CTSG

cathepsin G, the group of Cathepsins|Granule associated serine proteases of immune defence|Receptor ligands

Basic information

Region (hg38): 14:24573517-24576250

Links

ENSG00000100448 ∙ NCBI:1511 ∙ OMIM:116830 ∙ HGNC:2532 ∙ Uniprot:P08311 ∙ 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 CTSG gene.

• Inborn genetic diseases (10 variants)
• not provided (3 variants)
• not specified (1 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the CTSG 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			9	1	3	13
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	9	1	4

Variants in CTSG

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

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

Position	Type	Phenotype	Significance	ClinVar
14-24573647-G-C		not specified	Uncertain significance (Jun 10, 2022)
14-24573654-T-C		not specified	Uncertain significance (Aug 08, 2022)
14-24573779-T-C		not specified	Uncertain significance (Nov 07, 2022)
14-24574311-G-A			Benign (Aug 06, 2018)
14-24574376-C-G		not specified	Likely benign (Mar 14, 2023)
14-24574378-C-T		not specified	Uncertain significance (May 08, 2023)
14-24574411-G-C		not specified	Uncertain significance (Feb 10, 2022)
14-24574465-T-C		not specified	Benign (Mar 28, 2016)
14-24574470-G-T		not specified	Uncertain significance (Dec 14, 2023)
14-24574678-C-A		not specified	Uncertain significance (Nov 15, 2021)
14-24574745-G-A			Benign (Jul 31, 2018)
14-24574763-T-G		not specified	Uncertain significance (Aug 04, 2023)
14-24574790-C-T		not specified	Uncertain significance (Nov 09, 2023)
14-24575275-A-C		not specified	Uncertain significance (Dec 12, 2023)
14-24575297-G-C		not specified	Uncertain significance (Jun 26, 2023)
14-24575377-A-C		not specified	Uncertain significance (Oct 03, 2022)
14-24575410-C-T		not specified	Uncertain significance (Jun 24, 2022)
14-24576180-C-G			Benign (Jul 31, 2018)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
CTSG	protein_coding	protein_coding	ENST00000216336	5	2739

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.00000956	0.565	125713	0	35	125748	0.000139

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.818	130	159	0.817	0.0000101	1622
Missense in Polyphen		45	65.16	0.6906		703
Synonymous	0.0986	64	65.0	0.984	0.00000408	543
Loss of Function	0.769	9	11.9	0.759	7.47e-7	106

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000185	0.000185
Ashkenazi Jewish	0.00	0.00
East Asian	0.000326	0.000326
Finnish	0.00	0.00
European (Non-Finnish)	0.000132	0.000132
Middle Eastern	0.000326	0.000326
South Asian	0.000359	0.000359
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Serine protease with trypsin- and chymotrypsin-like specificity. Cleaves complement C3. Has antibacterial activity against the Gram-negative bacterium P.aeruginosa, antibacterial activity is inhibited by LPS from P.aeruginosa, Z-Gly-Leu-Phe- CH2Cl and phenylmethylsulfonyl fluoride. {ECO:0000269|PubMed:1861080, ECO:0000269|PubMed:1937776, ECO:0000269|PubMed:8194606}.
• Pathway: Agents Acting on the Renin-Angiotensin System Pathway, Pharmacodynamics;Renin-angiotensin system - Homo sapiens (human);Systemic lupus erythematosus - Homo sapiens (human);Lysosome - Homo sapiens (human);Amoebiasis - Homo sapiens (human);Neuroactive ligand-receptor interaction - Homo sapiens (human);ACE Inhibitor Pathway, Pharmacodynamics;ACE Inhibitor Pathway;Neutrophil degranulation;Peptide hormone metabolism;Metabolism of proteins;Metabolism of Angiotensinogen to Angiotensins;Extracellular matrix organization;Antimicrobial peptides;Innate Immune System;Immune System;Activation of Matrix Metalloproteinases;Regulation of Insulin-like Growth Factor (IGF) transport and uptake by Insulin-like Growth Factor Binding Proteins (IGFBPs);Degradation of the extracellular matrix;Urokinase-type plasminogen activator (uPA) and uPAR-mediated signaling (Consensus)

Recessive Scores

• pRec: 0.485

Intolerance Scores

• loftool: 0.313
• rvis_EVS: 0.55
• rvis_percentile_EVS: 81.38

Haploinsufficiency Scores

• pHI: 0.0309
• hipred: N
• hipred_score: 0.458

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.697

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Ctsg
• Phenotype: liver/biliary system phenotype; immune system phenotype; hematopoietic system phenotype; normal phenotype; 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); neoplasm

Gene ontology

• Biological process: angiotensin maturation;protein phosphorylation;proteolysis;immune response;antimicrobial humoral response;antibacterial humoral response;extracellular matrix disassembly;neutrophil degranulation;negative regulation of growth of symbiont in host;cellular protein metabolic process;positive regulation of immune response;defense response to Gram-negative bacterium;defense response to fungus;neutrophil mediated killing of gram-positive bacterium;cellular response to lipopolysaccharide
• Cellular component: extracellular region;extracellular space;nucleus;cytoplasm;plasma membrane;cell surface;cytoplasmic stress granule;secretory granule;azurophil granule lumen;collagen-containing extracellular matrix;extracellular exosome
• Molecular function: serine-type endopeptidase activity;protein binding;heparin binding;peptidase activity;serine-type peptidase activity