TMT1B

protein-coding

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

Gene summary

Enables thiol S-methyltransferase activity. Predicted to be involved in methylation. Predicted to be located in cytosol; endoplasmic reticulum membrane; and lipid droplet. [provided by Alliance of Genome Resources, Jul 2025]

Previous symbols:

METTL7B

MANE transcript

NM_152637.3

Inheritance

—

ClinVar variants

U:46B:7

Top phenotype

Congenital muscular dystrophy due to integrin alpha-7 deficiency

gnomAD constraint

pLI —, LoF o/e 0.38

Max pathogenic AF

—

Genomic locus

chr12:55,681,736-55,684,611

External References & Databases

Ensembl (ENSG00000170439)

Transcript & Mutation Effects

hg38 • Region Span ~2.9 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 TMT1B variants in ClinVar

3 Conditions Cataloged

not specifiedTotal: 44

not providedTotal: 5

Congenital muscular dystrophy due to integrin alpha-7 deficiencyTotal: 1

ClinVar Variants & Pathogenicity by Type

Statistics based on transcript NM_152637.3. 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			3 clinvar		1 clinvar	4
missense			43 clinvar	2 clinvar	3 clinvar	48
nonsense					1 clinvar	1
start loss						0
frameshift						0
splice donor/acceptor (+/-2bp)						0
Total	0	0	46	2	5	53

Loading ClinVar variants...

Transcript Catalog

Annotated transcript isoforms across RefSeq and Ensembl databases

Showing 4 of 6 transcripts

Transcript ID	Source	Protein ID	Coding Exons	MANE Status
NM_152637.3	RefSeq	NP_689850.2	2	MANE Select
ENST00000394252.4	Ensembl	ENSP00000377796.3	2	MANE Select
ENST00001117134.1	Ensembl	ENSP00000786939.1	2	Standard
ENST00001117135.1	Ensembl	ENSP00000786940.1	2	Standard

Gene Ontology (GO) Annotations & Pathways

Biological processes, molecular functions, cellular components and pathways

Biological Process

methylation

Molecular Function

methyltransferase activity

gnomAD Constraint

Source: gnomAD

Gene type: protein_coding
Transcript type: protein_coding
Transcript: ENST00000394252
Coding exons: 2
Length: 3066
Individuals with no LoFs: 125714
Homozygous LoFs: 0
Heterozygous LoFs: 33
Defined: 125747
p: 0.000131

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible
Missense	-0.172	140	134	1.04	0.00000704	1582
Missense (PolyPhen)		36	30.997	1.1614		380
Synonymous	-0.0813	56	55.2	1.01	0.00000285	498
Loss of Function	1.61	3	7.87	0.381	3.38e-7	88

Population LoF Frequency

Population	CAF	p-value	Status
African	0.00074	0.00074	rare
Latino/Admixed American	0.000058	0.000058	rare
Ashkenazi Jewish	0.00020	0.00020	rare
East Asian	0.00066	0.00060	rare
Finnish	0	0.0	absent
European (Non-Finnish)	0.000044	0.000044	rare
South Asian	0	0.0	absent
Other	0.00018	0.00016	rare

dbNSFP Gene Annotations

Source: dbNSFP

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

Recessive Scores

pRec: 0.109

Intolerance Scores

LoFtool: 0.426
RVIS EVS: 1.11
RVIS percentile EVS: 91.99

Essentials

Essential (CRISPR): N
Essential (CRISPR2): N
Essential (gene trap): N
Indispensability pred.: N
Indispensability score: 0.288

Gene Damage Prediction

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