UPF3A
Basic information
Region (hg38): 13:114281601-114305817
Links
Phenotypes
GenCC
Source:
ClinVar
This is a list of variants' phenotypes submitted to
- not_specified (85 variants)
- not_provided (1 variants)
Variants pathogenicity by type
Statistics on ClinVar variants can assist in determining whether a specific variant type in the UPF3A gene is commonly pathogenic or not. These statistics are base on transcript: NM_000023011.4. 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.
Effect | PathogenicP | Likely pathogenicLP | VUSVUS | Likely benignLB | BenignB | Sum |
---|---|---|---|---|---|---|
synonymous | 0 | |||||
missense | 83 | 85 | ||||
nonsense | 0 | |||||
start loss | 0 | |||||
frameshift | 0 | |||||
splice donor/acceptor (+/-2bp) | 0 | |||||
Total | 0 | 0 | 83 | 2 | 0 |
GnomAD
Source:
Gene | Type | Bio Type | Transcript | Coding Exons | Length |
---|---|---|---|---|---|
UPF3A | protein_coding | protein_coding | ENST00000375299 | 10 | 24225 |
pLI Probability LOF Intolerant | pRec Probability LOF Recessive | Individuals with no LOFs | Individuals with Homozygous LOFs | Individuals with Heterozygous LOFs | Defined | p |
---|---|---|---|---|---|---|
9.17e-7 | 0.929 | 125680 | 0 | 35 | 125715 | 0.000139 |
Z-Score | Observed | Expected | Observed/Expected | Mutation Rate | Total Possible in Transcript | |
---|---|---|---|---|---|---|
Missense | -0.605 | 275 | 248 | 1.11 | 0.0000133 | 3042 |
Missense in Polyphen | 54 | 63.329 | 0.85269 | 865 | ||
Synonymous | -2.99 | 132 | 95.0 | 1.39 | 0.00000528 | 877 |
Loss of Function | 1.76 | 13 | 21.9 | 0.594 | 0.00000107 | 305 |
LoF frequencies by population
Ethnicity | Sum of pLOFs | p |
---|---|---|
African & African-American | 0.000190 | 0.000183 |
Ashkenazi Jewish | 0.00 | 0.00 |
East Asian | 0.000339 | 0.000326 |
Finnish | 0.0000926 | 0.0000924 |
European (Non-Finnish) | 0.000165 | 0.000158 |
Middle Eastern | 0.000339 | 0.000326 |
South Asian | 0.000185 | 0.000163 |
Other | 0.00 | 0.00 |
dbNSFP
Source:
- Function
- FUNCTION: Involved in nonsense-mediated decay (NMD) of mRNAs containing premature stop codons by associating with the nuclear exon junction complex (EJC) and serving as link between the EJC core and NMD machinery. Recruits UPF2 at the cytoplasmic side of the nuclear envelope and the subsequent formation of an UPF1-UPF2- UPF3 surveillance complex (including UPF1 bound to release factors at the stalled ribosome) is believed to activate NMD. However, UPF3A is shown to be only marginally active in NMD as compared to UPF3B. Binds spliced mRNA upstream of exon-exon junctions. In vitro, weakly stimulates translation. {ECO:0000269|PubMed:11163187, ECO:0000269|PubMed:16601204}.;
- Pathway
- mRNA surveillance pathway - Homo sapiens (human);RNA transport - Homo sapiens (human);Metabolism of RNA;Nonsense-Mediated Decay (NMD);Nonsense Mediated Decay (NMD) enhanced by the Exon Junction Complex (EJC)
(Consensus)
Recessive Scores
- pRec
- 0.0943
Intolerance Scores
- loftool
- 0.886
- rvis_EVS
- 0.17
- rvis_percentile_EVS
- 65.96
Haploinsufficiency Scores
- pHI
- 0.0757
- hipred
- Y
- hipred_score
- 0.641
- ghis
- 0.507
Essentials
- essential_gene_CRISPR
- N
- essential_gene_CRISPR2
- N
- essential_gene_gene_trap
- N
- gene_indispensability_pred
- N
- gene_indispensability_score
- 0.238
Gene Damage Prediction
All | Recessive | Dominant | |
---|---|---|---|
Mendelian | Medium | Medium | Medium |
Primary Immunodeficiency | Medium | Medium | Medium |
Cancer | Medium | Medium | Medium |
Mouse Genome Informatics
- Gene name
- Upf3a
- 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); reproductive system phenotype; cellular phenotype;
Zebrafish Information Network
- Gene name
- upf3a
- Affected structure
- brain morphogenesis
- Phenotype tag
- abnormal
- Phenotype quality
- process quality
Gene ontology
- Biological process
- nuclear-transcribed mRNA catabolic process, nonsense-mediated decay;nucleocytoplasmic transport;positive regulation of translation;mRNA transport
- Cellular component
- nucleus;nucleolus;cytoplasm;cytosol;exon-exon junction complex;intracellular membrane-bounded organelle
- Molecular function
- RNA binding;protein binding;structural constituent of nuclear pore;telomeric DNA binding