TAF1D

TATA-box binding protein associated factor, RNA polymerase I subunit D, the group of Small nucleolar RNA protein coding host genes

Basic information

Region (hg38): 11:93729948-93784391

Previous symbols: [ "JOSD3" ]

Links

ENSG00000166012 ∙ NCBI:79101 ∙ OMIM:612823 ∙ HGNC:28759 ∙ Uniprot:Q9H5J8 ∙ 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 TAF1D gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the TAF1D 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			18	2		20
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding			1		1	2
Total	0	0	19	2	1

Variants in TAF1D

This is a list of pathogenic ClinVar variants found in the TAF1D region.

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

Position	Type	Phenotype	Significance	ClinVar
11-93730049-G-T		not specified	Uncertain significance (Jun 03, 2024)
11-93730101-C-G		not specified	Uncertain significance (Apr 06, 2023)
11-93730151-G-A			Benign (Aug 02, 2017)
11-93730164-GGA-G			Likely benign (Dec 14, 2023)
11-93730221-C-T			Benign (Aug 02, 2017)
11-93730235-C-G		not specified	Uncertain significance (Aug 12, 2021)
11-93736183-C-T		not specified	Uncertain significance (Sep 13, 2023)
11-93736240-T-C		not specified	Uncertain significance (Feb 16, 2023)
11-93736714-C-T		not specified	Uncertain significance (Aug 02, 2023)
11-93737065-T-C		not specified	Likely benign (Jun 30, 2022)
11-93737080-G-A		not specified	Uncertain significance (Jan 24, 2023)
11-93737088-G-C		not specified	Uncertain significance (Dec 02, 2024)
11-93737194-A-G		not specified	Uncertain significance (Dec 20, 2023)
11-93737212-A-G		not specified	Uncertain significance (Aug 26, 2022)
11-93738114-A-G		not specified	Uncertain significance (Nov 29, 2021)
11-93738138-C-A		not specified	Uncertain significance (May 03, 2023)
11-93738139-G-T		not specified	Likely benign (Nov 09, 2024)
11-93738147-C-T		not specified	Uncertain significance (Dec 21, 2023)
11-93738179-C-G		not specified	Uncertain significance (Feb 28, 2023)
11-93738179-C-T		not specified	Uncertain significance (Sep 29, 2023)
11-93738251-C-T		not specified	Uncertain significance (Jan 23, 2023)
11-93738318-A-C		not specified	Uncertain significance (Apr 07, 2022)
11-93738375-A-C		not specified	Uncertain significance (Jan 19, 2022)
11-93738401-G-A		not specified	Uncertain significance (Aug 12, 2021)
11-93738407-C-T		not specified	Likely benign (Dec 17, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
TAF1D	protein_coding	protein_coding	ENST00000448108	5	54444

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.00000840	0.537	124949	0	6	124955	0.0000240

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.365	126	138	0.913	0.00000676	1825
Missense in Polyphen		31	37.556	0.82543		589
Synonymous	-0.0900	47	46.2	1.02	0.00000222	488
Loss of Function	0.719	9	11.6	0.773	6.79e-7	161

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000125	0.000124
Ashkenazi Jewish	0.00	0.00
East Asian	0.00	0.00
Finnish	0.00	0.00
European (Non-Finnish)	0.0000183	0.0000177
Middle Eastern	0.00	0.00
South Asian	0.00	0.00
Other	0.000167	0.000165

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Component of the transcription factor SL1/TIF-IB complex, which is involved in the assembly of the PIC (preinitiation complex) during RNA polymerase I-dependent transcription. The rate of PIC formation probably is primarily dependent on the rate of association of SL1/TIF-IB with the rDNA promoter. SL1/TIF-IB is involved in stabilization of nucleolar transcription factor 1/UBTF on rDNA. Formation of SL1/TIF-IB excludes the association of TBP with TFIID subunits. {ECO:0000269|PubMed:15970593, ECO:0000269|PubMed:17318177}.
• 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: 0.0882

Intolerance Scores

• loftool: 0.390
• rvis_EVS: 0.26
• rvis_percentile_EVS: 70.26

Haploinsufficiency Scores

• pHI: 0.397
• hipred: N
• hipred_score: 0.461
• ghis: 0.495

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: E
• gene_indispensability_pred: E
• gene_indispensability_score: 0.860

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Taf1d

Gene ontology

• Biological process: regulation of transcription, DNA-templated;transcription initiation from RNA polymerase I promoter;termination of RNA polymerase I transcription;positive regulation of gene expression, epigenetic
• Cellular component: nucleoplasm;RNA polymerase transcription factor SL1 complex;microtubule organizing center
• Molecular function: DNA binding;protein binding