CASP6

caspase 6, the group of Caspases

Basic information

Region (hg38): 4:109688621-109703583

Links

ENSG00000138794 ∙ NCBI:839 ∙ OMIM:601532 ∙ HGNC:1507 ∙ Uniprot:P55212 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

Phenotypes

GenCC

Source: genCC

No genCC data.

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the CASP6 gene.

• Inborn genetic diseases (5 variants)

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			5			5
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	5	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
4-109689410-T-C		not specified	Uncertain significance (Jan 03, 2024)
4-109690870-A-G		not specified	Uncertain significance (Jun 28, 2022)
4-109690904-C-T		not specified	Uncertain significance (Jan 30, 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)

GnomAD

Source: gnomAD

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: dbNSFP

• 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