LTC4S
leukotriene C4 synthase
Basic information
Region (hg38): 5:179793980-179796647
Links
Phenotypes
GenCC
Source:
No genCC data.
Clinical Genomic Database
Source:
| 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
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.
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.
| Variant type | Pathogenic | Likely pathogenic | VUS | Likely benign | Benign | Sum |
|---|---|---|---|---|---|---|
| synonymous | 1 | |||||
| missense | 4 | |||||
| nonsense | 0 | |||||
| start loss | 0 | |||||
| frameshift | 0 | |||||
| inframe indel | 0 | |||||
| splice donor/acceptor (+/-2bp) | 1 | |||||
| splice region | 1 | 1 | 2 | |||
| non coding | 0 | |||||
| Total | 0 | 0 | 5 | 0 | 1 |
Variants in LTC4S
This is a list of pathogenic ClinVar variants found in the LTC4S region.
You can filter this list by clicking the number of variants in the Variants pathogenicity by type table.
| Position | Type | Phenotype | Significance | ClinVar |
|---|---|---|---|---|
| 5-179794104-G-A | Benign (Dec 20, 2017) | |||
| 5-179795687-A-C | Hypotonia-failure to thrive-microcephaly syndrome | Uncertain significance (Mar 29, 2021) | ||
| 5-179795793-T-C | not specified | Uncertain significance (Aug 28, 2023) | ||
| 5-179795857-G-A | Asthma, nasal polyps, and aspirin intolerance | Uncertain significance (Mar 29, 2024) | ||
| 5-179795863-G-A | Likely benign (Mar 01, 2018) | |||
| 5-179795982-C-T | not specified | Uncertain significance (May 26, 2022) | ||
| 5-179795983-T-G | not specified | Uncertain significance (Jul 20, 2021) | ||
| 5-179796263-C-A | not specified | Uncertain significance (Sep 26, 2023) | ||
| 5-179796332-C-T | not specified | Uncertain significance (Jun 07, 2024) |
GnomAD
Source:
| 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 |
|---|---|---|---|---|---|---|
| 0.000846 | 0.572 | 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:
- 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
Haploinsufficiency Scores
- pHI
- 0.125
- hipred
- N
- hipred_score
- 0.398
- ghis
- 0.405
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 |
Mouse Genome Informatics
- Gene name
- Ltc4s
- Phenotype
- immune system phenotype; cardiovascular system phenotype (the observable morphological and physiological characteristics of the mammalian heart, blood vessels, or circulatory system that are manifested through development and lifespan); respiratory system phenotype; integument phenotype (the observable morphological and physiological characteristics of the skin and its associated structures, such as the hair, nails, sweat glands, sebaceous glands and other secretory glands that are manifested through development and lifespan);
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