CARD9
protein-codingcaspase recruitment domain family member 9, the group of Caspase recruitment domain containing
Gene summary
The protein encoded by this gene is a member of the CARD protein family, which is defined by the presence of a characteristic caspase-associated recruitment domain (CARD). CARD is a protein interaction domain known to participate in activation or suppression of CARD containing members of the caspase family, and thus plays an important regulatory role in cell apoptosis. This protein was identified by its selective association with the CARD domain of BCL10, a postive regulator of apoptosis and NF-kappaB activation, and is thought to function as a molecular scaffold for the assembly of a BCL10 signaling complex that activates NF-kappaB. Several alternatively spliced transcript variants have been observed, but their full-length nature is not clearly defined. [provided by RefSeq, Jul 2008]
MANE transcript
Inheritance
ClinVar variants
Top phenotype
gnomAD constraint
Max pathogenic AF
Genomic locus
External References & Databases
Transcript & Mutation Effects
hg38 • Region Span ~9.7 kbGenCC Phenotypes & Disease Associations
Curated gene-disease validity assertions and inheritance patterns
Inheritance Pattern: AR
Disease ID:MONDO:0008905
Submitter: Labcorp Genetics (formerly Invitae)
Inheritance Pattern: AR
Disease ID:MONDO:0008905
Submitter: Orphanet
Inheritance Pattern: AR
Disease ID:MONDO:0018335
Submitter: Genomics England PanelApp
Inheritance Pattern: AR
Disease ID:MONDO:0008905
Submitter: Ambry Genetics
Clinical Genomic Database (CGD)
Manifestation: Allergy/Immunology/Infectious
Intervention: Allergy/Immunology/Infectious
Rationale: Individuals can have recurrent (and lethal) fungal infections, and surveillance, prophylaxis, and early treatment may be beneficial
ClinVar Associated Diseases & Phenotypes
Reported disease conditions connected to CARD9 variants in ClinVar
ClinVar Variants & Pathogenicity by Type
Statistics based on transcript NM_052813.5. Only rare variants are included.
We include only reliable ClinVar variants with their consequences to MANE Select, MANE Plus Clinical transcripts, or transcripts with TSL equal to 1. Click a count to filter the variants table below.
Slight differences between displayed counts and ClinVar may occur due to a different transcript/consequence chosen by our variant effect predictor, or because we classify Benign/Likely benign as Likely benign and Pathogenic/Likely pathogenic as Likely pathogenic.
| Effect | PathogenicP | Likely pathogenicLP | VUS | Likely benignLB | BenignB | Sum |
|---|---|---|---|---|---|---|
| synonymous | 3 | 165 | 2 | 170 | ||
| missense | 1 | 260 | 16 | 277 | ||
| nonsense | 9 | 1 | 3 | 13 | ||
| start loss | 1 | 1 | ||||
| frameshift | 7 | 2 | 1 | 10 | ||
| splice donor/acceptor (+/-2bp) | 5 | 2 | 1 | 8 | ||
| Total | 16 | 9 | 270 | 182 | 2 | 479 |
Highest pathogenic variant AF is 0.00002311948
Transcript Catalog
Annotated transcript isoforms across RefSeq and Ensembl databases
| Transcript ID | Source | Protein ID | Coding Exons | MANE Status |
|---|---|---|---|---|
| RefSeq | NP_434700.2 | 12 | MANE Select | |
| Ensembl | ENSP00000360797.5 | 12 | MANE Select | |
| RefSeq | NP_434701.1 | 12 | Standard | |
| Ensembl | ENSP00000360799.3 | 12 | Standard |
Gene Ontology (GO) Annotations & Pathways
Biological processes, molecular functions, cellular components and pathways
Pathways ConsensusPathDB
- NOD-like receptor signaling pathway - Homo sapiens (human)
- C-type lectin receptor signaling pathway - Homo sapiens (human)
- Tuberculosis - Homo sapiens (human)
- Nucleotide-binding Oligomerization Domain (NOD) pathway
- NOD1/2 Signaling Pathway
Biological Process
- stimulatory C-type lectin receptor signaling pathway
- I-kappaB kinase/NF-kappaB signaling
- response to fungus
- response to peptidoglycan
- response to muramyl dipeptide
Molecular Function
- protein binding
- protein homodimerization activity
- CARD domain binding
Cellular Component
- cytoplasm
- cytosol
- plasma membrane
gnomAD Constraint
Source:
- Gene type
- protein_coding
- Transcript type
- protein_coding
- Transcript
- ENST00000371732
- Coding exons
- 12
- Length
- 11779
- Individuals with no LoFs
- 124676
- Homozygous LoFs
- 2
- Heterozygous LoFs
- 856
- Defined
- 125534
- p
- 0.00342
| Z-Score | Observed | Expected | Observed/Expected | Mutation Rate | Total Possible | |
|---|---|---|---|---|---|---|
| Missense | 0.0997 | 355 | 360 | 0.985 | 0.0000263 | 3444 |
| Missense (PolyPhen) | 79 | 108.54 | 0.72786 | 975 | ||
| Synonymous | -1.56 | 184 | 159 | 1.16 | 0.0000113 | 1023 |
| Loss of Function | 1.04 | 22 | 27.9 | 0.788 | 0.00000128 | 312 |
Population LoF Frequency
| Population | CAF | p-value | Status |
|---|---|---|---|
| African | 0.00069 | 0.00068 | rare |
| Latino/Admixed American | 0.0015 | 0.0014 | notable |
| Ashkenazi Jewish | 0.0072 | 0.0072 | notable |
| East Asian | 0.00044 | 0.00044 | rare |
| Finnish | 0.00093 | 0.00088 | rare |
| European (Non-Finnish) | 0.0055 | 0.0055 | notable |
| South Asian | 0.0021 | 0.0021 | notable |
| Other | 0.0025 | 0.0025 | notable |
dbNSFP Gene Annotations
Source:
- Function
- FUNCTION: Adapter protein that plays a key role in innate immune response to a number of intracellular pathogens, such as C.albicans and L.monocytogenes. Is at the crossroads of ITAM- tyrosine kinase and the Toll-like receptors (TLR) and NOD2 signaling pathways. Probably controls various innate immune response pathways depending on the intracellular pathogen. In response to L.monocytogenes infection, acts by connecting NOD2 recognition of peptidoglycan to downstream activation of MAP kinases (MAPK) without activating NF-kappa-B. Also involved in activation of myeloid cells via classical ITAM-associated receptors and TLR: required for TLR-mediated activation of MAPK, while it is not required for TLR-induced activation of NF-kappa-B (By similarity). Controls CLEC7A (dectin-1)-mediated myeloid cell activation induced by the yeast cell wall component zymosan, leading to cytokine production and innate anti-fungal immunity: acts by regulating BCL10-MALT1-mediated NF-kappa-B activation pathway. Activates NF-kappa-B via BCL10. In response to the hyphal form of C.albicans, mediates CLEC6A (dectin-2)-induced I-kappa-B kinase ubiquitination, leading to NF-kappa-B activation via interaction with BCL10. In response to fungal infection, may be required for the development and subsequent differentiation of interleukin 17-producing T helper (TH-17) cells. {ECO:0000250, ECO:0000269|PubMed:11053425}.;
- Disease
- DISEASE: Candidiasis, familial, 2 (CANDF2) [MIM:212050]: A primary immunodeficiency disorder with altered immune responses and impaired clearance of fungal infections, selective against Candida. It is characterized by persistent and/or recurrent infections of the skin, nails and mucous membranes caused by organisms of the genus Candida, mainly Candida albicans. {ECO:0000269|PubMed:19864672, ECO:0000269|PubMed:23335372, ECO:0000269|PubMed:24131138}. Note=The disease is caused by mutations affecting the gene represented in this entry. Defects induce reduced numbers of CD4(+) Th17 lymphocytes as well as a lack of monocyte-derived cytokines in response to Candida strains. Neutrophils show a selective Candida albicans killing defect with abnormal ultrastructural phagolysosomes and outgrowth of hyphae (PubMed:23335372). {ECO:0000269|PubMed:23335372}.;
Recessive Scores
- pRec
- 0.139
Intolerance Scores
- LoFtool
- 0.827
- RVIS EVS
- -0.59
- RVIS percentile EVS
- 18.23
Essentials
- Essential (CRISPR)
- N
- Essential (CRISPR2)
- S
- Essential (gene trap)
- N
- Indispensability pred.
- E
- Indispensability score
- 0.814
Gene Damage Prediction
| All | Recessive | Dominant | |
|---|---|---|---|
| Mendelian | Medium | Medium | Medium |
| Primary Immunodeficiency | Medium | Medium | Medium |
| Cancer | Medium | Medium | Medium |