TAF1B

TATA-box binding protein associated factor, RNA polymerase I subunit B

Basic information

Region (hg38): 2:9843442-9934416

Links

ENSG00000115750 ∙ NCBI:9014 ∙ OMIM:604904 ∙ HGNC:11533 ∙ Uniprot:Q53T94 ∙ 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 TAF1B gene.

• Inborn genetic diseases (17 variants)
• Orofacial cleft 1 (1 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the TAF1B 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			17			17
nonsense						0
start loss						0
frameshift			1			1
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	18	0	0

Variants in TAF1B

This is a list of pathogenic ClinVar variants found in the TAF1B region.

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

Position	Type	Phenotype	Significance	ClinVar
2-9845265-G-T		not specified	Uncertain significance (Dec 15, 2023)
2-9845296-C-T		not specified	Uncertain significance (Jan 08, 2024)
2-9845314-C-T		not specified	Uncertain significance (Dec 19, 2022)
2-9849392-A-G		not specified	Uncertain significance (Feb 15, 2023)
2-9849441-T-TA		Orofacial cleft 1	Uncertain significance (Nov 22, 2022)
2-9851628-C-A		not specified	Uncertain significance (Mar 29, 2023)
2-9854420-C-T		not specified	Uncertain significance (Oct 27, 2022)
2-9868348-C-G		not specified	Uncertain significance (Oct 10, 2023)
2-9868367-C-T		not specified	Uncertain significance (Dec 22, 2023)
2-9868400-C-G		not specified	Uncertain significance (Mar 28, 2022)
2-9868424-A-T		not specified	Uncertain significance (Nov 07, 2023)
2-9875906-T-G		not specified	Uncertain significance (Sep 26, 2023)
2-9875913-G-A		not specified	Uncertain significance (Jan 05, 2022)
2-9875996-A-G		not specified	Uncertain significance (May 30, 2023)
2-9882734-A-G		not specified	Uncertain significance (Oct 05, 2023)
2-9882774-A-G		not specified	Uncertain significance (Jun 27, 2022)
2-9882794-T-C		not specified	Uncertain significance (Jun 05, 2023)
2-9904953-A-G		not specified	Uncertain significance (Jan 30, 2024)
2-9904968-T-C		not specified	Uncertain significance (Aug 02, 2021)
2-9910747-A-C		not specified	Uncertain significance (Mar 07, 2023)
2-9910751-T-C		not specified	Uncertain significance (Oct 12, 2022)
2-9910813-A-G		not specified	Uncertain significance (Jun 11, 2021)
2-9911551-A-G		not specified	Uncertain significance (Jan 18, 2023)
2-9919603-G-A		not specified	Uncertain significance (May 17, 2023)
2-9919645-A-G		not specified	Likely benign (Feb 23, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
TAF1B	protein_coding	protein_coding	ENST00000263663	15	91063

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
7.98e-15	0.388	125612	1	135	125748	0.000541

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.775	257	294	0.873	0.0000144	3868
Missense in Polyphen		61	88.515	0.68915		1189
Synonymous	-0.265	105	102	1.03	0.00000516	1012
Loss of Function	1.44	27	36.3	0.743	0.00000171	462

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.00120	0.00120
Ashkenazi Jewish	0.000397	0.000397
East Asian	0.000598	0.000489
Finnish	0.000278	0.000277
European (Non-Finnish)	0.000786	0.000712
Middle Eastern	0.000598	0.000489
South Asian	0.000236	0.000229
Other	0.000326	0.000326

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Component of RNA polymerase I core factor complex that acts as a GTF2B/TFIIB-like factor and plays a key role in multiple steps during transcription initiation such as pre-initiation complex (PIC) assembly and postpolymerase recruitment events in polymerase I (Pol I) transcription. Binds rDNA promoters and plays a role in Pol I recruitment as a component of the SL1/TIF-IB complex and, possibly, directly through its interaction with RRN3. {ECO:0000269|PubMed:15970593, ECO:0000269|PubMed:21921198, ECO:0000269|PubMed:21921199, ECO:0000269|PubMed:7491500, ECO:0000269|PubMed:7801123, ECO:0000269|PubMed:7801130}.
• Pathway: B-WICH complex positively regulates rRNA expression;Positive epigenetic regulation of rRNA expression;SIRT1 negatively regulates rRNA expression;NoRC negatively regulates rRNA expression;Negative epigenetic regulation of rRNA expression;Epigenetic regulation of gene expression;Gene expression (Transcription);RNA Polymerase I Promoter Clearance;RNA Polymerase I Transcription Termination;RNA Polymerase I Transcription;RNA Polymerase I Transcription Initiation;RNA Polymerase I Promoter Escape;RNA Polymerase I Chain Elongation (Consensus)

Recessive Scores

• pRec: 0.127

Intolerance Scores

• loftool: 0.941
• rvis_EVS: 0.76
• rvis_percentile_EVS: 86.8

Haploinsufficiency Scores

• pHI: 0.211
• hipred: Y
• hipred_score: 0.551
• ghis: 0.458

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: E
• essential_gene_gene_trap: E
• gene_indispensability_pred: E
• gene_indispensability_score: 0.713

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Taf1b

Zebrafish Information Network

• Gene name: taf1b
• Affected structure: head
• Phenotype tag: abnormal
• Phenotype quality: pointed

Gene ontology

• Biological process: RNA polymerase I preinitiation complex assembly;transcription, DNA-templated;transcription initiation from RNA polymerase I promoter;termination of RNA polymerase I transcription;nucleolar large rRNA transcription by RNA polymerase I;positive regulation of gene expression, epigenetic
• Cellular component: nucleus;nucleoplasm;RNA polymerase transcription factor SL1 complex;RNA polymerase I core factor complex
• Molecular function: RNA polymerase I CORE element sequence-specific DNA binding;protein binding;TBP-class protein binding;metal ion binding