UPF3A
UPF3A regulator of nonsense mediated mRNA decay
Basic information
Region (hg38): 13:114281601-114305817
Links
Phenotypes
GenCC
Source:
No genCC data.
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 UPF3A 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 | 55 | 57 | ||||
| nonsense | 0 | |||||
| start loss | 0 | |||||
| frameshift | 0 | |||||
| inframe indel | 0 | |||||
| splice donor/acceptor (+/-2bp) | 0 | |||||
| splice region | 1 | 1 | ||||
| non coding | 0 | |||||
| Total | 0 | 0 | 55 | 2 | 0 |
Variants in UPF3A
This is a list of pathogenic ClinVar variants found in the UPF3A region.
You can filter this list by clicking the number of variants in the Variants pathogenicity by type table.
| Position | Type | Phenotype | Significance | ClinVar |
|---|---|---|---|---|
| 13-114281649-G-A | not specified | Uncertain significance (Dec 02, 2021) | ||
| 13-114281655-G-A | not specified | Uncertain significance (Jan 23, 2024) | ||
| 13-114281661-G-A | not specified | Uncertain significance (Oct 16, 2023) | ||
| 13-114281662-C-T | not specified | Uncertain significance (Sep 30, 2021) | ||
| 13-114281682-G-A | not specified | Uncertain significance (Mar 15, 2023) | ||
| 13-114281689-C-T | not specified | Uncertain significance (Nov 09, 2022) | ||
| 13-114281707-G-A | not specified | Uncertain significance (Sep 06, 2022) | ||
| 13-114281724-C-A | not specified | Uncertain significance (Aug 26, 2024) | ||
| 13-114281782-C-T | not specified | Uncertain significance (Dec 21, 2022) | ||
| 13-114281800-G-A | not specified | Uncertain significance (Nov 08, 2024) | ||
| 13-114281828-G-C | not specified | Uncertain significance (Sep 01, 2021) | ||
| 13-114282016-C-T | Likely benign (Oct 01, 2022) | |||
| 13-114282040-C-T | not specified | Uncertain significance (Jun 29, 2022) | ||
| 13-114282043-C-T | not specified | Uncertain significance (Sep 16, 2021) | ||
| 13-114282078-C-T | not specified | Uncertain significance (Jul 19, 2022) | ||
| 13-114282104-C-A | not specified | Uncertain significance (Sep 22, 2023) | ||
| 13-114282107-G-C | not specified | Uncertain significance (Jun 02, 2023) | ||
| 13-114282844-C-T | not specified | Uncertain significance (Jun 17, 2024) | ||
| 13-114282883-C-T | not specified | Uncertain significance (May 14, 2024) | ||
| 13-114282892-A-G | not specified | Uncertain significance (May 30, 2023) | ||
| 13-114282899-T-G | not specified | Uncertain significance (Jun 16, 2023) | ||
| 13-114282923-A-G | not specified | Uncertain significance (Aug 05, 2024) | ||
| 13-114282923-A-T | not specified | Uncertain significance (Jun 29, 2023) | ||
| 13-114282931-C-T | not specified | Uncertain significance (May 09, 2023) | ||
| 13-114286317-C-T | not specified | Uncertain significance (Aug 19, 2024) |
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