LOXHD1

lipoxygenase homology PLAT domains 1

Basic information

Region (hg38): 18:46476972-46657220

Previous symbols: [ "DFNB77" ]

Links

ENSG00000167210NCBI:125336OMIM:613072HGNC:26521Uniprot:Q8IVV2AlphaFoldGenCCjaxSfariGnomADPubmedClinVar

Phenotypes

GenCC

Source: genCC

  • autosomal recessive nonsyndromic hearing loss 77 (Strong), mode of inheritance: AR
  • hearing loss, autosomal recessive (Supportive), mode of inheritance: AR
  • Fuchs' endothelial dystrophy (Limited), mode of inheritance: AD
  • autosomal recessive nonsyndromic hearing loss 77 (Strong), mode of inheritance: AR
  • nonsyndromic genetic hearing loss (Definitive), mode of inheritance: AR
  • autosomal recessive nonsyndromic hearing loss 77 (Definitive), mode of inheritance: AR
  • autosomal recessive nonsyndromic hearing loss 77 (Definitive), mode of inheritance: AR

Clinical Genomic Database

Source: CGD

ConditionInheritanceIntervention CategoriesIntervention/Rationale Manifestation CategoriesReferences
Deafness, autosomal recessive 77ARGeneralGenetic knowledge may be beneficial related to issues such as selection of optimal supportive care, informed medical decision-making, prognostic considerations, and avoidance of unnecessary testingAudiologic/Otolaryngologic19732867; 23226338

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the LOXHD1 gene.

  • not_provided (2186 variants)
  • Autosomal_recessive_nonsyndromic_hearing_loss_77 (743 variants)
  • Inborn_genetic_diseases (359 variants)
  • not_specified (301 variants)
  • LOXHD1-related_disorder (66 variants)
  • Hearing_impairment (15 variants)
  • Rare_genetic_deafness (12 variants)
  • Nonsyndromic_genetic_hearing_loss (12 variants)
  • Hearing_loss,_autosomal_recessive (5 variants)
  • Autosomal_dominant_nonsyndromic_hearing_loss (4 variants)
  • Deafness (3 variants)
  • VATER_association (2 variants)
  • Variant_of_unknown_significance (1 variants)
  • concomitant_exotropia (1 variants)
  • Stickler_syndrome (1 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the LOXHD1 gene is commonly pathogenic or not. These statistics are base on transcript: NM_001384474.1. Only rare variants are included in the table.

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.

EffectPLPVUSLBBSum
synonymous
31
clinvar
954
clinvar
9
clinvar
994
missense
21
clinvar
739
clinvar
70
clinvar
8
clinvar
838
nonsense
82
clinvar
50
clinvar
132
start loss
1
1
frameshift
105
clinvar
58
clinvar
1
clinvar
1
clinvar
165
splice donor/acceptor (+/-2bp)
14
clinvar
90
clinvar
1
clinvar
105
Total 202 219 772 1025 17

Highest pathogenic variant AF is 0.00103703

Loading clinvar variants...

GnomAD

Source: gnomAD

GeneTypeBio TypeTranscript Coding Exons Length
LOXHD1protein_codingprotein_codingENST00000300591 22180062
pLI Probability
LOF Intolerant
pRec Probability
LOF Recessive
Individuals with
no LOFs
Individuals with
Homozygous LOFs
Individuals with
Heterozygous LOFs
Defined p
5.59e-260.032200000.00
Z-Score Observed Expected Observed/Expected Mutation Rate Total Possible in Transcript
Missense1.385776780.8510.00004187398
Missense in Polyphen351432.110.81234862
Synonymous1.612452790.8780.00001942061
Loss of Function1.474658.10.7920.00000314621

LoF frequencies by population

EthnicitySum of pLOFs p
African & African-American0.000.00
Ashkenazi Jewish0.000.00
East Asian0.000.00
Finnish0.000.00
European (Non-Finnish)0.000.00
Middle Eastern0.000.00
South Asian0.000.00
Other0.000.00

dbNSFP

Source: dbNSFP

Function
FUNCTION: Involved in hearing. Required for normal function of hair cells in the inner ear (By similarity). {ECO:0000250, ECO:0000269|PubMed:19732867}.;
Disease
DISEASE: Deafness, autosomal recessive, 77 (DFNB77) [MIM:613079]: A form of non-syndromic deafness characterized by preserved low- frequency hearing, and a trend toward mild to moderate mid- frequency and high-frequency hearing loss during childhood and adolescence. Hearing loss progresses to become moderate to severe at mid and high frequencies during adulthood. {ECO:0000269|PubMed:19732867}. Note=The disease is caused by mutations affecting the gene represented in this entry.;

Recessive Scores

pRec
0.100

Intolerance Scores

loftool
rvis_EVS
1.18
rvis_percentile_EVS
92.83

Haploinsufficiency Scores

pHI
0.176
hipred
hipred_score
ghis
0.401

Essentials

essential_gene_CRISPR
N
essential_gene_CRISPR2
N
essential_gene_gene_trap
N
gene_indispensability_pred
E
gene_indispensability_score
0.868

Gene Damage Prediction

AllRecessiveDominant
MendelianHighHighHigh
Primary ImmunodeficiencyHighHighHigh
CancerHighHighHigh

Mouse Genome Informatics

Gene name
Loxhd1
Phenotype
behavior/neurological phenotype (the observable actions or reactions of mammalian organisms that are manifested through development and lifespan); 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);

Gene ontology

Biological process
sensory perception of sound;oxidation-reduction process;cellular oxidant detoxification
Cellular component
stereocilium
Molecular function
catalase activity;heme binding