CTSF

cathepsin F, the group of Cathepsins

Basic information

Region (hg38): 11:66563463-66568879

Links

ENSG00000174080 ∙ NCBI:8722 ∙ OMIM:603539 ∙ HGNC:2531 ∙ Uniprot:Q9UBX1 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

Phenotypes

GenCC

Source: genCC

• neuronal ceroid lipofuscinosis 13 (Strong), mode of inheritance: AR
• neuronal ceroid lipofuscinosis 13 (Supportive), mode of inheritance: AR
• neuronal ceroid lipofuscinosis 13 (Strong), mode of inheritance: AR
• neuronal ceroid lipofuscinosis 13 (Limited), mode of inheritance: Unknown
• adult neuronal ceroid lipofuscinosis (Definitive), mode of inheritance: AR

Clinical Genomic Database

Source: CGD

Condition	Inheritance	Intervention Categories	Intervention/Rationale	Manifestation Categories	References
Neuronal ceroid lipofuscinosis 13	AR	General	Genetic knowledge may be beneficial related to issues such as selection of optimal supportive care, informed medical decision-making, prognostic considerations, and avoidance of unnecessary testing	Biochemical; Neurologic	20301601; 23297359

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the CTSF gene.

• Neuronal ceroid lipofuscinosis 13 (90 variants)
• not provided (90 variants)
• Inborn genetic diseases (82 variants)
• not specified (16 variants)
• Neuronal ceroid lipofuscinosis (6 variants)
• Neurodevelopmental disorder (2 variants)
• CTSF-related condition (2 variants)
• Developmental disorder (1 variants)
• See cases (1 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the CTSF 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				32	5	37
missense	2		76	5	2	85
nonsense	2	3	2			7
start loss						0
frameshift	3	6	1			10
inframe indel	1		1			2
splice donor/acceptor (+/-2bp)		3				3
splice region			2	5	1	8
non coding				23	11	34
Total	8	12	80	60	18

Highest pathogenic variant AF is 0.0000197

Variants in CTSF

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

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

Position	Type	Phenotype	Significance	ClinVar
11-66563698-C-T			Benign (Jul 17, 2018)
11-66563714-TACC-T			Likely benign (Jul 21, 2018)
11-66563938-C-G			Uncertain significance (Mar 09, 2021)
11-66563944-C-T			Uncertain significance (Feb 24, 2022)
11-66563946-G-A		Inborn genetic diseases	Uncertain significance (Apr 27, 2022)
11-66563949-G-A		Neuronal ceroid lipofuscinosis 13	Uncertain significance (Mar 29, 2024)
11-66563961-G-C		Inborn genetic diseases	Uncertain significance (Jun 23, 2017)
11-66563974-A-T		Inborn genetic diseases	Uncertain significance (Feb 07, 2018)
11-66563980-C-T			Uncertain significance (Sep 09, 2021)
11-66563981-G-A		Neuronal ceroid lipofuscinosis 13 • Inborn genetic diseases	Benign/Likely benign (Jan 11, 2024)
11-66563987-A-G		not specified • Neuronal ceroid lipofuscinosis 13 • Inborn genetic diseases	Benign (Jan 30, 2024)
11-66563987-ACG-GCA		Inborn genetic diseases	Uncertain significance (Apr 26, 2019)
11-66563989-G-A		Neuronal ceroid lipofuscinosis 13 • Inborn genetic diseases	Uncertain significance (Oct 20, 2023)
11-66564068-GC-G		Neuronal ceroid lipofuscinosis 13	Likely benign (May 23, 2022)
11-66564075-C-T		Neuronal ceroid lipofuscinosis 13	Likely benign (Jan 28, 2024)
11-66564093-C-T		Inborn genetic diseases	Uncertain significance (Oct 13, 2023)
11-66564095-C-G		Neuronal ceroid lipofuscinosis 13	Pathogenic (Apr 01, 2013)
11-66564095-C-T		Inborn genetic diseases	Uncertain significance (May 31, 2023)
11-66564098-C-T		not specified	Uncertain significance (Dec 14, 2021)
11-66564100-G-A		not specified • Neuronal ceroid lipofuscinosis 13 • Inborn genetic diseases	Benign/Likely benign (Jan 19, 2024)
11-66564105-T-C			Uncertain significance (Nov 08, 2019)
11-66564110-C-T		not specified	Uncertain significance (Jul 26, 2021)
11-66564117-TC-T		Neuronal ceroid lipofuscinosis 13	Uncertain significance (Feb 08, 2018)
11-66564119-T-C			Uncertain significance (Feb 03, 2022)
11-66564138-C-T		Inborn genetic diseases	Likely benign (Mar 14, 2018)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
CTSF	protein_coding	protein_coding	ENST00000310325	13	5379

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
1.94e-13	0.112	125693	0	55	125748	0.000219

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.744	217	250	0.868	0.0000145	3086
Missense in Polyphen		88	113.43	0.7758		1329
Synonymous	-0.246	105	102	1.03	0.00000625	959
Loss of Function	0.753	22	26.2	0.841	0.00000121	304

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000518	0.000518
Ashkenazi Jewish	0.00	0.00
East Asian	0.000875	0.000870
Finnish	0.0000462	0.0000462
European (Non-Finnish)	0.000132	0.000132
Middle Eastern	0.000875	0.000870
South Asian	0.000393	0.000392
Other	0.000163	0.000163

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Thiol protease which is believed to participate in intracellular degradation and turnover of proteins. Has also been implicated in tumor invasion and metastasis.
• Pathway: Lysosome - Homo sapiens (human);Apoptosis - Homo sapiens (human);MHC class II antigen presentation;Immune System;Adaptive Immune System (Consensus)

Recessive Scores

• pRec: 0.152

Intolerance Scores

• loftool: 0.466
• rvis_EVS: 0.49
• rvis_percentile_EVS: 79.46

Haploinsufficiency Scores

• pHI: 0.133
• hipred: N
• hipred_score: 0.123
• ghis: 0.441

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: S
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.199

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Ctsf
• Phenotype: nervous system phenotype (the observable morphological and physiological characteristics of the extensive, intricate network of electochemical structures in the body that is comprised of the brain, spinal cord, nerves, ganglia and parts of the receptor organs that are manifested through development and lifespan); behavior/neurological phenotype (the observable actions or reactions of mammalian organisms that are manifested through development and lifespan); mortality/aging (the observable characteristics related to the ability of a mammalian organism to live and age that are manifested throughout development and life span); growth/size/body region phenotype

Gene ontology

• Biological process: proteolysis;antigen processing and presentation of exogenous peptide antigen via MHC class II;proteolysis involved in cellular protein catabolic process
• Cellular component: extracellular space;lysosome;lysosomal lumen;extracellular exosome;extracellular vesicle
• Molecular function: cysteine-type endopeptidase activity