LRRC51

leucine rich repeat containing 51

Basic information

Region (hg38): 11:72080337-72096895

Links

ENSG00000184154 ∙ NCBI:120356739 ∙ ∙ HGNC:55526 ∙ Uniprot:Q96E66 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

Phenotypes

GenCC

Source: genCC

No genCC data.

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the LRRC51 gene.

• Autosomal recessive nonsyndromic hearing loss 63 (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.

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			3	2		5
missense			6	6	1	13
nonsense						0
start loss						0
frameshift	1		2			3
inframe indel						0
splice donor/acceptor (+/-2bp)			1			1
splice region		1	1			2
non coding			8	8	9	25
Total	1	0	20	16	10

Highest pathogenic variant AF is 0.0000132

Variants in LRRC51

This is a list of pathogenic ClinVar variants found in the LRRC51 region.

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

Position	Type	Phenotype	Significance	ClinVar
11-72080391-C-T		Autosomal recessive nonsyndromic hearing loss 63	Uncertain significance (Jan 13, 2018)
11-72080445-C-A		Autosomal recessive nonsyndromic hearing loss 63	Uncertain significance (Jan 12, 2018)
11-72080446-C-T		Autosomal recessive nonsyndromic hearing loss 63	Uncertain significance (Jan 15, 2018)
11-72080464-G-A		Autosomal recessive nonsyndromic hearing loss 63	Likely benign (Jan 12, 2018)
11-72080482-T-G		Autosomal recessive nonsyndromic hearing loss 63	Uncertain significance (Jan 13, 2018)
11-72080502-A-G		Autosomal recessive nonsyndromic hearing loss 63	Uncertain significance (Jan 12, 2018)
11-72080504-C-G		Autosomal recessive nonsyndromic hearing loss 63	Uncertain significance (Apr 27, 2017)
11-72080605-G-A		Hearing loss, autosomal recessive	Conflicting classifications of pathogenicity (Apr 01, 2023)
11-72080653-G-A		Autosomal recessive nonsyndromic hearing loss 63	Uncertain significance (Jan 13, 2018)
11-72080681-T-A		Hearing loss, autosomal recessive	Uncertain significance (Jun 14, 2016)
11-72080726-G-T		Autosomal recessive nonsyndromic hearing loss 63	Uncertain significance (Jan 13, 2018)
11-72080754-A-G		Autosomal recessive nonsyndromic hearing loss 63	Uncertain significance (Jan 12, 2018)
11-72080785-T-C		Autosomal recessive nonsyndromic hearing loss 63	Uncertain significance (Jan 13, 2018)
11-72080798-G-A		Autosomal recessive nonsyndromic hearing loss 63	Uncertain significance (Jan 13, 2018)
11-72080828-T-C		Autosomal recessive nonsyndromic hearing loss 63	Uncertain significance (Jan 13, 2018)
11-72080863-G-A		Autosomal recessive nonsyndromic hearing loss 63	Uncertain significance (Jan 13, 2018)
11-72080886-G-T		Autosomal recessive nonsyndromic hearing loss 63	Uncertain significance (Jan 01, 2019)
11-72080890-G-A		Autosomal recessive nonsyndromic hearing loss 63	Uncertain significance (Jan 12, 2018)
11-72088058-G-A			Benign (Nov 12, 2018)
11-72088556-C-T			Likely benign (Apr 24, 2019)
11-72088622-A-C			Benign (Nov 12, 2018)
11-72088834-A-G			Likely benign (Feb 28, 2019)
11-72088919-T-C			Benign (Dec 17, 2018)
11-72089120-G-A			Likely benign (Jan 01, 2024)
11-72089135-T-C		LRTOMT-related disorder	Likely benign (Sep 16, 2021)

GnomAD

Source: gnomAD

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: dbNSFP

• 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