UPF3A

UPF3A regulator of nonsense mediated mRNA decay

Basic information

Region (hg38): 13:114281600-114305817

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.

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			39	2		41
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	39	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)
13-114281782-C-T		not specified	Uncertain significance (Dec 21, 2022)
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 (Apr 08, 2022)
13-114282923-A-T		not specified	Uncertain significance (Jun 29, 2023)
13-114282931-C-T		not specified	Uncertain significance (May 09, 2023)
13-114286579-A-T		not specified	Uncertain significance (Jun 07, 2024)
13-114286580-C-A		not specified	Uncertain significance (Dec 20, 2023)
13-114291653-G-A		not specified	Uncertain significance (Oct 06, 2021)

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