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

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; AllianceGenome:HGNC:22948
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; OZEMA18
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: all
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Genomic context

Location:: 19q13.42

Exon count:: 14

Annotation release	Status	Assembly	Chr	Location
RS_2024_08	current	GRCh38.p14 (GCF_000001405.40)	19	NC_000019.10 (54965284..55001138)
RS_2024_08	current	T2T-CHM13v2.0 (GCF_009914755.1)	19	NC_060943.1 (58059583..58095245)
RS_2024_09	previous assembly	GRCh37.p13 (GCF_000001405.25)	19	NC_000019.9 (55476652..55512506)

Chromosome 19 - NC_000019.10 Genomic Context describing neighboring genes

Genomic regions, transcripts, and products

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Go to reference sequence details

Genomic Sequence:

Go to nucleotide: Graphics FASTA GenBank

Expression

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See details

Project title: HPA RNA-seq normal tissues 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

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GeneRIFs: Gene References Into Functions

What's a GeneRIF?

Variants in NLRP2 and ZFP36L2, non-core components of the human subcortical maternal complex, cause female infertility with embryonic development arrest.
Title: Variants in NLRP2 and ZFP36L2, non-core components of the human subcortical maternal complex, cause female infertility with embryonic development arrest.
HLA-C expression in extravillous trophoblasts is determined by an ELF3-NLRP2/NLRP7 regulatory axis.
Title: HLA-C expression in extravillous trophoblasts is determined by an ELF3-NLRP2/NLRP7 regulatory axis.
Nlrp2 deletion ameliorates kidney damage in a mouse model of cystinosis.
Title: Nlrp2 deletion ameliorates kidney damage in a mouse model of cystinosis.
NLRP2 in health and disease.
Title: NLRP2 in health and disease.
Gene body hypomethylation of pyroptosis-related genes NLRP7, NLRP2, and NLRP3 facilitate non-invasive surveillance of hepatocellular carcinoma.
Title: Gene body hypomethylation of pyroptosis-related genes NLRP7, NLRP2, and NLRP3 facilitate non-invasive surveillance of hepatocellular carcinoma.
Somatic Mutation of NLRP Genes in Gastric and Colonic Cancers.
Title: Somatic Mutation of NLRP Genes in Gastric and Colonic Cancers.
NLRP2 and NLRP5 are novel mutant genes responsible for human early embryonic arrest.
Title: Mutations in NLRP2 and NLRP5 cause female infertility characterised by early embryonic arrest.
We now report 15 further pedigrees in which offspring had disturbance of imprinting, while their mothers had rare, predicted-deleterious variants in maternal effect genes, including NLRP2, NLRP7 and PADI6
Title: Maternal variants in NLRP and other maternal effect proteins are associated with multilocus imprinting disturbance in offspring.
Early-onset childhood atopic dermatitis is related to NLRP2 repression.
Title: Early-onset childhood atopic dermatitis is related to NLRP2 repression.
NLRP2 served an important role in maintaining cell viability.
Title: Downregulation of NLRP2 inhibits HUVEC viability by inhibiting the MAPK signaling pathway.

Submit: New GeneRIF Correction See all GeneRIFs (34)

Phenotypes

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Review eQTL and phenotype association data in this region using PheGenI

Associated conditions

Description	Tests
Oocyte/zygote/embryo maturation arrest 18 MedGen: C5830441 OMIM: 620332 GeneReviews: Not available	not available

EBI GWAS Catalog

Description
Host-microbe interactions have shaped the genetic architecture of inflammatory bowel disease. EBI GWAS Catalog EBI GWAS CatalogPubMed

Variation

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See variants in ClinVar

See studies and variants in dbVar

See Variation Viewer (GRCh37.p13)

See Variation Viewer (GRCh38)

Interactions

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Products	Interactant	Other Gene	Complex	Source	Pubs	Description

General gene information

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Markers

D19S654E (e-PCR)
- UniSTS:150569

RH47501 (e-PCR)
- UniSTS:2376

D19S926 (e-PCR)
- UniSTS:68569

Gene Ontology Provided by GOA

Function	Evidence Code	Pubs
enables ATP binding	IEA Inferred from Electronic Annotation more info
enables Pyrin domain binding	IPI Inferred from Physical Interaction more info	PubMed
enables protein binding	IPI Inferred from Physical Interaction more info	PubMed

Process	Evidence Code	Pubs
involved_in apoptotic process	IEA Inferred from Electronic Annotation more info
involved_in inflammatory response	IEA Inferred from Electronic Annotation more info
involved_in innate immune response	IEA Inferred from Electronic Annotation more info
involved_in negative regulation of non-canonical NF-kappaB signal transduction	IGI Inferred from Genetic Interaction more info	PubMed
involved_in positive regulation of interleukin-1 beta production	IDA Inferred from Direct Assay more info	PubMed
involved_in regulation of inflammatory response	IBA Inferred from Biological aspect of Ancestor more info

Component	Evidence Code	Pubs
located_in Golgi apparatus	IDA Inferred from Direct Assay more info
colocalizes_with chromosome, telomeric region	IDA Inferred from Direct Assay more info	PubMed
is_active_in cytoplasm	IBA Inferred from Biological aspect of Ancestor more info
located_in cytoplasm	IDA Inferred from Direct Assay more info	PubMed
located_in cytosol	IDA Inferred from Direct Assay more info
is_active_in intracellular membrane-bounded organelle	IBA Inferred from Biological aspect of Ancestor more info
located_in intracellular membrane-bounded organelle	IDA Inferred from Direct Assay more info

General protein information

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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)

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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

NG_052633.1 RefSeqGene

Range

18245..53009

Download

GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

NM_001174081.3 → NP_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, DA856893

Consensus CDS

CCDS12913.1

UniProtKB/Swiss-Prot

B4DZL7, I3L0G4, Q53FL5, Q59G09, Q8IXT0, Q9BVN5, Q9H6G6, Q9HAV9, Q9NWK3, Q9NX02

UniProtKB/TrEMBL

A0A0G2JPQ2

Related

ENSP00000445135.1, ENST00000543010.5

Conserved Domains (5) summary

smart00382
Location:208 → 355

AAA; ATPases associated with a variety of cellular activities

cd00116
Location:788 → 1018

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:11 → 94

Pyrin_NALPs; Pyrin death domain found in NALP proteins

sd00033
Location:757 → 784

LRR_RI; leucine-rich repeat [structural motif]

pfam05729
Location:207 → 375

NACHT; NACHT domain
NM_001174082.3 → NP_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

Consensus CDS

CCDS54319.1

UniProtKB/TrEMBL

A0A0G2JLX3

Related

ENSP00000440601.1, ENST00000537859.5

Conserved Domains (5) summary

smart00382
Location:186 → 333

AAA; ATPases associated with a variety of cellular activities

cd00116
Location:766 → 996

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:11 → 94

Pyrin_NALPs; Pyrin death domain found in NALP proteins

sd00033
Location:735 → 762

LRR_RI; leucine-rich repeat [structural motif]

pfam05729
Location:185 → 353

NACHT; NACHT domain
NM_001174083.2 → NP_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/TrEMBL

A0A0G2JMG8

Related

ENSP00000402474.2, ENST00000427260.6

Conserved Domains (5) summary

smart00382
Location:185 → 332

AAA; ATPases associated with a variety of cellular activities

cd00116
Location:765 → 995

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:734 → 761

LRR_RI; leucine-rich repeat [structural motif]

pfam05729
Location:184 → 352

NACHT; NACHT domain

cl14633
Location:11 → 71

DD; Death Domain Superfamily of protein-protein interaction domains
NM_001348003.2 → NP_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/TrEMBL

A0A0G2JPQ2, J3KN39

Related

ENSP00000263437.6, ENST00000263437.10

Conserved Domains (4) summary

cd08320
Location:11 → 94

Pyrin_NALPs; Pyrin death domain found in NALP proteins

sd00033
Location:754 → 781

LRR_RI; leucine-rich repeat [structural motif]

pfam05729
Location:204 → 372

NACHT; NACHT domain

cl26161
Location:785 → 1015

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 ...
NM_017852.5 → NP_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

B4DZL7, I3L0G4, Q53FL5, Q59G09, Q8IXT0, Q9BVN5, Q9H6G6, Q9HAV9, Q9NWK3, Q9NX02

UniProtKB/TrEMBL

A0A0G2JPQ2

Related

ENSP00000409370.2, ENST00000448584.7

Conserved Domains (5) summary

smart00382
Location:208 → 355

AAA; ATPases associated with a variety of cellular activities

cd00116
Location:788 → 1018

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:11 → 94

Pyrin_NALPs; Pyrin death domain found in NALP proteins

sd00033
Location:757 → 784

LRR_RI; leucine-rich repeat [structural motif]

pfam05729
Location:207 → 375

NACHT; NACHT domain

RNA

NR_145325.2 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