UPF3A

UPF3A regulator of nonsense mediated mRNA decay

Basic information

Region (hg38): 13:114281601-114305817

Links

ENSG00000169062NCBI:65110OMIM:605530HGNC:20332Uniprot:Q9H1J1AlphaFoldGenCCjaxSfariGnomADPubmedClinVar

Phenotypes

GenCC

Source: genCC

No genCC data.

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the UPF3A gene.

  • 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.

EffectPLPVUSLBBSum
synonymous
0
missense
83
clinvar
2
clinvar
85
nonsense
0
start loss
0
frameshift
0
splice donor/acceptor (+/-2bp)
0
Total 0 0 83 2 0
Loading clinvar variants...

GnomAD

Source: gnomAD

GeneTypeBio TypeTranscript Coding Exons Length
UPF3Aprotein_codingprotein_codingENST00000375299 1024225
pLI Probability
LOF Intolerant
pRec Probability
LOF Recessive
Individuals with
no LOFs
Individuals with
Homozygous LOFs
Individuals with
Heterozygous LOFs
Defined p
9.17e-70.9291256800351257150.000139
Z-Score Observed Expected Observed/Expected Mutation Rate Total Possible in Transcript
Missense-0.6052752481.110.00001333042
Missense in Polyphen5463.3290.85269865
Synonymous-2.9913295.01.390.00000528877
Loss of Function1.761321.90.5940.00000107305

LoF frequencies by population

EthnicitySum of pLOFs p
African & African-American0.0001900.000183
Ashkenazi Jewish0.000.00
East Asian0.0003390.000326
Finnish0.00009260.0000924
European (Non-Finnish)0.0001650.000158
Middle Eastern0.0003390.000326
South Asian0.0001850.000163
Other0.000.00

dbNSFP

Source: dbNSFP

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

AllRecessiveDominant
MendelianMediumMediumMedium
Primary ImmunodeficiencyMediumMediumMedium
CancerMediumMediumMedium

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