TMT1A

protein-coding

thiol methyltransferase 1A, the group of 7BS small molecule methyltransferases

Gene summary

Enables mRNA m(6)A methyltransferase activity and thiol S-methyltransferase activity. Involved in lncRNA processing; odontogenesis; and osteoblast differentiation. Located in endoplasmic reticulum and lipid droplet. [provided by Alliance of Genome Resources, Jul 2025]

Previous symbols:

METTL7A

MANE transcript

NM_014033.4

Inheritance

—

ClinVar variants

U:42B:1

Top phenotype

—

gnomAD constraint

pLI —, LoF o/e 0.7

Max pathogenic AF

—

Genomic locus

chr12:50,923,472-50,932,510

External References & Databases

Ensembl (ENSG00000185432)

Transcript & Mutation Effects

hg38 • Region Span ~9.0 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 TMT1A variants in ClinVar

1 Conditions Cataloged

not specifiedTotal: 38

ClinVar Variants & Pathogenicity by Type

Statistics based on transcript NM_014033.4. 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						0
missense			38 clinvar	1 clinvar		39
nonsense			1 clinvar			1
start loss						0
frameshift						0
splice donor/acceptor (+/-2bp)			3 clinvar			3
Total	0	0	42	1	0	43

Loading ClinVar variants...

Transcript Catalog

Annotated transcript isoforms across RefSeq and Ensembl databases

Showing 4 of 14 transcripts

Transcript ID	Source	Protein ID	Coding Exons	MANE Status
NM_014033.4	RefSeq	NP_054752.3	2	MANE Select
ENST00000332160.5	Ensembl	ENSP00000331787.4	2	MANE Select
ENST00000547104.1	Ensembl	ENSP00000447542.1	2	Standard
ENST00000548553.1	Ensembl	ENSP00000448785.1	2	Standard

Gene Ontology (GO) Annotations & Pathways

Biological processes, molecular functions, cellular components and pathways

Pathways ConsensusPathDB

miR-targeted genes in lymphocytes - TarBase
miR-targeted genes in muscle cell - TarBase
Neutrophil degranulation
Innate Immune System
Immune System

Biological Process

methylation
neutrophil degranulation

Molecular Function

methyltransferase activity

Cellular Component

extracellular region
endoplasmic reticulum
lipid droplet
membrane
tertiary granule lumen

gnomAD Constraint

Source: gnomAD

Gene type: protein_coding
Transcript type: protein_coding
Transcript: ENST00000548553
Coding exons: 2
Length: 9046
Individuals with no LoFs: 125690
Homozygous LoFs: 0
Heterozygous LoFs: 56
Defined: 125746
p: 0.000223

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible
Missense	-0.0479	134	132	1.01	0.00000676	1597
Missense (PolyPhen)		26	26.622	0.97663		346
Synonymous	-0.389	59	55.3	1.07	0.00000266	485
Loss of Function	0.807	6	8.55	0.702	4.21e-7	93

Population LoF Frequency

Population	CAF	p-value	Status
African	0.00012	0.00012	rare
Latino/Admixed American	0.00036	0.00035	rare
Ashkenazi Jewish	0.00020	0.00020	rare
East Asian	0.00060	0.00060	rare
Finnish	0	0.0	absent
European (Non-Finnish)	0.00024	0.00024	rare
South Asian	0	0.0	absent
Other	0.00033	0.00033	rare

dbNSFP Gene Annotations

Source: dbNSFP

Function: FUNCTION: Probable methyltransferase. {ECO:0000250}.;

Recessive Scores

pRec: 0.0968

Intolerance Scores

LoFtool: 0.590
RVIS EVS: 0.1
RVIS percentile EVS: 61.28

Essentials

Essential (CRISPR): N
Essential (CRISPR2): N
Indispensability pred.: E
Indispensability score: 0.877

Gene Damage Prediction

	All	Recessive	Dominant
Mendelian	Medium	Medium	Medium
Primary Immunodeficiency	Medium	Medium	Medium
Cancer	Medium	Medium	Medium