U2AF1L4

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

Basic information

Region (hg38): 19:35742463-35745445

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.

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.

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			21	3		24
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	21	3	0

Variants in U2AF1L4

This is a list of pathogenic ClinVar variants found in the U2AF1L4 region.

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

Position	Type	Phenotype	Significance	ClinVar
19-35742636-A-G		not specified	Uncertain significance (Dec 17, 2023)
19-35742645-A-G		not specified	Uncertain significance (Oct 26, 2022)
19-35742674-G-A		not specified	Likely benign (Aug 22, 2023)
19-35742689-T-C		not specified	Uncertain significance (Oct 05, 2021)
19-35742753-C-T		not specified	Uncertain significance (Dec 14, 2023)
19-35742798-G-A		not specified	Uncertain significance (Apr 22, 2022)
19-35743812-C-A		not specified	Uncertain significance (Apr 25, 2022)
19-35743812-C-T		not specified	Likely benign (Jan 19, 2024)
19-35743830-T-C		not specified	Uncertain significance (Nov 29, 2021)
19-35743863-C-T		not specified	Uncertain significance (Dec 11, 2023)
19-35743871-C-A		not specified	Uncertain significance (Jul 25, 2023)
19-35743880-G-C		not specified	Uncertain significance (Nov 17, 2023)
19-35743899-C-G		not specified	Uncertain significance (Oct 26, 2022)
19-35744102-C-T		not specified	Likely benign (Jan 12, 2024)
19-35744106-G-A		not specified	Uncertain significance (Dec 14, 2023)
19-35744120-C-G		not specified	Uncertain significance (Apr 10, 2023)
19-35744142-G-A		not specified	Uncertain significance (Nov 15, 2021)
19-35744325-T-C		not specified	Uncertain significance (Aug 01, 2022)
19-35744364-C-T		not specified	Uncertain significance (Aug 13, 2021)
19-35744378-T-C		not specified	Uncertain significance (Jul 20, 2021)
19-35745158-G-C		not specified	Uncertain significance (Sep 13, 2023)
19-35745166-C-A		not specified	Uncertain significance (Oct 10, 2023)
19-35745181-C-A		not specified	Uncertain significance (Dec 19, 2022)
19-35745384-T-C		not specified	Uncertain significance (May 23, 2023)

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