CARD16

caspase recruitment domain family member 16, the group of Caspase recruitment domain containing

Basic information

Region (hg38): 11:105041325-105101431

Links

ENSG00000204397 ∙ NCBI:114769 ∙ OMIM:615680 ∙ HGNC:33701 ∙ Uniprot:Q5EG05 ∙ 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 CARD16 gene.

• Inborn genetic diseases (13 variants)
• not provided (1 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the CARD16 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					1	1
missense			8	1		9
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding			4			4
Total	0	0	12	1	1

Variants in CARD16

This is a list of pathogenic ClinVar variants found in the CARD16 region.

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

Position	Type	Phenotype	Significance	ClinVar
11-105041421-A-C			Benign (Dec 11, 2017)
11-105041422-G-T		not specified	Uncertain significance (Oct 17, 2023)
11-105041443-C-T		not specified	Uncertain significance (Sep 06, 2022)
11-105041506-C-T		not specified	Likely benign (Nov 30, 2021)
11-105041577-C-G		not specified	Uncertain significance (Jun 22, 2023)
11-105041589-A-C		not specified	Uncertain significance (May 05, 2023)
11-105041702-C-G		not specified	Uncertain significance (Oct 26, 2021)
11-105041707-A-G		not specified	Uncertain significance (Nov 08, 2022)
11-105044421-T-C		not specified	Uncertain significance (Jun 30, 2023)
11-105044425-T-C		not specified	Uncertain significance (Jun 30, 2022)
11-105044491-C-T		not specified	Uncertain significance (May 23, 2023)
11-105044496-A-G		not specified	Uncertain significance (Dec 16, 2023)
11-105044505-G-T		not specified	Uncertain significance (Jun 30, 2023)
11-105044524-C-A		not specified	Uncertain significance (Sep 14, 2022)
11-105044532-C-T		not specified	Uncertain significance (Jan 31, 2024)
11-105044551-C-G		not specified	Uncertain significance (Dec 04, 2023)
11-105044557-G-T		not specified	Uncertain significance (Mar 16, 2022)
11-105044619-G-T		not specified	Uncertain significance (Mar 07, 2023)
11-105100546-T-G		not specified	Uncertain significance (Jun 05, 2023)
11-105100564-A-G		not specified	Likely benign (May 17, 2023)
11-105100582-A-G		not specified	Uncertain significance (Apr 08, 2022)
11-105100590-G-A		not specified	Uncertain significance (Oct 26, 2022)
11-105100600-G-A		not specified	Uncertain significance (Mar 07, 2024)
11-105100612-C-T		not specified	Uncertain significance (Dec 20, 2023)
11-105100615-G-A		not specified	Uncertain significance (Oct 10, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
CARD16	protein_coding	protein_coding	ENST00000375706	3	60106

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.383	0.577	125715	0	16	125731	0.0000636

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	-0.471	115	102	1.13	0.00000528	1285
Missense in Polyphen		24	17.754	1.3518		258
Synonymous	-1.50	50	38.2	1.31	0.00000201	367
Loss of Function	1.62	1	4.86	0.206	2.95e-7	54

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000738	0.000739
Ashkenazi Jewish	0.00	0.00
East Asian	0.00	0.00
Finnish	0.00	0.00
European (Non-Finnish)	0.0000264	0.0000264
Middle Eastern	0.00	0.00
South Asian	0.0000327	0.0000327
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Caspase inhibitor. Acts as a regulator of procaspase- 1/CASP1 activation implicated in the regulation of the proteolytic maturation of pro-interleukin-1 beta (IL1B) and its release during inflammation. Inhibits the release of IL1B in response to LPS in monocytes. Also induces NF-kappa-B activation during the pro- inflammatory cytokine response. Also able to inhibit CASP1- mediated neuronal cell death, TNF-alpha, hypoxia-, UV-, and staurosporine-mediated cell death but not ER stress-mediated cell death. Acts by preventing activation of caspases CASP1 and CASP4, possibly by preventing the interaction between CASP1 and RIPK2. {ECO:0000269|PubMed:11432859, ECO:0000269|PubMed:11536016, ECO:0000269|PubMed:16920334}.
• Pathway: NOD-like receptor signaling pathway - Homo sapiens (human) (Consensus)

Intolerance Scores

• loftool: 0.890
• rvis_EVS: 0.19
• rvis_percentile_EVS: 67.03

Haploinsufficiency Scores

• hipred: N
• hipred_score: 0.330
• ghis: 0.454

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.0302

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Cop1
• Phenotype: cardiovascular system phenotype (the observable morphological and physiological characteristics of the mammalian heart, blood vessels, or circulatory system that are manifested through development and lifespan); hematopoietic system phenotype; reproductive 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); pigmentation phenotype; neoplasm; homeostasis/metabolism phenotype; growth/size/body region phenotype; integument phenotype (the observable morphological and physiological characteristics of the skin and its associated structures, such as the hair, nails, sweat glands, sebaceous glands and other secretory glands that are manifested through development and lifespan); endocrine/exocrine gland phenotype

Gene ontology

• Biological process: proteolysis;negative regulation of tumor necrosis factor-mediated signaling pathway;negative regulation of lipopolysaccharide-mediated signaling pathway;negative regulation of protein binding;positive regulation of I-kappaB kinase/NF-kappaB signaling;negative regulation of cysteine-type endopeptidase activity involved in apoptotic process;negative regulation of interleukin-1 beta secretion;positive regulation of NF-kappaB transcription factor activity;cellular response to lipopolysaccharide;cellular response to hypoxia;cellular response to UV-C;inhibition of cysteine-type endopeptidase activity
• Cellular component: protein-containing complex;protease inhibitor complex
• Molecular function: cysteine-type endopeptidase activity;cysteine-type endopeptidase inhibitor activity;protein binding;kinase binding;identical protein binding;CARD domain binding;caspase binding