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NLRC4 NLR family CARD domain containing 4 [ Homo sapiens (human) ]

Gene ID: 58484, updated on 2-Mar-2021

Summary

Official Symbol
NLRC4provided by HGNC
Official Full Name
NLR family CARD domain containing 4provided by HGNC
Primary source
HGNC:HGNC:16412
See related
Ensembl:ENSG00000091106 MIM:606831
Gene type
protein coding
RefSeq status
REVIEWED
Organism
Homo sapiens
Lineage
Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Primates; Haplorrhini; Catarrhini; Hominidae; Homo
Also known as
CLAN; IPAF; AIFEC; CLAN1; CLANA; CLANB; CLANC; CLAND; FCAS4; CARD12; CLR2.1
Summary
This gene encodes a member of the caspase recruitment domain-containing NLR family. Family members play essential roles in innate immune response to a wide range of pathogenic organisms, tissue damage and other cellular stresses. Mutations in this gene result in autoinflammation with infantile enterocolitis. Alternative splicing results in multiple transcript variants. [provided by RefSeq, Oct 2014]
Expression
Broad expression in appendix (RPKM 5.7), bone marrow (RPKM 3.2) and 17 other tissues See more
Orthologs
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Genomic context

See NLRC4 in Genome Data Viewer
Location:
2p22.3
Exon count:
11
Annotation release Status Assembly Chr Location
109.20210226 current GRCh38.p13 (GCF_000001405.39) 2 NC_000002.12 (32224449..32265743, complement)
105.20201022 previous assembly GRCh37.p13 (GCF_000001405.25) 2 NC_000002.11 (32449518..32490812, complement)

Chromosome 2 - NC_000002.12Genomic Context describing neighboring genes Neighboring gene solute carrier family 30 member 6 Neighboring gene DEAD-box helicase 50 pseudogene 1 Neighboring gene RNA, U6 small nuclear 647, pseudogene Neighboring gene Yip1 domain family member 4 Neighboring gene baculoviral IAP repeat containing 6 Neighboring gene microRNA 558

Genomic regions, transcripts, and products

Expression

  • Project title: HPA RNA-seq normal tissues
  • Description: RNA-seq was performed of tissue samples from 95 human individuals representing 27 different tissues in order to determine tissue-specificity of all protein-coding genes
  • BioProject: PRJEB4337
  • Publication: PMID 24309898
  • Analysis date: Wed Apr 4 07:08:55 2018

Bibliography

GeneRIFs: Gene References Into Functions

What's a GeneRIF?

Phenotypes

Associated conditions

Description Tests
Autoinflammation with infantile enterocolitis
MedGen: C4015067 OMIM: 616050 GeneReviews: Not available
Compare labs
Familial cold autoinflammatory syndrome 4
MedGen: C4015276 OMIM: 616115 GeneReviews: Not available
Compare labs
Novel gene variants predict serum levels of the cytokines IL-18 and IL-1ra in older adults.
GeneReviews: Not available

Pathways from PubChem

Interactions

Products Interactant Other Gene Complex Source Pubs Description

General gene information

Markers

Homology

Gene Ontology Provided by GOA

Function Evidence Code Pubs
ATP binding IDA
Inferred from Direct Assay
more info
PubMed 
caspase binding IPI
Inferred from Physical Interaction
more info
PubMed 
endopeptidase activator activity IGI
Inferred from Genetic Interaction
more info
PubMed 
identical protein binding IPI
Inferred from Physical Interaction
more info
PubMed 
magnesium ion binding TAS
Traceable Author Statement
more info
PubMed 
protein binding IPI
Inferred from Physical Interaction
more info
PubMed 
protein homodimerization activity IDA
Inferred from Direct Assay
more info
PubMed 
Process Evidence Code Pubs
activation of cysteine-type endopeptidase activity IGI
Inferred from Genetic Interaction
more info
PubMed 
activation of cysteine-type endopeptidase activity IMP
Inferred from Mutant Phenotype
more info
PubMed 
activation of cysteine-type endopeptidase activity involved in apoptotic process IDA
Inferred from Direct Assay
more info
PubMed 
activation of innate immune response ISS
Inferred from Sequence or Structural Similarity
more info
 
apoptotic process IEA
Inferred from Electronic Annotation
more info
 
defense response to bacterium IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
defense response to bacterium IDA
Inferred from Direct Assay
more info
PubMed 
detection of bacterium IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
detection of bacterium IDA
Inferred from Direct Assay
more info
PubMed 
inflammatory response ISS
Inferred from Sequence or Structural Similarity
more info
 
innate immune response IEA
Inferred from Electronic Annotation
more info
 
positive regulation of NF-kappaB transcription factor activity IDA
Inferred from Direct Assay
more info
PubMed 
positive regulation of apoptotic process IDA
Inferred from Direct Assay
more info
PubMed 
positive regulation of interleukin-1 beta production IGI
Inferred from Genetic Interaction
more info
PubMed 
positive regulation of protein processing IGI
Inferred from Genetic Interaction
more info
PubMed 
protein homooligomerization ISS
Inferred from Sequence or Structural Similarity
more info
 
pyroptosis ISS
Inferred from Sequence or Structural Similarity
more info
 
regulation of apoptotic process TAS
Traceable Author Statement
more info
 
Component Evidence Code Pubs
IPAF inflammasome complex ISS
Inferred from Sequence or Structural Similarity
more info
 
cytosol ISS
Inferred from Sequence or Structural Similarity
more info
 
cytosol TAS
Traceable Author Statement
more info
 

General protein information

Preferred Names
NLR family CARD domain-containing protein 4
Names
CARD, LRR, and NACHT-containing protein
ICE-protease activating factor
NOD-like receptor C4
caspase recruitment domain family, member 12
caspase recruitment domain-containing protein 12
nucleotide-binding oligomerization domain, leucine rich repeat and CARD domain containing 4

NCBI Reference Sequences (RefSeq)

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RefSeqs maintained independently of Annotated Genomes

These reference sequences exist independently of genome builds. Explain

These reference sequences are curated independently of the genome annotation cycle, so their versions may not match the RefSeq versions in the current genome build. Identify version mismatches by comparing the version of the RefSeq in this section to the one reported in Genomic regions, transcripts, and products above.

Genomic

  1. NG_041780.1 RefSeqGene

    Range
    5858..46291
    Download
    GenBank, FASTA, Sequence Viewer (Graphics), LRG_1317

mRNA and Protein(s)

  1. NM_001199138.2NP_001186067.1  NLR family CARD domain-containing protein 4 isoform a

    See identical proteins and their annotated locations for NP_001186067.1

    Status: REVIEWED

    Description
    Transcript Variant: This variant (2) has an alternate 5' UTR exon and encodes the same protein, as compared to variant 1.
    Source sequence(s)
    AK095467, AL121653, BC031555
    Consensus CDS
    CCDS33174.1
    UniProtKB/Swiss-Prot
    Q9NPP4
    Related
    ENSP00000385428.1, ENST00000402280.6
    Conserved Domains (5) summary
    cd00116
    Location:738978
    LRR_RI; Leucine-rich repeats (LRRs), ribonuclease inhibitor (RI)-like subfamily. LRRs are 20-29 residue sequence motifs present in many proteins that participate in protein-protein interactions and have different functions and cellular locations. LRRs correspond ...
    sd00033
    Location:738764
    LRR_RI; leucine-rich repeat [structural motif]
    sd00034
    Location:691713
    LRR_AMN1; leucine-rich repeat [structural motif]
    pfam00619
    Location:187
    CARD; Caspase recruitment domain
    pfam05729
    Location:163316
    NACHT; NACHT domain
  2. NM_001199139.1NP_001186068.1  NLR family CARD domain-containing protein 4 isoform a

    See identical proteins and their annotated locations for NP_001186068.1

    Status: REVIEWED

    Description
    Transcript Variant: This variant (3) has an alternate splice site in the 5' UTR and encodes the same protein, as compared to variant 1.
    Source sequence(s)
    AW337918, AY035391
    Consensus CDS
    CCDS33174.1
    UniProtKB/Swiss-Prot
    Q9NPP4
    Conserved Domains (5) summary
    cd00116
    Location:738978
    LRR_RI; Leucine-rich repeats (LRRs), ribonuclease inhibitor (RI)-like subfamily. LRRs are 20-29 residue sequence motifs present in many proteins that participate in protein-protein interactions and have different functions and cellular locations. LRRs correspond ...
    sd00033
    Location:738764
    LRR_RI; leucine-rich repeat [structural motif]
    sd00034
    Location:691713
    LRR_AMN1; leucine-rich repeat [structural motif]
    pfam00619
    Location:187
    CARD; Caspase recruitment domain
    pfam05729
    Location:163316
    NACHT; NACHT domain
  3. NM_001302504.1NP_001289433.1  NLR family CARD domain-containing protein 4 isoform b

    See identical proteins and their annotated locations for NP_001289433.1

    Status: REVIEWED

    Description
    Transcript Variant: This variant (4) lacks an alternate in-frame exon in the 5' coding region compared to variant 1. It encodes isoform b, which is shorter than isoform a.
    Source sequence(s)
    AL121653, AW337918, AY027788
    Consensus CDS
    CCDS77400.1
    UniProtKB/Swiss-Prot
    Q9NPP4
    Related
    ENSP00000339666.6, ENST00000342905.10
    Conserved Domains (4) summary
    COG4886
    Location:79329
    LRR; Leucine-rich repeat (LRR) protein [Transcription]
    cd00116
    Location:71313
    LRR_RI; Leucine-rich repeats (LRRs), ribonuclease inhibitor (RI)-like subfamily. LRRs are 20-29 residue sequence motifs present in many proteins that participate in protein-protein interactions and have different functions and cellular locations. LRRs correspond ...
    sd00033
    Location:100124
    LRR_RI; leucine-rich repeat [structural motif]
    pfam00619
    Location:187
    CARD; Caspase recruitment domain
  4. NM_021209.4NP_067032.3  NLR family CARD domain-containing protein 4 isoform a

    See identical proteins and their annotated locations for NP_067032.3

    Status: REVIEWED

    Description
    Transcript Variant: This variant (1) represents the longest transcript. Variants 1, 2 and 3 encode the same protein.
    Source sequence(s)
    AW337918, BC031555, DN998613
    Consensus CDS
    CCDS33174.1
    UniProtKB/Swiss-Prot
    Q9NPP4
    Related
    ENSP00000354159.5, ENST00000360906.9
    Conserved Domains (5) summary
    cd00116
    Location:738978
    LRR_RI; Leucine-rich repeats (LRRs), ribonuclease inhibitor (RI)-like subfamily. LRRs are 20-29 residue sequence motifs present in many proteins that participate in protein-protein interactions and have different functions and cellular locations. LRRs correspond ...
    sd00033
    Location:738764
    LRR_RI; leucine-rich repeat [structural motif]
    sd00034
    Location:691713
    LRR_AMN1; leucine-rich repeat [structural motif]
    pfam00619
    Location:187
    CARD; Caspase recruitment domain
    pfam05729
    Location:163316
    NACHT; NACHT domain

RefSeqs of Annotated Genomes: Homo sapiens Updated Annotation Release 109.20210226

The following sections contain reference sequences that belong to a specific genome build. Explain

Reference GRCh38.p13 Primary Assembly

Genomic

  1. NC_000002.12 Reference GRCh38.p13 Primary Assembly

    Range
    32224449..32265743 complement
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_017004619.1XP_016860108.1  NLR family CARD domain-containing protein 4 isoform X1

    Related
    ENSP00000385090.3, ENST00000404025.3

RNA

  1. XR_001738872.1 RNA Sequence

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