U2AF1L4
protein-codingU2 small nuclear RNA auxiliary factor 1 like 4, the group of RNA binding motif containing
Gene summary
Predicted to enable pre-mRNA 3'-splice site binding activity. Predicted to be involved in mRNA splicing, via spliceosome. Predicted to be located in nucleoplasm. Predicted to be part of U2AF complex and spliceosomal complex. [provided by Alliance of Genome Resources, Jul 2025]
- U2AF1L3
MANE transcript
Inheritance
ClinVar variants
Top phenotype
gnomAD constraint
Max pathogenic AF
Genomic locus
External References & Databases
Transcript & Mutation Effects
hg38 • Region Span ~3.0 kbGenCC Phenotypes & Disease Associations
Curated gene-disease validity assertions and inheritance patterns
No GenCC data available for this gene.
ClinVar Associated Diseases & Phenotypes
Reported disease conditions connected to U2AF1L4 variants in ClinVar
ClinVar Variants & Pathogenicity by Type
Statistics based on transcript NM_001040425.3. Only rare variants are included.
We include only reliable ClinVar variants with their consequences to MANE Select, MANE Plus Clinical transcripts, or transcripts with TSL equal to 1. Click a count to filter the variants table below.
Slight differences between displayed counts and ClinVar may occur due to a different transcript/consequence chosen by our variant effect predictor, or because we classify Benign/Likely benign as Likely benign and Pathogenic/Likely pathogenic as Likely pathogenic.
| Effect | PathogenicP | Likely pathogenicLP | VUS | Likely benignLB | BenignB | Sum |
|---|---|---|---|---|---|---|
| synonymous | 0 | |||||
| missense | 26 | 10 | 36 | |||
| nonsense | 0 | |||||
| start loss | 0 | |||||
| frameshift | 0 | |||||
| splice donor/acceptor (+/-2bp) | 0 | |||||
| Total | 0 | 0 | 26 | 10 | 0 | 36 |
Transcript Catalog
Annotated transcript isoforms across RefSeq and Ensembl databases
| Transcript ID | Source | Protein ID | Coding Exons | MANE Status |
|---|---|---|---|---|
| RefSeq | NP_001035515.1 | 6 | MANE Select | |
| Ensembl | ENSP00000368258.2 | 6 | MANE Select | |
| RefSeq | NP_001356753.1 | 6 | Standard | |
| RefSeq | NP_659424.2 | 6 | Standard |
Gene Ontology (GO) Annotations & Pathways
Biological processes, molecular functions, cellular components and pathways
Pathways ConsensusPathDB
- Shigellosis - Homo sapiens (human)
- Spliceosome - Homo sapiens (human)
- Gene expression (Transcription)
- RNA Polymerase II Transcription
- Metabolism of RNA
Biological Process
- mRNA splicing, via spliceosome
- RNA export from nucleus
- mRNA export from nucleus
- mRNA 3'-end processing
Molecular Function
- pre-mRNA 3'-splice site binding
- metal ion binding
Cellular Component
- nucleoplasm
- spliceosomal complex
- cytoplasm
- nuclear speck
- U2AF
gnomAD Constraint
Source:
- Gene type
- protein_coding
- Transcript type
- protein_coding
- Transcript
- ENST00000292879
- Coding exons
- 6
- Length
- 2982
- Individuals with no LoFs
- 125643
- Homozygous LoFs
- 2
- Heterozygous LoFs
- 103
- Defined
- 125748
- p
- 0.000418
| Z-Score | Observed | Expected | Observed/Expected | Mutation Rate | Total Possible | |
|---|---|---|---|---|---|---|
| Missense | -0.309 | 137 | 127 | 1.08 | 0.00000708 | 1308 |
| Missense (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 |
Population LoF Frequency
| Population | CAF | p-value | Status |
|---|---|---|---|
| African | 0.000062 | 0.000062 | rare |
| Latino/Admixed American | 0.00026 | 0.00023 | rare |
| Ashkenazi Jewish | 0 | 0.0 | absent |
| East Asian | 0.000054 | 0.000054 | rare |
| Finnish | 0 | 0.0 | absent |
| European (Non-Finnish) | 0.000036 | 0.000035 | rare |
| South Asian | 0.0029 | 0.0029 | notable |
| Other | 0.00049 | 0.00049 | rare |
dbNSFP Gene Annotations
Source:
- 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}.;
Intolerance Scores
- LoFtool
- 0.470
- RVIS EVS
- -0.16
- RVIS percentile EVS
- 41.64
Essentials
- Essential (CRISPR)
- N
- Essential (CRISPR2)
- N
- Essential (gene trap)
- N
- Indispensability pred.
- E
- Indispensability score
- 0.653
Gene Damage Prediction
| All | Recessive | Dominant | |
|---|---|---|---|
| Mendelian | Medium | Medium | Medium |
| Primary Immunodeficiency | Medium | Medium | Medium |
| Cancer | Medium | Medium | Medium |