SLBP
stem-loop binding protein
Basic information
Region (hg38): 4:1692731-1712344
Links
Phenotypes
GenCC
Source:
No genCC data.
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 SLBP 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 | 11 | 12 | ||||
| nonsense | 0 | |||||
| start loss | 0 | |||||
| frameshift | 0 | |||||
| inframe indel | 0 | |||||
| splice donor/acceptor (+/-2bp) | 0 | |||||
| splice region | 0 | |||||
| non coding | 0 | |||||
| Total | 0 | 0 | 11 | 1 | 0 |
Variants in SLBP
This is a list of pathogenic ClinVar variants found in the SLBP region.
You can filter this list by clicking the number of variants in the Variants pathogenicity by type table.
| Position | Type | Phenotype | Significance | ClinVar |
|---|---|---|---|---|
| 4-1693698-T-A | not specified | Uncertain significance (Mar 28, 2023) | ||
| 4-1694827-G-A | not specified | Uncertain significance (Apr 04, 2023) | ||
| 4-1696235-G-A | not specified | Uncertain significance (Mar 12, 2024) | ||
| 4-1696292-C-G | not specified | Uncertain significance (Aug 08, 2023) | ||
| 4-1696295-C-A | not specified | Uncertain significance (May 26, 2024) | ||
| 4-1696314-T-C | not specified | Uncertain significance (Dec 14, 2021) | ||
| 4-1696345-A-G | Likely benign (Sep 01, 2024) | |||
| 4-1699586-G-A | not specified | Uncertain significance (Oct 29, 2024) | ||
| 4-1699659-A-C | not specified | Likely benign (Sep 21, 2023) | ||
| 4-1700054-G-C | not specified | Uncertain significance (Jan 26, 2023) | ||
| 4-1703638-T-C | not specified | Uncertain significance (Jul 05, 2023) | ||
| 4-1703671-C-T | not specified | Uncertain significance (May 26, 2023) | ||
| 4-1711899-G-A | not specified | Uncertain significance (Sep 14, 2023) | ||
| 4-1711959-G-C | not specified | Uncertain significance (Feb 21, 2024) | ||
| 4-1712166-G-A | not specified | Uncertain significance (Jun 02, 2023) |
GnomAD
Source:
| Gene | Type | Bio Type | Transcript | Coding Exons | Length |
|---|---|---|---|---|---|
| SLBP | protein_coding | protein_coding | ENST00000489418 | 8 | 19756 |
| pLI Probability LOF Intolerant | pRec Probability LOF Recessive | Individuals with no LOFs | Individuals with Homozygous LOFs | Individuals with Heterozygous LOFs | Defined | p |
|---|---|---|---|---|---|---|
| 0.0681 | 0.920 | 125733 | 0 | 15 | 125748 | 0.0000596 |
| Z-Score | Observed | Expected | Observed/Expected | Mutation Rate | Total Possible in Transcript | |
|---|---|---|---|---|---|---|
| Missense | 0.526 | 105 | 121 | 0.866 | 0.00000602 | 1770 |
| Missense in Polyphen | 33 | 44.308 | 0.74479 | 619 | ||
| Synonymous | -0.417 | 44 | 40.6 | 1.08 | 0.00000203 | 478 |
| Loss of Function | 2.18 | 4 | 12.2 | 0.327 | 5.17e-7 | 182 |
LoF frequencies by population
| Ethnicity | Sum of pLOFs | p |
|---|---|---|
| African & African-American | 0.000161 | 0.000161 |
| Ashkenazi Jewish | 0.00 | 0.00 |
| East Asian | 0.00 | 0.00 |
| Finnish | 0.000186 | 0.000185 |
| European (Non-Finnish) | 0.0000627 | 0.0000615 |
| Middle Eastern | 0.00 | 0.00 |
| South Asian | 0.00 | 0.00 |
| Other | 0.000175 | 0.000163 |
dbNSFP
Source:
- Function
- FUNCTION: RNA-binding protein involved in the histone pre-mRNA processing. Binds the stem-loop structure of replication-dependent histone pre-mRNAs and contributes to efficient 3'-end processing by stabilizing the complex between histone pre-mRNA and U7 small nuclear ribonucleoprotein (snRNP), via the histone downstream element (HDE). Plays an important role in targeting mature histone mRNA from the nucleus to the cytoplasm and to the translation machinery. Stabilizes mature histone mRNA and could be involved in cell-cycle regulation of histone gene expression. Involved in the mechanism by which growing oocytes accumulate histone proteins that support early embryogenesis. Binds to the 5' side of the stem-loop structure of histone pre-mRNAs. {ECO:0000269|PubMed:12588979, ECO:0000269|PubMed:19155325}.;
- 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;Transport of the SLBP Dependant Mature mRNA;Transport of Mature mRNAs Derived from Intronless Transcripts;Transport of Mature Transcript to Cytoplasm;Processing of Capped Intron-Containing Pre-mRNA
(Consensus)
Recessive Scores
- pRec
- 0.0792
Intolerance Scores
- loftool
- 0.314
- rvis_EVS
- 0.06
- rvis_percentile_EVS
- 58.26
Haploinsufficiency Scores
- pHI
- 0.150
- hipred
- Y
- hipred_score
- 0.629
- ghis
- 0.615
Essentials
- essential_gene_CRISPR
- N
- essential_gene_CRISPR2
- S
- essential_gene_gene_trap
- E
- gene_indispensability_pred
- E
- gene_indispensability_score
- 0.867
Gene Damage Prediction
| All | Recessive | Dominant | |
|---|---|---|---|
| Mendelian | Medium | Medium | Medium |
| Primary Immunodeficiency | Medium | Medium | Medium |
| Cancer | Medium | Medium | Medium |
Mouse Genome Informatics
- Gene name
- Slbp
- Phenotype
Zebrafish Information Network
- Gene name
- slbp
- Affected structure
- retinal ganglion cell
- Phenotype tag
- abnormal
- Phenotype quality
- decreased amount
Gene ontology
- Biological process
- termination of RNA polymerase II transcription;mRNA 3'-end processing by stem-loop binding and cleavage;mRNA export from nucleus;histone mRNA metabolic process;nuclear DNA replication;cell cycle phase transition;mRNA transport
- Cellular component
- nucleus;nucleoplasm;nucleolus;cytoplasm;cytosol;histone pre-mRNA 3'end processing complex;ribonucleoprotein complex
- Molecular function
- RNA binding;mRNA binding;protein binding;histone pre-mRNA stem-loop binding;histone pre-mRNA DCP binding