CASP1

caspase 1, the group of Caspase recruitment domain containing|Caspases

Basic information

Region (hg38): 11:105025396-105035250

Previous symbols: [ "IL1BC" ]

Links

ENSG00000137752 ∙ NCBI:834 ∙ OMIM:147678 ∙ HGNC:1499 ∙ Uniprot:P29466 ∙ 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 CASP1 gene.

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				3	1	4
missense			22	7	2	31
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	22	10	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)
11-105029750-A-G			Likely benign (Aug 22, 2018)
11-105029808-C-T		CASP1-related disorder	Likely benign (Mar 13, 2023)
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)
11-105030461-G-C		not specified	Uncertain significance (Aug 11, 2022)
11-105030476-G-A		not specified	Uncertain significance (Aug 22, 2023)
11-105030478-C-T		not specified	Uncertain significance (Apr 26, 2023)
11-105030485-T-C		not specified	Uncertain significance (Dec 08, 2023)
11-105031189-C-T			Benign (Jul 06, 2018)
11-105031197-C-T		not specified	Uncertain significance (Dec 22, 2023)

GnomAD

Source: gnomAD

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: dbNSFP

• 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