UPF2

UPF2 regulator of nonsense mediated mRNA decay, the group of MIF4G domain containing proteins|DECID complex

Basic information

Region (hg38): 10:11920022-12043170

Links

ENSG00000151461 ∙ NCBI:26019 ∙ OMIM:605529 ∙ HGNC:17854 ∙ Uniprot:Q9HAU5 ∙ 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 UPF2 gene.

• not provided (1 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the UPF2 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				2	4	6
missense			44	2		46
nonsense						0
start loss						0
frameshift	1					1
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region				5	2	7
non coding					1	1
Total	1	0	44	4	5

Highest pathogenic variant AF is 0.00000657

Variants in UPF2

This is a list of pathogenic ClinVar variants found in the UPF2 region.

You can filter this list by clicking the number of variants in the Variants pathogenicity by type table.

Position	Type	Phenotype	Significance	ClinVar
10-11929857-T-A			Likely benign (Jun 08, 2018)
10-11929858-G-A			Likely benign (Jun 08, 2018)
10-11931735-G-C		not specified	Uncertain significance (Jul 19, 2023)
10-11931759-C-T		not specified	Uncertain significance (Sep 01, 2021)
10-11936703-C-T		not specified	Uncertain significance (Apr 24, 2024)
10-11942657-T-C			Likely benign (May 08, 2018)
10-11942682-T-C		not specified	Uncertain significance (Jun 24, 2022)
10-11942727-G-T		not specified	Uncertain significance (Dec 07, 2021)
10-11943060-G-A			Likely benign (Jan 01, 2019)
10-11943119-T-A		not specified	Uncertain significance (Jan 10, 2022)
10-11948506-G-T		not specified	Uncertain significance (Jun 10, 2024)
10-11952102-C-A		not specified	Uncertain significance (Aug 31, 2022)
10-11952192-T-C		not specified	Uncertain significance (Sep 29, 2023)
10-11952212-G-A		not specified	Uncertain significance (Oct 27, 2022)
10-11952248-C-T		not specified	Uncertain significance (Apr 25, 2023)
10-11955227-T-C			Benign (Dec 31, 2019)
10-11955340-C-T			Benign (Jan 02, 2018)
10-11955489-T-A		not specified	Uncertain significance (Jan 19, 2024)
10-11956313-T-C			Likely benign (Jan 01, 2019)
10-11956362-G-T		not specified	Uncertain significance (Apr 01, 2024)
10-11956400-C-A		not specified	Uncertain significance (Jun 05, 2024)
10-11956529-A-T			Benign (Jan 01, 2019)
10-11959276-G-A			Benign (Jan 01, 2019)
10-11959316-G-A		not specified	Uncertain significance (Sep 14, 2022)
10-11964796-T-C			Benign (Jun 01, 2022)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
UPF2	protein_coding	protein_coding	ENST00000356352	21	123149

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
1.00	2.42e-9	125740	0	6	125746	0.0000239

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	3.19	438	671	0.653	0.0000348	8529
Missense in Polyphen		86	214.15	0.40158		2778
Synonymous	-0.438	232	224	1.04	0.0000110	2230
Loss of Function	7.15	2	63.4	0.0315	0.00000352	795

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.0000289	0.0000289
Ashkenazi Jewish	0.00	0.00
East Asian	0.00	0.00
Finnish	0.00	0.00
European (Non-Finnish)	0.0000469	0.0000352
Middle Eastern	0.00	0.00
South Asian	0.0000327	0.0000327
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). Recruited by UPF3B associated with the EJC core 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. In cooperation with UPF3B stimulates both ATPase and RNA helicase activities of UPF1. Binds spliced mRNA. {ECO:0000269|PubMed:11163187, ECO:0000269|PubMed:16209946, ECO:0000269|PubMed:18066079}.
• 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)

Intolerance Scores

• loftool: 0.168
• rvis_EVS: -0.89
• rvis_percentile_EVS: 10.46

Haploinsufficiency Scores

• pHI: 0.897
• hipred: Y
• hipred_score: 0.775
• ghis: 0.622

Essentials

• essential_gene_CRISPR: E
• essential_gene_CRISPR2: E
• essential_gene_gene_trap: E
• gene_indispensability_pred: E
• gene_indispensability_score: 0.928

Gene Damage Prediction

	All	Recessive	Dominant
Mendelian	Medium	Medium	Medium
Primary Immunodeficiency	Medium	Medium	Medium
Cancer	Medium	Medium	Medium

Mouse Genome Informatics

• Gene name: Upf2
• Phenotype: immune system 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); hematopoietic system phenotype; endocrine/exocrine gland phenotype

Zebrafish Information Network

• Gene name: upf2
• Affected structure: extension
• Phenotype tag: abnormal
• Phenotype quality: decreased thickness

Gene ontology

• Biological process: nuclear-transcribed mRNA catabolic process, nonsense-mediated decay;liver development;mRNA export from nucleus;animal organ regeneration
• Cellular component: nucleus;cytoplasm;cytosol;polysome;exon-exon junction complex;cytoplasmic ribonucleoprotein granule;perinuclear region of cytoplasm
• Molecular function: RNA binding;protein binding;telomeric DNA binding