LRRC51
leucine rich repeat containing 51
Basic information
Region (hg38): 11:72080337-72096895
Links
Phenotypes
GenCC
Source:
No genCC data.
ClinVar
This is a list of variants' phenotypes submitted to
- not_provided (21 variants)
- Autosomal_recessive_nonsyndromic_hearing_loss_63 (10 variants)
- LRTOMT-related_disorder (6 variants)
- not_specified (4 variants)
- Hearing_loss,_autosomal_recessive (2 variants)
- Rare_genetic_deafness (1 variants)
Variants pathogenicity by type
Statistics on ClinVar variants can assist in determining whether a specific variant type in the LRRC51 gene is commonly pathogenic or not. These statistics are base on transcript: NM_000145309.6. 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 | 8 | |||||
| missense | 16 | |||||
| nonsense | 1 | |||||
| start loss | 0 | |||||
| frameshift | 4 | |||||
| splice donor/acceptor (+/-2bp) | 1 | |||||
| Total | 1 | 2 | 14 | 12 | 1 |
Highest pathogenic variant AF is 0.000004337298
Loading clinvar variants...
GnomAD
Source:
| Gene | Type | Bio Type | Transcript | Coding Exons | Length |
|---|---|---|---|---|---|
| LRRC51 | protein_coding | protein_coding | ENST00000435085 | 5 | 30447 |
| pLI Probability LOF Intolerant | pRec Probability LOF Recessive | Individuals with no LOFs | Individuals with Homozygous LOFs | Individuals with Heterozygous LOFs | Defined | p |
|---|---|---|---|---|---|---|
| 0.0000700 | 0.752 | 125465 | 0 | 2 | 125467 | 0.00000797 |
| Z-Score | Observed | Expected | Observed/Expected | Mutation Rate | Total Possible in Transcript | |
|---|---|---|---|---|---|---|
| Missense | 1.09 | 128 | 168 | 0.763 | 0.0000109 | 1792 |
| Missense in Polyphen | 52 | 74.067 | 0.70206 | 852 | ||
| Synonymous | 2.23 | 44 | 67.3 | 0.654 | 0.00000348 | 668 |
| Loss of Function | 1.07 | 8 | 12.0 | 0.666 | 8.44e-7 | 126 |
LoF frequencies by population
| Ethnicity | Sum of pLOFs | p |
|---|---|---|
| African & African-American | 0.0000615 | 0.0000615 |
| Ashkenazi Jewish | 0.00 | 0.00 |
| East Asian | 0.00 | 0.00 |
| Finnish | 0.00 | 0.00 |
| European (Non-Finnish) | 0.00000882 | 0.00000882 |
| Middle Eastern | 0.00 | 0.00 |
| South Asian | 0.00 | 0.00 |
| Other | 0.00 | 0.00 |
dbNSFP
Source:
- Function
- FUNCTION: Catalyzes the O-methylation, and thereby the inactivation, of catecholamine neurotransmitters and catechol hormones (By similarity). Required for auditory function (PubMed:18794526). Component of the cochlear hair cell's mechanotransduction (MET) machinery. Involved in the assembly of the asymmetric tip-link MET complex. Required for transportation of TMC1 and TMC2 proteins into the mechanically sensitive stereocilia of the hair cells. The function in MET is independent of the enzymatic activity (By similarity). {ECO:0000250|UniProtKB:A1Y9I9, ECO:0000250|UniProtKB:P21964, ECO:0000269|PubMed:18794526}.;
- Disease
- DISEASE: Deafness, autosomal recessive, 63 (DFNB63) [MIM:611451]: A form of non-syndromic sensorineural hearing loss. Sensorineural deafness results from damage to the neural receptors of the inner ear, the nerve pathways to the brain, or the area of the brain that receives sound information. {ECO:0000269|PubMed:18794526, ECO:0000269|PubMed:18953341, ECO:0000269|PubMed:28281779}. Note=The disease is caused by mutations affecting the gene represented in this entry.;
- Pathway
- Dopaminergic synapse - Homo sapiens (human);Steroid hormone biosynthesis - Homo sapiens (human);Tyrosine metabolism - Homo sapiens (human);Neuronal System;Enzymatic degradation of dopamine by COMT;Dopamine clearance from the synaptic cleft;Neurotransmitter clearance;Transmission across Chemical Synapses;noradrenaline and adrenaline degradation
(Consensus)
Recessive Scores
- pRec
- 0.0891
Intolerance Scores
- loftool
- 0.480
- rvis_EVS
- 0.33
- rvis_percentile_EVS
- 73.54
Haploinsufficiency Scores
- pHI
- 0.105
- hipred
- N
- hipred_score
- 0.198
- ghis
- 0.438
Essentials
- essential_gene_CRISPR
- N
- essential_gene_CRISPR2
- N
- essential_gene_gene_trap
- N
- gene_indispensability_pred
- N
- gene_indispensability_score
- 0.231
Gene Damage Prediction
| All | Recessive | Dominant | |
|---|---|---|---|
| Mendelian | Medium | Medium | Medium |
| Primary Immunodeficiency | Medium | Medium | Medium |
| Cancer | Medium | Medium | Medium |
Mouse Genome Informatics
- Gene name
- Tomt
- Phenotype
- growth/size/body region 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); hearing/vestibular/ear phenotype; behavior/neurological phenotype (the observable actions or reactions of mammalian organisms that are manifested through development and lifespan);
Gene ontology
- Biological process
- sensory perception of sound;methylation;developmental process;neurotransmitter catabolic process;dopamine metabolic process;catecholamine catabolic process;auditory receptor cell development
- Cellular component
- cellular_component;endoplasmic reticulum;plasma membrane;integral component of membrane
- Molecular function
- catechol O-methyltransferase activity;L-dopa O-methyltransferase activity;orcinol O-methyltransferase activity