CASP9
caspase 9, the group of Apoptosome|Caspases|Caspase recruitment domain containing|Protein phosphatase 1 regulatory subunits
Basic information
Region (hg38): 1:15490832-15526534
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 CASP9 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 | 9 | |||||
| missense | 27 | 37 | ||||
| nonsense | 0 | |||||
| start loss | 0 | |||||
| frameshift | 0 | |||||
| inframe indel | 0 | |||||
| splice donor/acceptor (+/-2bp) | 0 | |||||
| splice region | 2 | 2 | ||||
| non coding | 1 | |||||
| Total | 0 | 0 | 27 | 10 | 10 |
Variants in CASP9
This is a list of pathogenic ClinVar variants found in the CASP9 region.
You can filter this list by clicking the number of variants in the Variants pathogenicity by type table.
| Position | Type | Phenotype | Significance | ClinVar |
|---|---|---|---|---|
| 1-15491299-T-C | not specified | Uncertain significance (Nov 28, 2023) | ||
| 1-15492963-G-T | not specified | Uncertain significance (Jul 20, 2021) | ||
| 1-15492971-C-T | not specified | Uncertain significance (Jan 26, 2023) | ||
| 1-15492994-C-A | not specified | Likely benign (Sep 14, 2022) | ||
| 1-15492997-C-A | not specified | Uncertain significance (Dec 03, 2021) | ||
| 1-15493007-A-T | not specified | Uncertain significance (Dec 04, 2023) | ||
| 1-15493898-C-G | CASP9-related disorder | Likely benign (Jun 21, 2019) | ||
| 1-15493903-G-A | not specified | Uncertain significance (Apr 15, 2024) | ||
| 1-15493908-T-C | not specified | Uncertain significance (Jun 24, 2022) | ||
| 1-15493953-G-T | CASP9-related disorder | Benign (Dec 31, 2019) | ||
| 1-15493997-A-C | not specified | Uncertain significance (Nov 06, 2023) | ||
| 1-15495299-A-G | not specified | Uncertain significance (Jan 18, 2023) | ||
| 1-15495350-C-T | not specified | Uncertain significance (Jul 12, 2022) | ||
| 1-15495401-G-T | not specified | Uncertain significance (Aug 17, 2022) | ||
| 1-15495437-C-G | not specified | Uncertain significance (Apr 20, 2024) | ||
| 1-15495452-T-C | not specified | Uncertain significance (Jan 16, 2024) | ||
| 1-15504656-G-T | not specified | Uncertain significance (Jul 19, 2023) | ||
| 1-15504674-C-T | not specified | Uncertain significance (May 27, 2022) | ||
| 1-15504763-A-G | CASP9-related disorder | Benign (Aug 28, 2019) | ||
| 1-15505981-G-A | CASP9-related disorder | Benign (Dec 31, 2019) | ||
| 1-15505999-G-A | CASP9-related disorder | Likely benign (Mar 01, 2023) | ||
| 1-15506028-C-A | not specified | Uncertain significance (Sep 23, 2023) | ||
| 1-15506048-T-C | CASP9-related disorder | Benign (Oct 18, 2019) | ||
| 1-15506050-C-T | CASP9-related disorder | Likely benign (Apr 12, 2019) | ||
| 1-15506969-C-T | not specified | Uncertain significance (Aug 26, 2022) |
GnomAD
Source:
| Gene | Type | Bio Type | Transcript | Coding Exons | Length |
|---|---|---|---|---|---|
| CASP9 | protein_coding | protein_coding | ENST00000333868 | 9 | 35703 |
| pLI Probability LOF Intolerant | pRec Probability LOF Recessive | Individuals with no LOFs | Individuals with Homozygous LOFs | Individuals with Heterozygous LOFs | Defined | p |
|---|---|---|---|---|---|---|
| 0.00000738 | 0.916 | 125689 | 0 | 59 | 125748 | 0.000235 |
| Z-Score | Observed | Expected | Observed/Expected | Mutation Rate | Total Possible in Transcript | |
|---|---|---|---|---|---|---|
| Missense | 0.0269 | 239 | 240 | 0.995 | 0.0000141 | 2679 |
| Missense in Polyphen | 97 | 95.484 | 1.0159 | 1082 | ||
| Synonymous | 0.232 | 94 | 96.9 | 0.970 | 0.00000590 | 835 |
| Loss of Function | 1.65 | 11 | 18.7 | 0.588 | 9.47e-7 | 209 |
LoF frequencies by population
| Ethnicity | Sum of pLOFs | p |
|---|---|---|
| African & African-American | 0.000529 | 0.000510 |
| Ashkenazi Jewish | 0.00 | 0.00 |
| East Asian | 0.000231 | 0.000217 |
| Finnish | 0.000110 | 0.0000924 |
| European (Non-Finnish) | 0.000342 | 0.000325 |
| Middle Eastern | 0.000231 | 0.000217 |
| South Asian | 0.0000980 | 0.0000980 |
| Other | 0.000163 | 0.000163 |
dbNSFP
Source:
- Function
- FUNCTION: Involved in the activation cascade of caspases responsible for apoptosis execution. Binding of caspase-9 to Apaf- 1 leads to activation of the protease which then cleaves and activates caspase-3. Promotes DNA damage-induced apoptosis in a ABL1/c-Abl-dependent manner. Proteolytically cleaves poly(ADP- ribose) polymerase (PARP).;
- Pathway
- PI3K-Akt signaling pathway - Homo sapiens (human);Non-small cell lung cancer - Homo sapiens (human);Kaposi,s sarcoma-associated herpesvirus infection - Homo sapiens (human);Legionellosis - Homo sapiens (human);VEGF signaling pathway - 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);Influenza A - Homo sapiens (human);Alzheimer,s disease - Homo sapiens (human);Amyotrophic lateral sclerosis (ALS) - Homo sapiens (human);Huntington,s disease - Homo sapiens (human);Thyroid hormone signaling pathway - Homo sapiens (human);Prostate cancer - Homo sapiens (human);Tuberculosis - Homo sapiens (human);Toxoplasmosis - Homo sapiens (human);Pathways in cancer - Homo sapiens (human);Hepatitis B - Homo sapiens (human);Parkinson,s disease - Homo sapiens (human);Apoptosis - Homo sapiens (human);Pancreatic cancer - Homo sapiens (human);Endometrial cancer - Homo sapiens (human);Colorectal cancer - Homo sapiens (human);Celecoxib Pathway, Pharmacodynamics;Nucleotide-binding Oligomerization Domain (NOD) pathway;miRNA Regulation of DNA Damage Response;Apoptosis Modulation and Signaling;Integrated Breast Cancer Pathway;Alzheimers Disease;TNF alpha Signaling Pathway;AGE-RAGE pathway;Allograft Rejection;Corticotropin-releasing hormone signaling pathway;Parkinsons Disease Pathway;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;Rac1-Pak1-p38-MMP-2 pathway;Apoptotic Signaling Pathway;Hepatitis C and Hepatocellular Carcinoma;Apoptosis Modulation by HSP70;Focal Adhesion-PI3K-Akt-mTOR-signaling pathway;Oxidative Damage;miRNA regulation of prostate cancer signaling pathways;miRNA regulation of p53 pathway in prostate cancer;NO-cGMP-PKG mediated Neuroprotection;apoptotic signaling in response to dna damage;Endometrial cancer;PI3K-Akt Signaling Pathway;Chromosomal and microsatellite instability in colorectal cancer;DNA Damage Response;Disease;Signal Transduction;trefoil factors initiate mucosal healing;caspase cascade in apoptosis;role of mitochondria in apoptotic signaling;akt signaling pathway;ras signaling pathway;hiv-1 nef: negative effector of fas and tnf;west nile virus;stress induction of hsp regulation;regulation of cell cycle progression by plk3;internal ribosome entry pathway;Fas;NOD1/2 Signaling Pathway;Nucleotide-binding domain, leucine rich repeat containing receptor (NLR) signaling pathways;Caspase activation via extrinsic apoptotic signalling pathway;DroToll-like;Formation of apoptosome;SMAC-mediated dissociation of IAP:caspase complexes ;SMAC-mediated apoptotic response;Apoptotic factor-mediated response;Intrinsic Pathway for Apoptosis;Innate Immune System;Immune System;Apoptosis;Programmed Cell Death;Activation of caspases through apoptosome-mediated cleavage;BCR;EGFR1;SMAC binds to IAPs ;PIP3 activates AKT signaling;Ligand-independent caspase activation via DCC;Constitutive Signaling by AKT1 E17K in Cancer;PI3K/AKT Signaling in Cancer;TNF;AKT phosphorylates targets in the cytosol;Cytochrome c-mediated apoptotic response;Intracellular signaling by second messengers;Caspase Cascade in Apoptosis;HIV-1 Nef: Negative effector of Fas and TNF-alpha;Diseases of signal transduction;p75(NTR)-mediated signaling;Class I PI3K signaling events mediated by Akt
(Consensus)
Recessive Scores
- pRec
- 0.734
Intolerance Scores
- loftool
- 0.882
- rvis_EVS
- 0.82
- rvis_percentile_EVS
- 88.02
Haploinsufficiency Scores
- pHI
- 0.188
- hipred
- Y
- hipred_score
- 0.669
- ghis
- 0.413
Essentials
- essential_gene_CRISPR
- N
- essential_gene_CRISPR2
- S
- essential_gene_gene_trap
- N
- gene_indispensability_pred
- E
- gene_indispensability_score
- 0.971
Gene Damage Prediction
| All | Recessive | Dominant | |
|---|---|---|---|
| Mendelian | Medium | Medium | Medium |
| Primary Immunodeficiency | Medium | Medium | Medium |
| Cancer | Medium | Medium | Medium |
Mouse Genome Informatics
- Gene name
- Casp9
- Phenotype
- growth/size/body region phenotype; taste/olfaction phenotype; endocrine/exocrine gland phenotype; craniofacial phenotype; cellular phenotype; embryo phenotype; respiratory system 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); 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); immune system phenotype;
Zebrafish Information Network
- Gene name
- casp9
- Affected structure
- retinal ganglion cell
- Phenotype tag
- abnormal
- Phenotype quality
- occurrence
Gene ontology
- Biological process
- kidney development;response to ischemia;proteolysis;apoptotic process;cellular response to DNA damage stimulus;aging;intrinsic apoptotic signaling pathway in response to DNA damage;activation of cysteine-type endopeptidase activity involved in apoptotic process by cytochrome c;platelet formation;response to cobalt ion;response to estradiol;response to lipopolysaccharide;glial cell apoptotic process;cellular response to UV;signal transduction in response to DNA damage;positive regulation of apoptotic process;positive regulation of neuron apoptotic process;response to antibiotic;cellular response to dexamethasone stimulus;leukocyte apoptotic process;extrinsic apoptotic signaling pathway in absence of ligand;regulation of response to DNA damage stimulus
- Cellular component
- nucleus;cytoplasm;mitochondrion;cytosol;protein-containing complex;apoptosome
- Molecular function
- cysteine-type endopeptidase activity;protein binding;enzyme activator activity;peptidase activity;SH3 domain binding;protein kinase binding;cysteine-type endopeptidase activity involved in apoptotic process;cysteine-type endopeptidase activity involved in apoptotic signaling pathway