CASP6
Basic information
Region (hg38): 4:109688622-109703583
Links
Phenotypes
GenCC
Source:
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 CASP6 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 | 0 | |||||
missense | 9 | |||||
nonsense | 0 | |||||
start loss | 0 | |||||
frameshift | 0 | |||||
inframe indel | 0 | |||||
splice donor/acceptor (+/-2bp) | 0 | |||||
splice region | 0 | |||||
non coding | 0 | |||||
Total | 0 | 0 | 9 | 0 | 0 |
Variants in CASP6
This is a list of pathogenic ClinVar variants found in the CASP6 region.
You can filter this list by clicking the number of variants in the Variants pathogenicity by type table.
Position | Type | Phenotype | Significance | ClinVar |
---|---|---|---|---|
4-109689358-T-A | not specified | Uncertain significance (Sep 08, 2024) | ||
4-109689371-T-C | not specified | Uncertain significance (Jun 26, 2024) | ||
4-109689410-T-C | not specified | Uncertain significance (Jan 03, 2024) | ||
4-109689412-G-T | not specified | Uncertain significance (Aug 28, 2024) | ||
4-109689433-C-T | not specified | Uncertain significance (Apr 04, 2024) | ||
4-109689440-G-C | not specified | Uncertain significance (May 30, 2024) | ||
4-109689553-C-T | not specified | Uncertain significance (Aug 26, 2024) | ||
4-109690870-A-G | not specified | Uncertain significance (Jun 28, 2022) | ||
4-109690904-C-T | not specified | Uncertain significance (Jan 30, 2024) | ||
4-109690963-A-G | not specified | Likely benign (Mar 16, 2024) | ||
4-109690999-C-A | not specified | Uncertain significance (Feb 09, 2022) | ||
4-109694649-C-G | not specified | Uncertain significance (Mar 01, 2024) | ||
4-109697625-C-T | not specified | Uncertain significance (Nov 12, 2021) | ||
4-109697626-G-A | not specified | Uncertain significance (Dec 06, 2021) | ||
4-109697680-G-A | not specified | Uncertain significance (Nov 30, 2021) | ||
4-109697695-C-G | not specified | Uncertain significance (Dec 26, 2023) | ||
4-109698309-A-C | not specified | Uncertain significance (Aug 05, 2024) |
GnomAD
Source:
Gene | Type | Bio Type | Transcript | Coding Exons | Length |
---|---|---|---|---|---|
CASP6 | protein_coding | protein_coding | ENST00000265164 | 7 | 14955 |
pLI Probability LOF Intolerant | pRec Probability LOF Recessive | Individuals with no LOFs | Individuals with Homozygous LOFs | Individuals with Heterozygous LOFs | Defined | p |
---|---|---|---|---|---|---|
0.000127 | 0.855 | 125691 | 0 | 57 | 125748 | 0.000227 |
Z-Score | Observed | Expected | Observed/Expected | Mutation Rate | Total Possible in Transcript | |
---|---|---|---|---|---|---|
Missense | 0.796 | 130 | 158 | 0.822 | 0.00000831 | 1935 |
Missense in Polyphen | 49 | 59.583 | 0.82238 | 733 | ||
Synonymous | 0.441 | 54 | 58.3 | 0.927 | 0.00000327 | 536 |
Loss of Function | 1.34 | 8 | 13.2 | 0.604 | 6.42e-7 | 181 |
LoF frequencies by population
Ethnicity | Sum of pLOFs | p |
---|---|---|
African & African-American | 0.000389 | 0.000386 |
Ashkenazi Jewish | 0.000198 | 0.000198 |
East Asian | 0.000657 | 0.000653 |
Finnish | 0.00 | 0.00 |
European (Non-Finnish) | 0.000187 | 0.000185 |
Middle Eastern | 0.000657 | 0.000653 |
South Asian | 0.000201 | 0.000196 |
Other | 0.000815 | 0.000815 |
dbNSFP
Source:
- Function
- FUNCTION: Involved in the activation cascade of caspases responsible for apoptosis execution. Cleaves poly(ADP-ribose) polymerase in vitro, as well as lamins. Overexpression promotes programmed cell death.;
- Pathway
- Apoptosis - Homo sapiens (human);Apoptosis Modulation and Signaling;Parkinsons Disease Pathway;Nanomaterial induced apoptosis;Integrated Lung Cancer Pathway;Apoptosis;Fas Ligand (FasL) pathway and Stress induction of Heat Shock Proteins (HSP) regulation;Apoptotic Signaling Pathway;TP53 Regulates Transcription of Cell Death Genes;Apoptosis Modulation by HSP70;apoptotic signaling in response to dna damage;Gene expression (Transcription);trefoil factors initiate mucosal healing;caspase cascade in apoptosis;induction of apoptosis through dr3 and dr4/5 death receptors;hiv-1 nef: negative effector of fas and tnf;west nile virus;regulation of cell cycle progression by plk3;internal ribosome entry pathway;Generic Transcription Pathway;TP53 Regulates Transcription of Cell Death Genes;RNA Polymerase II Transcription;DroToll-like;Caspase-mediated cleavage of cytoskeletal proteins;Breakdown of the nuclear lamina;Apoptotic cleavage of cellular proteins;Apoptotic execution phase;Apoptosis;Programmed Cell Death;TP53 Regulates Transcription of Caspase Activators and Caspases;C-MYB transcription factor network;Transcriptional Regulation by TP53;Direct p53 effectors;Caspase Cascade in Apoptosis;HIV-1 Nef: Negative effector of Fas and TNF-alpha;p75(NTR)-mediated signaling
(Consensus)
Recessive Scores
- pRec
- 0.253
Intolerance Scores
- loftool
- 0.886
- rvis_EVS
- 0.31
- rvis_percentile_EVS
- 72.23
Haploinsufficiency Scores
- pHI
- 0.292
- hipred
- Y
- hipred_score
- 0.550
- ghis
- 0.436
Essentials
- essential_gene_CRISPR
- N
- essential_gene_CRISPR2
- N
- essential_gene_gene_trap
- N
- gene_indispensability_pred
- E
- gene_indispensability_score
- 0.928
Gene Damage Prediction
All | Recessive | Dominant | |
---|---|---|---|
Mendelian | Medium | Medium | Medium |
Primary Immunodeficiency | Medium | Medium | Medium |
Cancer | Medium | Medium | Medium |
Mouse Genome Informatics
- Gene name
- Casp6
- Phenotype
- behavior/neurological phenotype (the observable actions or reactions of mammalian organisms that are manifested through development and lifespan); 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); vision/eye phenotype; growth/size/body region phenotype; cellular phenotype; homeostasis/metabolism phenotype;
Gene ontology
- Biological process
- proteolysis;apoptotic process;epithelial cell differentiation;regulation of apoptotic process;cellular response to staurosporine;execution phase of apoptosis
- Cellular component
- nucleoplasm;cytoplasm;cytosol
- Molecular function
- cysteine-type endopeptidase activity;protein binding;cysteine-type peptidase activity;identical protein binding;cysteine-type endopeptidase activity involved in apoptotic process;cysteine-type endopeptidase activity involved in execution phase of apoptosis