LOXL1

lysyl oxidase like 1

Basic information

Region (hg38): 15:73925988-73952137

Links

ENSG00000129038 ∙ NCBI:4016 ∙ OMIM:153456 ∙ HGNC:6665 ∙ Uniprot:Q08397 ∙ 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 LOXL1 gene.

• Inborn genetic diseases (19 variants)
• not provided (3 variants)

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.

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
missense			19	1		20
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	19	1	2

Variants in LOXL1

This is a list of pathogenic ClinVar variants found in the LOXL1 region.

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

Position	Type	Phenotype	Significance	ClinVar
15-73926926-A-G		not specified	Uncertain significance (Aug 14, 2023)
15-73926985-C-T		not specified	Uncertain significance (Oct 20, 2021)
15-73926986-G-A		not specified	Uncertain significance (Dec 16, 2022)
15-73927004-G-C		not specified	Uncertain significance (Aug 12, 2021)
15-73927042-C-G		not specified	Uncertain significance (Sep 27, 2021)
15-73927056-C-A		not specified	Uncertain significance (Jan 08, 2024)
15-73927071-G-T		not specified	Uncertain significance (Feb 05, 2024)
15-73927110-C-T		LOXL1-related disorder	Likely benign (Mar 22, 2019)
15-73927140-C-A		not specified	Uncertain significance (Jan 30, 2024)
15-73927205-G-T		Exfoliation syndrome, susceptibility to	risk factor (May 01, 2009)
15-73927210-C-T		not specified	Uncertain significance (Jul 26, 2022)
15-73927215-C-T		LOXL1-related disorder	Benign/Likely benign (Sep 12, 2019)
15-73927241-G-A		Exfoliation syndrome, susceptibility to • LOXL1-related disorder	Benign (Jun 27, 2019)
15-73927258-T-G		LOXL1-related disorder	Benign (Jan 24, 2020)
15-73927261-G-C			Likely benign (Jan 01, 2023)
15-73927265-C-T		LOXL1-related disorder	Benign (Sep 25, 2019)
15-73927364-C-A		not specified	Uncertain significance (Jun 29, 2023)
15-73927481-G-T		not specified	Uncertain significance (Mar 17, 2023)
15-73927541-C-T		not specified	Uncertain significance (Feb 07, 2023)
15-73927659-C-T		LOXL1-related disorder	Benign (Apr 25, 2019)
15-73927693-G-A		not specified	Uncertain significance (Jan 23, 2024)
15-73927693-G-C		not specified	Uncertain significance (Feb 22, 2023)
15-73927771-C-T		not specified	Uncertain significance (Jul 20, 2021)
15-73927781-C-G		not specified	Uncertain significance (Sep 01, 2021)
15-73927825-G-A		not specified	Uncertain significance (Jul 19, 2022)

GnomAD

Source: gnomAD

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: dbNSFP

• 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
• 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