CARD9

protein-coding

caspase 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

NM_052813.5

Inheritance

AR

ClinVar variants

P:25U:270B:184

Top phenotype

Immunodeficiency 103, susceptibility to fungal infections

gnomAD constraint

pLI —, LoF o/e 0.79

Max pathogenic AF

—

Genomic locus

chr9:136,363,956-136,373,681

External References & Databases

Transcript & Mutation Effects

hg38 • Region Span ~9.7 kb
Loading mutation effect viewer...

GenCC Phenotypes & Disease Associations

Curated gene-disease validity assertions and inheritance patterns

predisposition to invasive fungal disease due to CARD9 deficiencySTRONG

Inheritance Pattern: AR

Disease ID:MONDO:0008905

Submitter: Labcorp Genetics (formerly Invitae)

predisposition to invasive fungal disease due to CARD9 deficiencySUPPORTIVE

Inheritance Pattern: AR

Disease ID:MONDO:0008905

Submitter: Orphanet

deep dermatophytosisSTRONG

Inheritance Pattern: AR

Disease ID:MONDO:0018335

Submitter: Genomics England PanelApp

predisposition to invasive fungal disease due to CARD9 deficiencySTRONG

Inheritance Pattern: AR

Disease ID:MONDO:0008905

Submitter: Ambry Genetics

Clinical Genomic Database (CGD)

Immunodeficiency 103, susceptibility to fungal infectionsAR

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

Refs: 19864672; 22703878; 23335372; 24131138Source: CGD (NHGRI)

ClinVar Associated Diseases & Phenotypes

Reported disease conditions connected to CARD9 variants in ClinVar

7 Conditions Cataloged
Predisposition to invasive fungal disease due to CARD9 deficiencyTotal: 550
Inborn genetic diseasesTotal: 99
not specifiedTotal: 55
not providedTotal: 40
CARD9-related disorderTotal: 20
Inherited Immunodeficiency DiseasesTotal: 1
Primary ciliary dyskinesiaTotal: 1

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.

EffectPLPVUSLBBSum
synonymous
3
clinvar
165
clinvar
2
clinvar
170
missense
1
clinvar
260
clinvar
16
clinvar
277
nonsense
9
clinvar
1
clinvar
3
clinvar
13
start loss
1
clinvar
1
frameshift
7
clinvar
2
clinvar
1
clinvar
10
splice donor/acceptor (+/-2bp)
5
clinvar
2
clinvar
1
clinvar
8
Total1692701822479

Highest pathogenic variant AF is 0.00002311948

Loading ClinVar variants...

Transcript Catalog

Annotated transcript isoforms across RefSeq and Ensembl databases

Showing 4 of 25 transcripts
Transcript IDSourceProtein IDCoding ExonsMANE Status
NM_052813.5RefSeqNP_434700.212MANE Select
ENST00000371732.10EnsemblENSP00000360797.512MANE Select
NM_052814.4RefSeqNP_434701.112Standard
ENST00000371734.7EnsemblENSP00000360799.312Standard

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: gnomAD

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-ScoreObservedExpectedObserved/ExpectedMutation RateTotal Possible
Missense0.09973553600.9850.00002633444
Missense (PolyPhen)79108.540.72786975
Synonymous-1.561841591.160.00001131023
Loss of Function1.042227.90.7880.00000128312

Population LoF Frequency

PopulationCAFp-valueStatus
African0.000690.00068rare
Latino/Admixed American0.00150.0014notable
Ashkenazi Jewish0.00720.0072notable
East Asian0.000440.00044rare
Finnish0.000930.00088rare
European (Non-Finnish)0.00550.0055notable
South Asian0.00210.0021notable
Other0.00250.0025notable

dbNSFP Gene Annotations

Source: dbNSFP

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

AllRecessiveDominant
MendelianMediumMediumMedium
Primary ImmunodeficiencyMediumMediumMedium
CancerMediumMediumMedium
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