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

    Gene ID: 84695, updated on 2-Nov-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_2024_08 current GRCh38.p14 (GCF_000001405.40) 2 NC_000002.12 (74532258..74555702, complement)
    RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 2 NC_060926.1 (74540824..74564305, complement)
    RS_2024_09 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 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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    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
    		Compare labs

    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 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 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_2024_08

    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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