SF3A3
Splicing Factor 3a Subunit 3
Gene Information Card
| Symbol | SF3A3 |
|---|---|
| Full Name | Splicing Factor 3a Subunit 3 |
| Gene Type | protein-coding |
| Chromosomal Location | 1p34.3 |
| NCBI Gene ID | 10946 ncbi.nlm.nih.gov/gene/10946 |
| Ensembl ID | ENSG00000134243 |
| UniProt ID | Q12874 |
| OMIM ID | 605596 |
| HGNC ID | 10767 |
| Aliases | PRP9, SAP61, SF3a60 |
Description
SF3A3 encodes a subunit of the splicing factor 3a complex, which is essential for the assembly of the U2 small nuclear ribonucleoprotein (snRNP) onto the pre-mRNA branch site. This protein interacts with other spliceosomal components to facilitate pre-mRNA splicing. Mutations in SF3A3 have been implicated in various cancers and developmental disorders.
Disease Associations
| Disease category | Pathophysiological mechanism | Genomic evidence |
|---|---|---|
| Myelodysplastic syndrome | Spliceosomal mutations lead to aberrant RNA splicing and hematopoietic dysfunction | COSMIC, ClinVar |
| Acute myeloid leukemia | Recurrent mutations in SF3A3 alter splicing of key regulatory genes | COSMIC, ClinVar |
| Retinitis pigmentosa | Missense mutations disrupt U2 snRNP assembly, affecting retinal cell survival | OMIM, ClinVar |
Expression Profile
Tissue Expression
| Tissue | nTPM | level |
|---|---|---|
| Testis | 28.5 | High |
| Lymph node | 18.2 | Medium |
| Brain | 12.1 | Medium |
| Liver | 8.9 | Low |
| Heart | 7.4 | Low |
Cell Line Expression
| Cell Line | nTPM | Notes |
|---|---|---|
| K562 | 22.3 | Leukemia cell line |
| HeLa | 19.8 | Cervical carcinoma |
| HepG2 | 15.6 | Hepatocellular carcinoma |
| A549 | 14.2 | Lung adenocarcinoma |
Data source：Human Protein Atlas（proteinatlas.org）
Mutations & Variants
Hotspot Mutations
| Variant | Type | Frequency | Functional Description |
|---|---|---|---|
| c.128A>G (p.Asn43Ser) | Missense | 0.5% in AML | Alters splicing factor activity |
| c.625C>T (p.Arg209Trp) | Missense | 0.3% in MDS | Disrupts U2 snRNP binding |
| c.1024_1026del (p.Lys342del) | In-frame deletion | Rare | Impairs spliceosome assembly |
Mutation functional classification
Loss of Function (LOF)
Missense mutations in the zinc finger domain reduce RNA binding and splicing efficiency.
Gain of Function (GOF)
Not reported.
Dominant Negative (DN)
Mutant SF3A3 can interfere with wild-type spliceosome assembly, leading to global splicing defects.
View complete mutation data：
Gene Ontology (GO)
| • RNA splicing | • mRNA processing |
| • spliceosomal complex assembly | • U2 snRNP binding |
| • nucleus |
Pathways
• Spliceosome (KEGG hsa03040)
• mRNA Splicing - Major Pathway (Reactome R-HSA-72163)
Protein Summary
SF3A3 is a 501-amino acid protein (UniProt Q12874) that contains a zinc finger domain and is part of the SF3a complex. It localizes to the nucleus and is essential for the early steps of spliceosome assembly. The protein interacts with SF3A1, SF3A2, and U2 snRNA to form the active U2 snRNP.
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