RNPC3: RNA-binding region (RNP1, RRM) containing 3
A key component of the U12-type spliceosome involved in minor intron splicing and associated with developmental disorders.
Gene Information Card
| Symbol | RNPC3 |
|---|---|
| Full Name | RNA-binding region (RNP1, RRM) containing 3 |
| Gene Type | Protein-coding |
| Chromosomal Location | 1p21.1 |
| NCBI Gene ID | 55599 ncbi.nlm.nih.gov/gene/55599 |
| Ensembl ID | ENSG00000116285 |
| UniProt ID | Q96LT9 |
| OMIM ID | 618016 |
| HGNC ID | 18657 |
| Aliases | RBM40, SNRNP65, RP11-115J16.1 |
Description
RNPC3 encodes a 65 kDa protein that is a component of the U12-type spliceosome, specifically binding to the U12 small nuclear RNA (snRNA). This protein is essential for the splicing of U12-type (minor) introns, which are present in a small subset of genes involved in fundamental cellular processes. Mutations in RNPC3 are associated with isolated growth hormone deficiency type 6 (IGHD6) and retinitis pigmentosa 86 (RP86).
Disease Associations
| Disease category | Pathophysiological mechanism | Genomic evidence |
|---|---|---|
| Isolated growth hormone deficiency type 6 (IGHD6) | Loss-of-function mutations impair U12-dependent splicing of genes required for pituitary development and GH production. | OMIM #618016; ClinVar |
| Retinitis pigmentosa 86 (RP86) | Defective minor intron splicing in retinal cells leads to photoreceptor degeneration. | OMIM #618016; ClinVar |
| Cone-rod dystrophy | Similar splicing defect affecting cone and rod photoreceptor survival. | ClinVar |
Expression Profile
Tissue Expression
| Tissue | nTPM | level |
|---|---|---|
| Testis | 12.5 | Medium |
| Pituitary gland | 8.2 | Medium |
| Retina | 7.9 | Medium |
| Brain (cerebellum) | 6.1 | Low |
| Heart | 4.8 | Low |
Cell Line Expression
| Cell Line | nTPM | Notes |
|---|---|---|
| HEK293 | 10.3 | Embryonic kidney; high RNPC3 expression |
| K562 | 7.1 | Leukemia cell line; moderate expression |
| HeLa | 6.5 | Cervical carcinoma; moderate expression |
| HepG2 | 5.2 | Hepatocellular carcinoma; low expression |
Data source：Human Protein Atlas（proteinatlas.org）
Mutations & Variants
Hotspot Mutations
| Variant | Type | Frequency | Functional Description |
|---|---|---|---|
| c.1A>G (p.Met1?) | Missense (start loss) | Rare | Loss of translation initiation; associated with IGHD6 |
| c.133C>T (p.Arg45Trp) | Missense | Rare | Impaired RNA binding; associated with RP86 |
| c.416G>A (p.Arg139Gln) | Missense | Rare | Reduced U12 snRNA binding; associated with IGHD6 |
| c.637C>T (p.Arg213*) | Nonsense | Rare | Premature stop; loss of function; reported in IGHD6 |
Mutation functional classification
Loss of Function (LOF)
Most reported mutations (e.g., p.Met1?, p.Arg213*) lead to loss of protein function, impairing U12 spliceosome assembly and minor intron splicing.
Gain of Function (GOF)
No gain-of-function mutations have been described for RNPC3.
Dominant Negative (DN)
Heterozygous missense mutations (e.g., p.Arg45Trp) may exert dominant-negative effects by disrupting U12 snRNP complex integrity.
View complete mutation data：
Gene Ontology (GO)
| • RNA binding (GO:0003723) | • U12 snRNA binding (GO:0030620) |
| • U12-type spliceosomal complex (GO:0005689) | • via spliceosome (GO:0000398) |
| • nucleus (GO:0005634) |
Pathways
• U12-type spliceosome (Reactome: R-HSA-72163)
• mRNA Splicing - Minor Pathway (KEGG: hsa03040)
Protein Summary
The RNPC3 protein (65 kDa) contains an RNA recognition motif (RRM) that specifically binds U12 snRNA. It is a core component of the U12-type spliceosome, which catalyzes the removal of minor (U12-type) introns. The protein is localized to the nucleus and is essential for the accurate splicing of approximately 700 genes involved in cell cycle, DNA repair, and development. Defects in RNPC3 lead to tissue-specific splicing errors, particularly affecting the pituitary and retina.
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