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LOXL3 lysyl oxidase like 3 [ Homo sapiens (human) ]

Gene ID: 84695, updated on 13-Apr-2024

Summary

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Official Symbol
LOXL3provided by HGNC
Official Full Name
lysyl oxidase like 3provided by HGNC
Primary source
HGNC:HGNC:13869
See related
Ensembl:ENSG00000115318 MIM:607163; AllianceGenome:HGNC:13869
Gene type
protein coding
RefSeq status
REVIEWED
Organism
Homo sapiens
Lineage
Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Primates; Haplorrhini; Catarrhini; Hominidae; Homo
Also known as
LOXL; MYP28
Summary
This gene encodes a lysyl oxidase, which likely functions as an amine oxidase and plays a role in the formation of crosslinks in collagens and elastin. Deletion of the related gene in mouse causes neonatal mortality with cleft palate, spine deformity, and defects in collagen organization. A mutation in this gene was found in a family with Stickler syndrome. [provided by RefSeq, Sep 2016]
Expression
Ubiquitous expression in placenta (RPKM 7.6), bone marrow (RPKM 5.2) and 24 other tissues See more
Orthologs
mouse all
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Genomic context

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See LOXL3 in Genome Data Viewer
Location:
2p13.1
Exon count:
16
Annotation release Status Assembly Chr Location
RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 2 NC_000002.12 (74532258..74555702, complement)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 2 NC_060926.1 (74540824..74564305, complement)
105.20220307 previous assembly GRCh37.p13 (GCF_000001405.25) 2 NC_000002.11 (74759385..74781069, complement)

Chromosome 2 - NC_000002.12Genomic Context describing neighboring genes Neighboring gene ATAC-STARR-seq lymphoblastoid active region 16070 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr2:74756279-74757161 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 16072 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 16073 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 16074 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 16075 Neighboring gene DEAQ-box RNA dependent ATPase 1 Neighboring gene H3K27ac hESC enhancer GRCh37_chr2:74763605-74764106 Neighboring gene AUP1 lipid droplet regulating VLDL assembly factor Neighboring gene HtrA serine peptidase 2 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 16076 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 11669 Neighboring gene Sharpr-MPRA regulatory regions 4995 and 13004 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 11670 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr2:74781947-74782464 Neighboring gene docking protein 1 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 16078 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 16079 Neighboring gene meiosis 1 associated protein Neighboring gene ATAC-STARR-seq lymphoblastoid active region 16080 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 16081 Neighboring gene TOR1B pseudogene 1 Neighboring gene TVP23B pseudogene 2

Genomic regions, transcripts, and products

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Go to nucleotide: Graphics FASTA GenBank

Expression

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  • Project title: HPA RNA-seq normal tissues
  • Description: RNA-seq was performed of tissue samples from 95 human individuals representing 27 different tissues in order to determine tissue-specificity of all protein-coding genes
  • BioProject: PRJEB4337
  • Publication: PMID 24309898
  • Analysis date: Wed Apr 4 07:08:55 2018

Bibliography

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Related articles in PubMed

  1. The Genetic Confirmation and Clinical Characterization of LOXL3-Associated MYP28: A Common Type of Recessive Extreme High Myopia. Jiang Y, et al. Invest Ophthalmol Vis Sci, 2023 Mar 1. PMID 36917121, Free PMC Article
  2. Apoptosis Activation and Autophagy Inhibition of Chondrocytes by Leptin by the Upregulation of LOXL3 in Osteoarthritis Pathogenesis. Wei Q. J Healthc Eng, 2022. PMID 35035830, Free PMC Article
  3. Identification of LOXL3-associating immune infiltration landscape and prognostic value in hepatocellular carcinoma. Wang N, et al. Virchows Arch, 2021 Dec. PMID 34448895
  4. LOXL3 Silencing Affected Cell Adhesion and Invasion in U87MG Glioma Cells. Laurentino TS, et al. Int J Mol Sci, 2021 Jul 28. PMID 34360836, Free PMC Article
  5. LOXL3 Function Beyond Amino Oxidase and Role in Pathologies, Including Cancer. Laurentino TS, et al. Int J Mol Sci, 2019 Jul 23. PMID 31340433, Free PMC Article

See all (34) citations in PubMed

GeneRIFs: Gene References Into Functions

What's a GeneRIF?
  1. The Genetic Confirmation and Clinical Characterization of LOXL3-Associated MYP28: A Common Type of Recessive Extreme High Myopia.
    Title: The Genetic Confirmation and Clinical Characterization of LOXL3-Associated MYP28: A Common Type of Recessive Extreme High Myopia.
  2. LOXL3-promoted hepatocellular carcinoma progression via promotion of Snail1/USP4-mediated epithelial-mesenchymal transition.
    Title: LOXL3-promoted hepatocellular carcinoma progression via promotion of Snail1/USP4-mediated epithelial-mesenchymal transition.
  3. Apoptosis Activation and Autophagy Inhibition of Chondrocytes by Leptin by the Upregulation of LOXL3 in Osteoarthritis Pathogenesis.
    Title: Apoptosis Activation and Autophagy Inhibition of Chondrocytes by Leptin by the Upregulation of LOXL3 in Osteoarthritis Pathogenesis.
  4. Identification of LOXL3-associating immune infiltration landscape and prognostic value in hepatocellular carcinoma.
    Title: Identification of LOXL3-associating immune infiltration landscape and prognostic value in hepatocellular carcinoma.
  5. LOXL3 Silencing Affected Cell Adhesion and Invasion in U87MG Glioma Cells.
    Title: LOXL3 Silencing Affected Cell Adhesion and Invasion in U87MG Glioma Cells.
  6. we present here a child and his father with Stickler syndrome and homozygous novel mutation in LOXL3 c.1036C>T (p.Arg346Trp). This report adds more evidence that biallelic mutations in LOXL3 cause autosomal recessive Stickler syndrome.
    Title: LOXL3 novel mutation causing a rare form of autosomal recessive Stickler syndrome.
  7. LOXL3 function beyond amino oxidase and role in pathologies, including cancer, has been described. (Review)
    Title: LOXL3 Function Beyond Amino Oxidase and Role in Pathologies, Including Cancer.
  8. results reveal an unexpected role for LOXL3 in the control of genome stability and melanoma progression, exposing its potential as a novel therapeutic target in malignant melanoma, a very aggressive condition yet in need for more effective treatment options.
    Title: Lysyl oxidase-like 3 is required for melanoma cell survival by maintaining genomic stability.
  9. LOXL1, LOXL3, and LOXL4 expressions are associated with distant metastasis of gastric cancer.
    Title: Significance of the Lysyl Oxidase Members Lysyl Oxidase Like 1, 3, and 4 in Gastric Cancer.
  10. Missense variant in LOXL3 gene is associated with nonsyndromic cleft palate.
    Title: Association between a common missense variant in LOXL3 gene and the risk of non-syndromic cleft palate.
Submit: New GeneRIF Correction See all GeneRIFs (20)

Phenotypes

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Find tests for this gene in the NIH Genetic Testing Registry (GTR)

Review eQTL and phenotype association data in this region using PheGenI

Associated conditions

Description Tests
Myopia 28, autosomal recessive
MedGen: C5676935 OMIM: 619781 GeneReviews: Not available
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Variation

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See variants in ClinVar

See studies and variants in dbVar

See Variation Viewer (GRCh37.p13)

See Variation Viewer (GRCh38)

Genotypes

Pathways from PubChem

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Interactions

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Products Interactant Other Gene Complex Source Pubs Description

General gene information

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Markers

Homology

Gene Ontology Provided by GOA

Function Evidence Code Pubs
enables copper ion binding NAS
Non-traceable Author Statement
more info
 PubMed 
enables fibronectin binding ISS
Inferred from Sequence or Structural Similarity
more info
  
enables protein binding IPI
Inferred from Physical Interaction
more info
 PubMed 
enables protein-lysine 6-oxidase activity IBA
Inferred from Biological aspect of Ancestor
more info
  
enables protein-lysine 6-oxidase activity IDA
Inferred from Direct Assay
more info
 PubMed 
enables protein-lysine 6-oxidase activity NAS
Non-traceable Author Statement
more info
 PubMed 
Process Evidence Code Pubs
involved_in collagen fibril organization IBA
Inferred from Biological aspect of Ancestor
more info
  
involved_in epithelial to mesenchymal transition IDA
Inferred from Direct Assay
more info
 PubMed 
involved_in fibronectin fibril organization ISS
Inferred from Sequence or Structural Similarity
more info
  
involved_in inflammatory response IBA
Inferred from Biological aspect of Ancestor
more info
  
involved_in inflammatory response ISS
Inferred from Sequence or Structural Similarity
more info
  
involved_in lung development ISS
Inferred from Sequence or Structural Similarity
more info
  
involved_in negative regulation of DNA-templated transcription IDA
Inferred from Direct Assay
more info
 PubMed 
involved_in negative regulation of T-helper 17 cell lineage commitment IDA
Inferred from Direct Assay
more info
 PubMed 
involved_in negative regulation of T-helper 17 cell lineage commitment ISS
Inferred from Sequence or Structural Similarity
more info
  
involved_in peptidyl-lysine oxidation IBA
Inferred from Biological aspect of Ancestor
more info
  
involved_in peptidyl-lysine oxidation IDA
Inferred from Direct Assay
more info
 PubMed 
involved_in positive regulation of integrin-mediated signaling pathway ISS
Inferred from Sequence or Structural Similarity
more info
  
involved_in roof of mouth development ISS
Inferred from Sequence or Structural Similarity
more info
  
involved_in somite development ISS
Inferred from Sequence or Structural Similarity
more info
  
involved_in spinal cord development ISS
Inferred from Sequence or Structural Similarity
more info
  
Component Evidence Code Pubs
is_active_in collagen-containing extracellular matrix IBA
Inferred from Biological aspect of Ancestor
more info
  
located_in cytoplasm IDA
Inferred from Direct Assay
more info
 PubMed 
located_in extracellular region IDA
Inferred from Direct Assay
more info
 PubMed 
is_active_in extracellular space IBA
Inferred from Biological aspect of Ancestor
more info
  
located_in extracellular space ISS
Inferred from Sequence or Structural Similarity
more info
  
located_in membrane IEA
Inferred from Electronic Annotation
more info
  
located_in nucleus IDA
Inferred from Direct Assay
more info
 PubMed 
located_in nucleus TAS
Traceable Author Statement
more info
 PubMed 

General protein information

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Preferred Names
lysyl oxidase homolog 3
Names
lysyl oxidase-like protein 3
NP_001276093.1
NP_001276094.1
NP_115992.1
XP_011531436.1
XP_024308944.1
XP_024308945.1
XP_024308946.1
XP_054200194.1
XP_054200195.1
XP_054200196.1
XP_054200197.1

NCBI Reference Sequences (RefSeq)

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RefSeqs maintained independently of Annotated Genomes

These reference sequences exist independently of genome builds. Explain

These reference sequences are curated independently of the genome annotation cycle, so their versions may not match the RefSeq versions in the current genome build. Identify version mismatches by comparing the version of the RefSeq in this section to the one reported in Genomic regions, transcripts, and products above.

Genomic

  1. NG_033047.1 RefSeqGene

    Range
    4994..26678
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. NM_001289164.3 → NP_001276093.1  lysyl oxidase homolog 3 isoform 2 precursor

    See identical proteins and their annotated locations for NP_001276093.1

    Status: REVIEWED

    Description
    Transcript Variant: This variant (2) lacks an alternate in-frame exon in the 5' coding region, compared to variant 1. Its encodes isoform 2, which is shorter than isoform 1.
    Source sequence(s)
    AC005033, AC005041
    Consensus CDS
    CCDS74527.1
    UniProtKB/TrEMBL
    B9A025
    Related
    ENSP00000377512.2, ENST00000393937.6
    Conserved Domains (2) summary
    smart00202
    Location:162 → 262
    SR; Scavenger receptor Cys-rich
    pfam01186
    Location:385 → 583
    Lysyl_oxidase; Lysyl oxidase

  2. NM_001289165.2 → NP_001276094.1  lysyl oxidase homolog 3 isoform 3

    See identical proteins and their annotated locations for NP_001276094.1

    Status: REVIEWED

    Description
    Transcript Variant: This variant (3, also known as sv1) represents the use of an alternate promoter, differs in the 5' UTR, and lacks a portion of the 5' coding region, compared to variant 1. This results in an isoform (3) which has a shorter N-terminus, compared to isoform 1.
    Source sequence(s)
    DQ378059
    UniProtKB/Swiss-Prot
    P58215
    Related
    ENST00000470907.6
    Conserved Domains (3) summary
    smart00202
    Location:56 → 164
    SR; Scavenger receptor Cys-rich
    pfam00530
    Location:61 → 164
    SRCR; Scavenger receptor cysteine-rich domain
    pfam01186
    Location:169 → 363
    Lysyl_oxidase; Lysyl oxidase

  3. NM_032603.5 → NP_115992.1  lysyl oxidase homolog 3 isoform 1 precursor

    See identical proteins and their annotated locations for NP_115992.1

    Status: REVIEWED

    Description
    Transcript Variant: This variant (1) represents the longest transcript and encodes the longest isoform (1).
    Source sequence(s)
    AC005033, AF284815, DQ378059
    Consensus CDS
    CCDS1953.1
    UniProtKB/Swiss-Prot
    D6W5J1, P58215, Q2EHP2, Q6IPL7, Q96RS1
    UniProtKB/TrEMBL
    E7END4
    Related
    ENSP00000264094.3, ENST00000264094.8
    Conserved Domains (2) summary
    smart00202
    Location:307 → 407
    SR; Scavenger receptor Cys-rich
    pfam01186
    Location:530 → 728
    Lysyl_oxidase; Lysyl oxidase

RefSeqs of Annotated Genomes: GCF_000001405.40-RS_2023_10

The following sections contain reference sequences that belong to a specific genome build. Explain

Reference GRCh38.p14 Primary Assembly

Genomic

  1. NC_000002.12 Reference GRCh38.p14 Primary Assembly

    Range
    74532258..74555702 complement
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_011533134.3 → XP_011531436.1  lysyl oxidase homolog 3 isoform X1

    See identical proteins and their annotated locations for XP_011531436.1

    UniProtKB/Swiss-Prot
    D6W5J1, P58215, Q2EHP2, Q6IPL7, Q96RS1
    UniProtKB/TrEMBL
    E7END4
    Related
    ENSP00000386696.1, ENST00000409549.5
    Conserved Domains (2) summary
    smart00202
    Location:307 → 407
    SR; Scavenger receptor Cys-rich
    pfam01186
    Location:530 → 728
    Lysyl_oxidase; Lysyl oxidase

  2. XM_024453176.2 → XP_024308944.1  lysyl oxidase homolog 3 isoform X1

    UniProtKB/Swiss-Prot
    D6W5J1, P58215, Q2EHP2, Q6IPL7, Q96RS1
    UniProtKB/TrEMBL
    E7END4
    Conserved Domains (2) summary
    smart00202
    Location:307 → 407
    SR; Scavenger receptor Cys-rich
    pfam01186
    Location:530 → 728
    Lysyl_oxidase; Lysyl oxidase

  3. XM_024453178.2 → XP_024308946.1  lysyl oxidase homolog 3 isoform X1

    UniProtKB/Swiss-Prot
    D6W5J1, P58215, Q2EHP2, Q6IPL7, Q96RS1
    UniProtKB/TrEMBL
    E7END4
    Conserved Domains (2) summary
    smart00202
    Location:307 → 407
    SR; Scavenger receptor Cys-rich
    pfam01186
    Location:530 → 728
    Lysyl_oxidase; Lysyl oxidase

  4. XM_024453177.2 → XP_024308945.1  lysyl oxidase homolog 3 isoform X1

    UniProtKB/Swiss-Prot
    D6W5J1, P58215, Q2EHP2, Q6IPL7, Q96RS1
    UniProtKB/TrEMBL
    E7END4
    Conserved Domains (2) summary
    smart00202
    Location:307 → 407
    SR; Scavenger receptor Cys-rich
    pfam01186
    Location:530 → 728
    Lysyl_oxidase; Lysyl oxidase

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060926.1 Alternate T2T-CHM13v2.0

    Range
    74540824..74564305 complement
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_054344221.1 → XP_054200196.1  lysyl oxidase homolog 3 isoform X1

    UniProtKB/Swiss-Prot
    D6W5J1, P58215, Q2EHP2, Q6IPL7, Q96RS1

  2. XM_054344222.1 → XP_054200197.1  lysyl oxidase homolog 3 isoform X1

    UniProtKB/Swiss-Prot
    D6W5J1, P58215, Q2EHP2, Q6IPL7, Q96RS1

  3. XM_054344219.1 → XP_054200194.1  lysyl oxidase homolog 3 isoform X1

    UniProtKB/Swiss-Prot
    D6W5J1, P58215, Q2EHP2, Q6IPL7, Q96RS1

  4. XM_054344220.1 → XP_054200195.1  lysyl oxidase homolog 3 isoform X1

    UniProtKB/Swiss-Prot
    D6W5J1, P58215, Q2EHP2, Q6IPL7, Q96RS1
Nucleotide Protein
Heading Accession and Version
Protein Accession Links
GenPept Link UniProtKB Link
P58215.1 GenPept UniProtKB/Swiss-Prot:P58215

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