LSM2
protein-codingLSM2 homolog, U6 small nuclear RNA and 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. Pseudogenes of this gene are located on the short arm of chromosomes 6 and 19. [provided by RefSeq, Nov 2011]
- C6orf28
MANE transcript
Inheritance
ClinVar variants
Top phenotype
gnomAD constraint
Max pathogenic AF
Genomic locus
External References & Databases
Transcript & Mutation Effects
hg38 • Region Span ~9.6 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 LSM2 variants in ClinVar
No annotated ClinVar phenotypes.
ClinVar Variants & Pathogenicity by Type
Statistics based on transcript NM_021177.5. 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 | 0 | |||||
| nonsense | 0 | |||||
| start loss | 0 | |||||
| frameshift | 0 | |||||
| splice donor/acceptor (+/-2bp) | 3 | 3 | ||||
| Total | 0 | 0 | 3 | 0 | 0 | 3 |
Transcript Catalog
Annotated transcript isoforms across RefSeq and Ensembl databases
| Transcript ID | Source | Protein ID | Coding Exons | MANE Status |
|---|---|---|---|---|
| RefSeq | NP_067000.1 | 5 | MANE Select | |
| Ensembl | ENSP00000364813.5 | 5 | MANE Select | |
| Ensembl | ENSP00000574377.1 | 5 | Standard | |
| Ensembl | ENSP00000574377.1 | 5 | Standard |
Gene Ontology (GO) Annotations & Pathways
Biological processes, molecular functions, cellular components and pathways
Pathways ConsensusPathDB
- RNA degradation - Homo sapiens (human)
- Spliceosome - Homo sapiens (human)
- mRNA Processing
- Metabolism of RNA
- mRNA Splicing - Major Pathway
Biological Process
- mRNA splicing, via spliceosome
- exonucleolytic nuclear-transcribed mRNA catabolic process involved in deadenylation-dependent decay
Molecular Function
- RNA binding
- protein binding
- U6 snRNA binding
- Ral GTPase binding
Cellular Component
- P-body
- nucleus
- nucleoplasm
- U6 snRNP
- cytosol
gnomAD Constraint
Source:
- Gene type
- protein_coding
- Transcript type
- protein_coding
- Transcript
- ENST00000375661
- Coding exons
- 5
- Length
- 9589
- Individuals with no LoFs
- 123436
- Homozygous LoFs
- 0
- Heterozygous LoFs
- 14
- Defined
- 123450
- p
- 0.0000567
| Z-Score | Observed | Expected | Observed/Expected | Mutation Rate | Total Possible | |
|---|---|---|---|---|---|---|
| Missense | 1.83 | 14 | 50.5 | 0.277 | 0.00000260 | 610 |
| Missense (PolyPhen) | 3 | 12.931 | 0.232 | 151 | ||
| Synonymous | 0.805 | 17 | 21.8 | 0.781 | 0.00000124 | 181 |
| Loss of Function | 0.0218 | 7 | 7.06 | 0.991 | 3.84e-7 | 78 |
Population LoF Frequency
| Population | CAF | p-value | Status |
|---|---|---|---|
| African | 0.000066 | 0.000066 | rare |
| Latino/Admixed American | 0 | 0.0 | absent |
| Ashkenazi Jewish | 0 | 0.0 | absent |
| East Asian | 0.000056 | 0.000055 | rare |
| Finnish | 0.000048 | 0.000046 | rare |
| European (Non-Finnish) | 0.000065 | 0.000063 | rare |
| South Asian | 0.000099 | 0.000099 | rare |
| Other | 0.00017 | 0.00016 | rare |
dbNSFP Gene Annotations
Source:
- Function
- FUNCTION: Plays role in pre-mRNA splicing as component of the U4/U6-U5 tri-snRNP complex that is involved in spliceosome assembly, and as component of the precatalytic spliceosome (spliceosome B complex) (PubMed:28781166). The heptameric LSM2-8 complex binds specifically to the 3'-terminal U-tract of U6 snRNA (PubMed:10523320). {ECO:0000269|PubMed:10523320, ECO:0000269|PubMed:28781166}.;
Recessive Scores
- pRec
- 0.118
Intolerance Scores
- LoFtool
- 0.677
- RVIS EVS
- 0.19
- RVIS percentile EVS
- 66.32
Essentials
- Essential (CRISPR)
- E
- Essential (CRISPR2)
- N
- Essential (gene trap)
- E
- Indispensability pred.
- E
- Indispensability score
- 0.731