TOMT

protein-coding

transmembrane O-methyltransferase

Gene summary

This gene encodes 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. Readthrough transcription is observed across this gene and the adjacent leucine-rich repeat containing 51 gene. A third locus (GeneID:220074) is defined to represent the readthrough transcripts. [provided by RefSeq, Feb 2021]

MANE transcript

NM_001393500.2

Inheritance

—

ClinVar variants

P:29U:84B:30

Top phenotype

Autosomal recessive nonsyndromic hearing loss 63

Max pathogenic AF

—

Genomic locus

chr11:72,105,924-72,109,596

External References & Databases

Ensembl (ENSG00000284844)

NCBI Gene (120356740)

Transcript & Mutation Effects

hg38 • Region Span ~3.7 kb

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GenCC Phenotypes & Disease Associations

Curated gene-disease validity assertions and inheritance patterns

No GenCC data available for this gene.

ClinVar Associated Diseases & Phenotypes

Reported disease conditions connected to TOMT variants in ClinVar

7 Conditions Cataloged

not providedTotal: 79

Autosomal recessive nonsyndromic hearing loss 63Total: 54

Inborn genetic diseasesTotal: 52

not specifiedTotal: 21

LRTOMT-related disorderTotal: 7

Rare genetic deafnessTotal: 2

Hearing impairmentTotal: 1

ClinVar Variants & Pathogenicity by Type

Statistics based on transcript NM_001393500.2. Only rare variants are included.

We include only reliable ClinVar variants with their consequences to MANE Select, MANE Plus Clinical transcripts, or transcripts with TSL equal to 1. Click a count to filter the variants table below.

Slight differences between displayed counts and ClinVar may occur due to a different transcript/consequence chosen by our variant effect predictor, or because we classify Benign/Likely benign as Likely benign and Pathogenic/Likely pathogenic as Likely pathogenic.

Effect	PathogenicP	Likely pathogenicLP	VUS	Likely benignLB	BenignB	Sum
synonymous		1 clinvar	4 clinvar	21 clinvar		26
missense	2 clinvar	7 clinvar	80 clinvar	8 clinvar	1 clinvar	98
nonsense	6 clinvar	2 clinvar				8
start loss	1 clinvar					1
frameshift	4 clinvar	4 clinvar				8
splice donor/acceptor (+/-2bp)	2 clinvar					2
Total	15	14	84	29	1	143

Highest pathogenic variant AF is 0.00004467789

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Transcript Catalog

Annotated transcript isoforms across RefSeq and Ensembl databases

Showing 4 of 5 transcripts

Transcript ID	Source	Protein ID	Coding Exons	MANE Status
NM_001393500.2	RefSeq	NP_001380429.1	3	MANE Select
ENST00000541899.3	Ensembl	ENSP00000494667.1	3	MANE Select
ENST00000864603.1	Ensembl	ENSP00000534662.1	3	Standard
ENST00000864603.2	Ensembl	ENSP00000534662.1	3	Standard