LOXHD1
Basic information
Region (hg38): 18:46476972-46657220
Previous symbols: [ "DFNB77" ]
Links
Phenotypes
GenCC
Source:
- 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:
Condition | Inheritance | Intervention Categories | Intervention/Rationale | Manifestation Categories | References |
---|---|---|---|---|---|
Deafness, autosomal recessive 77 | AR | General | Genetic knowledge may be beneficial related to issues such as selection of optimal supportive care, informed medical decision-making, prognostic considerations, and avoidance of unnecessary testing | Audiologic/Otolaryngologic | 19732867; 23226338 |
ClinVar
This is a list of variants' phenotypes submitted to
- 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.
Effect | PathogenicP | Likely pathogenicLP | VUSVUS | Likely benignLB | BenignB | Sum |
---|---|---|---|---|---|---|
synonymous | 31 | 954 | 994 | |||
missense | 21 | 739 | 70 | 838 | ||
nonsense | 82 | 50 | 132 | |||
start loss | 1 | 1 | ||||
frameshift | 105 | 58 | 165 | |||
splice donor/acceptor (+/-2bp) | 14 | 90 | 105 | |||
Total | 202 | 219 | 772 | 1025 | 17 |
Highest pathogenic variant AF is 0.00103703
GnomAD
Source:
Gene | Type | Bio Type | Transcript | Coding Exons | Length |
---|---|---|---|---|---|
LOXHD1 | protein_coding | protein_coding | ENST00000300591 | 22 | 180062 |
pLI Probability LOF Intolerant | pRec Probability LOF Recessive | Individuals with no LOFs | Individuals with Homozygous LOFs | Individuals with Heterozygous LOFs | Defined | p |
---|---|---|---|---|---|---|
5.59e-26 | 0.0322 | 0 | 0 | 0 | 0 | 0.00 |
Z-Score | Observed | Expected | Observed/Expected | Mutation Rate | Total Possible in Transcript | |
---|---|---|---|---|---|---|
Missense | 1.38 | 577 | 678 | 0.851 | 0.0000418 | 7398 |
Missense in Polyphen | 351 | 432.11 | 0.8123 | 4862 | ||
Synonymous | 1.61 | 245 | 279 | 0.878 | 0.0000194 | 2061 |
Loss of Function | 1.47 | 46 | 58.1 | 0.792 | 0.00000314 | 621 |
LoF frequencies by population
Ethnicity | Sum of pLOFs | p |
---|---|---|
African & African-American | 0.00 | 0.00 |
Ashkenazi Jewish | 0.00 | 0.00 |
East Asian | 0.00 | 0.00 |
Finnish | 0.00 | 0.00 |
European (Non-Finnish) | 0.00 | 0.00 |
Middle Eastern | 0.00 | 0.00 |
South Asian | 0.00 | 0.00 |
Other | 0.00 | 0.00 |
dbNSFP
Source:
- 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
All | Recessive | Dominant | |
---|---|---|---|
Mendelian | High | High | High |
Primary Immunodeficiency | High | High | High |
Cancer | High | High | High |
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