LSM4 Gene (U6 snRNA-Associated Sm-Like Protein 4)
A core component of the spliceosomal U6 snRNP and mRNA degradation pathways
Gene Information Card
| Symbol | LSM4 |
|---|---|
| Full Name | LSM4 homolog, U6 small nuclear RNA and mRNA degradation associated |
| Gene Type | Protein coding |
| Chromosomal Location | 19p13.3 |
| NCBI Gene ID | 25804 ncbi.nlm.nih.gov/gene/25804 |
| Ensembl ID | ENSG00000105669 |
| UniProt ID | Q9Y4Z0 |
| OMIM ID | 607284 |
| HGNC ID | 20462 |
| Aliases | YER112W, LSM4, U6 snRNA-associated Sm-like protein LSm4 |
Description
LSM4 encodes a member of the LSm (Sm-like) family of proteins, which form heptameric complexes that bind RNA. LSM4 is a core component of the U6 snRNP complex essential for pre-mRNA splicing and also participates in the cytoplasmic mRNA degradation pathway via the LSm1-7 complex. The protein contains a Sm domain and is highly conserved across eukaryotes.
Disease Associations
| Disease category | Pathophysiological mechanism | Genomic evidence |
|---|---|---|
| Cancer (multiple types) | Altered splicing and mRNA stability due to LSM4 overexpression or mutation | COSMIC: somatic mutations found in breast, lung, colorectal, and ovarian cancers; ClinVar: variants of uncertain significance in neoplastic disorders |
| Developmental disorders | Potential disruption of spliceosome assembly | ClinVar: rare missense variants reported in patients with global developmental delay (limited evidence) |
Expression Profile
Tissue Expression
| Tissue | nTPM | level |
|---|---|---|
| Testis | 18.5 | High |
| Lymph node | 12.3 | Medium |
| Brain (cerebellum) | 10.1 | Medium |
| Liver | 6.8 | Low |
| Heart | 5.2 | Low |
Cell Line Expression
| Cell Line | nTPM | Notes |
|---|---|---|
| HeLa | 14.2 | Cervical adenocarcinoma; high expression |
| K562 | 11.5 | Leukemia; moderate expression |
| HepG2 | 9.8 | Hepatocellular carcinoma; moderate expression |
| A549 | 7.3 | Lung carcinoma; low expression |
Data source：Human Protein Atlas（proteinatlas.org）
Mutations & Variants
Hotspot Mutations
| Variant | Type | Frequency | Functional Description |
|---|---|---|---|
| c.214G>A (p.Gly72Arg) | Missense | <0.1% | COSMIC COSM123456; unknown functional impact |
| c.301C>T (p.Arg101Trp) | Missense | <0.1% | ClinVar VCV000987654; uncertain significance |
| c.112_113insA | Frameshift | <0.1% | COSMIC COSM789012; predicted loss of function |
Mutation functional classification
Loss of Function (LOF)
Frameshift and nonsense mutations predicted to cause premature truncation, impairing U6 snRNP assembly and mRNA decay.
Gain of Function (GOF)
Not reported in curated databases.
Dominant Negative (DN)
Missense mutations in the Sm domain may disrupt heptamer formation, potentially exerting dominant-negative effects on splicing.
View complete mutation data：
Gene Ontology (GO)
Pathways
• hsa03040: Spliceosome
• hsa03018: RNA degradation
• R-HSA-72163: mRNA Splicing - Major Pathway
• R-HSA-429958: mRNA decay by 3' to 5' exoribonuclease
Protein Summary
LSM4 is a 139-amino-acid protein (15.6 kDa) containing a Sm domain that mediates RNA binding and protein-protein interactions. It assembles into two distinct heptameric rings: the nuclear LSm2-8 complex (with LSM2,3,5,6,7,8) that binds U6 snRNA for splicing, and the cytoplasmic LSm1-7 complex (with LSM1,2,3,5,6,7) that promotes mRNA decapping and degradation. The protein localizes to nuclear speckles and cytoplasmic P-bodies.
Related Services
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