GeneBe

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.

  • not_specified (43 variants)
  • not_provided (4 variants)
  • Cardiomyopathy,_familial_restrictive,_6 (2 variants)
  • Primary_dilated_cardiomyopathy (1 variants)

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. These statistics are base on transcript: NM_000005681.4. Only rare variants are included in the table.

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.

EffectPLPVUSLBBSum
synonymous
0
missense
42
clinvar
4
clinvar
1
clinvar
 47
nonsense
0
start loss
0
frameshift
0
splice donor/acceptor (+/-2bp)
0
Total 0 0 42 4 1
Loading clinvar variants...

GnomAD

Source: gnomAD

GeneTypeBio TypeTranscript Coding Exons Length
TAF1Aprotein_codingprotein_codingENST00000350027 1032032
pLI Probability
LOF Intolerant 		pRec Probability
LOF Recessive 		Individuals with
no LOFs 		Individuals with
Homozygous LOFs 		Individuals with
Heterozygous LOFs 		Defined p
1.23e-90.7871256730701257430.000278
Z-Score Observed Expected Observed/Expected Mutation Rate Total Possible in Transcript
Missense1.001862290.8140.00001102980
Missense in Polyphen5268.8380.7554945
Synonymous0.1278081.50.9820.00000396758
Loss of Function1.561826.70.6740.00000119349

LoF frequencies by population

EthnicitySum of pLOFs p
African & African-American0.0007670.000767
Ashkenazi Jewish0.0001050.0000992
East Asian0.0001700.000163
Finnish0.000.00
European (Non-Finnish)0.0003400.000334
Middle Eastern0.0001700.000163
South Asian0.0001700.000163
Other0.0003590.000326

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

AllRecessiveDominant
MendelianMediumMediumMedium
Primary ImmunodeficiencyMediumMediumMedium
CancerMediumMediumMedium

Mouse Genome Informatics

Gene name
Taf1a
Phenotype

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