CASP12

caspase 12 (gene/pseudogene), the group of Caspases|Caspase recruitment domain containing

Basic information

Region (hg38): 11:104885718-104898670

Previous symbols: [ "CASP12P1" ]

Links

ENSG00000204403 ∙ NCBI:100506742 ∙ OMIM:608633 ∙ HGNC:19004 ∙ Uniprot:Q6UXS9 ∙ 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 CASP12 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the CASP12 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		2
missense			17	2	4	23
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)					1	1
splice region						0
non coding				1	1	2
Total	0	0	17	5	6

Variants in CASP12

This is a list of pathogenic ClinVar variants found in the CASP12 region.

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

Position	Type	Phenotype	Significance	ClinVar
11-104886708-T-C		CASP12-related disorder	Benign (Jun 05, 2019)
11-104886733-T-C		not specified	Uncertain significance (Jan 08, 2024)
11-104886747-C-G		not specified	Uncertain significance (Dec 31, 2023)
11-104886781-A-T		not specified	Uncertain significance (Nov 08, 2024)
11-104887202-A-G		CASP12-related disorder	Likely benign (May 02, 2019)
11-104887216-G-T		not specified	Uncertain significance (Feb 07, 2023)
11-104887276-C-T		CASP12-related disorder	Likely benign (May 31, 2022)
11-104887305-T-C		CASP12-related disorder	Benign (Sep 24, 2019)
11-104890373-C-C		not specified	Benign (Mar 28, 2016)
11-104890379-G-A		not specified	Uncertain significance (Jul 14, 2024)
11-104890403-T-A		not specified	Uncertain significance (Dec 08, 2023)
11-104890425-T-G		not specified	Uncertain significance (Apr 06, 2024)
11-104890482-C-T		not specified	Uncertain significance (Nov 09, 2021)
11-104891194-T-C		CASP12-related disorder	Benign (Feb 26, 2020)
11-104891198-C-T		CASP12-related disorder	Likely benign (Aug 16, 2019)
11-104891214-A-C		not specified	Uncertain significance (Apr 28, 2023)
11-104891229-C-T		not specified	Uncertain significance (May 24, 2023)
11-104891230-G-A		not specified	Uncertain significance (Nov 27, 2023)
11-104891241-A-C		not specified	Uncertain significance (Oct 21, 2024)
11-104891260-C-T		CASP12-related disorder	Benign (Feb 26, 2020)
11-104891301-C-T		not specified	Uncertain significance (Dec 22, 2023)
11-104891322-T-C		not specified	Uncertain significance (Sep 29, 2023)
11-104892335-G-T		not specified	Uncertain significance (Oct 18, 2021)
11-104892390-A-G		Sepsis, susceptibility to	risk factor (May 06, 2004)
11-104892390-A-A		not specified • CASP12-related disorder	Likely benign (Mar 28, 2016)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
CASP12	protein_coding	protein_coding	ENST00000422698	7	12953

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.000127	0.856	0	0	0	0	0.00

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	1.26	117	162	0.722	0.00000765	2257
Missense in Polyphen		33	43.195	0.76398		630
Synonymous	2.39	34	56.9	0.597	0.00000270	617
Loss of Function	1.34	8	13.3	0.603	7.04e-7	177

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.00	0.00
Ashkenazi Jewish	0.00	0.00
East Asian	0.00	0.00
Finnish	0.00	0.00
European (Non-Finnish)	0.00	0.00
Middle Eastern	0.00	0.00
South Asian	0.00	0.00
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Has no protease activity. May reduce cytokine release in response to bacterial lipopolysaccharide during infections. Reduces activation of NF-kappa-B in response to TNF. {ECO:0000269|PubMed:12054529, ECO:0000269|PubMed:15129283}.
• Pathway: Prion diseases - Homo sapiens (human);Protein processing in endoplasmic reticulum - Homo sapiens (human);Alzheimer,s disease - Homo sapiens (human);Amyotrophic lateral sclerosis (ALS) - Homo sapiens (human);NOD-like receptor signaling pathway - Homo sapiens (human);Hepatitis B - Homo sapiens (human);Apoptosis - Homo sapiens (human);Alzheimers Disease;Corticotropin-releasing hormone signaling pathway;Amyotrophic lateral sclerosis (ALS);Prion disease pathway (Consensus)

Haploinsufficiency Scores

• pHI: 0.0580
• hipred: N
• hipred_score: 0.112
• ghis: 0.464

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.539

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Casp12
• Phenotype: cellular phenotype; homeostasis/metabolism 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); normal 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); behavior/neurological phenotype (the observable actions or reactions of mammalian organisms that are manifested through development and lifespan); immune system phenotype

Gene ontology

• Biological process: proteolysis;apoptotic process;activation of cysteine-type endopeptidase activity involved in apoptotic process;apoptotic signaling pathway;execution phase of apoptosis
• Cellular component: cytoplasm;endoplasmic reticulum
• Molecular function: cysteine-type endopeptidase activity;cysteine-type endopeptidase activity involved in apoptotic process;cysteine-type endopeptidase activity involved in apoptotic signaling pathway