CASP3
caspase 3, the group of Caspases|Small nucleolar RNA protein coding host genes
Basic information
Region (hg38): 4:184627695-184650062
Links
Phenotypes
GenCC
Source:
No genCC data.
ClinVar
This is a list of variants' phenotypes submitted to
- Inborn genetic diseases (6 variants)
- not provided (5 variants)
Variants pathogenicity by type
Statistics on ClinVar variants can assist in determining whether a specific variant type in the CASP3 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 | 2 | |||||
| missense | 6 | |||||
| nonsense | 0 | |||||
| start loss | 0 | |||||
| frameshift | 0 | |||||
| inframe indel | 1 | |||||
| splice donor/acceptor (+/-2bp) | 0 | |||||
| splice region ? | 0 | |||||
| non coding ? | 1 | |||||
| Total | 0 | 0 | 5 | 4 | 1 |
Variants in CASP3
This is a list of pathogenic ClinVar variants found in the CASP3 region.
You can filter this list by clicking the number of variants in the Variants pathogenicity by type table.
| Position | Type | Phenotype | Significance | ClinVar |
|---|---|---|---|---|
| 4-184628935-A-G | Benign (Feb 23, 2021) | |||
| 4-184629342-G-A | not specified | Uncertain significance (Nov 07, 2022) | ||
| 4-184629346-C-T | not specified | Uncertain significance (Feb 05, 2024) | ||
| 4-184629409-T-C | not specified | Uncertain significance (May 03, 2023) | ||
| 4-184629416-A-C | Likely benign (Dec 31, 2019) | |||
| 4-184629436-T-C | not specified | Uncertain significance (Jun 05, 2023) | ||
| 4-184631112-CACT-C | Uncertain significance (Aug 01, 2019) | |||
| 4-184631143-T-G | Likely benign (Jun 26, 2018) | |||
| 4-184631871-A-G | not specified | Uncertain significance (Jan 09, 2023) | ||
| 4-184632273-C-T | Likely benign (Dec 31, 2019) | |||
| 4-184632338-T-A | not specified | Uncertain significance (Dec 16, 2023) | ||
| 4-184635330-T-C | not specified | Uncertain significance (Jun 27, 2022) | ||
| 4-184635399-C-T | not specified | Likely benign (Apr 07, 2023) |
GnomAD
Source:
| Gene | Type | Bio Type | Transcript | Coding Exons | Length |
|---|---|---|---|---|---|
| CASP3 | protein_coding | protein_coding | ENST00000308394 | 6 | 21814 |
| pLI Probability LOF Intolerant | pRec Probability LOF Recessive | Individuals with no LOFs | Individuals with Homozygous LOFs | Individuals with Heterozygous LOFs | Defined | p |
|---|---|---|---|---|---|---|
| 0.100 | 0.893 | 125730 | 0 | 18 | 125748 | 0.0000716 |
| Z-Score | Observed | Expected | Observed/Expected | Mutation Rate | Total Possible in Transcript | |
|---|---|---|---|---|---|---|
| Missense | 1.66 | 99 | 158 | 0.628 | 0.00000841 | 1862 |
| Missense in Polyphen | 29 | 54.7 | 0.53017 | 720 | ||
| Synonymous | 1.31 | 40 | 52.1 | 0.768 | 0.00000284 | 485 |
| Loss of Function | 2.37 | 4 | 13.3 | 0.300 | 8.16e-7 | 158 |
LoF frequencies by population
| Ethnicity | Sum of pLOFs | p |
|---|---|---|
| African & African-American | 0.000153 | 0.000152 |
| Ashkenazi Jewish | 0.00 | 0.00 |
| East Asian | 0.00 | 0.00 |
| Finnish | 0.0000465 | 0.0000462 |
| European (Non-Finnish) | 0.0000975 | 0.0000967 |
| Middle Eastern | 0.00 | 0.00 |
| South Asian | 0.0000665 | 0.0000653 |
| Other | 0.000167 | 0.000163 |
dbNSFP
Source:
- Function
- FUNCTION: Involved in the activation cascade of caspases responsible for apoptosis execution. At the onset of apoptosis it proteolytically cleaves poly(ADP-ribose) polymerase (PARP) at a '216-Asp-|-Gly-217' bond. Cleaves and activates sterol regulatory element binding proteins (SREBPs) between the basic helix-loop- helix leucine zipper domain and the membrane attachment domain. Cleaves and activates caspase-6, -7 and -9. Involved in the cleavage of huntingtin. Triggers cell adhesion in sympathetic neurons through RET cleavage. {ECO:0000269|PubMed:21357690, ECO:0000269|PubMed:7596430}.;
- Pathway
- Kaposi,s sarcoma-associated herpesvirus infection - Homo sapiens (human);Pertussis - Homo sapiens (human);Legionellosis - Homo sapiens (human);Serotonergic synapse - Homo sapiens (human);Non-alcoholic fatty liver disease (NAFLD) - Homo sapiens (human);AGE-RAGE signaling pathway in diabetic complications - Homo sapiens (human);Viral myocarditis - Homo sapiens (human);p53 signaling pathway - Homo sapiens (human);Small cell lung cancer - Homo sapiens (human);Apoptosis - multiple species - Homo sapiens (human);Alzheimer,s disease - Homo sapiens (human);Amyotrophic lateral sclerosis (ALS) - Homo sapiens (human);Huntington,s disease - Homo sapiens (human);TNF signaling pathway - Homo sapiens (human);Amoebiasis - Homo sapiens (human);Epithelial cell signaling in Helicobacter pylori infection - Homo sapiens (human);Tuberculosis - Homo sapiens (human);MAPK signaling pathway - Homo sapiens (human);Natural killer cell mediated cytotoxicity - Homo sapiens (human);IL-17 signaling pathway - Homo sapiens (human);Toxoplasmosis - Homo sapiens (human);Proteoglycans in cancer - Homo sapiens (human);MicroRNAs in cancer - Homo sapiens (human);Pathways in cancer - Homo sapiens (human);Viral carcinogenesis - Homo sapiens (human);Hepatitis B - Homo sapiens (human);Parkinson,s disease - Homo sapiens (human);Apoptosis - Homo sapiens (human);Colorectal cancer - Homo sapiens (human);Human papillomavirus infection - Homo sapiens (human);Herpes simplex infection - Homo sapiens (human);Celecoxib Pathway, Pharmacodynamics;miRNA Regulation of DNA Damage Response;Apoptosis Modulation and Signaling;Integrated Breast Cancer Pathway;Prolactin Signaling Pathway;Alzheimers Disease;TNF alpha Signaling Pathway;AGE-RAGE pathway;Allograft Rejection;Corticotropin-releasing hormone signaling pathway;Parkinsons Disease Pathway;Oncostatin M Signaling Pathway;Brain-Derived Neurotrophic Factor (BDNF) signaling pathway;Spinal Cord Injury;Amyotrophic lateral sclerosis (ALS);Nanomaterial induced apoptosis;Integrated Lung Cancer Pathway;Apoptosis;Fas Ligand (FasL) pathway and Stress induction of Heat Shock Proteins (HSP) regulation;Copper homeostasis;Apoptotic Signaling Pathway;Hepatitis C and Hepatocellular Carcinoma;MAPK Signaling Pathway;Apoptosis Modulation by HSP70;ERK Pathway in Huntington,s Disease;Oxidative Damage;miRNA regulation of p53 pathway in prostate cancer;Prion disease pathway;apoptotic signaling in response to dna damage;Chromosomal and microsatellite instability in colorectal cancer;Sudden Infant Death Syndrome (SIDS) Susceptibility Pathways;DNA Damage Response;Signal Transduction;Other interleukin signaling;Signaling by Interleukins;tnfr1 signaling pathway;trefoil factors initiate mucosal healing;caspase cascade in apoptosis;granzyme a mediated apoptosis pathway;tsp-1 induced apoptosis in microvascular endothelial cell;induction of apoptosis through dr3 and dr4/5 death receptors;hiv-1 nef: negative effector of fas and tnf;b cell survival pathway;west nile virus;apoptotic dna-fragmentation and tissue homeostasis;stress induction of hsp regulation;regulation of cell cycle progression by plk3;internal ribosome entry pathway;Cytokine Signaling in Immune system;Fas;Extracellular matrix organization;Caspase activation via extrinsic apoptotic signalling pathway;DroToll-like;SMAC-mediated dissociation of IAP:caspase complexes ;SMAC-mediated apoptotic response;Apoptotic factor-mediated response;Intrinsic Pathway for Apoptosis;Caspase-mediated cleavage of cytoskeletal proteins;Apoptotic cleavage of cell adhesion proteins;Apoptotic cleavage of cellular proteins;Immune System;Activation of DNA fragmentation factor;Apoptosis induced DNA fragmentation;Stimulation of the cell death response by PAK-2p34;Apoptotic execution phase;Apoptosis;Programmed Cell Death;Activation of caspases through apoptosome-mediated cleavage;fas signaling pathway (cd95);AndrogenReceptor;d4gdi signaling pathway;SMAC binds to IAPs ;NADE modulates death signalling;Degradation of the extracellular matrix;Posttranslational regulation of adherens junction stability and dissassembly;Ligand-independent caspase activation via DCC;Death Receptor Signalling;p75 NTR receptor-mediated signalling;Signaling by Hippo;TNFalpha;TNF;Cytochrome c-mediated apoptotic response;Caspase Cascade in Apoptosis;HIV-1 Nef: Negative effector of Fas and TNF-alpha;LPA receptor mediated events;Calcineurin-regulated NFAT-dependent transcription in lymphocytes;p75(NTR)-mediated signaling;Cell death signalling via NRAGE, NRIF and NADE;FAS (CD95) signaling pathway;Role of Calcineurin-dependent NFAT signaling in lymphocytes;Syndecan-2-mediated signaling events
(Consensus)
Recessive Scores
- pRec
- 0.987
Intolerance Scores
- loftool
- 0.628
- rvis_EVS
- -0.38
- rvis_percentile_EVS
- 27.42
Haploinsufficiency Scores
- pHI
- 0.942
- hipred
- Y
- hipred_score
- 0.798
- ghis
- 0.652
Essentials
- essential_gene_CRISPR
- N
- essential_gene_CRISPR2
- N
- essential_gene_gene_trap
- N
- gene_indispensability_pred
- E
- gene_indispensability_score
- 0.764
Gene Damage Prediction
| All | Recessive | Dominant | |
|---|---|---|---|
| Mendelian | Medium | Medium | Medium |
| Primary Immunodeficiency | Medium | Medium | Medium |
| Cancer | Medium | Medium | Medium |
Mouse Genome Informatics
- Gene name
- Casp3
- Phenotype
- taste/olfaction phenotype; endocrine/exocrine gland phenotype; growth/size/body region phenotype; integument phenotype (the observable morphological and physiological characteristics of the skin and its associated structures, such as the hair, nails, sweat glands, sebaceous glands and other secretory glands that are manifested through development and lifespan); homeostasis/metabolism phenotype; cellular phenotype; craniofacial phenotype; digestive/alimentary phenotype; muscle phenotype; hearing/vestibular/ear 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); pigmentation phenotype; cardiovascular system phenotype (the observable morphological and physiological characteristics of the mammalian heart, blood vessels, or circulatory system that are manifested through development and lifespan); 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); reproductive system phenotype; behavior/neurological phenotype (the observable actions or reactions of mammalian organisms that are manifested through development and lifespan); respiratory system phenotype; skeleton phenotype; immune system phenotype; vision/eye phenotype;
Zebrafish Information Network
- Gene name
- casp3a
- Affected structure
- retinal ganglion cell
- Phenotype tag
- abnormal
- Phenotype quality
- occurrence
Gene ontology
- Biological process
- luteolysis;response to hypoxia;B cell homeostasis;apoptotic DNA fragmentation;proteolysis;apoptotic process;activation of cysteine-type endopeptidase activity involved in apoptotic process;cellular response to DNA damage stimulus;axonal fasciculation;heart development;sensory perception of sound;learning or memory;intrinsic apoptotic signaling pathway in response to osmotic stress;response to UV;response to glucose;response to X-ray;regulation of macroautophagy;protein processing;cytokine-mediated signaling pathway;hippocampus development;neuron differentiation;keratinocyte differentiation;erythrocyte differentiation;platelet formation;negative regulation of B cell proliferation;regulation of protein stability;response to cobalt ion;response to estradiol;response to lipopolysaccharide;glial cell apoptotic process;response to tumor necrosis factor;response to nicotine;hippo signaling;wound healing;response to hydrogen peroxide;T cell homeostasis;negative regulation of apoptotic process;response to amino acid;positive regulation of neuron apoptotic process;cell fate commitment;negative regulation of cyclin-dependent protein serine/threonine kinase activity;negative regulation of activated T cell proliferation;neurotrophin TRK receptor signaling pathway;striated muscle cell differentiation;response to glucocorticoid;neuron apoptotic process;leukocyte apoptotic process;cellular response to staurosporine;apoptotic signaling pathway;extrinsic apoptotic signaling pathway in absence of ligand;execution phase of apoptosis;positive regulation of amyloid-beta formation
- Cellular component
- nucleus;nucleoplasm;cytoplasm;cytosol;death-inducing signaling complex;neuronal cell body;membrane raft
- Molecular function
- protease binding;aspartic-type endopeptidase activity;cysteine-type endopeptidase activity;cyclin-dependent protein serine/threonine kinase inhibitor activity;death receptor binding;protein binding;peptidase activity;cysteine-type endopeptidase activator activity involved in apoptotic process;phospholipase A2 activator activity;protein-containing complex binding;cysteine-type endopeptidase activity involved in apoptotic process;cysteine-type endopeptidase activity involved in apoptotic signaling pathway;cysteine-type endopeptidase activity involved in execution phase of apoptosis