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LRTOMT

Synonyms
CFAP111, DFNB63, LRRC51, LRRC51-TOMT, TOMT
External resources
Summary
This gene has evolved in primates as a fusion of two ancestral neighboring genes, Lrrc51 and Tomt, which exist as two independent genes in rodents. The fusion gene contains some shared exons, but encodes structurally unrelated proteins, LRTOMT1 and LRTOMT2. Those variants that utilize the more centromere-proximal 3' terminal exon (short transcript form) encode LRTOMT1, while those variants that use a more centromere-distal 3' terminal exon (long transcript form) encode the LRTOMT2 protein. There is a small region within one of the exons of this gene that contains overlapping alternate reading frames for both LRTOMT1 and LRTOMT2. LRTOMT1 shares similarity with the protein encoded by mouse Lrrc51, while LRTOMT2 shares similarity with the protein encoded by mouse Tomt. Alternative splicing results in multiple transcript variants, encoding different isoforms of both LRTOMT1 and LRTOMT2. The LRTOMT1 protein is a leucine-rich repeat-containing protein, while the LRTOMT2 protein is a catechol-O-methyltransferase that catalyzes the transfer of a methyl group from S-adenosyl-L-methionine to a hydroxyl group of catechols and is essential for auditory and vestibular function. Mutations in this gene have been associated with nonsyndromic deafness.

Variant counts

The variants found in rare patients tested by 3billion are classified and counted according to ACMG guidelines. The variants with over 5% variant frequency in population genome databases ( gnomAD, dbSNP, etc) are excluded.

Pathogenic
25
Likely pathogenic
13
VUS
4,619
Likely benign
5,235
Benign
180

Patient phenotypes

Proportions of phenotypes among 37 patients carrying pathogenic or likely pathogenic variants on LRTOMT gene are displayed below.

Phenotype class
Patients in 3billion (%)
Abnormality of the nervous system
32.4%
Abnormality of the ear
27%
Abnormality of head or neck
18.9%
Abnormality of the eye
16.2%
Abnormality of the musculoskeletal system
16.2%
Abnormality of the cardiovascular system
10.8%
Abnormality of the digestive system
10.8%
Abnormality of the genitourinary system
10.8%
Growth abnormality
10.8%
Abnormality of the integument
8.1%
Abnormality of the endocrine system
5.4%
Abnormality of limbs
2.7%
Abnormality of prenatal development or birth
2.7%
Abnormality of the respiratory system
2.7%
Neoplasm
2.7%
Abnormal cellular phenotype
0%
Abnormality of blood and blood-forming tissues
0%
Abnormality of metabolism homeostasis
0%
Abnormality of the breast
0%
Abnormality of the immune system
0%
Abnormality of the thoracic cavity
0%
Abnormality of the voice
0%
Constitutional symptom
0%

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