UBTF

upstream binding transcription factor, the group of MicroRNA protein coding host genes

Basic information

Region (hg38): 17:44205033-44221626

Links

ENSG00000108312NCBI:7343OMIM:600673HGNC:12511Uniprot:P17480AlphaFoldGenCCjaxSfariGnomADPubmedClinVar

Phenotypes

GenCC

Source: genCC

  • childhood-onset motor and cognitive regression syndrome with extrapyramidal movement disorder (Strong), mode of inheritance: AD
  • childhood-onset motor and cognitive regression syndrome with extrapyramidal movement disorder (Supportive), mode of inheritance: AD
  • childhood-onset motor and cognitive regression syndrome with extrapyramidal movement disorder (Definitive), mode of inheritance: AD
  • childhood-onset motor and cognitive regression syndrome with extrapyramidal movement disorder (Definitive), mode of inheritance: AD
  • childhood-onset motor and cognitive regression syndrome with extrapyramidal movement disorder (Strong), mode of inheritance: AD

Clinical Genomic Database

Source: CGD

ConditionInheritanceIntervention CategoriesIntervention/Rationale Manifestation CategoriesReferences
Neurodegeneration, childhood-onset, with brain atrophyADGeneralGenetic knowledge may be beneficial related to issues such as selection of optimal supportive care, informed medical decision-making, prognostic considerations, and avoidance of unnecessary testingNeurologic28777933

ClinVar

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

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the UBTF gene is commonly pathogenic or not. These statistics are base on transcript: . 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.

Variant type Pathogenic Likely pathogenic VUS Likely benign Benign Sum
synonymous
1
clinvar
3
clinvar
4
clinvar
8
missense
2
clinvar
51
clinvar
2
clinvar
55
nonsense
2
clinvar
3
clinvar
5
start loss
0
frameshift
5
clinvar
5
splice donor/acceptor (+/-2bp)
1
clinvar
1
Total 0 5 60 5 4
Loading clinvar variants...

GnomAD

Source: gnomAD

GeneTypeBio TypeTranscript Coding Exons Length
UBTFprotein_codingprotein_codingENST00000302904 2016594
pLI Probability
LOF Intolerant
pRec Probability
LOF Recessive
Individuals with
no LOFs
Individuals with
Homozygous LOFs
Individuals with
Heterozygous LOFs
Defined p
1.001.41e-8125659011256600.00000398
Z-Score Observed Expected Observed/Expected Mutation Rate Total Possible in Transcript
Missense4.751724580.3760.00002775111
Missense in Polyphen26176.520.147291928
Synonymous-1.422101851.130.00001221302
Loss of Function6.55049.90.000.00000258571

LoF frequencies by population

EthnicitySum of pLOFs p
African & African-American0.000.00
Ashkenazi Jewish0.000.00
East Asian0.000.00
Finnish0.000.00
European (Non-Finnish)0.00001760.00000880
Middle Eastern0.000.00
South Asian0.000.00
Other0.000.00

dbNSFP

Source: dbNSFP

Function
FUNCTION: Recognizes the ribosomal RNA gene promoter and activates transcription mediated by RNA polymerase I through cooperative interactions with the transcription factor SL1/TIF-IB complex. It binds specifically to the upstream control element. {ECO:0000269|PubMed:28777933, ECO:0000269|PubMed:7982918}.;
Disease
DISEASE: Neurodegeneration, childhood-onset, with brain atrophy (CONDBA) [MIM:617672]: An autosomal dominant neurodegenerative disease with onset in childhood, characterized by progressive cortical atrophy, developmental delay, developmental regression, loss of motor skills and ambulation, absence of language, and intellectual disability. {ECO:0000269|PubMed:28777933}. Note=The disease is caused by mutations affecting the gene represented in this entry.;
Pathway
Ectoderm Differentiation;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 Promoter Opening;RNA Polymerase I Transcription Termination;RNA Polymerase I Transcription;RNA Polymerase I Transcription Initiation;RNA Polymerase I Promoter Escape;RNA Polymerase I Chain Elongation;Validated targets of C-MYC transcriptional activation (Consensus)

Recessive Scores

pRec
0.172

Intolerance Scores

loftool
0.00537
rvis_EVS
-1.16
rvis_percentile_EVS
6.17

Haploinsufficiency Scores

pHI
0.820
hipred
Y
hipred_score
0.825
ghis
0.704

Essentials

essential_gene_CRISPR
E
essential_gene_CRISPR2
E
essential_gene_gene_trap
E
gene_indispensability_pred
E
gene_indispensability_score
0.878

Gene Damage Prediction

AllRecessiveDominant
MendelianMediumMediumMedium
Primary ImmunodeficiencyMediumMediumMedium
CancerMediumMediumMedium

Mouse Genome Informatics

Gene name
Ubtf
Phenotype
embryo phenotype; mortality/aging (the observable characteristics related to the ability of a mammalian organism to live and age that are manifested throughout development and life span); normal phenotype;

Gene ontology

Biological process
RNA polymerase I preinitiation complex assembly;regulation of transcription by RNA polymerase I;regulation of transcription by RNA polymerase II;transcription by RNA polymerase I;transcription initiation from RNA polymerase I promoter;termination of RNA polymerase I transcription;positive regulation of transcription by RNA polymerase I;regulation of glucose mediated signaling pathway
Cellular component
fibrillar center;nucleus;nucleoplasm;nucleolus
Molecular function
DNA-binding transcription factor activity, RNA polymerase II-specific;RNA polymerase I CORE element sequence-specific DNA binding;RNA polymerase I upstream control element sequence-specific DNA binding;chromatin binding;RNA binding;protein binding;scaffold protein binding