TMT1B

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

Basic information

Region (hg38): 12:55681736-55684611

Previous symbols: [ "METTL7B" ]

Links

ENSG00000170439 ∙ NCBI:196410 ∙ ∙ HGNC:28276 ∙ Uniprot:Q6UX53 ∙ 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 TMT1B gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the TMT1B 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						0
missense			22	1	3	26
nonsense					1	1
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region					1	1
non coding						0
Total	0	0	22	1	4

Variants in TMT1B

This is a list of pathogenic ClinVar variants found in the TMT1B region.

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

Position	Type	Phenotype	Significance	ClinVar
12-55681788-G-A		not specified	Uncertain significance (Jan 04, 2024)
12-55681815-C-T			Benign (Jul 27, 2018)
12-55681822-C-T		not specified	Uncertain significance (Oct 03, 2022)
12-55681908-G-C		not specified	Uncertain significance (Jul 13, 2022)
12-55681951-C-A		not specified	Uncertain significance (Jan 20, 2023)
12-55681953-G-A		not specified	Uncertain significance (Jan 20, 2023)
12-55681981-A-T		not specified	Uncertain significance (Nov 19, 2022)
12-55681998-G-A		not specified	Uncertain significance (Apr 07, 2022)
12-55682016-T-C		not specified	Uncertain significance (Aug 11, 2022)
12-55682049-C-A		not specified	Uncertain significance (Aug 26, 2022)
12-55682056-C-T			Benign (Jan 01, 2023)
12-55682064-G-A		not specified	Uncertain significance (Apr 25, 2022)
12-55682116-G-T		not specified	Uncertain significance (Apr 08, 2024)
12-55682127-G-A		not specified	Uncertain significance (Mar 14, 2023)
12-55682131-C-A			Benign (Jan 10, 2019)
12-55682149-A-T		not specified	Uncertain significance (Dec 08, 2022)
12-55682251-C-T		not specified	Uncertain significance (Oct 12, 2021)
12-55683815-A-T			Benign (Jul 27, 2018)
12-55683816-G-A		not specified	Uncertain significance (Aug 31, 2022)
12-55683870-A-G		not specified	Uncertain significance (Dec 13, 2022)
12-55683871-T-A		not specified	Uncertain significance (Jun 01, 2023)
12-55683888-G-A		not specified	Uncertain significance (Jun 03, 2022)
12-55683907-T-C		not specified	Uncertain significance (Jul 09, 2021)
12-55683946-A-G		not specified	Uncertain significance (Feb 28, 2023)
12-55683969-G-A		not specified	Uncertain significance (Feb 13, 2024)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
TMT1B	protein_coding	protein_coding	ENST00000394252	2	3066

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.0662	0.877	125714	0	33	125747	0.000131

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	-0.172	140	134	1.04	0.00000704	1582
Missense in 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

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000797	0.000796
Ashkenazi Jewish	0.000198	0.000198
East Asian	0.000665	0.000598
Finnish	0.00	0.00
European (Non-Finnish)	0.0000439	0.0000439
Middle Eastern	0.000665	0.000598
South Asian	0.00	0.00
Other	0.000178	0.000163

dbNSFP

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

Haploinsufficiency Scores

• pHI: 0.0790
• hipred: N
• hipred_score: 0.281

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.288

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Mettl7b
• Phenotype: homeostasis/metabolism phenotype; integument phenotype (the observable morphological and physiological characteristics of the skin and its associated structures, such as the hair, nails, sweat glands, sebaceous glands and other secretory glands that are manifested through development and lifespan); pigmentation phenotype; behavior/neurological phenotype (the observable actions or reactions of mammalian organisms that are manifested through development and lifespan)

Gene ontology

• Biological process: methylation
• Molecular function: methyltransferase activity