CTSG
cathepsin G, the group of Cathepsins|Granule associated serine proteases of immune defence|Receptor ligands
Basic information
Region (hg38): 14:24573518-24576250
Links
Phenotypes
GenCC
Source:
No genCC data.
ClinVar
This is a list of variants' phenotypes submitted to
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 | |||||
| missense | 13 | 17 | ||||
| nonsense | 0 | |||||
| start loss | 0 | |||||
| frameshift | 0 | |||||
| inframe indel | 0 | |||||
| splice donor/acceptor (+/-2bp) | 0 | |||||
| splice region | 0 | |||||
| non coding | 0 | |||||
| Total | 0 | 0 | 13 | 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) | ||
| 14-24574493-T-C | not specified | Uncertain significance (May 14, 2024) | ||
| 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:
| 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:
- 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
- ghis
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