U2AF1L4

U2 small nuclear RNA auxiliary factor 1 like 4, the group of RNA binding motif containing

Basic information

Region (hg38): 19:35742464-35745445

Previous symbols: [ "U2AF1L3" ]

Links

ENSG00000161265

∙ NCBI:199746 ∙ OMIM:601080 ∙ HGNC:23020 ∙ Uniprot:Q8WU68 ∙ 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 U2AF1L4 gene.

not_specified (29 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the U2AF1L4 gene is commonly pathogenic or not. These statistics are base on transcript: NM_001040425.3. 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			21 clinvar	8 clinvar		29
nonsense						0
start loss						0
frameshift						0
splice donor/acceptor (+/-2bp)						0
Total	0	0	21	8	0

Loading clinvar variants...

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
U2AF1L4	protein_coding	protein_coding	ENST00000292879	6	2982

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.00000671	0.291	125643	2	103	125748	0.000418

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	-0.309	137	127	1.08	0.00000708	1308
Missense in Polyphen		23	29.101	0.79036		333
Synonymous	0.545	48	53.1	0.905	0.00000342	412
Loss of Function	0.0896	8	8.28	0.966	3.50e-7	100

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000324	0.000324
Ashkenazi Jewish	0.00	0.00
East Asian	0.0000544	0.0000544
Finnish	0.00	0.00
European (Non-Finnish)	0.0000357	0.0000352
Middle Eastern	0.0000544	0.0000544
South Asian	0.00291	0.00288
Other	0.000489	0.000489

dbNSFP

Source: dbNSFP

Function: FUNCTION: RNA-binding protein that function as a pre-mRNA splicing factor. Plays a critical role in both constitutive and enhancer- dependent splicing by mediating protein-protein interactions and protein-RNA interactions required for accurate 3'-splice site selection. Acts by enhancing the binding of U2AF2 to weak pyrimidine tracts. Also participates in the regulation of alternative pre-mRNA splicing. Activates exon 5 skipping of PTPRC during T-cell activation; an event reversed by GFI1. Binds to RNA at the AG dinucleotide at the 3'-splice site (By similarity). Shows a preference for AGC or AGA (By similarity). {ECO:0000250|UniProtKB:Q8BGJ9}.;
Pathway: Shigellosis - Homo sapiens (human);Spliceosome - Homo sapiens (human);Gene expression (Transcription);RNA Polymerase II Transcription;Metabolism of RNA;Cleavage of Growing Transcript in the Termination Region ;RNA Polymerase II Transcription Termination;mRNA Splicing - Major Pathway;Transport of Mature mRNA derived from an Intron-Containing Transcript;mRNA Splicing;mRNA 3,-end processing;Transport of Mature Transcript to Cytoplasm;Processing of Capped Intron-Containing Pre-mRNA (Consensus)

Intolerance Scores

loftool: 0.470
rvis_EVS: -0.16
rvis_percentile_EVS: 41.64

Haploinsufficiency Scores

pHI: 0.0884
hipred: N
hipred_score: 0.146
ghis: 0.547

Essentials

essential_gene_CRISPR: N
essential_gene_CRISPR2: N
essential_gene_gene_trap: N
gene_indispensability_pred: E
gene_indispensability_score: 0.653

Gene Damage Prediction

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

Mouse Genome Informatics

Gene name: U2af1l4
Phenotype: behavior/neurological phenotype (the observable actions or reactions of mammalian organisms that are manifested through development and lifespan);

Gene ontology

Biological process: mRNA splicing, via spliceosome;RNA export from nucleus;mRNA export from nucleus;mRNA 3'-end processing
Cellular component: nucleoplasm;spliceosomal complex;cytoplasm;nuclear speck;U2AF
Molecular function: pre-mRNA 3'-splice site binding;metal ion binding