TFB2M

transcription factor B2, mitochondrial, the group of 7BS N6-adenosine DNA/RNA methyltransferases

Basic information

Region (hg38): 1:246540560-246566261

Links

ENSG00000162851 ∙ NCBI:64216 ∙ OMIM:607055 ∙ HGNC:18559 ∙ Uniprot:Q9H5Q4 ∙ 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 TFB2M gene.

• Inborn genetic diseases (15 variants)
• not provided (6 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the TFB2M 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	2	3
missense			14	3		17
nonsense			1			1
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	15	4	2

Variants in TFB2M

This is a list of pathogenic ClinVar variants found in the TFB2M region.

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

Position	Type	Phenotype	Significance	ClinVar
1-246541046-G-A			Likely benign (Dec 01, 2022)
1-246541061-C-T			Uncertain significance (Jul 17, 2019)
1-246541065-T-C		not specified	Uncertain significance (Dec 21, 2023)
1-246541087-G-A		not specified	Likely benign (Dec 18, 2023)
1-246541172-T-C		not specified	Uncertain significance (Apr 28, 2023)
1-246544522-G-A		not specified	Uncertain significance (Jun 29, 2023)
1-246544534-T-C		not specified	Uncertain significance (Nov 30, 2022)
1-246544540-T-C		not specified	Uncertain significance (Jan 27, 2022)
1-246544548-C-T		not specified	Uncertain significance (Nov 01, 2022)
1-246544662-T-G		not specified	Uncertain significance (Sep 14, 2023)
1-246548573-T-G		not specified	Uncertain significance (May 04, 2022)
1-246548576-C-T		not specified	Likely benign (Sep 22, 2023)
1-246548579-G-T		not specified	Uncertain significance (Jun 28, 2023)
1-246551284-C-T		not specified	Likely benign (Aug 04, 2023)
1-246557447-G-A		not specified	Uncertain significance (Apr 18, 2023)
1-246557457-T-C			Benign (May 31, 2018)
1-246564370-G-A			Benign (May 31, 2018)
1-246564414-C-T		not specified	Uncertain significance (May 02, 2023)
1-246565846-A-G		not specified	Uncertain significance (Jan 22, 2024)
1-246565886-C-A		not specified	Uncertain significance (Oct 10, 2023)
1-246565910-C-A		not specified	Uncertain significance (Jan 24, 2024)
1-246565916-C-T		not specified	Likely benign (Dec 22, 2023)
1-246565918-T-A		not specified	Uncertain significance (Mar 29, 2023)
1-246565949-C-T			Likely benign (Feb 01, 2023)
1-246565952-T-C		not specified	Uncertain significance (Sep 25, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
TFB2M	protein_coding	protein_coding	ENST00000366514	8	25765

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.00000877	0.932	125739	0	7	125746	0.0000278

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	-0.123	225	220	1.02	0.0000113	2579
Missense in Polyphen		57	69.211	0.82357		905
Synonymous	1.05	67	78.9	0.850	0.00000396	752
Loss of Function	1.72	11	19.1	0.576	0.00000106	222

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.00	0.00
Ashkenazi Jewish	0.00	0.00
East Asian	0.00	0.00
Finnish	0.00	0.00
European (Non-Finnish)	0.0000264	0.0000264
Middle Eastern	0.00	0.00
South Asian	0.0000654	0.0000653
Other	0.000329	0.000326

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. Compared to TFB1M, it activates transcription of mitochondrial DNA more efficiently, while it has less methyltransferase activity. {ECO:0000269|PubMed:12068295, ECO:0000269|PubMed:12897151, ECO:0000269|PubMed:15526033, ECO:0000269|PubMed:20410300}.
• Pathway: Energy Metabolism;Mitochondrial biogenesis;Mitochondrial Gene Expression;Gene expression (Transcription);Transcriptional activation of mitochondrial biogenesis;Mitochondrial biogenesis;Mitochondrial transcription initiation;Transcription from mitochondrial promoters;Organelle biogenesis and maintenance (Consensus)

Recessive Scores

• pRec: 0.0597

Intolerance Scores

• rvis_EVS: -0.14
• rvis_percentile_EVS: 43.77

Haploinsufficiency Scores

• pHI: 0.0487
• hipred: N
• hipred_score: 0.386
• ghis: 0.528

Essentials

• essential_gene_CRISPR: E
• essential_gene_CRISPR2: S
• essential_gene_gene_trap: E
• gene_indispensability_pred: E
• gene_indispensability_score: 0.953

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Tfb2m

Gene ontology

• Biological process: mitochondrial transcription;transcription initiation from mitochondrial promoter;mitochondrion organization;rRNA methylation;positive regulation of transcription, DNA-templated
• Cellular component: mitochondrion;mitochondrial matrix;mitochondrial nucleoid
• Molecular function: rRNA (adenine-N6,N6-)-dimethyltransferase activity;transcription coregulator activity;RNA binding