TAF1A

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

Basic information

Region (hg38): 1:222557902-222589933

Links

ENSG00000143498 ∙ NCBI:9015 ∙ OMIM:604903 ∙ HGNC:11532 ∙ Uniprot:Q15573 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

Phenotypes

GenCC

Source: genCC

• familial isolated dilated cardiomyopathy (Supportive), mode of inheritance: AD

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the TAF1A gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the TAF1A 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			16	3	1	20
nonsense						0
start loss						0
frameshift						0
inframe indel			1			1
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding					1	1
Total	0	0	17	3	2

Variants in TAF1A

This is a list of pathogenic ClinVar variants found in the TAF1A region.

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

Position	Type	Phenotype	Significance	ClinVar
1-222558703-T-C		not specified	Uncertain significance (Jun 24, 2022)
1-222558709-C-T			Likely benign (Dec 31, 2019)
1-222561411-G-A		not specified	Uncertain significance (Feb 07, 2023)
1-222561507-G-A		not specified	Likely benign (Sep 13, 2023)
1-222563156-C-T			Benign (Apr 24, 2020)
1-222563237-C-T		Cardiomyopathy, familial restrictive, 6 • Primary dilated cardiomyopathy	Uncertain significance (Jul 06, 2022)
1-222563285-GTTC-G			Uncertain significance (Jul 06, 2022)
1-222569566-A-G		not specified	Uncertain significance (Mar 02, 2023)
1-222569571-T-C		not specified	Uncertain significance (Oct 03, 2023)
1-222569623-T-G		Cardiomyopathy, familial restrictive, 6	Uncertain significance (Sep 19, 2022)
1-222570665-T-A		not specified	Uncertain significance (Dec 07, 2021)
1-222577447-A-G		not specified	Uncertain significance (Jun 19, 2024)
1-222577463-T-C		not specified	Uncertain significance (Feb 13, 2024)
1-222577483-T-A		not specified	Uncertain significance (Aug 30, 2021)
1-222577534-C-T		not specified	Likely benign (Jun 22, 2021)
1-222579816-C-G		not specified	Uncertain significance (Jan 16, 2024)
1-222579870-A-C			Benign (Dec 31, 2019)
1-222584139-C-T		not specified	Uncertain significance (Mar 16, 2022)
1-222584188-C-T		not specified	Uncertain significance (Jun 03, 2022)
1-222584216-T-A		not specified	Uncertain significance (Jun 21, 2023)
1-222584234-T-C		not specified	Uncertain significance (Sep 22, 2022)
1-222584252-G-A		not specified	Uncertain significance (Dec 14, 2022)
1-222584254-A-T		not specified	Uncertain significance (Jun 11, 2021)
1-222588479-G-C		not specified	Uncertain significance (May 30, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
TAF1A	protein_coding	protein_coding	ENST00000350027	10	32032

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
1.23e-9	0.787	125673	0	70	125743	0.000278

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	1.00	186	229	0.814	0.0000110	2980
Missense in Polyphen		52	68.838	0.7554		945
Synonymous	0.127	80	81.5	0.982	0.00000396	758
Loss of Function	1.56	18	26.7	0.674	0.00000119	349

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000767	0.000767
Ashkenazi Jewish	0.000105	0.0000992
East Asian	0.000170	0.000163
Finnish	0.00	0.00
European (Non-Finnish)	0.000340	0.000334
Middle Eastern	0.000170	0.000163
South Asian	0.000170	0.000163
Other	0.000359	0.000326

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Component of the transcription factor SL1/TIF-IB complex, which is involved in the assembly of the PIC (pre- initiation 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:7801123}.
• 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: 0.0680

Intolerance Scores

• loftool: 0.626
• rvis_EVS: 0.6
• rvis_percentile_EVS: 82.66

Haploinsufficiency Scores

• pHI: 0.0583
• hipred: N
• hipred_score: 0.394
• ghis: 0.465

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: E
• essential_gene_gene_trap: K
• gene_indispensability_pred: E
• gene_indispensability_score: 0.888

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Taf1a

Zebrafish Information Network

• Gene name: taf1a
• Affected structure: whole organism
• Phenotype tag: abnormal
• Phenotype quality: decreased life span

Gene ontology

• Biological process: transcription by RNA polymerase I;transcription initiation from RNA polymerase I promoter;termination of RNA polymerase I transcription;transcription by RNA polymerase II;positive regulation of gene expression, epigenetic
• Cellular component: RNA polymerase I transcription factor complex;nucleoplasm;microtubule cytoskeleton
• Molecular function: DNA binding;protein binding