SLU7
SLU7 homolog, splicing factor, the group of Spliceosomal C complex|U11 small nuclear ribonucleoprotein|Spliceosomal P complex|NTC associated proteins
Basic information
Region (hg38): 5:160401641-160421711
Links
Phenotypes
GenCC
Source:
No genCC data.
ClinVar
This is a list of variants' phenotypes submitted to
- not_specified (45 variants)
- not_provided (4 variants)
Variants pathogenicity by type
Statistics on ClinVar variants can assist in determining whether a specific variant type in the SLU7 gene is commonly pathogenic or not. These statistics are base on transcript: NM_000006425.5. 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 | 0 | |||||
| missense | 44 | 46 | ||||
| nonsense | 0 | |||||
| start loss | 0 | |||||
| frameshift | 0 | |||||
| splice donor/acceptor (+/-2bp) | 0 | |||||
| Total | 0 | 0 | 44 | 1 | 1 |
Loading clinvar variants...
GnomAD
Source:
| Gene | Type | Bio Type | Transcript | Coding Exons | Length |
|---|---|---|---|---|---|
| SLU7 | protein_coding | protein_coding | ENST00000297151 | 15 | 20071 |
| pLI Probability LOF Intolerant | pRec Probability LOF Recessive | Individuals with no LOFs | Individuals with Homozygous LOFs | Individuals with Heterozygous LOFs | Defined | p |
|---|---|---|---|---|---|---|
| 1.63e-9 | 0.998 | 125691 | 0 | 57 | 125748 | 0.000227 |
| Z-Score | Observed | Expected | Observed/Expected | Mutation Rate | Total Possible in Transcript | |
|---|---|---|---|---|---|---|
| Missense | 1.99 | 203 | 300 | 0.677 | 0.0000147 | 3893 |
| Missense in Polyphen | 53 | 118.86 | 0.44592 | 1550 | ||
| Synonymous | 1.27 | 82 | 98.0 | 0.837 | 0.00000453 | 981 |
| Loss of Function | 2.79 | 21 | 40.1 | 0.524 | 0.00000233 | 487 |
LoF frequencies by population
| Ethnicity | Sum of pLOFs | p |
|---|---|---|
| African & African-American | 0.000582 | 0.000578 |
| Ashkenazi Jewish | 0.000630 | 0.000595 |
| East Asian | 0.000109 | 0.000109 |
| Finnish | 0.000139 | 0.000139 |
| European (Non-Finnish) | 0.000187 | 0.000185 |
| Middle Eastern | 0.000109 | 0.000109 |
| South Asian | 0.000364 | 0.000359 |
| Other | 0.000164 | 0.000163 |
dbNSFP
Source:
- Function
- FUNCTION: Participates in the second catalytic step of pre-mRNA splicing, when the free hydroxyl group of exon I attacks the 3'- splice site to generate spliced mRNA and the excised lariat intron. Required for holding exon 1 properly in the spliceosome and for correct AG identification when more than one possible AG exists in 3'-splicing site region. May be involved in the activation of proximal AG. Probably also involved in alternative splicing regulation. {ECO:0000269|PubMed:10197984, ECO:0000269|PubMed:10647016, ECO:0000269|PubMed:12764196, ECO:0000269|PubMed:15728250}.;
- Pathway
- Spliceosome - Homo sapiens (human);Gene expression (Transcription);RNA Polymerase II Transcription;Metabolism of RNA;Cleavage of Growing Transcript in the Termination Region ;RNA Polymerase II Transcription Termination;Transport of Mature mRNA derived from an Intron-Containing Transcript;mRNA 3,-end processing;Transport of Mature Transcript to Cytoplasm;Processing of Capped Intron-Containing Pre-mRNA
(Consensus)
Recessive Scores
- pRec
- 0.125
Intolerance Scores
- loftool
- 0.892
- rvis_EVS
- -0.09
- rvis_percentile_EVS
- 46.92
Haploinsufficiency Scores
- pHI
- 0.252
- hipred
- Y
- hipred_score
- 0.706
- ghis
- 0.600
Essentials
- essential_gene_CRISPR
- N
- essential_gene_CRISPR2
- E
- essential_gene_gene_trap
- E
- gene_indispensability_pred
- E
- gene_indispensability_score
- 0.681
Gene Damage Prediction
| All | Recessive | Dominant | |
|---|---|---|---|
| Mendelian | Medium | Medium | Medium |
| Primary Immunodeficiency | Medium | Medium | Medium |
| Cancer | Medium | Medium | Medium |
Mouse Genome Informatics
- Gene name
- Slu7
- Phenotype
- integument phenotype (the observable morphological and physiological characteristics of the skin and its associated structures, such as the hair, nails, sweat glands, sebaceous glands and other secretory glands that are manifested through development and lifespan); immune system phenotype; 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); hematopoietic system phenotype;
Gene ontology
- Biological process
- RNA splicing, via transesterification reactions;alternative mRNA splicing, via spliceosome;mRNA 3'-splice site recognition;mRNA splicing, via spliceosome;RNA export from nucleus;mRNA export from nucleus;intracellular protein transport;mRNA 3'-end processing;cellular response to heat
- Cellular component
- nucleus;nucleoplasm;spliceosomal complex;cytoplasm;cytosol;membrane;nuclear speck;small nuclear ribonucleoprotein complex;intracellular membrane-bounded organelle;catalytic step 2 spliceosome
- Molecular function
- second spliceosomal transesterification activity;protein binding;zinc ion binding;pre-mRNA 3'-splice site binding