LTC4S

leukotriene C4 synthase

Basic information

Region (hg38): 5:179793980-179796647

Links

ENSG00000213316 ∙ NCBI:4056 ∙ OMIM:246530 ∙ HGNC:6719 ∙ Uniprot:Q16873 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

Phenotypes

GenCC

Source: genCC

No genCC data.

Clinical Genomic Database

Source: CGD

Condition	Inheritance	Intervention Categories	Intervention/Rationale	Manifestation Categories	References
Asthma, aspirin-induced, susceptibility to	AR	Pharmacogenomic	The relative risk/odds ratios of identified variants are overall relatively low, but variants may have pharmacogenomic importance	General	10970818; 19862937; 22884858; 23101307

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the LTC4S gene.

• not_specified (17 variants)
• not_provided (2 variants)
• Asthma,_nasal_polyps,_and_aspirin_intolerance (1 variants)
• Hypotonia-failure_to_thrive-microcephaly_syndrome (1 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the LTC4S gene is commonly pathogenic or not. These statistics are base on transcript: NM_000145867.2. Only rare variants are included in the table.

In the table, we include only reliable ClinVar variants with their consequences to MANE Select, Mane Plus Clinical transcripts, or transcripts with TSL equals 1. Click the count to view the source variants.

Warning: slight differences between displayed counts and the number of variants in ClinVar may occur, primarily due to (1) the application of a different transcript and/or consequence by our variant effect predictor or (2) differences in clinical significance: we classify Benign/Likely benign variants as Likely benign and Pathogenic/Likely pathogenic variants as Likely pathogenic.

Effect	Pathogenic	Likely pathogenic	VUS	Likely benign	Benign	Sum
synonymous					1	1
missense			17			17
nonsense						0
start loss						0
frameshift						0
splice donor/acceptor (+/-2bp)			2			2
Total	0	0	19	0	1

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
LTC4S	protein_coding	protein_coding	ENST00000292596	5	2668

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
		125020	1	518	125539	0.00207

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	-0.132	72	68.9	1.04	0.00000323	892
Missense in Polyphen		32	29.749	1.0757		346
Synonymous	-0.810	43	36.8	1.17	0.00000180	348
Loss of Function	0.439	5	6.18	0.809	2.63e-7	75

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.00120	0.00112
Ashkenazi Jewish	0.0129	0.0121
East Asian	0.000171	0.000163
Finnish	0.00205	0.00176
European (Non-Finnish)	0.00277	0.00247
Middle Eastern	0.000171	0.000163
South Asian	0.00138	0.00134
Other	0.00124	0.00114

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Catalyzes the conjugation of leukotriene A4 with reduced glutathione to form leukotriene C4.
• Pathway: Arachidonic acid metabolism - Homo sapiens (human);Leukotriene modifiers pathway, Pharmacodynamics;Etodolac Action Pathway;Ketoprofen Action Pathway;Ibuprofen Action Pathway;Rofecoxib Action Pathway;Acetylsalicylic Acid Action Pathway;Diflunisal Action Pathway;Leukotriene C4 Synthesis Deficiency;Acetaminophen Action Pathway;Celecoxib Action Pathway;Sulindac Action Pathway;Diclofenac Action Pathway;Ketorolac Action Pathway;Naproxen Action Pathway;Etoricoxib Action Pathway;Carprofen Action Pathway;Flurbiprofen Action Pathway;Fenoprofen Action Pathway;Antrafenine Action Pathway;Antipyrine Action Pathway;Lumiracoxib Action Pathway;Magnesium salicylate Action Pathway;Trisalicylate-choline Action Pathway;Nepafenac Action Pathway;Phenylbutazone Action Pathway;Lornoxicam Action Pathway;Salsalate Action Pathway;Tenoxicam Action Pathway;Tiaprofenic Acid Action Pathway;Tolmetin Action Pathway;Salicylic Acid Action Pathway;Salicylate-sodium Action Pathway;Oxaprozin Action Pathway;Valdecoxib Action Pathway;Nabumetone Action Pathway;Indomethacin Action Pathway;Meloxicam Action Pathway;Suprofen Action Pathway;Bromfenac Action Pathway;Mefenamic Acid Action Pathway;Arachidonic Acid Metabolism;Piroxicam Action Pathway;NOTCH-Ncore;Eicosanoid Synthesis;Metabolism of lipids;Prostaglandin Leukotriene metabolism;Synthesis of Leukotrienes (LT) and Eoxins (EX);Synthesis of 5-eicosatetraenoic acids;Arachidonic acid metabolism;Biosynthesis of protectin and resolvin conjugates in tissue regeneration (PCTR and RCTR);Biosynthesis of DHA-derived sulfido conjugates;Synthesis of Lipoxins (LX);Metabolism;Biosynthesis of maresin conjugates in tissue regeneration (MCTR);Biosynthesis of DHA-derived SPMs;Biosynthesis of specialized proresolving mediators (SPMs);Fatty acid metabolism;leukotriene biosynthesis (Consensus)

Recessive Scores

• pRec: 0.108

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.934

Gene Damage Prediction

	All	Recessive	Dominant
Mendelian	Medium	Medium	Medium
Primary Immunodeficiency	Medium	Medium	Medium
Cancer	Medium	Medium	Medium

Gene ontology

• Biological process: leukotriene metabolic process;leukotriene biosynthetic process;long-chain fatty acid biosynthetic process;positive regulation of catalytic activity;cellular oxidant detoxification
• Cellular component: nuclear envelope;nuclear outer membrane;endoplasmic reticulum;endoplasmic reticulum membrane;integral component of membrane;intracellular membrane-bounded organelle
• Molecular function: glutathione transferase activity;leukotriene-C4 synthase activity;glutathione peroxidase activity;protein binding;enzyme activator activity;lipid binding;identical protein binding