UPF3A

UPF3A regulator of nonsense mediated mRNA decay

Basic information

Region (hg38): 13:114281601-114305817

Links

ENSG00000169062

∙ NCBI:65110 ∙ OMIM:605530 ∙ HGNC:20332 ∙ Uniprot:Q9H1J1 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

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.

Effect	PathogenicP	Likely pathogenicLP	VUSVUS	Likely benignLB	BenignB	Sum
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

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: 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

	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