LSM1
protein-codingLSM1 homolog, mRNA degradation associated, the group of LSm proteins
Gene summary
This gene encodes a member of the LSm family of RNA-binding proteins. LSm proteins form stable heteromers that bind specifically to the 3'-terminal oligo(U) tract of U6 snRNA and may play a role in pre-mRNA splicing by mediating U4/U6 snRNP formation. Increased expression of this gene may play a role in cellular transformation and the progression of several malignancies including lung cancer, mesothelioma and breast cancer. Alternatively spliced transcript variants have been observed for this gene, and a pseudogene of this gene is located on the short arm of chromosome 9. [provided by RefSeq, Nov 2011]
MANE transcript
Inheritance
ClinVar variants
Top phenotype
gnomAD constraint
Max pathogenic AF
Genomic locus
External References & Databases
Transcript & Mutation Effects
hg38 • Region Span ~13.4 kbGenCC Phenotypes & Disease Associations
Curated gene-disease validity assertions and inheritance patterns
Inheritance Pattern: AR
Disease ID:MONDO:0700092
Submitter: PanelApp Australia
ClinVar Associated Diseases & Phenotypes
Reported disease conditions connected to LSM1 variants in ClinVar
ClinVar Variants & Pathogenicity by Type
Statistics based on transcript NM_014462.3. 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 | 1 | 1 | ||||
| missense | 1 | 16 | 17 | |||
| nonsense | 0 | |||||
| start loss | 1 | 1 | ||||
| frameshift | 0 | |||||
| splice donor/acceptor (+/-2bp) | 2 | 2 | ||||
| Total | 0 | 1 | 20 | 0 | 0 | 21 |
Transcript Catalog
Annotated transcript isoforms across RefSeq and Ensembl databases
| Transcript ID | Source | Protein ID | Coding Exons | MANE Status |
|---|---|---|---|---|
| RefSeq | NP_055277.1 | 4 | MANE Select | |
| Ensembl | ENSP00000310596.4 | 4 | MANE Select | |
| Ensembl | ENSP00000430021.1 | 3 | Standard | |
| Ensembl | ENSP00000430021.1 | 3 | Standard |
Gene Ontology (GO) Annotations & Pathways
Biological processes, molecular functions, cellular components and pathways
Pathways ConsensusPathDB
- RNA degradation - Homo sapiens (human)
- Metabolism of RNA
- mRNA decay by 5, to 3, exoribonuclease
- Deadenylation-dependent mRNA decay
Biological Process
- deadenylation-dependent decapping of nuclear-transcribed mRNA
- RNA splicing, via transesterification reactions
- mRNA processing
- RNA splicing
- RNA metabolic process
Molecular Function
- RNA cap binding
- RNA binding
- mRNA binding
- protein binding
- pre-mRNA binding
Cellular Component
- P-body
- nucleus
- cytoplasm
- cytosol
- axon
gnomAD Constraint
Source:
- Gene type
- protein_coding
- Transcript type
- protein_coding
- Transcript
- ENST00000311351
- Coding exons
- 4
- Length
- 13410
- Individuals with no LoFs
- 125738
- Homozygous LoFs
- 0
- Heterozygous LoFs
- 7
- Defined
- 125745
- p
- 0.0000278
| Z-Score | Observed | Expected | Observed/Expected | Mutation Rate | Total Possible | |
|---|---|---|---|---|---|---|
| Missense | 1.00 | 48 | 71.9 | 0.668 | 0.00000359 | 862 |
| Missense (PolyPhen) | 14 | 22.173 | 0.63141 | 262 | ||
| Synonymous | 0.554 | 22 | 25.6 | 0.861 | 0.00000120 | 262 |
| Loss of Function | 1.20 | 4 | 7.57 | 0.528 | 4.53e-7 | 79 |
Population LoF Frequency
| Population | CAF | p-value | Status |
|---|---|---|---|
| African | 0.000062 | 0.000062 | rare |
| Latino/Admixed American | 0 | 0.0 | absent |
| Ashkenazi Jewish | 0 | 0.0 | absent |
| East Asian | 0.000054 | 0.000054 | rare |
| Finnish | 0 | 0.0 | absent |
| European (Non-Finnish) | 0.000026 | 0.000026 | rare |
| South Asian | 0.000066 | 0.000065 | rare |
| Other | 0 | 0.0 | absent |
dbNSFP Gene Annotations
Source:
- Function
- FUNCTION: Plays a role in the degradation of histone mRNAs, the only eukaryotic mRNAs that are not polyadenylated (PubMed:18172165). Probably also part of an LSm subunits- containing complex involved in the general process of mRNA degradation (By similarity). {ECO:0000250|UniProtKB:P47017, ECO:0000269|PubMed:18172165}.;
Recessive Scores
- pRec
- 0.132
Intolerance Scores
- RVIS EVS
- -0.05
- RVIS percentile EVS
- 49.39
Essentials
- Essential (CRISPR)
- N
- Essential (CRISPR2)
- N
- Essential (gene trap)
- N
- Indispensability pred.
- E
- Indispensability score
- 0.801
Gene Damage Prediction
| All | Recessive | Dominant | |
|---|---|---|---|
| Mendelian | Medium | Low | Low |
| Primary Immunodeficiency | Medium | Low | Medium |
| Cancer | Medium | Low | Medium |