CASP1
caspase 1, the group of Caspase recruitment domain containing|Caspases
Basic information
Region (hg38): 11:105025397-105035250
Previous symbols: [ "IL1BC" ]
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 CASP1 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 | 4 | |||||
| missense | 32 | 39 | ||||
| nonsense | 0 | |||||
| start loss | 0 | |||||
| frameshift | 0 | |||||
| inframe indel | 0 | |||||
| splice donor/acceptor (+/-2bp) | 0 | |||||
| splice region | 0 | |||||
| non coding | 0 | |||||
| Total | 0 | 0 | 32 | 8 | 3 |
Variants in CASP1
This is a list of pathogenic ClinVar variants found in the CASP1 region.
You can filter this list by clicking the number of variants in the Variants pathogenicity by type table.
| Position | Type | Phenotype | Significance | ClinVar |
|---|---|---|---|---|
| 11-105026263-G-A | not specified | Likely benign (Feb 28, 2023) | ||
| 11-105026316-A-C | not specified | Uncertain significance (May 24, 2024) | ||
| 11-105026322-G-A | not specified | Likely benign (Oct 27, 2023) | ||
| 11-105026870-G-A | not specified | Uncertain significance (Jun 24, 2022) | ||
| 11-105026870-G-C | not specified | Uncertain significance (Nov 18, 2022) | ||
| 11-105026889-T-G | not specified | Likely benign (Oct 29, 2021) | ||
| 11-105026893-T-A | not specified | Uncertain significance (Mar 24, 2023) | ||
| 11-105026922-C-T | not specified | Uncertain significance (Jun 16, 2024) | ||
| 11-105026931-G-T | not specified | Uncertain significance (Jan 02, 2024) | ||
| 11-105029146-G-A | Likely benign (Aug 06, 2018) | |||
| 11-105029148-T-A | not specified | Uncertain significance (Oct 12, 2021) | ||
| 11-105029686-T-C | not specified | Uncertain significance (Jan 19, 2022) | ||
| 11-105029692-C-A | not specified | Uncertain significance (Feb 22, 2023) | ||
| 11-105029692-C-T | not specified | Uncertain significance (Aug 27, 2024) | ||
| 11-105029750-A-G | Likely benign (Aug 22, 2018) | |||
| 11-105029762-T-C | not specified | Uncertain significance (Oct 28, 2024) | ||
| 11-105029808-C-T | CASP1-related disorder | Likely benign (Mar 13, 2023) | ||
| 11-105029809-G-A | not specified | Uncertain significance (Nov 15, 2024) | ||
| 11-105029818-G-A | not specified | Uncertain significance (Dec 19, 2023) | ||
| 11-105029858-C-T | Likely benign (Jun 05, 2018) | |||
| 11-105029866-G-A | CASP1-related disorder | Likely benign (Jan 19, 2023) | ||
| 11-105029878-C-A | not specified | Uncertain significance (Aug 16, 2021) | ||
| 11-105029895-A-G | not specified | Uncertain significance (Jul 07, 2024) | ||
| 11-105030341-G-A | not specified | Uncertain significance (Sep 09, 2024) | ||
| 11-105030461-G-C | not specified | Uncertain significance (Aug 11, 2022) |
GnomAD
Source:
| Gene | Type | Bio Type | Transcript | Coding Exons | Length |
|---|---|---|---|---|---|
| CASP1 | protein_coding | protein_coding | ENST00000533400 | 9 | 75989 |
| pLI Probability LOF Intolerant | pRec Probability LOF Recessive | Individuals with no LOFs | Individuals with Homozygous LOFs | Individuals with Heterozygous LOFs | Defined | p |
|---|---|---|---|---|---|---|
| 0.0000352 | 0.952 | 125703 | 0 | 39 | 125742 | 0.000155 |
| Z-Score | Observed | Expected | Observed/Expected | Mutation Rate | Total Possible in Transcript | |
|---|---|---|---|---|---|---|
| Missense | -0.0593 | 226 | 224 | 1.01 | 0.0000119 | 2669 |
| Missense in Polyphen | 71 | 83.158 | 0.8538 | 1024 | ||
| Synonymous | 0.154 | 76 | 77.7 | 0.978 | 0.00000410 | 761 |
| Loss of Function | 1.81 | 10 | 18.4 | 0.545 | 8.68e-7 | 229 |
LoF frequencies by population
| Ethnicity | Sum of pLOFs | p |
|---|---|---|
| African & African-American | 0.000580 | 0.000580 |
| Ashkenazi Jewish | 0.0000994 | 0.0000992 |
| East Asian | 0.00 | 0.00 |
| Finnish | 0.0000463 | 0.0000462 |
| European (Non-Finnish) | 0.0000798 | 0.0000791 |
| Middle Eastern | 0.00 | 0.00 |
| South Asian | 0.000267 | 0.000261 |
| Other | 0.00 | 0.00 |
dbNSFP
Source:
- Function
- FUNCTION: Thiol protease that cleaves IL-1 beta between an Asp and an Ala, releasing the mature cytokine which is involved in a variety of inflammatory processes. Important for defense against pathogens. Cleaves and activates sterol regulatory element binding proteins (SREBPs). Can also promote apoptosis. Upon inflammasome activation, during DNA virus infection but not RNA virus challenge, controls antiviral immunity through the cleavage of CGAS, rendering it inactive (PubMed:28314590). {ECO:0000269|PubMed:15498465, ECO:0000269|PubMed:1574116, ECO:0000269|PubMed:28314590, ECO:0000269|PubMed:7876192}.;
- Pathway
- Pertussis - Homo sapiens (human);Salmonella infection - Homo sapiens (human);Legionellosis - Homo sapiens (human);Influenza A - Homo sapiens (human);Amyotrophic lateral sclerosis (ALS) - Homo sapiens (human);Cytosolic DNA-sensing pathway - Homo sapiens (human);Necroptosis - Homo sapiens (human);NOD-like receptor signaling pathway - Homo sapiens (human);C-type lectin receptor signaling pathway - Homo sapiens (human);Nucleotide-binding Oligomerization Domain (NOD) pathway;Apoptosis Modulation and Signaling;Parkin-Ubiquitin Proteasomal System pathway;Amyotrophic lateral sclerosis (ALS);Apoptosis;Apoptotic Signaling Pathway;TP53 Regulates Transcription of Cell Death Genes;Gene expression (Transcription);Signaling by Interleukins;caspase cascade in apoptosis;internal ribosome entry pathway;Generic Transcription Pathway;Cytokine Signaling in Immune system;The NLRP3 inflammasome;NOD1/2 Signaling Pathway;Inflammasomes;Nucleotide-binding domain, leucine rich repeat containing receptor (NLR) signaling pathways;TP53 Regulates Transcription of Cell Death Genes;RNA Polymerase II Transcription;DroToll-like;Innate Immune System;Immune System;AndrogenReceptor;TP53 Regulates Transcription of Caspase Activators and Caspases;d4gdi signaling pathway;Transcriptional Regulation by TP53;IFN-gamma pathway;Direct p53 effectors;The AIM2 inflammasome;The IPAF inflammasome;Interleukin-1 processing;IL1-mediated signaling events;Cellular roles of Anthrax toxin;Interleukin-1 family signaling
(Consensus)
Recessive Scores
- pRec
- 0.586
Intolerance Scores
- loftool
- 0.831
- rvis_EVS
- 0.44
- rvis_percentile_EVS
- 77.8
Haploinsufficiency Scores
- pHI
- 0.0966
- hipred
- Y
- hipred_score
- 0.556
- ghis
- 0.440
Essentials
- essential_gene_CRISPR
- N
- essential_gene_CRISPR2
- N
- essential_gene_gene_trap
- N
- gene_indispensability_pred
- E
- gene_indispensability_score
- 0.509
Gene Damage Prediction
| All | Recessive | Dominant | |
|---|---|---|---|
| Mendelian | Medium | Medium | Medium |
| Primary Immunodeficiency | Medium | Medium | Medium |
| Cancer | Medium | Medium | Medium |
Mouse Genome Informatics
- Gene name
- Casp1
- Phenotype
- homeostasis/metabolism phenotype; cellular phenotype; endocrine/exocrine gland phenotype; renal/urinary system phenotype; immune system phenotype; digestive/alimentary 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); neoplasm; hematopoietic system 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);
Gene ontology
- Biological process
- proteolysis;apoptotic process;activation of cysteine-type endopeptidase activity involved in apoptotic process;signal transduction;protein autoprocessing;cytokine-mediated signaling pathway;regulation of apoptotic process;positive regulation of I-kappaB kinase/NF-kappaB signaling;positive regulation of cysteine-type endopeptidase activity involved in apoptotic process;positive regulation of interleukin-1 beta secretion;cellular response to lipopolysaccharide;cellular response to mechanical stimulus;cellular response to organic substance;cellular response to cytokine stimulus;cellular response to interferon-gamma;apoptotic signaling pathway;execution phase of apoptosis;positive regulation of tumor necrosis factor-mediated signaling pathway
- Cellular component
- cytoplasm;cytosol;protein-containing complex;IPAF inflammasome complex;NLRP1 inflammasome complex;NLRP3 inflammasome complex;AIM2 inflammasome complex;protease inhibitor complex
- Molecular function
- endopeptidase activity;cysteine-type endopeptidase activity;protein binding;cysteine-type endopeptidase activator activity involved in apoptotic process;kinase binding;identical protein binding;CARD domain binding;cysteine-type endopeptidase activity involved in apoptotic process;cysteine-type endopeptidase activity involved in apoptotic signaling pathway