CASP2

caspase 2, the group of Caspases|Protein phosphatase 1 regulatory subunits|Caspase recruitment domain containing

Basic information

Region (hg38): 7:143288215-143307696

Previous symbols: [ "NEDD2" ]

Links

ENSG00000106144NCBI:835OMIM:600639HGNC:1503Uniprot:P42575AlphaFoldGenCCjaxSfariGnomADPubmedClinVar

Phenotypes

GenCC

Source: genCC

  • 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: CGD

ConditionInheritanceIntervention CategoriesIntervention/Rationale Manifestation CategoriesReferences
Intellectual developmental disorder, autosomal recessive 80, with variant lissencephalyARGeneralGenetic knowledge may be beneficial related to issues such as selection of optimal supportive care, informed medical decision-making, prognostic considerations, and avoidance of unnecessary testingNeurologic37880421

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the CASP2 gene.

  • 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
2
clinvar
5
clinvar
7
missense
24
clinvar
24
nonsense
2
clinvar
2
start loss
0
frameshift
1
clinvar
1
clinvar
2
inframe indel
0
splice donor/acceptor (+/-2bp)
1
clinvar
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)2492289
7-143288510-G-A CASP2-related disorder Likely benign (Sep 08, 2022)3057249
7-143288526-G-T not specified Uncertain significance (Sep 28, 2022)3137593
7-143291550-G-A not specified Uncertain significance (Nov 09, 2023)3137595
7-143291552-G-A Benign (Feb 01, 2025)715721
7-143291595-C-T Intellectual developmental disorder, autosomal recessive 80, with variant lissencephaly • Inborn genetic diseases Pathogenic (Apr 09, 2023)2499471
7-143291615-G-C not specified Uncertain significance (Aug 23, 2021)2219761
7-143291627-C-G not specified Uncertain significance (Dec 20, 2023)3137590
7-143292656-T-C not specified Uncertain significance (Dec 19, 2023)3137591
7-143292676-C-T Benign (Dec 31, 2019)768215
7-143292686-C-T not specified Uncertain significance (Oct 19, 2024)3485197
7-143294285-G-T not specified Uncertain significance (Jul 11, 2023)2589645
7-143294286-C-G CASP2-related disorder Likely benign (May 30, 2023)3036802
7-143294298-G-A not specified Uncertain significance (Oct 12, 2021)2254917
7-143294309-AAC-A Inborn genetic diseases Likely pathogenic (Mar 29, 2018)985938
7-143294622-G-A not specified Uncertain significance (Feb 22, 2023)2470872
7-143294667-A-G not specified Uncertain significance (Dec 28, 2023)3137592
7-143299928-G-A not specified Uncertain significance (Nov 09, 2023)3137594
7-143299937-A-G Benign (Nov 20, 2017)774665
7-143299968-C-G not specified Conflicting classifications of pathogenicity (Jun 01, 2022)2658111
7-143299976-G-A Benign/Likely benign (Mar 01, 2025)710251
7-143299989-G-A not specified Uncertain significance (Dec 02, 2024)3485196
7-143299993-C-T not specified Uncertain significance (Apr 01, 2024)3263426
7-143300052-G-T Inborn genetic diseases • Intellectual developmental disorder, autosomal recessive 80, with variant lissencephaly Pathogenic (Apr 04, 2023)2499511
7-143300060-A-G CASP2-related disorder Likely benign (Oct 28, 2019)3040385

GnomAD

Source: gnomAD

GeneTypeBio TypeTranscript Coding Exons Length
CASP2protein_codingprotein_codingENST00000310447 1119482
pLI Probability
LOF Intolerant
pRec Probability
LOF Recessive
Individuals with
no LOFs
Individuals with
Homozygous LOFs
Individuals with
Heterozygous LOFs
Defined p
0.001500.9971257200281257480.000111
Z-Score Observed Expected Observed/Expected Mutation Rate Total Possible in Transcript
Missense0.4972332550.9130.00001582973
Missense in Polyphen74106.890.692311229
Synonymous-0.5511071001.070.00000632865
Loss of Function2.82923.90.3770.00000133272

LoF frequencies by population

EthnicitySum of pLOFs p
African & African-American0.0005780.000578
Ashkenazi Jewish0.000.00
East Asian0.0001630.000163
Finnish0.000.00
European (Non-Finnish)0.00007910.0000703
Middle Eastern0.0001630.000163
South Asian0.00009800.0000980
Other0.0001630.000163

dbNSFP

Source: dbNSFP

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

AllRecessiveDominant
MendelianMediumMediumMedium
Primary ImmunodeficiencyMediumMediumMedium
CancerMediumMediumMedium

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