LOXL1
lysyl oxidase like 1
Basic information
Region (hg38): 15:73925989-73952137
Links
Phenotypes
GenCC
Source:
No genCC data.
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 LOXL1 gene is commonly pathogenic or not. These statistics are base on transcript: . 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.
| Variant type | Pathogenic | Likely pathogenic | VUS | Likely benign | Benign | Sum |
|---|---|---|---|---|---|---|
| synonymous | 2 | |||||
| missense | 34 | 36 | ||||
| nonsense | 0 | |||||
| start loss | 0 | |||||
| frameshift | 0 | |||||
| splice donor/acceptor (+/-2bp) | 0 | |||||
| Total | 0 | 0 | 34 | 2 | 2 |
Loading clinvar variants...
GnomAD
Source:
| Gene | Type | Bio Type | Transcript | Coding Exons | Length |
|---|---|---|---|---|---|
| LOXL1 | protein_coding | protein_coding | ENST00000261921 | 7 | 26149 |
| pLI Probability LOF Intolerant | pRec Probability LOF Recessive | Individuals with no LOFs | Individuals with Homozygous LOFs | Individuals with Heterozygous LOFs | Defined | p |
|---|---|---|---|---|---|---|
| 0.887 | 0.113 | 125715 | 0 | 5 | 125720 | 0.0000199 |
| Z-Score | Observed | Expected | Observed/Expected | Mutation Rate | Total Possible in Transcript | |
|---|---|---|---|---|---|---|
| Missense | 1.13 | 217 | 269 | 0.807 | 0.0000148 | 3603 |
| Missense in Polyphen | 103 | 145.82 | 0.70633 | 1748 | ||
| Synonymous | 1.93 | 92 | 119 | 0.775 | 0.00000685 | 1196 |
| Loss of Function | 3.56 | 3 | 20.3 | 0.148 | 8.77e-7 | 260 |
LoF frequencies by population
| Ethnicity | Sum of pLOFs | p |
|---|---|---|
| African & African-American | 0.0000302 | 0.0000302 |
| Ashkenazi Jewish | 0.00 | 0.00 |
| East Asian | 0.00 | 0.00 |
| Finnish | 0.0000550 | 0.0000462 |
| European (Non-Finnish) | 0.0000192 | 0.0000176 |
| Middle Eastern | 0.00 | 0.00 |
| South Asian | 0.0000356 | 0.0000327 |
| Other | 0.00 | 0.00 |
dbNSFP
Source:
- Function
- FUNCTION: Active on elastin and collagen substrates. {ECO:0000250}.;
- Disease
- DISEASE: Exfoliation syndrome (XFS) [MIM:177650]: A disorder characterized by accumulation of abnormal fibrillar deposits in the anterior segment of the eye. In addition to being a cause of glaucoma and glaucomatous optic neuropathy, exfoliation syndrome has also been associated with lens zonule weakness, cataract formation, and systemic vascular complications due to deposition of exfoliation material in extraocular tissues. {ECO:0000269|PubMed:18037624, ECO:0000269|PubMed:19343041}. Note=Disease susceptibility is associated with variations affecting the gene represented in this entry. Susceptibility to exfoliation syndrome is conferred by a risk haplotype that includes two LOXL1 coding non-synonymous SNPs (Arg141Leu and Gly153Asp) and one intronic SNP. Arg141Leu and Gly153Asp are sufficient to confer disease susceptibility in some populations.;
- Pathway
- Canonical and Non-Canonical TGF-B signaling;Crosslinking of collagen fibrils;Assembly of collagen fibrils and other multimeric structures;Collagen formation;Extracellular matrix organization
(Consensus)
Recessive Scores
- pRec
- 0.295
Haploinsufficiency Scores
- pHI
- 0.931
- hipred
- hipred_score
- ghis
- 0.453
Essentials
- essential_gene_CRISPR
- E
- essential_gene_CRISPR2
- N
- essential_gene_gene_trap
- N
- gene_indispensability_pred
- E
- gene_indispensability_score
- 0.980
Gene Damage Prediction
| All | Recessive | Dominant | |
|---|---|---|---|
| Mendelian | High | High | High |
| Primary Immunodeficiency | High | High | High |
| Cancer | High | High | High |
Mouse Genome Informatics
- Gene name
- Loxl1
- Phenotype
- respiratory system phenotype; behavior/neurological phenotype (the observable actions or reactions of mammalian organisms that are manifested through development and lifespan); 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); reproductive system phenotype; digestive/alimentary phenotype; hearing/vestibular/ear phenotype; nervous system phenotype (the observable morphological and physiological characteristics of the extensive, intricate network of electochemical structures in the body that is comprised of the brain, spinal cord, nerves, ganglia and parts of the receptor organs that are manifested through development and lifespan); growth/size/body region 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); homeostasis/metabolism phenotype;
Zebrafish Information Network
- Gene name
- loxl1
- Affected structure
- somite
- Phenotype tag
- abnormal
- Phenotype quality
- morphology
Gene ontology
- Biological process
- peptidyl-lysine oxidation;protein deamination;response to lipopolysaccharide;aorta development;oxidation-reduction process
- Cellular component
- acrosomal vesicle;extracellular region;basement membrane;extracellular space;collagen-containing extracellular matrix
- Molecular function
- protein-lysine 6-oxidase activity;copper ion binding