CARD10

caspase recruitment domain family member 10, the group of Caspase recruitment domain containing|Membrane associated guanylate kinases

Basic information

Region (hg38): 22:37490361-37519542

Links

ENSG00000100065 ∙ NCBI:29775 ∙ OMIM:607209 ∙ HGNC:16422 ∙ Uniprot:Q9BWT7 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

Phenotypes

GenCC

Source: genCC

• immunodeficiency 89 and autoimmunity (Limited), mode of inheritance: Unknown

Clinical Genomic Database

Source: CGD

Condition	Inheritance	Intervention Categories	Intervention/Rationale	Manifestation Categories	References
Immunodeficiency 89 and autoimmunity	AR	Allergy/Immunology/Infectious	The condition may involve susceptibility to infections (including involving pulmonary sequelae), and and prophylactic measures, as well as early and aggressive treatment of infections may be beneficial	Allergy/Immunology/Infectious	32238915

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the CARD10 gene.

• Inborn genetic diseases (35 variants)
• not provided (7 variants)
• Immunodeficiency 89 and autoimmunity (1 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the CARD10 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	3	5
missense			36		2	38
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	2	5

Variants in CARD10

This is a list of pathogenic ClinVar variants found in the CARD10 region.

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

Position	Type	Phenotype	Significance	ClinVar
22-37491163-G-T		CARD10-related disorder	Uncertain significance (Feb 05, 2024)
22-37491181-C-T		CARD10-related disorder	Benign (Sep 17, 2019)
22-37491186-T-G		not specified	Uncertain significance (Apr 13, 2022)
22-37491199-C-T		not specified	Uncertain significance (Oct 25, 2023)
22-37491203-C-G		CARD10-related disorder	Uncertain significance (Feb 05, 2024)
22-37491239-G-A		not specified	Uncertain significance (Sep 27, 2021)
22-37491246-C-G			Likely benign (Mar 01, 2022)
22-37491799-G-A		CARD10-related disorder	Benign/Likely benign (Dec 31, 2019)
22-37491811-C-G		not specified	Uncertain significance (Dec 01, 2022)
22-37491831-G-A		not specified	Uncertain significance (Feb 15, 2023)
22-37491855-G-T		not specified	Uncertain significance (Feb 13, 2024)
22-37492533-C-T		not specified	Uncertain significance (Mar 07, 2024)
22-37492762-C-T		CARD10-related disorder	Benign (Feb 28, 2019)
22-37492785-T-C		not specified	Uncertain significance (Feb 07, 2023)
22-37492794-G-A		Primary open angle glaucoma	risk factor (Mar 29, 2016)
22-37492809-C-G		CARD10-related disorder	Likely benign (Jul 16, 2019)
22-37495539-C-G		not specified	Uncertain significance (Sep 07, 2022)
22-37495539-C-T		not specified	Uncertain significance (Jul 27, 2021)
22-37495549-G-A		not specified	Uncertain significance (Jan 26, 2022)
22-37495781-C-A		not specified	Uncertain significance (Feb 02, 2022)
22-37495834-C-T		CARD10-related disorder	Likely benign (Aug 09, 2019)
22-37495950-C-T		CARD10-related disorder	Benign (Jun 07, 2019)
22-37495951-G-A		CARD10-related disorder	Likely benign (Jul 23, 2019)
22-37496452-T-G		not specified	Uncertain significance (Dec 16, 2022)
22-37496515-C-T		not specified	Uncertain significance (Jun 27, 2022)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
CARD10	protein_coding	protein_coding	ENST00000403299	20	29150

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.00226	0.998	125685	0	63	125748	0.000251

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	2.20	465	619	0.751	0.0000408	6427
Missense in Polyphen		78	124.16	0.6282		1235
Synonymous	0.604	250	262	0.953	0.0000153	2174
Loss of Function	4.71	15	51.4	0.292	0.00000259	571

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000754	0.000726
Ashkenazi Jewish	0.00	0.00
East Asian	0.000112	0.000109
Finnish	0.0000489	0.0000462
European (Non-Finnish)	0.000308	0.000299
Middle Eastern	0.000112	0.000109
South Asian	0.000203	0.000196
Other	0.000685	0.000652

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Activates NF-kappa-B via BCL10 and IKK.
• Pathway: NF-kappa B signaling pathway - Homo sapiens (human) (Consensus)

Recessive Scores

• pRec: 0.0937

Intolerance Scores

• loftool: 0.659
• rvis_EVS: -1.15
• rvis_percentile_EVS: 6.32

Haploinsufficiency Scores

• pHI: 0.125
• hipred: Y
• hipred_score: 0.762
• ghis: 0.623

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.911

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Card10
• 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); 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)

Gene ontology

• Biological process: activation of NF-kappaB-inducing kinase activity;regulation of apoptotic process;protein-containing complex assembly;negative regulation of cell migration involved in sprouting angiogenesis;positive regulation of protein localization to nucleus
• Cellular component: cytoplasm;CBM complex
• Molecular function: protein binding;receptor signaling complex scaffold activity