LTA4H

leukotriene A4 hydrolase, the group of M1 metallopeptidases

Basic information

Region (hg38): 12:96000752-96043520

Links

ENSG00000111144 ∙ NCBI:4048 ∙ OMIM:151570 ∙ HGNC:6710 ∙ Uniprot:P09960 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

Phenotypes

GenCC

Source: genCC

No genCC data.

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the LTA4H gene.

• Inborn genetic diseases (15 variants)
• not provided (8 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the LTA4H 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				2	2	4
missense			14	2	1	17
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding					1	1
Total	0	0	14	4	4

Variants in LTA4H

This is a list of pathogenic ClinVar variants found in the LTA4H region.

You can filter this list by clicking the number of variants in the Variants pathogenicity by type table.

Position	Type	Phenotype	Significance	ClinVar
12-96001014-A-G		not specified	Uncertain significance (Nov 10, 2022)
12-96001015-C-A		not specified	Uncertain significance (Jan 10, 2023)
12-96001062-G-C		not specified	Uncertain significance (Dec 22, 2023)
12-96001065-C-T		not specified	Uncertain significance (Sep 16, 2021)
12-96003014-G-A		not specified	Uncertain significance (Jan 23, 2024)
12-96006381-T-C		not specified	Likely benign (Oct 12, 2021)
12-96006401-T-A			Benign (Jul 31, 2018)
12-96006403-C-T		not specified	Uncertain significance (Mar 28, 2023)
12-96006408-G-A		not specified	Uncertain significance (Aug 16, 2021)
12-96006409-C-T		not specified	Uncertain significance (Jul 12, 2023)
12-96013217-G-A			Benign (Dec 31, 2019)
12-96013781-T-C		not specified	Uncertain significance (Apr 19, 2023)
12-96013817-T-G		not specified	Uncertain significance (Dec 06, 2022)
12-96014866-A-T		not specified	Uncertain significance (Feb 05, 2024)
12-96014959-A-G		not specified	Uncertain significance (Oct 25, 2022)
12-96014963-G-C		not specified	Uncertain significance (Jul 15, 2021)
12-96014985-C-T			Benign/Likely benign (Apr 01, 2022)
12-96015652-G-A			Likely benign (Apr 01, 2022)
12-96018811-A-G			Benign (Jun 18, 2018)
12-96018819-A-C		not specified	Uncertain significance (Dec 15, 2021)
12-96019211-G-C		not specified	Uncertain significance (Dec 28, 2022)
12-96022208-C-T		not specified	Uncertain significance (May 30, 2023)
12-96027509-G-A		not specified	Uncertain significance (Apr 25, 2022)
12-96027546-T-C		not specified	Uncertain significance (Mar 07, 2024)
12-96029046-C-G			Benign (Jul 31, 2018)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
LTA4H	protein_coding	protein_coding	ENST00000228740	19	42693

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
2.96e-8	0.999	125682	0	66	125748	0.000262

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	1.48	242	316	0.766	0.0000151	3975
Missense in Polyphen		85	108.19	0.78565		1375
Synonymous	1.59	92	114	0.810	0.00000568	1144
Loss of Function	2.96	19	39.0	0.487	0.00000192	466

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000517	0.000512
Ashkenazi Jewish	0.00	0.00
East Asian	0.000163	0.000163
Finnish	0.000324	0.000323
European (Non-Finnish)	0.000316	0.000308
Middle Eastern	0.000163	0.000163
South Asian	0.000171	0.000163
Other	0.000669	0.000652

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Epoxide hydrolase that catalyzes the final step in the biosynthesis of the proinflammatory mediator leukotriene B4. Has also aminopeptidase activity. {ECO:0000269|PubMed:11917124, ECO:0000269|PubMed:12207002, ECO:0000269|PubMed:15078870, ECO:0000269|PubMed:18804029, ECO:0000269|PubMed:1897988, ECO:0000269|PubMed:1975494, ECO:0000269|PubMed:2244921}.
• 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;Eicosanoid Synthesis;Neutrophil degranulation;Metabolism of lipids;Prostaglandin Leukotriene metabolism;Synthesis of Leukotrienes (LT) and Eoxins (EX);Arachidonic acid metabolism;Innate Immune System;Immune System;Metabolism;Biosynthesis of E-series 18(S)-resolvins;Biosynthesis of E-series 18(R)-resolvins;Biosynthesis of EPA-derived SPMs;Biosynthesis of D-series resolvins;Biosynthesis of aspirin-triggered D-series resolvins;Biosynthesis of protectins;Biosynthesis of DHA-derived SPMs;Biosynthesis of specialized proresolving mediators (SPMs);Fatty acid metabolism;leukotriene biosynthesis (Consensus)

Recessive Scores

• pRec: 0.208

Intolerance Scores

• loftool: 0.814
• rvis_EVS: 0.02
• rvis_percentile_EVS: 55.45

Haploinsufficiency Scores

• pHI: 0.120
• hipred: N
• hipred_score: 0.492
• ghis: 0.486

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.999

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Lta4h
• Phenotype: immune system phenotype

Zebrafish Information Network

• Gene name: lta4h
• Affected structure: epiboly involved in gastrulation with mouth forming second
• Phenotype tag: abnormal
• Phenotype quality: delayed

Gene ontology

• Biological process: proteolysis;leukotriene metabolic process;leukotriene biosynthetic process;long-chain fatty acid biosynthetic process;peptide catabolic process;neutrophil degranulation;cellular lipid metabolic process;cellular protein metabolic process
• Cellular component: extracellular region;nucleus;nucleoplasm;cytosol;extracellular exosome;tertiary granule lumen;ficolin-1-rich granule lumen
• Molecular function: RNA binding;aminopeptidase activity;epoxide hydrolase activity;leukotriene-A4 hydrolase activity;protein binding;peptidase activity;zinc ion binding;metalloaminopeptidase activity