscinosis Neuronal	GENOMICS_ENGLAND_DG	16508006, 23746550, 25274848		★★☆☆☆ Found in Text Mining + Unknown/Other Associations
CEROID LIPOFUSCINOSIS, NEURONAL, 13	Ceroid Lipofuscinosis Neuronal	UNIPROT_DG	23297359		★★☆☆☆ Found in Text Mining + Unknown/Other Associations
CEROID LIPOFUSCINOSIS, NEURONAL, 13	Ceroid Lipofuscinosis Neuronal	ORPHANET_DG	23297359		★★☆☆☆ Found in Text Mining + Unknown/Other Associations
CEROID LIPOFUSCINOSIS, NEURONAL, 13	Ceroid Lipofuscinosis Neuronal	CLINVAR_DG			★★☆☆☆ Found in Text Mining + Unknown/Other Associations
CEROID LIPOFUSCINOSIS, NEURONAL, 13	Ceroid Lipofuscinosis Neuronal	CTD_human_DG			★★☆☆☆ Found in Text Mining + Unknown/Other Associations
CLN13 disease	Neuronal Ceroid Lipofuscinosis	Orphanet			★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Dementia	Dementia	BEFREE	23297359		★☆☆☆☆ Found in Text Mining only
Dementia	Dementia	HPO_DG			★☆☆☆☆ Found in Text Mining only
Depressive disorder	Mental Depression	HPO_DG			★☆☆☆☆ Found in Text Mining only
Dermatitis	Dermatitis	Pubtator	36057013	Associate	★☆☆☆☆ Found in Text Mining only
Diabetes Mellitus	Diabetes mellitus	Pubtator	16186340, 24255036, 25446319, 27077448, 33181273	Associate	★☆☆☆☆ Found in Text Mining only
Diabetic Retinopathy	Diabetic Retinopathy	BEFREE	16186340		★☆☆☆☆ Found in Text Mining only
Diabetic Retinopathy	Diabetic retinopathy	Pubtator	16186340	Stimulate	★☆☆☆☆ Found in Text Mining only
Dysarthria	Dysarthria	HPO_DG			★☆☆☆☆ Found in Text Mining only
Esophageal Neoplasms	Esophageal neoplasm	Pubtator	34716287	Associate	★☆☆☆☆ Found in Text Mining only
Fabry Disease	Fabry disease	BEFREE	31378672		★☆☆☆☆ Found in Text Mining only
Fabry Disease	Fabry disease	Pubtator	31378672	Associate	★☆☆☆☆ Found in Text Mining only
Frontotemporal Dementia	Frontotemporal dementia	Pubtator	28749476, 34561610	Associate	★☆☆☆☆ Found in Text Mining only
Lung Neoplasms	Lung neoplasms	Pubtator	34923982	Associate	★☆☆☆☆ Found in Text Mining only
Lymphatic Metastasis	Lymphatic metastasis	Pubtator	28474574	Associate	★☆☆☆☆ Found in Text Mining only
Macular Degeneration	Macular degeneration	Pubtator	36705323	Associate	★☆☆☆☆ Found in Text Mining only
Malignant neoplasm of stomach	Stomach Neoplasms	BEFREE	28474574		★☆☆☆☆ Found in Text Mining only
Malignant Neoplasms	Malignant Neoplasm	BEFREE	28474574		★☆☆☆☆ Found in Text Mining only
Mood swings	Mood swings	HPO_DG			★☆☆☆☆ Found in Text Mining only
Neoplasms	Neoplasms	BEFREE	28474574		★☆☆☆☆ Found in Text Mining only
Neuronal Ceroid-Lipofuscinoses	Neuronal Ceroid Lipofuscinosis	BEFREE	23297359, 25576872, 29120254		★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Presenile dementia	Senile Dementia	BEFREE	23297359		★☆☆☆☆ Found in Text Mining only
Stomach Carcinoma	Stomach Carcinoma	BEFREE	28474574		★☆☆☆☆ Found in Text Mining only
Stomach Neoplasms	Stomach neoplasms	Pubtator	28474574, 33236952	Associate	★☆☆☆☆ Found in Text Mining only
Uterine Cervical Neoplasms	Uterine neoplasm	Pubtator	15989693	Associate	★☆☆☆☆ Found in Text Mining only