LACC1 (laccase domain containing 1)

Gene

• Entrez ID: 144811
• Gene name: Laccase domain containing 1
• Gene symbol: LACC1
• Synonyms (NCBI Gene): C13orf31, FAMIN, JUVAR
• Chromosome: 13
• Chromosome location: 13q14.11
• Summary: This gene encodes an oxidoreductase that promotes fatty-acid oxidation, with concomitant inflammasome activation, mitochondrial and NADPH-oxidase-dependent reactive oxygen species production, and bactericidal activity of macrophages. The encoded protein f

SNPs

SNP ID	Visualize variation	Clinical significance	Consequence
rs184370809	C>T	Pathogenic	Stop gained, genic downstream transcript variant, coding sequence variant, intron variant
rs730880295	T>C	Likely-pathogenic, pathogenic	Missense variant, coding sequence variant
rs776489319	ATT>-	Pathogenic	Coding sequence variant, genic downstream transcript variant, inframe deletion
rs1594890601	C>-	Pathogenic	Frameshift variant, coding sequence variant

miRNA

miRTarBase ID	miRNA	Experiments	Reference
MIRT043065	hsa-miR-324-5p	CLASH	23622248
MIRT620124	hsa-miR-5003-3p	HITS-CLIP	23824327
MIRT620123	hsa-miR-3148	HITS-CLIP	23824327
MIRT620122	hsa-miR-4668-5p	HITS-CLIP	23824327
MIRT620121	hsa-miR-3153	HITS-CLIP	23824327
MIRT620120	hsa-miR-6733-5p	HITS-CLIP	23824327
MIRT620119	hsa-miR-6739-5p	HITS-CLIP	23824327
MIRT620124	hsa-miR-5003-3p	HITS-CLIP	23824327
MIRT620123	hsa-miR-3148	HITS-CLIP	23824327
MIRT620122	hsa-miR-4668-5p	HITS-CLIP	23824327
MIRT620121	hsa-miR-3153	HITS-CLIP	23824327
MIRT620120	hsa-miR-6733-5p	HITS-CLIP	23824327
MIRT620119	hsa-miR-6739-5p	HITS-CLIP	23824327

Gene ontology (GO)

GO ID	Ontology	Definition	Evidence	Reference
GO:0002221	Process	Pattern recognition receptor signaling pathway	IDA	28593945, 31875558
GO:0002376	Process	Immune system process	IEA
GO:0002720	Process	Positive regulation of cytokine production involved in immune response	IDA	28593945
GO:0004000	Function	Adenosine deaminase activity	IDA	31978345
GO:0004000	Function	Adenosine deaminase activity	IEA
GO:0004731	Function	Purine-nucleoside phosphorylase activity	IDA	31978345
GO:0004731	Function	Purine-nucleoside phosphorylase activity	IEA
GO:0005507	Function	Copper ion binding	IBA
GO:0005515	Function	Protein binding	IPI	27478939, 28514442, 31875558, 33961781
GO:0005634	Component	Nucleus	IEA
GO:0005634	Component	Nucleus	ISS
GO:0005737	Component	Cytoplasm	IEA
GO:0005777	Component	Peroxisome	IDA	27478939, 27959965
GO:0005777	Component	Peroxisome	IEA
GO:0005783	Component	Endoplasmic reticulum	IDA	31875558
GO:0005783	Component	Endoplasmic reticulum	IEA
GO:0006954	Process	Inflammatory response	IEA
GO:0016682	Function	Oxidoreductase activity, acting on diphenols and related substances as donors, oxygen as acceptor	IDA	27959965, 31978345
GO:0016740	Function	Transferase activity	IEA
GO:0016787	Function	Hydrolase activity	IEA
GO:0017061	Function	S-methyl-5-thioadenosine phosphorylase activity	IDA	31978345
GO:0017061	Function	S-methyl-5-thioadenosine phosphorylase activity	IEA
GO:0030641	Process	Regulation of cellular pH	IDA	31978345
GO:0031347	Process	Regulation of defense response	IEA
GO:0045087	Process	Innate immune response	IEA
GO:0046872	Function	Metal ion binding	IEA
GO:0047975	Function	Guanosine phosphorylase activity	IDA	31978345
GO:0047975	Function	Guanosine phosphorylase activity	IEA
GO:0050727	Process	Regulation of inflammatory response	IEA
GO:0050727	Process	Regulation of inflammatory response	ISS
GO:0070431	Process	Nucleotide-binding oligomerization domain containing 2 signaling pathway	IDA	31875558
GO:1900542	Process	Regulation of purine nucleotide metabolic process	IEA
GO:1900542	Process	Regulation of purine nucleotide metabolic process	ISS

Other IDs

• MIM: 613409
• HGNC: 26789
• e!Ensembl: ENSG00000179630

Protein

• UniProt ID: Q8IV20
• Protein name: Purine nucleoside phosphorylase LACC1 (EC 2.4.2.1) (Adenosine deaminase LACC1) (EC 3.5.4.4) (Fatty acid metabolism-immunity nexus) (Guanosine phosphorylase LACC1) (Laccase domain-containing protein 1) (S-methyl-5'-thioadenosine phosphorylase LACC1) (EC 2.
• Protein function: Purine nucleoside enzyme that catalyzes the phosphorolysis of adenosine, guanosine and inosine nucleosides, yielding D-ribose 1-phosphate and the respective free bases, adenine, guanine and hypoxanthine (PubMed:31978345). Also catalyzes the phos
• Family and domains:

  Pfam

  Accession	ID	Position in sequence	Description	Type
  PF02578	Cu-oxidase_4	195 → 427	Multi-copper polyphenol oxidoreductase laccase	Family

• Tissue specificity: TISSUE SPECIFICITY: Ubiquitously expressed, with higher expression levels in immune-related tissues such as lymph nodes and spleen (PubMed:27959965). Expressed in both intestinal and peripheral myeloid-derived cells (PubMed:28593945). {ECO:0000269|PubMed:
• Sequence:

  MAEAVLIDLFGLKLNSQKNCHQTLLKTLNAVQYHHAAKAKFLCIMCCSNISYERDGEQDN
  CEIETSNGLSALLEEFEIVSCPSMAATLYTIKQKIDEKNLSSIKVIVPRHRKTLMKAFID
  QLFTDVYNFEFEDLQVTFRGGLFKQSIEINVITAQELRGIQNEIETFLRSLPALRGKLTI
  ITSSLIPDIFIHGFTTRTGGISYIPTLSSFNLFSSSKRRDPKVVVQENLRRLANAAGFNV
  EKFYRIKTHHSNDIWIMGRKEPDSYDGITTNQRGVTIAALGADCIPIVFADPVKKACGVA
  HAGWKGTLLGVAMATVNAMIAEYGCSLEDIVVVLGPSVGPCCFTLPRESAEAFHNLHPAC
  VQLFDSPNPCIDIRKATRILLEQGGILPQNIQDQNQDLNLCTSCHPDKFFSHVRDGLNFG
  TQIGFISIKE

• Sequence length: 430

Pathways

KEGG:

Purine metabolism
Cysteine and methionine metabolism
Metabolic pathways
Nucleotide metabolism

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)

Causal
Phenotype Name	Clinical Significance	dbSNP ID	RCV Accession	Evidence Score
Juvenile arthritis due to defect in LACC1	Likely pathogenic; Pathogenic	rs2138301967, rs1594890601, rs1594882933, rs184370809, rs776489319, rs1594883470, rs1955020297	RCV002247148 RCV001005043 RCV001005044 RCV001005045 RCV001005046 RCV001005047 RCV001283808	★★★★★ ClinVar: Pathogenic / Likely Pathogenic (≥5 Variants)

Unknown / Other Associations
Phenotype Name	Clinical Significance	Source	Evidence Score
BEHCET'S SYNDROME	—	GWAS catalog	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
CROHN'S DISEASE	—	GWAS catalog	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
INFLAMMATORY BOWEL DISEASE	—	GWAS catalog	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
JUVENILE ARTHRITIS	—	Disgenet, HPO Disgenet, HPO	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
JUVENILE CHRONIC POLYARTHRITIS	—	Disgenet	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
LEPROSY	—	GWAS catalog	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Leprosy, susceptibility to, 1	Uncertain risk allele	ClinVar	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
MONOARTICULAR JUVENILE RHEUMATOID ARTHRITIS	—	Disgenet	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
PAUCIARTICULAR JUVENILE RHEUMATOID ARTHRITIS	—	Disgenet	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
SCHIZOPHRENIA	—	GWAS catalog	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
SYSTEMIC-ONSET JUVENILE IDIOPATHIC ARTHRITIS	—	Orphanet	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
ULCERATIVE COLITIS	—	GWAS catalog	★★☆☆☆ Found in Text Mining + Unknown/Other Associations

Associations from Text Mining
Disease Name	Disease (Merged)	Source	PMID	Relationship Type	Evidence Score
Anterior uveitis	Uveitis	HPO_DG			★☆☆☆☆ Found in Text Mining only
Arthritis	Arthritis	BEFREE	30510070		★☆☆☆☆ Found in Text Mining only
Arthritis	Arthritis	Pubtator	31978345	Associate	★☆☆☆☆ Found in Text Mining only
Arthritis Juvenile	Juvenile arthritis	Pubtator	27881174, 27959965, 30872671	Associate	★☆☆☆☆ Found in Text Mining only
Asthma	Asthma	GWASDB_DG	21150878		★☆☆☆☆ Found in Text Mining only
Autoimmune Diseases	Autoimmune disease	Pubtator	36604576	Associate	★☆☆☆☆ Found in Text Mining only
Autoinflammatory disorder	Autoinflammatory Disease	BEFREE	25220867		★☆☆☆☆ Found in Text Mining only
Behcet Syndrome	Behcet disease	Pubtator	28166214, 29907633, 33393726	Associate	★☆☆☆☆ Found in Text Mining only
Colitis Ulcerative	Ulcerative colitis	Pubtator	27959965	Associate	★☆☆☆☆ Found in Text Mining only
Crohn Disease	Crohn Disease	GWASCAT_DG	18587394, 21102463, 23128233, 28067908		★☆☆☆☆ Found in Text Mining only
Crohn Disease	Crohn Disease	GWASDB_DG	18587394, 21102463, 23128233		★☆☆☆☆ Found in Text Mining only
Crohn Disease	Crohn Disease	BEFREE	23135745, 25220867, 27098602, 27478939, 27959965, 28593945, 29538758		★☆☆☆☆ Found in Text Mining only
Crohn Disease	Crohn disease	Pubtator	23135745, 23598818, 27959965, 31978345, 36604576	Associate	★☆☆☆☆ Found in Text Mining only
Granulomatous Disease Chronic	Granulomatous disease	Pubtator	27861181	Associate	★☆☆☆☆ Found in Text Mining only
Inflammatory Bowel Diseases	Inflammatory Bowel Disease	GWASCAT_DG	26192919, 28067908		★☆☆☆☆ Found in Text Mining only
Inflammatory Bowel Diseases	Inflammatory Bowel Disease	BEFREE	27098602, 30510070		★☆☆☆☆ Found in Text Mining only
Inflammatory Bowel Diseases	Inflammatory bowel disease	Pubtator	27861181, 31978345	Associate	★☆☆☆☆ Found in Text Mining only
Juvenile arthritis	Arthritis	BEFREE	25220867, 27098602, 27959965, 30872671		★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Juvenile arthritis	Arthritis	HPO_DG			★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Juvenile-Onset Still Disease	Still Disease	ORPHANET_DG	25220867		★☆☆☆☆ Found in Text Mining only
Leprosy	Leprosy	GWASDB_DG	20018961, 22019778		★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Leprosy	Leprosy	GWASCAT_DG	20018961		★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Leprosy	Leprosy	Pubtator	20018961, 27959965, 28166214, 29706348, 31978345, 32421744, 32433683, 36604576	Associate	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Leprosy	Leprosy	BEFREE	25220867, 25367361, 26235265, 27098602, 27478939, 27959965, 29538758, 29706348, 30510070		★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Majeed syndrome	Majeed Syndrome	BEFREE	31741047		★☆☆☆☆ Found in Text Mining only
Multiple Sclerosis	Multiple Sclerosis	GWASDB_DG	22190364		★☆☆☆☆ Found in Text Mining only
Pericarditis	Pericarditis	HPO_DG			★☆☆☆☆ Found in Text Mining only
Pleural effusion disorder	Pleural effusion	HPO_DG			★☆☆☆☆ Found in Text Mining only
Polyarticular Juvenile Idiopathic Arthritis, Rheumatoid Factor Negative	Seronegative polyarthritis	BEFREE	30872671		★☆☆☆☆ Found in Text Mining only
Rheumatoid Arthritis, Systemic Juvenile	Rheumatoid arthritis	UNIPROT_DG	25220867		★☆☆☆☆ Found in Text Mining only
Skin lesion	Skin Lesion	BEFREE	29706348		★☆☆☆☆ Found in Text Mining only
Systemic onset juvenile chronic arthritis	Arthritis	BEFREE	25220867, 26196376, 27478939, 29538758, 30510070		★☆☆☆☆ Found in Text Mining only
Systemic onset juvenile chronic arthritis	Arthritis	ORPHANET_DG	25220867		★☆☆☆☆ Found in Text Mining only
Systemic-onset juvenile idiopathic arthritis	Arthritis	Orphanet			★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Ulcerative Colitis	Ulcerative colitis	BEFREE	23974994, 27098602, 27959965		★★☆☆☆ Found in Text Mining + Unknown/Other Associations