UBTF
Basic information
Region (hg38): 17:44205033-44221626
Links
Phenotypes
GenCC
Source:
- 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:
Condition | Inheritance | Intervention Categories | Intervention/Rationale | Manifestation Categories | References |
---|---|---|---|---|---|
Neurodegeneration, childhood-onset, with brain atrophy | AD | General | Genetic knowledge may be beneficial related to issues such as selection of optimal supportive care, informed medical decision-making, prognostic considerations, and avoidance of unnecessary testing | Neurologic | 28777933 |
ClinVar
This is a list of variants' phenotypes submitted to
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 | 8 | |||||
missense | 51 | 55 | ||||
nonsense | 5 | |||||
start loss | 0 | |||||
frameshift | 5 | |||||
splice donor/acceptor (+/-2bp) | 1 | |||||
Total | 0 | 5 | 60 | 5 | 4 |
GnomAD
Source:
Gene | Type | Bio Type | Transcript | Coding Exons | Length |
---|---|---|---|---|---|
UBTF | protein_coding | protein_coding | ENST00000302904 | 20 | 16594 |
pLI Probability LOF Intolerant | pRec Probability LOF Recessive | Individuals with no LOFs | Individuals with Homozygous LOFs | Individuals with Heterozygous LOFs | Defined | p |
---|---|---|---|---|---|---|
1.00 | 1.41e-8 | 125659 | 0 | 1 | 125660 | 0.00000398 |
Z-Score | Observed | Expected | Observed/Expected | Mutation Rate | Total Possible in Transcript | |
---|---|---|---|---|---|---|
Missense | 4.75 | 172 | 458 | 0.376 | 0.0000277 | 5111 |
Missense in Polyphen | 26 | 176.52 | 0.14729 | 1928 | ||
Synonymous | -1.42 | 210 | 185 | 1.13 | 0.0000122 | 1302 |
Loss of Function | 6.55 | 0 | 49.9 | 0.00 | 0.00000258 | 571 |
LoF frequencies by population
Ethnicity | Sum of pLOFs | p |
---|---|---|
African & African-American | 0.00 | 0.00 |
Ashkenazi Jewish | 0.00 | 0.00 |
East Asian | 0.00 | 0.00 |
Finnish | 0.00 | 0.00 |
European (Non-Finnish) | 0.0000176 | 0.00000880 |
Middle Eastern | 0.00 | 0.00 |
South Asian | 0.00 | 0.00 |
Other | 0.00 | 0.00 |
dbNSFP
Source:
- 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
All | Recessive | Dominant | |
---|---|---|---|
Mendelian | Medium | Medium | Medium |
Primary Immunodeficiency | Medium | Medium | Medium |
Cancer | Medium | Medium | Medium |
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