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NLRP2 NLR family pyrin domain containing 2 [ Homo sapiens (human) ]

Gene ID: 55655, updated on 7-Dec-2018

Summary

Official Symbol
NLRP2provided by HGNC
Official Full Name
NLR family pyrin domain containing 2provided by HGNC
Primary source
HGNC:HGNC:22948
See related
Ensembl:ENSG00000022556 MIM:609364
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
NBS1; PAN1; NALP2; PYPAF2; CLR19.9
Summary
This gene is a member of the nucleotide-binding and leucine-rich repeat receptor (NLR) family, and is predicted to contain an N-terminal pyrin effector domain (PYD), a centrally-located nucleotide-binding and oligomerization domain (NACHT) and C-terminal leucine-rich repeats (LRR). Members of this gene family are thought to be important regulators of immune responses. This gene product interacts with components of the IkB kinase (IKK) complex, and can regulate both caspase-1 and NF-kB (nuclear factor kappa-light-chain-enhancer of activated B cells) activity. The pyrin domain is necessary and sufficient for suppression of NF-kB activity. An allelic variant (rs147585490) has been found that is incapable of blocking the transcriptional activity of NF-kB. Alternative splicing results in multiple transcript variants encoding different isoforms. [provided by RefSeq, Dec 2016]
Expression
Broad expression in placenta (RPKM 9.2), urinary bladder (RPKM 9.0) and 16 other tissues See more
Orthologs

Genomic context

See NLRP2 in Genome Data Viewer
Location:
19q13.42
Exon count:
14
Annotation release Status Assembly Chr Location
109 current GRCh38.p12 (GCF_000001405.38) 19 NC_000019.10 (54965279..55001142)
105 previous assembly GRCh37.p13 (GCF_000001405.25) 19 NC_000019.9 (55476652..55512510)

Chromosome 19 - NC_000019.10Genomic Context describing neighboring genes Neighboring gene Fc fragment of IgA receptor Neighboring gene natural cytotoxicity triggering receptor 1 Neighboring gene NLR family pyrin domain containing 7 Neighboring gene ribosomal protein L36a pseudogene 50 Neighboring gene uncharacterized LOC107985325 Neighboring gene glycoprotein VI platelet Neighboring gene retinol dehydrogenase 13

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 FunctionsWhat's a GeneRIF?

Phenotypes

NHGRI GWAS Catalog

Description
Host-microbe interactions have shaped the genetic architecture of inflammatory bowel disease.
NHGRI GWA Catalog

Pathways from BioSystems

Interactions

Products Interactant Other Gene Complex Source Pubs Description

General gene information

Markers

Homology

Clone Names

  • FLJ20510

Gene Ontology Provided by GOA

Function Evidence Code Pubs
ATP binding IEA
Inferred from Electronic Annotation
more info
 
Pyrin domain binding IPI
Inferred from Physical Interaction
more info
PubMed 
protein binding IPI
Inferred from Physical Interaction
more info
PubMed 
Process Evidence Code Pubs
apoptotic process IEA
Inferred from Electronic Annotation
more info
 
inflammatory response IEA
Inferred from Electronic Annotation
more info
 
innate immune response IEA
Inferred from Electronic Annotation
more info
 
negative regulation of NF-kappaB transcription factor activity IGI
Inferred from Genetic Interaction
more info
PubMed 
positive regulation of cysteine-type endopeptidase activity involved in apoptotic process IDA
Inferred from Direct Assay
more info
PubMed 
positive regulation of interleukin-1 beta secretion IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
positive regulation of interleukin-1 beta secretion IDA
Inferred from Direct Assay
more info
PubMed 
Component Evidence Code Pubs
Golgi apparatus IDA
Inferred from Direct Assay
more info
 
cytoplasm IDA
Inferred from Direct Assay
more info
PubMed 
cytosol IDA
Inferred from Direct Assay
more info
 
intracellular membrane-bounded organelle IDA
Inferred from Direct Assay
more info
 
colocalizes_with nuclear chromosome, telomeric region IDA
Inferred from Direct Assay
more info
PubMed 

General protein information

Preferred Names
NACHT, LRR and PYD domains-containing protein 2
Names
NACHT, leucine rich repeat and PYD containing 2
PYRIN domain and NACHT domain-containing protein 1
PYRIN-containing APAF1-like protein 2
nucleotide-binding oligomerization domain, leucine rich repeat and pyrin domain containing 2
nucleotide-binding site protein 1

NCBI Reference Sequences (RefSeq)

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_052633.1 RefSeqGene

    Range
    18213..53013
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. NM_001174081.2NP_001167552.1  NACHT, LRR and PYD domains-containing protein 2 isoform 1

    See identical proteins and their annotated locations for NP_001167552.1

    Status: REVIEWED

    Description
    Transcript Variant: This variant (2) differs in the 5' UTR compared to variant 1. Both variants 1 and 2 encode the same isoform (1).
    Source sequence(s)
    AF464764, AK000784, BC003592, DA739916, DA856893
    Consensus CDS
    CCDS12913.1
    UniProtKB/Swiss-Prot
    Q9NX02
    Related
    ENSP00000445135.1, ENST00000543010.5
    Conserved Domains (5) summary
    smart00382
    Location:208355
    AAA; ATPases associated with a variety of cellular activities
    cd00116
    Location:7881018
    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 ...
    cd08320
    Location:1194
    Pyrin_NALPs; Pyrin death domain found in NALP proteins
    sd00033
    Location:757784
    LRR_RI; leucine-rich repeat [structural motif]
    pfam05729
    Location:207375
    NACHT; NACHT domain
  2. NM_001174082.2NP_001167553.1  NACHT, LRR and PYD domains-containing protein 2 isoform 2

    See identical proteins and their annotated locations for NP_001167553.1

    Status: REVIEWED

    Description
    Transcript Variant: This variant (3) lacks an alternate in-frame exon in the 5' coding region compared to variant 1. The encoded isoform (2) has the same N- and C-termini, but is shorter than isoform 1.
    Source sequence(s)
    AF310106, AK025952, BC001039, DB046128, DB066882
    Consensus CDS
    CCDS54319.1
    UniProtKB/Swiss-Prot
    Q9NX02
    Related
    ENSP00000440601.1, ENST00000537859.5
    Conserved Domains (5) summary
    smart00382
    Location:186333
    AAA; ATPases associated with a variety of cellular activities
    cd00116
    Location:766996
    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 ...
    cd08320
    Location:1194
    Pyrin_NALPs; Pyrin death domain found in NALP proteins
    sd00033
    Location:735762
    LRR_RI; leucine-rich repeat [structural motif]
    pfam05729
    Location:185353
    NACHT; NACHT domain
  3. NM_001174083.1NP_001167554.1  NACHT, LRR and PYD domains-containing protein 2 isoform 3

    Status: REVIEWED

    Description
    Transcript Variant: This variant (4) lacks an in-frame exon in the CDS, as compared to variant 1. The resulting isoform (3) lacks an internal segment, as compared to isoform 1.
    Source sequence(s)
    AF310106, AK025952, AK302989, BC001039, DB046128
    Consensus CDS
    CCDS54318.1
    UniProtKB/Swiss-Prot
    Q9NX02
    Related
    ENSP00000402474.2, ENST00000427260.6
    Conserved Domains (5) summary
    smart00382
    Location:185332
    AAA; ATPases associated with a variety of cellular activities
    cd00116
    Location:765995
    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:734761
    LRR_RI; leucine-rich repeat [structural motif]
    pfam05729
    Location:184352
    NACHT; NACHT domain
    cl14633
    Location:1171
    DD; Death Domain Superfamily of protein-protein interaction domains
  4. NM_001348003.1NP_001334932.1  NACHT, LRR and PYD domains-containing protein 2 isoform 4

    Status: REVIEWED

    Description
    Transcript Variant: This variant (5) uses an alternate in-frame splice site in the 5' coding region compared to variant 1. The encoded isoform (4) has the same N- and C-termini, but is shorter than isoform 1.
    Source sequence(s)
    AF310106, AK025952, AK292681, BC001039, DB046128, DB066882
    Consensus CDS
    CCDS86807.1
    UniProtKB/Swiss-Prot
    Q9NX02
    UniProtKB/TrEMBL
    A8K9G6, J3KN39
    Related
    ENSP00000263437.6, ENST00000263437.10
    Conserved Domains (4) summary
    cd08320
    Location:1194
    Pyrin_NALPs; Pyrin death domain found in NALP proteins
    sd00033
    Location:754781
    LRR_RI; leucine-rich repeat [structural motif]
    pfam05729
    Location:204372
    NACHT; NACHT domain
    cl26161
    Location:7851015
    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 ...
  5. NM_017852.5NP_060322.1  NACHT, LRR and PYD domains-containing protein 2 isoform 1

    See identical proteins and their annotated locations for NP_060322.1

    Status: REVIEWED

    Description
    Transcript Variant: This variant (1) encodes the longest isoform (1). Both variants 1 and 2 encode the same isoform (1).
    Source sequence(s)
    AF310106, AK025952, BC001039, DB046128, DB066882
    Consensus CDS
    CCDS12913.1
    UniProtKB/Swiss-Prot
    Q9NX02
    Related
    ENSP00000409370.2, ENST00000448584.6
    Conserved Domains (5) summary
    smart00382
    Location:208355
    AAA; ATPases associated with a variety of cellular activities
    cd00116
    Location:7881018
    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 ...
    cd08320
    Location:1194
    Pyrin_NALPs; Pyrin death domain found in NALP proteins
    sd00033
    Location:757784
    LRR_RI; leucine-rich repeat [structural motif]
    pfam05729
    Location:207375
    NACHT; NACHT domain

RNA

  1. NR_145325.1 RNA Sequence

    Status: REVIEWED

    Description
    Transcript Variant: This variant (6) uses an alternate splice site in an internal exon compared to variant 1. This variant is represented as non-coding because the use of the 5'-most expected translational start codon, as used in variant 1, renders the transcript a candidate for nonsense-mediated mRNA decay (NMD).
    Source sequence(s)
    AF310106, AK025952, BC001039, BC039269, DB046128, DB066882
    Related
    ENST00000540597.5

RefSeqs of Annotated Genomes: Homo sapiens Annotation Release 109

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

Reference GRCh38.p12 Primary Assembly

Genomic

  1. NC_000019.10 Reference GRCh38.p12 Primary Assembly

    Range
    54965279..55001142
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Reference GRCh38.p12 ALT_REF_LOCI_1

Genomic

  1. NW_003571054.1 Reference GRCh38.p12 ALT_REF_LOCI_1

    Range
    868677..904540
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Reference GRCh38.p12 ALT_REF_LOCI_2

Genomic

  1. NW_003571055.2 Reference GRCh38.p12 ALT_REF_LOCI_2

    Range
    610481..646344
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Reference GRCh38.p12 ALT_REF_LOCI_3

Genomic

  1. NW_003571056.2 Reference GRCh38.p12 ALT_REF_LOCI_3

    Range
    945265..981128
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Reference GRCh38.p12 ALT_REF_LOCI_4

Genomic

  1. NW_003571057.2 Reference GRCh38.p12 ALT_REF_LOCI_4

    Range
    972802..1008665
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Reference GRCh38.p12 ALT_REF_LOCI_5

Genomic

  1. NW_003571058.2 Reference GRCh38.p12 ALT_REF_LOCI_5

    Range
    947351..983214
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Reference GRCh38.p12 ALT_REF_LOCI_6

Genomic

  1. NW_003571059.2 Reference GRCh38.p12 ALT_REF_LOCI_6

    Range
    883644..919507
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Reference GRCh38.p12 ALT_REF_LOCI_7

Genomic

  1. NW_003571060.1 Reference GRCh38.p12 ALT_REF_LOCI_7

    Range
    869084..903924
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Reference GRCh38.p12 ALT_REF_LOCI_8

Genomic

  1. NW_003571061.2 Reference GRCh38.p12 ALT_REF_LOCI_8

    Range
    677440..713303
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Reference GRCh38.p12 ALT_REF_LOCI_9

Genomic

  1. NT_187693.1 Reference GRCh38.p12 ALT_REF_LOCI_9

    Range
    947761..983624
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
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