CASP5

caspase 5, the group of Caspases|Caspase recruitment domain containing

Basic information

Region (hg38): 11:104994235-105023168

Links

ENSG00000137757 ∙ NCBI:838 ∙ OMIM:602665 ∙ HGNC:1506 ∙ Uniprot:P51878 ∙ 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 CASP5 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the CASP5 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			36	4		40
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	36	4	0

Variants in CASP5

This is a list of pathogenic ClinVar variants found in the CASP5 region.

You can filter this list by clicking the number of variants in the Variants pathogenicity by type table.

Position	Type	Phenotype	Significance	ClinVar
11-104995788-G-A			Uncertain significance (Mar 07, 2024)
11-104995793-A-G		not specified	Uncertain significance (Nov 25, 2024)
11-104995826-T-C		not specified	Uncertain significance (Mar 18, 2024)
11-104997406-G-A		not specified	Uncertain significance (Oct 07, 2024)
11-104997445-C-G		not specified	Likely benign (Mar 16, 2022)
11-104997471-C-T		not specified	Uncertain significance (Nov 09, 2021)
11-104998899-C-G		not specified	Uncertain significance (Jan 18, 2023)
11-104998905-G-A		not specified	Uncertain significance (Aug 02, 2022)
11-105000275-T-C		not specified	Uncertain significance (Feb 10, 2022)
11-105000288-C-T		not specified	Uncertain significance (Dec 28, 2023)
11-105000299-T-C		not specified	Uncertain significance (Jun 07, 2023)
11-105000309-T-G		not specified	Uncertain significance (Nov 14, 2024)
11-105000390-C-T		not specified	Uncertain significance (Sep 16, 2021)
11-105000401-T-C		not specified	Uncertain significance (May 07, 2024)
11-105000443-G-A		not specified	Uncertain significance (Sep 22, 2023)
11-105002065-C-T		not specified	Uncertain significance (Nov 15, 2024)
11-105002078-G-A		not specified	Uncertain significance (Aug 02, 2021)
11-105002082-C-G		not specified	Uncertain significance (Sep 23, 2023)
11-105002134-T-A		not specified	Uncertain significance (Jun 28, 2022)
11-105002146-T-A		not specified	Uncertain significance (Oct 22, 2021)
11-105002162-C-T		not specified	Uncertain significance (Dec 22, 2023)
11-105002168-G-A		not specified	Uncertain significance (Dec 27, 2023)
11-105002173-C-T		not specified	Uncertain significance (Mar 02, 2023)
11-105002174-G-A		not specified	Uncertain significance (Dec 28, 2022)
11-105003320-C-A		not specified	Uncertain significance (Apr 26, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
CASP5	protein_coding	protein_coding	ENST00000393141	9	28934

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
1.75e-16	0.00362	125270	2	474	125746	0.00189

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.468	231	252	0.917	0.0000136	2960
Missense in Polyphen		58	67.072	0.86475		844
Synonymous	-1.60	112	92.5	1.21	0.00000538	829
Loss of Function	-0.407	23	21.0	1.10	0.00000117	257

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.00456	0.00455
Ashkenazi Jewish	0.000894	0.000893
East Asian	0.000109	0.000109
Finnish	0.000278	0.000277
European (Non-Finnish)	0.00266	0.00264
Middle Eastern	0.000109	0.000109
South Asian	0.000825	0.000817
Other	0.00296	0.00294

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Mediator of programmed cell death (apoptosis). During non-canonical inflammasome activation, cuts CGAS and may play a role in the regulation of antiviral innate immune activation (PubMed:28314590). {ECO:0000269|PubMed:28314590}.
• Pathway: NOD-like receptor signaling pathway - Homo sapiens (human);Nucleotide-binding Oligomerization Domain (NOD) pathway;Vitamin D Receptor Pathway;internal ribosome entry pathway;DroToll-like (Consensus)

Recessive Scores

• pRec: 0.115

Intolerance Scores

• loftool: 0.996
• rvis_EVS: 1.2
• rvis_percentile_EVS: 92.98

Haploinsufficiency Scores

• pHI: 0.119
• hipred: N
• hipred_score: 0.133
• ghis: 0.387

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.235

Gene Damage Prediction

	All	Recessive	Dominant
Mendelian	Medium	Medium	Medium
Primary Immunodeficiency	Medium	Medium	Medium
Cancer	Medium	Medium	Medium

Gene ontology

• Biological process: proteolysis;apoptotic process;activation of cysteine-type endopeptidase activity involved in apoptotic process;substantia nigra development;cellular response to mechanical stimulus;apoptotic signaling pathway;execution phase of apoptosis
• Cellular component: cytoplasm;NLRP1 inflammasome complex
• Molecular function: cysteine-type endopeptidase activity;cysteine-type peptidase activity;cysteine-type endopeptidase activity involved in apoptotic process;cysteine-type endopeptidase activity involved in apoptotic signaling pathway