LSM1
LSM1 homolog, mRNA degradation associated, the group of LSm proteins
Basic information
Region (hg38): 8:38163335-38176730
Links
Phenotypes
GenCC
Source:
No genCC data.
ClinVar
This is a list of variants' phenotypes submitted to
- not_specified (14 variants)
- not_provided (1 variants)
- Fetal_pyelectasis (1 variants)
- Strabismus (1 variants)
- Generalized_hypotonia (1 variants)
- Triphalangeal_thumb (1 variants)
- Hemivertebrae (1 variants)
- Cryptorchidism (1 variants)
- Global_developmental_delay (1 variants)
- Neurodevelopmental_delay (1 variants)
- Penile_hypospadias (1 variants)
- Intellectual_disability (1 variants)
- Complex_neurodevelopmental_disorder (1 variants)
- Perimembranous_ventricular_septal_defect (1 variants)
- Feeding_difficulties (1 variants)
- Patent_ductus_arteriosus_after_premature_birth (1 variants)
- Hydroureter (1 variants)
- Oligohydramnios (1 variants)
- Inguinal_hernia (1 variants)
- Bicuspid_aortic_valve (1 variants)
- Abnormal_facial_shape (1 variants)
- FICUS_SYNDROME (1 variants)
- Constipation (1 variants)
- Mitral_stenosis (1 variants)
Variants pathogenicity by type
Statistics on ClinVar variants can assist in determining whether a specific variant type in the LSM1 gene is commonly pathogenic or not. These statistics are base on transcript: NM_000014462.3. Only rare variants are included in the table.
In the table, we include only reliable ClinVar variants with their consequences to MANE Select, Mane Plus Clinical transcripts, or transcripts with TSL equals 1. Click the count to view the source variants.
Warning: slight differences between displayed counts and the number of variants in ClinVar may occur, primarily due to (1) the application of a different transcript and/or consequence by our variant effect predictor or (2) differences in clinical significance: we classify Benign/Likely benign variants as Likely benign and Pathogenic/Likely pathogenic variants as Likely pathogenic.
| Effect | PathogenicP | Likely pathogenicLP | VUSVUS | Likely benignLB | BenignB | Sum |
|---|---|---|---|---|---|---|
| synonymous | 1 | |||||
| missense | 14 | 15 | ||||
| nonsense | 0 | |||||
| start loss | 1 | 1 | ||||
| frameshift | 0 | |||||
| splice donor/acceptor (+/-2bp) | 2 | |||||
| Total | 0 | 1 | 18 | 0 | 0 |
Loading clinvar variants...
GnomAD
Source:
| Gene | Type | Bio Type | Transcript | Coding Exons | Length |
|---|---|---|---|---|---|
| LSM1 | protein_coding | protein_coding | ENST00000311351 | 4 | 13410 |
| pLI Probability LOF Intolerant | pRec Probability LOF Recessive | Individuals with no LOFs | Individuals with Homozygous LOFs | Individuals with Heterozygous LOFs | Defined | p |
|---|---|---|---|---|---|---|
| 0.0110 | 0.850 | 125738 | 0 | 7 | 125745 | 0.0000278 |
| Z-Score | Observed | Expected | Observed/Expected | Mutation Rate | Total Possible in Transcript | |
|---|---|---|---|---|---|---|
| Missense | 1.00 | 48 | 71.9 | 0.668 | 0.00000359 | 862 |
| Missense in 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 |
LoF frequencies by population
| Ethnicity | Sum of pLOFs | p |
|---|---|---|
| African & African-American | 0.0000615 | 0.0000615 |
| Ashkenazi Jewish | 0.00 | 0.00 |
| East Asian | 0.0000544 | 0.0000544 |
| Finnish | 0.00 | 0.00 |
| European (Non-Finnish) | 0.0000264 | 0.0000264 |
| Middle Eastern | 0.0000544 | 0.0000544 |
| South Asian | 0.0000665 | 0.0000653 |
| Other | 0.00 | 0.00 |
dbNSFP
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}.;
- Pathway
- RNA degradation - Homo sapiens (human);Metabolism of RNA;mRNA decay by 5, to 3, exoribonuclease;Deadenylation-dependent mRNA decay
(Consensus)
Recessive Scores
- pRec
- 0.132
Intolerance Scores
- loftool
- rvis_EVS
- -0.05
- rvis_percentile_EVS
- 49.39
Haploinsufficiency Scores
- pHI
- 0.571
- hipred
- Y
- hipred_score
- 0.783
- ghis
- 0.599
Essentials
- essential_gene_CRISPR
- N
- essential_gene_CRISPR2
- N
- essential_gene_gene_trap
- N
- gene_indispensability_pred
- E
- gene_indispensability_score
- 0.801
Gene Damage Prediction
| All | Recessive | Dominant | |
|---|---|---|---|
| Mendelian | Medium | Low | Low |
| Primary Immunodeficiency | Medium | Low | Medium |
| Cancer | Medium | Low | Medium |
Mouse Genome Informatics
- Gene name
- Lsm1
- Phenotype
- behavior/neurological phenotype (the observable actions or reactions of mammalian organisms that are manifested through development and lifespan); cardiovascular system phenotype (the observable morphological and physiological characteristics of the mammalian heart, blood vessels, or circulatory system that are manifested through development and lifespan); mortality/aging (the observable characteristics related to the ability of a mammalian organism to live and age that are manifested throughout development and life span); vision/eye phenotype; hearing/vestibular/ear phenotype;
Gene ontology
- Biological process
- deadenylation-dependent decapping of nuclear-transcribed mRNA;RNA splicing, via transesterification reactions;mRNA processing;RNA splicing;RNA metabolic process;stem cell population maintenance;exonucleolytic nuclear-transcribed mRNA catabolic process involved in deadenylation-dependent decay;negative regulation of neuron differentiation;histone mRNA catabolic process
- Cellular component
- P-body;nucleus;cytoplasm;cytosol;axon;dendrite;neuronal cell body;messenger ribonucleoprotein complex;Lsm1-7-Pat1 complex
- Molecular function
- RNA cap binding;RNA binding;mRNA binding;protein binding;pre-mRNA binding