LSM10
Basic information
Region (hg38): 1:36391238-36397908
Links
Phenotypes
GenCC
Source:
ClinVar
This is a list of variants' phenotypes submitted to
Variants pathogenicity by type
Statistics on ClinVar variants can assist in determining whether a specific variant type in the LSM10 gene is commonly pathogenic or not.
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.
| Variant type | Pathogenic | Likely pathogenic | VUS | Likely benign | Benign | Sum |
|---|---|---|---|---|---|---|
| synonymous | 0 | |||||
| missense | 4 | |||||
| nonsense | 0 | |||||
| start loss | 0 | |||||
| frameshift | 0 | |||||
| inframe indel | 0 | |||||
| splice donor/acceptor (+/-2bp) | 0 | |||||
| splice region | 0 | |||||
| non coding | 0 | |||||
| Total | 0 | 0 | 4 | 0 | 0 |
Variants in LSM10
This is a list of pathogenic ClinVar variants found in the LSM10 region.
You can filter this list by clicking the number of variants in the Variants pathogenicity by type table.
| Position | Type | Phenotype | Significance | ClinVar |
|---|---|---|---|---|
| 1-36393784-C-G | not specified | Uncertain significance (Dec 28, 2023) | ||
| 1-36393793-C-G | not specified | Uncertain significance (May 31, 2023) | ||
| 1-36393868-C-T | not specified | Uncertain significance (Jun 24, 2022) | ||
| 1-36393882-T-C | not specified | Uncertain significance (Jun 19, 2024) | ||
| 1-36393941-C-A | not specified | Uncertain significance (Nov 23, 2022) | ||
| 1-36394018-C-T | Fraser syndrome 3 | Uncertain significance (-) |
GnomAD
Source:
| Gene | Type | Bio Type | Transcript | Coding Exons | Length |
|---|---|---|---|---|---|
| LSM10 | protein_coding | protein_coding | ENST00000315732 | 1 | 6655 |
| pLI Probability LOF Intolerant | pRec Probability LOF Recessive | Individuals with no LOFs | Individuals with Homozygous LOFs | Individuals with Heterozygous LOFs | Defined | p |
|---|---|---|---|---|---|---|
| 0.00407 | 0.435 | 125738 | 0 | 6 | 125744 | 0.0000239 |
| Z-Score | Observed | Expected | Observed/Expected | Mutation Rate | Total Possible in Transcript | |
|---|---|---|---|---|---|---|
| Missense | 0.468 | 72 | 84.1 | 0.856 | 0.00000626 | 801 |
| Missense in Polyphen | 28 | 32.308 | 0.86665 | 290 | ||
| Synonymous | -0.305 | 35 | 32.8 | 1.07 | 0.00000205 | 260 |
| Loss of Function | -0.433 | 3 | 2.29 | 1.31 | 9.94e-8 | 23 |
LoF frequencies by population
| Ethnicity | Sum of pLOFs | p |
|---|---|---|
| African & African-American | 0.00 | 0.00 |
| Ashkenazi Jewish | 0.00 | 0.00 |
| East Asian | 0.00 | 0.00 |
| Finnish | 0.00 | 0.00 |
| European (Non-Finnish) | 0.0000440 | 0.0000440 |
| Middle Eastern | 0.00 | 0.00 |
| South Asian | 0.0000327 | 0.0000327 |
| Other | 0.00 | 0.00 |
dbNSFP
Source:
- Function
- FUNCTION: Appears to function in the U7 snRNP complex that is involved in histone 3'-end processing. Increases U7 snRNA levels but not histone 3'-end pre-mRNA processing activity, when overexpressed. Required for cell cycle progression from G1 to S phases. Binds specifically to U7 snRNA. Binds to the downstream cleavage product (DCP) of histone pre-mRNA in a U7 snRNP dependent manner. {ECO:0000269|PubMed:16914750}.;
- Pathway
- Gene expression (Transcription);RNA Polymerase II Transcription;SLBP Dependent Processing of Replication-Dependent Histone Pre-mRNAs;Metabolism of RNA;Processing of Capped Intronless Pre-mRNA;Cleavage of Growing Transcript in the Termination Region ;RNA Polymerase II Transcription Termination;SLBP independent Processing of Histone Pre-mRNAs
(Consensus)
Recessive Scores
- pRec
- 0.105
Intolerance Scores
- loftool
- 0.178
- rvis_EVS
- -0.03
- rvis_percentile_EVS
- 51.04
Haploinsufficiency Scores
- pHI
- 0.133
- hipred
- Y
- hipred_score
- 0.744
- ghis
- 0.524
Essentials
- essential_gene_CRISPR
- N
- essential_gene_CRISPR2
- S
- essential_gene_gene_trap
- E
- gene_indispensability_pred
- E
- gene_indispensability_score
- 0.876
Gene Damage Prediction
| All | Recessive | Dominant | |
|---|---|---|---|
| Mendelian | Medium | Medium | Medium |
| Primary Immunodeficiency | Medium | Medium | Medium |
| Cancer | Medium | Medium | Medium |
Mouse Genome Informatics
- Gene name
- Lsm10
- Phenotype
Gene ontology
- Biological process
- termination of RNA polymerase II transcription;mRNA processing;histone mRNA metabolic process;RNA splicing;positive regulation of G1/S transition of mitotic cell cycle
- Cellular component
- nucleus;nucleoplasm;U7 snRNP;Cajal body;nuclear body
- Molecular function
- protein binding;histone pre-mRNA DCP binding;U7 snRNA binding