TMT1A

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

Basic information

Region (hg38): 12:50923471-50932510

Previous symbols: [ "METTL7A" ]

Links

ENSG00000185432 ∙ NCBI:25840 ∙ OMIM:618338 ∙ HGNC:24550 ∙ Uniprot:Q9H8H3 ∙ 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 TMT1A gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the TMT1A 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			11			11
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	11	0	0

Variants in TMT1A

This is a list of pathogenic ClinVar variants found in the TMT1A region.

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

Position	Type	Phenotype	Significance	ClinVar
12-50925232-T-C		not specified	Uncertain significance (Sep 14, 2022)
12-50925253-T-C		not specified	Uncertain significance (May 26, 2024)
12-50925262-T-C		not specified	Uncertain significance (Jul 14, 2021)
12-50925292-T-C		not specified	Uncertain significance (Apr 01, 2024)
12-50925334-C-G		not specified	Uncertain significance (Dec 02, 2022)
12-50925337-A-T		not specified	Uncertain significance (Oct 13, 2023)
12-50925400-G-A		not specified	Uncertain significance (Nov 22, 2022)
12-50925447-T-C		not specified	Uncertain significance (Dec 06, 2022)
12-50925510-C-T		not specified	Uncertain significance (Dec 21, 2023)
12-50929951-A-G		not specified	Uncertain significance (Jan 26, 2022)
12-50929968-T-C		not specified	Uncertain significance (Jan 03, 2024)
12-50929995-G-A		not specified	Uncertain significance (Nov 21, 2022)
12-50930052-G-A		not specified	Uncertain significance (Jun 18, 2024)
12-50930088-A-G		not specified	Uncertain significance (Apr 24, 2024)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
TMT1A	protein_coding	protein_coding	ENST00000548553	2	9046

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.000475	0.688	125690	0	56	125746	0.000223

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	-0.0479	134	132	1.01	0.00000676	1597
Missense in 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

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000478	0.000478
Ashkenazi Jewish	0.000199	0.000198
East Asian	0.000598	0.000598
Finnish	0.00	0.00
European (Non-Finnish)	0.000241	0.000237
Middle Eastern	0.000598	0.000598
South Asian	0.00	0.00
Other	0.000331	0.000326

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Probable methyltransferase. {ECO:0000250}.
• Pathway: miR-targeted genes in lymphocytes - TarBase;miR-targeted genes in muscle cell - TarBase;Neutrophil degranulation;Innate Immune System;Immune System (Consensus)

Recessive Scores

• pRec: 0.0968

Intolerance Scores

• loftool: 0.590
• rvis_EVS: 0.1
• rvis_percentile_EVS: 61.28

Haploinsufficiency Scores

• pHI: 0.0903
• hipred: N
• hipred_score: 0.146
• ghis: 0.542

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.877

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Mettl7a3

Gene ontology

• Biological process: methylation;neutrophil degranulation
• Cellular component: extracellular region;endoplasmic reticulum;lipid droplet;membrane;tertiary granule lumen
• Molecular function: methyltransferase activity