NLRP4 (NLR family pyrin domain containing 4)

Gene

• Entrez ID: 147945
• Gene name: NLR family pyrin domain containing 4
• Gene symbol: NLRP4
• Synonyms (NCBI Gene): CLR19.5, CT58, NALP4, PAN2, PYPAF4, RNH2
• Chromosome: 19
• Chromosome location: 19q13.43
• Summary: The protein encoded by 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

miRNA

miRTarBase ID	miRNA	Experiments	Reference
MIRT1187272	hsa-miR-1245b-5p	CLIP-seq
MIRT1187273	hsa-miR-3142	CLIP-seq
MIRT1187274	hsa-miR-4276	CLIP-seq
MIRT1187275	hsa-miR-4493	CLIP-seq
MIRT1187276	hsa-miR-487a	CLIP-seq
MIRT1187277	hsa-miR-548aa	CLIP-seq
MIRT1187278	hsa-miR-548ac	CLIP-seq
MIRT1187279	hsa-miR-548ae	CLIP-seq
MIRT1187280	hsa-miR-548aj	CLIP-seq
MIRT1187281	hsa-miR-548am	CLIP-seq
MIRT1187282	hsa-miR-548d-3p	CLIP-seq
MIRT1187283	hsa-miR-548x	CLIP-seq
MIRT1187284	hsa-miR-548z	CLIP-seq
MIRT2283399	hsa-miR-216a	CLIP-seq
MIRT2283400	hsa-miR-342-3p	CLIP-seq
MIRT2283401	hsa-miR-342-5p	CLIP-seq
MIRT2283402	hsa-miR-4651	CLIP-seq
MIRT2283403	hsa-miR-4664-5p	CLIP-seq
MIRT2283404	hsa-miR-4790-3p	CLIP-seq
MIRT2283405	hsa-miR-608	CLIP-seq
MIRT2283399	hsa-miR-216a	CLIP-seq
MIRT2283400	hsa-miR-342-3p	CLIP-seq
MIRT2283401	hsa-miR-342-5p	CLIP-seq
MIRT2283402	hsa-miR-4651	CLIP-seq
MIRT2283403	hsa-miR-4664-5p	CLIP-seq
MIRT2283404	hsa-miR-4790-3p	CLIP-seq
MIRT2283405	hsa-miR-608	CLIP-seq
MIRT2455261	hsa-miR-3922-5p	CLIP-seq
MIRT2455262	hsa-miR-4717-5p	CLIP-seq
MIRT2455263	hsa-miR-4753-5p	CLIP-seq
MIRT2455261	hsa-miR-3922-5p	CLIP-seq
MIRT2455262	hsa-miR-4717-5p	CLIP-seq
MIRT2455263	hsa-miR-4753-5p	CLIP-seq

Gene ontology (GO)

GO ID	Ontology	Definition	Evidence	Reference
GO:0000166	Function	Nucleotide binding	IEA
GO:0005524	Function	ATP binding	IEA
GO:0005737	Component	Cytoplasm	IBA
GO:0005737	Component	Cytoplasm	IDA	27692986
GO:0005829	Component	Cytosol	TAS
GO:0006954	Process	Inflammatory response	IEA
GO:0043161	Process	Proteasome-mediated ubiquitin-dependent protein catabolic process	IDA	27692986
GO:0045824	Process	Negative regulation of innate immune response	IDA	27692986
GO:0045824	Process	Negative regulation of innate immune response	IDA	27692986
GO:0050727	Process	Regulation of inflammatory response	IBA
GO:0060090	Function	Molecular adaptor activity	IDA	27692986
GO:0070936	Process	Protein K48-linked ubiquitination	IDA	27692986
GO:0140374	Process	Antiviral innate immune response	IDA	14703513
GO:1990168	Process	Protein K33-linked deubiquitination	IDA	27692986

Other IDs

• MIM: 609645
• HGNC: 22943
• e!Ensembl: ENSG00000160505

Protein

• UniProt ID: Q96MN2
• Protein name: NACHT, LRR and PYD domains-containing protein 4 (Cancer/testis antigen 58) (CT58) (PAAD and NACHT-containing protein 2) (PAN2) (PYRIN and NACHT-containing protein 2) (PYRIN-containing APAF1-like protein 4) (PYPAF4) (Ribonuclease inhibitor 2)
• Protein function: May be involved in inflammation and recognition of cytosolic pathogen-associated molecular patterns (PAMPs) not intercepted by membrane-bound receptors. Acts as a negative regulator of the type I interferon signaling pathway by serving as an ada
• PDB: 4EWI
• Family and domains:

  Pfam

  Accession	ID	Position in sequence	Description	Type
  PF02758	PYRIN	10 → 86	PAAD/DAPIN/Pyrin domain	Domain
  PF05729	NACHT	149 → 318	NACHT domain	Domain
  PF17779	NOD2_WH	394 → 450	NOD2 winged helix domain	Domain
  PF17776	NLRC4_HD2	452 → 568	NLRC4 helical domain HD2	Domain
  PF13516	LRR_6	749 → 766	Leucine Rich repeat	Repeat
  PF13516	LRR_6	805 → 828	Leucine Rich repeat	Repeat
  PF13516	LRR_6	862 → 885	Leucine Rich repeat	Repeat

• Sequence:

  MAASFFSDFGLMWYLEELKKEEFRKFKEHLKQMTLQLELKQIPWTEVKKASREELANLLI
  KHYEEQQAWNITLRIFQKMDRKDLCMKVMRERTGYTKTYQAHAKQKFSRLWSSKSVTEIH
  LYFEEEVKQEECDHLDRLFAPKEAGKQPRTVIIQGPQGIGKTTLLMKLMMAWSDNKIFRD
  RFLYTFYFCCRELRELPPTSLADLISREWPDPAAPITEIVSQPERLLFVIDSFEELQGGL
  NEPDSDLCGDLMEKRPVQVLLSSLLRKKMLPEASLLIAIKPVCPKELRDQVTISEIYQPR
  GFNESDRLVYFCCFFKDPKRAMEAFNLVRESEQLFSICQIPLLCWILCTSLKQEMQKGKD
  LALTCQSTTSVYSSFVFNLFTPEGAEGPTPQTQHQLKALCSLAAEGMWTDTFEFCEDDLR
  RNGVVDADIPALLGTKILLKYGERESSYVFLHVCIQEFCAALFYLLKSHLDHPHPAVRCV
  QELLVANFEKARRAHWIFLGCFLTGLLNKKEQEKLDAFFGFQLSQEIKQQIHQCLKSLGE
  RGNPQGQVDSLAIFYCLFEMQDPAFVKQAVNLLQEANFHIIDNVDLVVSAYCLKYCSSLR
  KLCFSVQNVFKKEDEHSSTSDYSLICWHHICSVLTTSGHLRELQVQDSTLSESTFVTWCN
  QLRHPSCRLQKLGINNVSFSGQSVLLFEVLFYQPDLKYLSFTLTKLSRDDIRSLCDALNY
  PAGNVKELALVNCHLSPIDCEVLAGLLTNNKKLTYLNVSCNQLDTGVPLLCEALCSPDTV
  LVYLMLAFCHLSEQCCEYISEMLLRNKSVRYLDLSANVLKDEGLKTLCEALKHPDCCLDS
  LCLVKCFITAAGCEDLASALISNQNLKILQIGCNEIGDVGVQLLCRALTHTDCRLEILGL
  EECGLTSTCCKDLASVLTCSKTLQQLNLTLNTLDHTGVVVLCEALRHPECALQVLGLRKT
  DFDEETQALLTAEEERNPNLTITDDCDTITRVEI

• Sequence length: 994

Pathways

KEGG:

Pathogenic Escherichia coli infection

Reactome:

IRF3 mediated activation of type 1 IFN
Regulation of innate immune responses to cytosolic DNA
IRF3-mediated induction of type I IFN

Associated diseases

Evidence Score:

• ★☆☆☆☆  Gene-disease association found in Text Mining only
• ★★☆☆☆  Found in Text Mining and Unknown/Other Associations
• ★★★☆☆  Reported in Unknown/Other Associations across ≥2 Sources
• ★★★★☆  ClinVar: Pathogenic/Likely Pathogenic (<5 Variants)
• ★★★★★  ClinVar: Pathogenic/Likely Pathogenic (≥5 Variants)

Unknown / Other Associations
Phenotype Name	Clinical Significance	Source	Evidence Score
AUTISM SPECTRUM DISORDER	—	GWAS catalog	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
INSOMNIA	—	GWAS catalog	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
MACULAR DEGENERATION	—	GWAS catalog	★★☆☆☆ Found in Text Mining + Unknown/Other Associations

Associations from Text Mining
Disease Name	Disease (Merged)	Source	PMID	Relationship Type	Evidence Score
Adenocarcinoma	Adenocarcinoma	BEFREE	10836999		★☆☆☆☆ Found in Text Mining only
Asthma	Asthma	BEFREE	30526007		★☆☆☆☆ Found in Text Mining only
Bladder Neoplasm	Bladder Neoplasm	BEFREE	17760744		★☆☆☆☆ Found in Text Mining only
Breast Carcinoma	Breast Carcinoma	BEFREE	29599486		★☆☆☆☆ Found in Text Mining only
Carcinoma of bladder	Bladder carcinoma	BEFREE	17760744		★☆☆☆☆ Found in Text Mining only
Cholestasis	Cholestasis	CTD_human_DG	26881866		★☆☆☆☆ Found in Text Mining only
Colorectal Carcinoma	Colorectal Cancer	UNIPROT_DG			★☆☆☆☆ Found in Text Mining only
Congenital Abnormalities	Congenital abnormalities	Pubtator	35304602	Associate	★☆☆☆☆ Found in Text Mining only
Demyelinating Diseases	Demyelinating diseases	Pubtator	27893410	Associate	★☆☆☆☆ Found in Text Mining only
Developmental Disabilities	Developmental disability	Pubtator	35304602	Associate	★☆☆☆☆ Found in Text Mining only
Growth Disorders	Growth disorder	Pubtator	35304602	Associate	★☆☆☆☆ Found in Text Mining only
Head and Neck Neoplasms	Head and neck neoplasm	Pubtator	35304602	Associate	★☆☆☆☆ Found in Text Mining only
Hearing Loss Sensorineural	Hearing loss	Pubtator	35304602	Associate	★☆☆☆☆ Found in Text Mining only
Heart Defects Congenital	Congenital heart defect	Pubtator	35304602	Associate	★☆☆☆☆ Found in Text Mining only
Intellectual Disability	Intellectual developmental disorder	Pubtator	35304602	Associate	★☆☆☆☆ Found in Text Mining only
Malignant neoplasm of urinary bladder	Urinary bladder cancer	BEFREE	17760744		★☆☆☆☆ Found in Text Mining only
Malignant Neoplasms	Malignant Neoplasm	BEFREE	9458099		★☆☆☆☆ Found in Text Mining only
Multiple Sclerosis	Multiple sclerosis	Pubtator	27893410	Associate	★☆☆☆☆ Found in Text Mining only
Pena Shokeir syndrome type 1	Pena-shokeir syndrome	Pubtator	35304602	Associate	★☆☆☆☆ Found in Text Mining only
Psoriasis	Psoriasis	Pubtator	29715312	Associate	★☆☆☆☆ Found in Text Mining only
Pulmonary Disease Chronic Obstructive	Chronic obstructive pulmonary disease	Pubtator	31601004	Associate	★☆☆☆☆ Found in Text Mining only
Tetralogy of Fallot	Tetralogy of fallot	Pubtator	35304602	Associate	★☆☆☆☆ Found in Text Mining only
Urothelial Carcinoma	Urothelial Carcinoma	BEFREE	28888400		★☆☆☆☆ Found in Text Mining only