ALOX12

arachidonate 12-lipoxygenase, 12S type, the group of Arachidonate lipoxygenases

Basic information

Region (hg38): 17:6996049-7010754

Links

ENSG00000108839 ∙ NCBI:239 ∙ OMIM:152391 ∙ HGNC:429 ∙ Uniprot:P18054 ∙ 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 ALOX12 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the ALOX12 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	5	6
missense			30	4	4	38
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding					22	22
Total	0	0	30	5	31

Variants in ALOX12

This is a list of pathogenic ClinVar variants found in the ALOX12 region.

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

Position	Type	Phenotype	Significance	ClinVar
17-6996178-C-A		not specified	Uncertain significance (Feb 28, 2024)
17-6996217-G-A		not specified	Uncertain significance (Nov 10, 2024)
17-6996240-C-G			Benign (Nov 10, 2018)
17-6996310-C-T			Benign (Nov 10, 2018)
17-6996412-T-C			Benign (Jun 18, 2021)
17-6996757-G-A			Benign (Nov 10, 2018)
17-6996865-C-A		not specified	Uncertain significance (Aug 20, 2024)
17-6996894-C-G		not specified	Uncertain significance (Aug 01, 2024)
17-6996897-C-A		not specified	Uncertain significance (Oct 30, 2023)
17-6996913-G-A		not specified	Uncertain significance (Oct 24, 2023)
17-6996965-T-C		not specified	Likely benign (May 04, 2022)
17-6997043-C-T			Benign (Nov 10, 2018)
17-6997064-T-C			Benign (Jun 18, 2021)
17-6997125-T-G			Benign (Nov 10, 2018)
17-6998353-G-A			Benign (Nov 10, 2018)
17-6998511-C-T		not specified	Uncertain significance (Aug 09, 2021)
17-6998512-G-A		not specified	Uncertain significance (Dec 26, 2023)
17-6998520-G-C			Likely benign (Apr 01, 2022)
17-6998566-T-G		not specified	Uncertain significance (Apr 18, 2023)
17-6998570-A-C			Likely benign (Jul 01, 2024)
17-6998575-G-A		not specified	Uncertain significance (Jan 31, 2023)
17-6998741-C-T		not specified	Uncertain significance (Nov 25, 2024)
17-6998836-G-A		not specified	Uncertain significance (Oct 03, 2023)
17-6998860-G-A			Benign (Nov 10, 2018)
17-6998958-T-C		not specified	Uncertain significance (Jan 19, 2024)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
ALOX12	protein_coding	protein_coding	ENST00000251535	14	14672

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
1.44e-15	0.290	125666	0	82	125748	0.000326

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	1.27	308	378	0.815	0.0000220	4274
Missense in Polyphen		80	111.29	0.71882		1363
Synonymous	1.57	123	147	0.836	0.00000838	1309
Loss of Function	1.36	28	36.9	0.758	0.00000199	381

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.00110	0.00110
Ashkenazi Jewish	0.0000993	0.0000992
East Asian	0.000163	0.000163
Finnish	0.0000462	0.0000462
European (Non-Finnish)	0.000362	0.000360
Middle Eastern	0.000163	0.000163
South Asian	0.000394	0.000392
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Non-heme iron-containing dioxygenase that catalyzes the stereo-specific peroxidation of free and esterified polyunsaturated fatty acids generating a spectrum of bioactive lipid mediators. Mainly converts arachidonic acid to (12S)- hydroperoxyeicosatetraenoic acid/(12S)-HPETE but can also metabolize linoleic acid. Has a dual activity since it also converts leukotriene A4/LTA4 into both the bioactive lipoxin A4/LXA4 and lipoxin B4/LXB4. Through the production of specific bioactive lipids like (12S)-HPETE it regulates different biological processes including platelet activation. It also probably positively regulates angiogenesis through regulation of the expression of the vascular endothelial growth factor. Plays a role in apoptotic process, promoting the survival of vascular smooth muscle cells for instance. May also play a role in the control of cell migration and proliferation. {ECO:0000269|PubMed:16638750, ECO:0000269|PubMed:22237009, ECO:0000269|PubMed:23578768, ECO:0000269|PubMed:8250832, ECO:0000269|PubMed:9751607}.
• Disease: DISEASE: Esophageal cancer (ESCR) [MIM:133239]: A malignancy of the esophagus. The most common types are esophageal squamous cell carcinoma and adenocarcinoma. Cancer of the esophagus remains a devastating disease because it is usually not detected until it has progressed to an advanced incurable stage. {ECO:0000269|PubMed:17460548}. Note=Disease susceptibility may be associated with variations affecting the gene represented in this entry. Gln at position 261 may confer interindividual susceptibility to esophageal cancer (PubMed:17460548). {ECO:0000269|PubMed:17460548}.; DISEASE: Colorectal cancer (CRC) [MIM:114500]: A complex disease characterized by malignant lesions arising from the inner wall of the large intestine (the colon) and the rectum. Genetic alterations are often associated with progression from premalignant lesion (adenoma) to invasive adenocarcinoma. Risk factors for cancer of the colon and rectum include colon polyps, long-standing ulcerative colitis, and genetic family history. {ECO:0000269|PubMed:17151091}. Note=Disease susceptibility may be associated with variations affecting the gene represented in this entry. Gln at position 261 may confer interindividual susceptibility to colorectal cancer (PubMed:17460548). {ECO:0000269|PubMed:17460548}.
• Pathway: Inflammatory mediator regulation of TRP channels - Homo sapiens (human);Serotonergic synapse - Homo sapiens (human);Arachidonic acid metabolism - Homo sapiens (human);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;Metabolism of lipids;Prostaglandin Leukotriene metabolism;Synthesis of 12-eicosatetraenoic acid derivatives;Synthesis of Hepoxilins (HX) and Trioxilins (TrX);Arachidonic acid metabolism;Synthesis of Lipoxins (LX);Metabolism;Biosynthesis of DHA-derived SPMs;Biosynthesis of DPAn-6 SPMs;Biosynthesis of DPAn-3 SPMs;Biosynthesis of DPA-derived SPMs;Biosynthesis of specialized proresolving mediators (SPMs);Fatty acid metabolism;Prostaglandin formation from arachidonate;lipoxin biosynthesis;Biosynthesis of DPAn-3-derived maresins;Arachidonic acid metabolism (Consensus)

Recessive Scores

• pRec: 0.243

Intolerance Scores

• loftool: 0.854
• rvis_EVS: 0.8
• rvis_percentile_EVS: 87.66

Haploinsufficiency Scores

• pHI: 0.240
• hipred: N
• hipred_score: 0.178
• ghis: 0.412

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.594

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Alox12
• Phenotype: homeostasis/metabolism 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); hematopoietic system phenotype

Zebrafish Information Network

• Gene name: alox12
• Affected structure: post-vent region
• Phenotype tag: abnormal
• Phenotype quality: bent

Gene ontology

• Biological process: negative regulation of muscle cell apoptotic process;arachidonic acid metabolic process;lipoxygenase pathway;fatty acid oxidation;superoxide anion generation;long-chain fatty acid biosynthetic process;linoleic acid metabolic process;hepoxilin metabolic process;hepoxilin biosynthetic process;establishment of skin barrier;negative regulation of platelet aggregation;leukotriene A4 metabolic process;lipoxin biosynthetic process;lipoxin A4 biosynthetic process;lipoxin B4 biosynthetic process
• Cellular component: cytoplasm;cytosol;membrane;sarcolemma;extracellular exosome
• Molecular function: arachidonate 12-lipoxygenase activity;iron ion binding;protein binding;linoleate 13S-lipoxygenase activity;oxidoreductase activity, acting on single donors with incorporation of molecular oxygen, incorporation of two atoms of oxygen;hepoxilin-epoxide hydrolase activity;hepoxilin A3 synthase activity