LOXL4

lysyl oxidase like 4, the group of Scavenger receptor cysteine rich domain containing

Basic information

Region (hg38): 10:98247690-98268194

Links

ENSG00000138131 ∙ NCBI:84171 ∙ OMIM:607318 ∙ HGNC:17171 ∙ Uniprot:Q96JB6 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

Phenotypes

GenCC

Source: genCC

• skeletal dysplasia (Limited), mode of inheritance: AD

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the LOXL4 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the LOXL4 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						0
missense			83	3		86
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	83	3	0

Variants in LOXL4

This is a list of pathogenic ClinVar variants found in the LOXL4 region.

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

Position	Type	Phenotype	Significance	ClinVar
10-98248943-C-T		not specified	Uncertain significance (Sep 20, 2023)
10-98248951-C-G		not specified	Uncertain significance (Dec 04, 2024)
10-98248991-C-G		not specified	Uncertain significance (Jul 17, 2024)
10-98251079-T-C		not specified	Uncertain significance (Feb 02, 2024)
10-98251091-C-T		not specified	Uncertain significance (Jan 14, 2025)
10-98251112-C-T		not specified	Uncertain significance (Mar 15, 2024)
10-98251576-T-A		not specified	Uncertain significance (Dec 03, 2024)
10-98251598-T-C		not specified	Uncertain significance (Nov 22, 2022)
10-98251660-C-T		not specified	Uncertain significance (Oct 19, 2024)
10-98251682-A-G		not specified	Uncertain significance (Jun 05, 2024)
10-98251693-C-T		not specified	Uncertain significance (Sep 02, 2024)
10-98252358-G-A		not specified	Uncertain significance (Nov 16, 2021)
10-98253581-C-T		not specified	Uncertain significance (Mar 06, 2025)
10-98253611-G-A		not specified	Uncertain significance (Feb 27, 2024)
10-98253620-T-C		not specified	Uncertain significance (Dec 11, 2024)
10-98253641-G-A		not specified	Uncertain significance (Nov 18, 2022)
10-98253652-C-T		not specified	Uncertain significance (Feb 25, 2025)
10-98253659-C-T		not specified	Uncertain significance (Sep 07, 2022)
10-98253661-T-G		not specified	Uncertain significance (Jun 29, 2022)
10-98253665-G-A		not specified	Uncertain significance (Jan 03, 2024)
10-98253666-C-G		not specified	Uncertain significance (Nov 19, 2024)
10-98253673-A-G		not specified	Uncertain significance (Dec 28, 2022)
10-98253698-A-G		not specified	Uncertain significance (Feb 10, 2022)
10-98253710-G-A		not specified	Uncertain significance (Aug 08, 2023)
10-98253719-A-G		not specified	Uncertain significance (Mar 05, 2025)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
LOXL4	protein_coding	protein_coding	ENST00000260702	14	20561

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
9.19e-20	0.0295	125491	1	256	125748	0.00102

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.158	471	481	0.980	0.0000308	4914
Missense in Polyphen		196	196.97	0.99505		1922
Synonymous	0.889	174	190	0.918	0.0000116	1508
Loss of Function	0.929	33	39.3	0.840	0.00000178	407

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.00109	0.00108
Ashkenazi Jewish	0.000199	0.000198
East Asian	0.000435	0.000435
Finnish	0.0000927	0.0000924
European (Non-Finnish)	0.000603	0.000598
Middle Eastern	0.000435	0.000435
South Asian	0.00494	0.00491
Other	0.000326	0.000326

dbNSFP

Source: dbNSFP

• Function: FUNCTION: May modulate the formation of a collagenous extracellular matrix.
• Pathway: Simplified Interaction Map Between LOXL4 and Oxidative Stress 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: 0.165

Intolerance Scores

• loftool: 0.924
• rvis_EVS: -0.37
• rvis_percentile_EVS: 28.29

Haploinsufficiency Scores

• pHI: 0.281
• hipred: N
• hipred_score: 0.197
• ghis: 0.506

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.808

Gene Damage Prediction

	All	Recessive	Dominant
Mendelian	Medium	Medium	Medium
Primary Immunodeficiency	High	Medium	High
Cancer	High	High	High

Mouse Genome Informatics

• Gene name: Loxl4

Gene ontology

• Biological process: receptor-mediated endocytosis;peptidyl-lysine oxidation;collagen fibril organization
• Cellular component: extracellular space;membrane;receptor complex;extracellular exosome
• Molecular function: protein-lysine 6-oxidase activity;scavenger receptor activity;copper ion binding;protein binding