TOMT

transmembrane O-methyltransferase

Basic information

Region (hg38): 11:72105924-72109596

Links

ENSG00000284844 ∙ NCBI:120356740 ∙ ∙ HGNC:55527 ∙ Uniprot:Q8WZ04 ∙ 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 TOMT gene.

• Autosomal recessive nonsyndromic hearing loss 63 (3 variants)
• not provided (2 variants)
• Inborn genetic diseases (1 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 TOMT 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	13		16
missense	1		59	2	1	63
nonsense	1		1			2
start loss	1					1
frameshift	1	1				2
inframe indel			1			1
splice donor/acceptor (+/-2bp)	1					1
splice region		1				1
non coding			11	3	1	15
Total	5	1	75	18	2

Highest pathogenic variant AF is 0.0000131

Variants in TOMT

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

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

Position	Type	Phenotype	Significance	ClinVar
11-72105937-G-A		Inborn genetic diseases	Likely benign (Apr 20, 2024)
11-72105946-GGGACCATGTCCCCT-G			Pathogenic (Dec 05, 2021)
11-72105969-A-G		not specified	Likely benign (Aug 21, 2015)
11-72105970-T-C		not specified	Likely benign (Aug 24, 2015)
11-72106006-C-T		Autosomal recessive nonsyndromic hearing loss 63	Uncertain significance (Jan 03, 2022)
11-72106007-G-A			Uncertain significance (Oct 28, 2022)
11-72106012-C-T		Inborn genetic diseases	Uncertain significance (Nov 17, 2022)
11-72106013-G-A		Autosomal recessive nonsyndromic hearing loss 63	Uncertain significance (Jan 03, 2022)
11-72106017-C-G		not specified	Uncertain significance (Mar 31, 2015)
11-72106024-C-T		Autosomal recessive nonsyndromic hearing loss 63	Conflicting classifications of pathogenicity (Dec 23, 2021)
11-72106025-G-A			Uncertain significance (Jan 19, 2022)
11-72106031-T-C		Autosomal recessive nonsyndromic hearing loss 63	Uncertain significance (May 13, 2021)
11-72106036-C-T		LRTOMT-related disorder	Likely benign (Feb 16, 2023)
11-72106040-C-T		not specified	Likely benign (Aug 24, 2015)
11-72106041-G-A		Autosomal recessive nonsyndromic hearing loss 63 • LRTOMT-related disorder	Uncertain significance (Mar 11, 2023)
11-72106043-T-G		not specified • Inborn genetic diseases	Uncertain significance (Jun 26, 2023)
11-72106048-C-G		not specified • Autosomal recessive nonsyndromic hearing loss 63	Uncertain significance (Jan 12, 2018)
11-72106051-C-T		Autosomal recessive nonsyndromic hearing loss 63	Pathogenic (May 06, 2021)
11-72106052-G-A		Inborn genetic diseases	Uncertain significance (Aug 04, 2021)
11-72106056-C-T		not specified	Likely benign (Nov 13, 2016)
11-72106061-G-A		Autosomal recessive nonsyndromic hearing loss 63 • not specified • Inborn genetic diseases	Conflicting classifications of pathogenicity (Sep 22, 2023)
11-72106074-A-G		not specified • Autosomal recessive nonsyndromic hearing loss 63	Conflicting classifications of pathogenicity (Apr 06, 2023)
11-72106082-G-A			Uncertain significance (Sep 13, 2022)
11-72106094-G-A		Autosomal recessive nonsyndromic hearing loss 63 • Rare genetic deafness	Pathogenic (Jul 29, 2022)
11-72106101-C-G		Hearing impairment	Uncertain significance (Oct 05, 2022)

GnomAD

Source: gnomAD

dbNSFP

Source: dbNSFP