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

Summary

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

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_000002.12 Genomic Context describing neighboring genes

Genomic regions, transcripts, and products

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Go to reference sequence details

Genomic Sequence:

Go to nucleotide: Graphics FASTA GenBank

Expression

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See details

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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GeneRIFs: Gene References Into Functions

What's a GeneRIF?

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.
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.
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.
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.
LOXL3 Silencing Affected Cell Adhesion and Invasion in U87MG Glioma Cells.
Title: LOXL3 Silencing Affected Cell Adhesion and Invasion in U87MG Glioma Cells.
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.
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.
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.
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.
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)

Interactions

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Products	Interactant	Other Gene	Complex	Source	Pubs	Description

General gene information

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Markers

Loxl3 (e-PCR), detects polymorphism
- UniSTS:507975

BCD2341 (e-PCR)
- UniSTS:82012

LOXL3__6411 (e-PCR)
- UniSTS:466274

RH15974 (e-PCR)
- UniSTS:3969

A006U29 (e-PCR)
- UniSTS:16002

D2S1958E (e-PCR)
- UniSTS:153730

RH125632 (e-PCR)
- UniSTS:163230

MARC_4349-4350:991938479:1 (e-PCR)
- UniSTS:231082

MARC_4349-4350:996679540:1 (e-PCR)
- UniSTS:231082

RH124140 (e-PCR)
- UniSTS:161004

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

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

NG_033047.1 RefSeqGene

Range

4994..26678

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GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

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
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
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

NC_000002.12 Reference GRCh38.p14 Primary Assembly

Range

74532258..74555702 complement

Download

GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

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
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
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
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