CASP2
Basic information
Region (hg38): 7:143288215-143307696
Previous symbols: [ "NEDD2" ]
Links
Phenotypes
GenCC
Source:
- intellectual developmental disorder, autosomal recessive 80, with variant lissencephaly (Limited), mode of inheritance: AR
- intellectual developmental disorder, autosomal recessive 80, with variant lissencephaly (Moderate), mode of inheritance: AR
Clinical Genomic Database
Source:
Condition | Inheritance | Intervention Categories | Intervention/Rationale | Manifestation Categories | References |
---|---|---|---|---|---|
Intellectual developmental disorder, autosomal recessive 80, with variant lissencephaly | AR | General | Genetic knowledge may be beneficial related to issues such as selection of optimal supportive care, informed medical decision-making, prognostic considerations, and avoidance of unnecessary testing | Neurologic | 37880421 |
ClinVar
This is a list of variants' phenotypes submitted to
- Intellectual developmental disorder, autosomal recessive 80, with variant lissencephaly (4 variants)
- Inborn genetic diseases (4 variants)
Variants pathogenicity by type
Statistics on ClinVar variants can assist in determining whether a specific variant type in the CASP2 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 | 7 | |||||
missense | 24 | 24 | ||||
nonsense | 2 | |||||
start loss | 0 | |||||
frameshift | 2 | |||||
inframe indel | 0 | |||||
splice donor/acceptor (+/-2bp) | 1 | |||||
splice region | 0 | |||||
non coding | 0 | |||||
Total | 4 | 1 | 24 | 2 | 5 |
Variants in CASP2
This is a list of pathogenic ClinVar variants found in the CASP2 region.
You can filter this list by clicking the number of variants in the Variants pathogenicity by type table.
Position | Type | Phenotype | Significance | ClinVar |
---|---|---|---|---|
7-143288487-C-T | not specified | Uncertain significance (Mar 01, 2023) | ||
7-143288510-G-A | CASP2-related disorder | Likely benign (Sep 08, 2022) | ||
7-143288526-G-T | not specified | Uncertain significance (Sep 28, 2022) | ||
7-143291550-G-A | not specified | Uncertain significance (Nov 09, 2023) | ||
7-143291552-G-A | Benign (Feb 01, 2025) | |||
7-143291595-C-T | Intellectual developmental disorder, autosomal recessive 80, with variant lissencephaly • Inborn genetic diseases | Pathogenic (Apr 09, 2023) | ||
7-143291615-G-C | not specified | Uncertain significance (Aug 23, 2021) | ||
7-143291627-C-G | not specified | Uncertain significance (Dec 20, 2023) | ||
7-143292656-T-C | not specified | Uncertain significance (Dec 19, 2023) | ||
7-143292676-C-T | Benign (Dec 31, 2019) | |||
7-143292686-C-T | not specified | Uncertain significance (Oct 19, 2024) | ||
7-143294285-G-T | not specified | Uncertain significance (Jul 11, 2023) | ||
7-143294286-C-G | CASP2-related disorder | Likely benign (May 30, 2023) | ||
7-143294298-G-A | not specified | Uncertain significance (Oct 12, 2021) | ||
7-143294309-AAC-A | Inborn genetic diseases | Likely pathogenic (Mar 29, 2018) | ||
7-143294622-G-A | not specified | Uncertain significance (Feb 22, 2023) | ||
7-143294667-A-G | not specified | Uncertain significance (Dec 28, 2023) | ||
7-143299928-G-A | not specified | Uncertain significance (Nov 09, 2023) | ||
7-143299937-A-G | Benign (Nov 20, 2017) | |||
7-143299968-C-G | not specified | Conflicting classifications of pathogenicity (Jun 01, 2022) | ||
7-143299976-G-A | Benign/Likely benign (Mar 01, 2025) | |||
7-143299989-G-A | not specified | Uncertain significance (Dec 02, 2024) | ||
7-143299993-C-T | not specified | Uncertain significance (Apr 01, 2024) | ||
7-143300052-G-T | Inborn genetic diseases • Intellectual developmental disorder, autosomal recessive 80, with variant lissencephaly | Pathogenic (Apr 04, 2023) | ||
7-143300060-A-G | CASP2-related disorder | Likely benign (Oct 28, 2019) |
GnomAD
Source:
Gene | Type | Bio Type | Transcript | Coding Exons | Length |
---|---|---|---|---|---|
CASP2 | protein_coding | protein_coding | ENST00000310447 | 11 | 19482 |
pLI Probability LOF Intolerant | pRec Probability LOF Recessive | Individuals with no LOFs | Individuals with Homozygous LOFs | Individuals with Heterozygous LOFs | Defined | p |
---|---|---|---|---|---|---|
0.00150 | 0.997 | 125720 | 0 | 28 | 125748 | 0.000111 |
Z-Score | Observed | Expected | Observed/Expected | Mutation Rate | Total Possible in Transcript | |
---|---|---|---|---|---|---|
Missense | 0.497 | 233 | 255 | 0.913 | 0.0000158 | 2973 |
Missense in Polyphen | 74 | 106.89 | 0.69231 | 1229 | ||
Synonymous | -0.551 | 107 | 100 | 1.07 | 0.00000632 | 865 |
Loss of Function | 2.82 | 9 | 23.9 | 0.377 | 0.00000133 | 272 |
LoF frequencies by population
Ethnicity | Sum of pLOFs | p |
---|---|---|
African & African-American | 0.000578 | 0.000578 |
Ashkenazi Jewish | 0.00 | 0.00 |
East Asian | 0.000163 | 0.000163 |
Finnish | 0.00 | 0.00 |
European (Non-Finnish) | 0.0000791 | 0.0000703 |
Middle Eastern | 0.000163 | 0.000163 |
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. Might function by either activating some proteins required for cell death or inactivating proteins necessary for cell survival.;
- Pathway
- Apoptosis - Homo sapiens (human);Apoptosis Modulation and Signaling;Parkinsons Disease Pathway;Apoptosis;Apoptotic Signaling Pathway;Apoptosis Modulation by HSP70;Signal Transduction;Gene expression (Transcription);tnfr1 signaling pathway;caspase cascade in apoptosis;hiv-1 nef: negative effector of fas and tnf;tnf/stress related signaling;internal ribosome entry pathway;Generic Transcription Pathway;NOD1/2 Signaling Pathway;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;p73 transcription factor network;TP53 Regulates Transcription of Caspase Activators and Caspases;NADE modulates death signalling;Death Receptor Signalling;p75 NTR receptor-mediated signalling;Transcriptional Regulation by TP53;TNFalpha;Caspase Cascade in Apoptosis;HIV-1 Nef: Negative effector of Fas and TNF-alpha;Cell death signalling via NRAGE, NRIF and NADE
(Consensus)
Recessive Scores
- pRec
- 0.213
Intolerance Scores
- loftool
- 0.574
- rvis_EVS
- -0.65
- rvis_percentile_EVS
- 16.44
Haploinsufficiency Scores
- pHI
- 0.256
- hipred
- Y
- hipred_score
- 0.736
- ghis
- 0.596
Essentials
- essential_gene_CRISPR
- N
- essential_gene_CRISPR2
- N
- essential_gene_gene_trap
- N
- gene_indispensability_pred
- E
- gene_indispensability_score
- 1.00
Gene Damage Prediction
All | Recessive | Dominant | |
---|---|---|---|
Mendelian | Medium | Medium | Medium |
Primary Immunodeficiency | Medium | Medium | Medium |
Cancer | Medium | Medium | Medium |
Mouse Genome Informatics
- Gene name
- Casp2
- 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); immune system phenotype; 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; endocrine/exocrine gland phenotype; cellular phenotype;
Gene ontology
- Biological process
- luteolysis;neural retina development;apoptotic process;DNA damage response, signal transduction by p53 class mediator resulting in cell cycle arrest;brain development;aging;intrinsic apoptotic signaling pathway in response to DNA damage;protein processing;ectopic germ cell programmed cell death;regulation of apoptotic process;positive regulation of apoptotic process;negative regulation of apoptotic process;positive regulation of neuron apoptotic process;cellular response to mechanical stimulus;apoptotic signaling pathway;extrinsic apoptotic signaling pathway in absence of ligand;execution phase of apoptosis;positive regulation of apoptotic signaling pathway
- Cellular component
- nucleus;cytoplasm;mitochondrion;cytosol;membrane
- Molecular function
- cysteine-type endopeptidase activity;protein binding;enzyme binding;protein domain specific binding;identical protein binding;cysteine-type endopeptidase activity involved in apoptotic process;cysteine-type endopeptidase activity involved in execution phase of apoptosis