TFB1M

transcription factor B1, mitochondrial, the group of 7BS N6-adenosine DNA/RNA methyltransferases

Basic information

Region (hg38): 6:155256134-155314493

Links

ENSG00000029639 ∙ NCBI:51106 ∙ OMIM:607033 ∙ HGNC:17037 ∙ Uniprot:Q8WVM0 ∙ 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 TFB1M gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the TFB1M 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					1	1
missense			15	2		17
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding			20		1	21
Total	0	0	35	2	2

Variants in TFB1M

This is a list of pathogenic ClinVar variants found in the TFB1M region.

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

Position	Type	Phenotype	Significance	ClinVar
6-155256572-C-A		not specified	Uncertain significance (Mar 29, 2022)
6-155256604-G-A		not specified	Uncertain significance (Oct 19, 2021)
6-155256705-G-C		not specified	Uncertain significance (Jan 23, 2024)
6-155256731-T-A			Benign (Jul 17, 2018)
6-155256859-C-T		not specified	Uncertain significance (Feb 13, 2024)
6-155256888-C-T		not specified	Uncertain significance (Jun 29, 2023)
6-155256903-G-A		not specified	Uncertain significance (Nov 17, 2023)
6-155256970-C-T		not specified	Uncertain significance (Jul 15, 2021)
6-155256998-T-A		not specified	Uncertain significance (Jun 24, 2022)
6-155257108-A-T		not specified	Uncertain significance (Dec 14, 2021)
6-155257110-G-A		not specified	Uncertain significance (Jan 08, 2024)
6-155257942-T-C		not specified	Uncertain significance (Jan 24, 2023)
6-155257961-C-T		not specified	Uncertain significance (Oct 05, 2023)
6-155257999-C-T		not specified	Uncertain significance (Sep 25, 2023)
6-155258060-G-A		not specified	Uncertain significance (Sep 25, 2023)
6-155260282-C-T		not specified	Uncertain significance (Nov 05, 2021)
6-155275834-A-G		not specified	Uncertain significance (Oct 25, 2022)
6-155275856-A-G		not specified	Uncertain significance (Nov 30, 2021)
6-155275864-G-A		not specified	Uncertain significance (Dec 19, 2022)
6-155275883-C-T		not specified	Uncertain significance (Dec 13, 2023)
6-155275958-C-T		not specified	Uncertain significance (Jan 23, 2023)
6-155276077-G-C		not specified	Uncertain significance (May 20, 2024)
6-155276123-C-T		not specified	Uncertain significance (Dec 03, 2021)
6-155276150-T-C		not specified	Uncertain significance (Oct 13, 2023)
6-155276174-T-C		not specified	Uncertain significance (Mar 06, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
TFB1M	protein_coding	protein_coding	ENST00000367166	7	56985

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
6.39e-10	0.133	125641	0	107	125748	0.000426

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.150	181	187	0.969	0.0000102	2246
Missense in Polyphen		76	77.083	0.98594		949
Synonymous	0.115	68	69.2	0.982	0.00000377	684
Loss of Function	0.338	15	16.5	0.910	0.00000100	172

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000868	0.000868
Ashkenazi Jewish	0.00	0.00
East Asian	0.000381	0.000381
Finnish	0.000326	0.000323
European (Non-Finnish)	0.000537	0.000536
Middle Eastern	0.000381	0.000381
South Asian	0.000261	0.000261
Other	0.000490	0.000489

dbNSFP

Source: dbNSFP

• Function: FUNCTION: S-adenosyl-L-methionine-dependent methyltransferase which specifically dimethylates mitochondrial 12S rRNA at the conserved stem loop. Also required for basal transcription of mitochondrial DNA, probably via its interaction with POLRMT and TFAM. Stimulates transcription independently of the methyltransferase activity. {ECO:0000269|PubMed:11809803, ECO:0000269|PubMed:12068295, ECO:0000269|PubMed:12897151}.
• Disease: DISEASE: Note=Variations in TFB1M may influence the clinical expression of aminoglycoside-induced deafness caused by the A1555G mutation in the mitochondrial 12S rRNA.
• Pathway: Energy Metabolism;Mitochondrial biogenesis;Mitochondrial Gene Expression;rRNA processing;rRNA modification in the mitochondrion;Metabolism of RNA;rRNA processing in the mitochondrion;Transcriptional activation of mitochondrial biogenesis;Mitochondrial biogenesis;Organelle biogenesis and maintenance (Consensus)

Recessive Scores

• pRec: 0.103

Intolerance Scores

• loftool: 0.903
• rvis_EVS: 0.26
• rvis_percentile_EVS: 70.44

Haploinsufficiency Scores

• pHI: 0.202
• hipred: N
• hipred_score: 0.174
• ghis: 0.514

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: E
• essential_gene_gene_trap: E
• gene_indispensability_pred: E
• gene_indispensability_score: 0.571

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Tfb1m
• Phenotype: muscle phenotype; cellular phenotype; growth/size/body region phenotype; cardiovascular system phenotype (the observable morphological and physiological characteristics of the mammalian heart, blood vessels, or circulatory system that are manifested through development and lifespan); mortality/aging (the observable characteristics related to the ability of a mammalian organism to live and age that are manifested throughout development and life span); vision/eye phenotype; nervous system phenotype (the observable morphological and physiological characteristics of the extensive, intricate network of electochemical structures in the body that is comprised of the brain, spinal cord, nerves, ganglia and parts of the receptor organs that are manifested through development and lifespan); embryo phenotype

Gene ontology

• Biological process: rRNA modification;mitochondrion organization;rRNA methylation
• Cellular component: mitochondrial matrix;mitochondrial nucleoid
• Molecular function: rRNA (adenine-N6,N6-)-dimethyltransferase activity;DNA binding;RNA binding;protein binding