LRTOMT

leucine rich transmembrane and O-methyltransferase domain containing, the group of Cilia and flagella associated

Basic information

Region (hg38): 11:72080330-72110782

Previous symbols: [ "LRRC51", "DFNB63" ]

Links

ENSG00000284922 ∙ NCBI:220074 ∙ OMIM:612414 ∙ HGNC:25033 ∙ ∙ ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

Phenotypes

GenCC

Source: genCC

• autosomal recessive nonsyndromic hearing loss 63 (Strong), mode of inheritance: AR
• autosomal recessive nonsyndromic hearing loss 63 (Strong), mode of inheritance: AR
• autosomal recessive nonsyndromic hearing loss 63 (Moderate), mode of inheritance: AR
• hearing loss, autosomal recessive (Supportive), mode of inheritance: AR
• autosomal recessive nonsyndromic hearing loss 63 (Definitive), mode of inheritance: AR

Clinical Genomic Database

Source: CGD

Condition	Inheritance	Intervention Categories	Intervention/Rationale	Manifestation Categories	References
Deafness, autosomal recessive 63	AR	Audiologic/Otolaryngologic	Early recognition and treatment of hearing impairment may improve outcomes, including speech and language development	Audiologic/Otolaryngologic	17166180; 17066295; 18953341; 18794526

ClinVar

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

• Autosomal recessive nonsyndromic hearing loss 63 (32 variants)
• Nonsyndromic Hearing Loss, Recessive (8 variants)
• not provided (6 variants)
• Inborn genetic diseases (4 variants)
• not specified (3 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the LRTOMT 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						0
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding	1		38	6	1	46
Total	1	0	38	6	1

Highest pathogenic variant AF is 0.0000132

Variants in LRTOMT

This is a list of pathogenic ClinVar variants found in the LRTOMT 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		Nonsyndromic Hearing Loss, 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		Nonsyndromic Hearing Loss, 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 22, 2023)

GnomAD

Source: gnomAD

dbNSFP

Source: dbNSFP