SAP18
Sin3A associated protein 18, the group of ASAP complex|Spliceosomal C complex|Spliceosomal Bact complex|SIN3 histone deacetylase complex subunits
Basic information
Region (hg38): 13:21140119-21149097
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 SAP18 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 | 6 | |||||
| nonsense | 0 | |||||
| start loss | 0 | |||||
| frameshift | 0 | |||||
| inframe indel | 0 | |||||
| splice donor/acceptor (+/-2bp) | 0 | |||||
| splice region | 0 | |||||
| non coding | 0 | |||||
| Total | 0 | 0 | 6 | 0 | 0 |
Variants in SAP18
This is a list of pathogenic ClinVar variants found in the SAP18 region.
You can filter this list by clicking the number of variants in the Variants pathogenicity by type table.
| Position | Type | Phenotype | Significance | ClinVar |
|---|---|---|---|---|
| 13-21140566-G-A | not specified | Uncertain significance (Apr 05, 2023) | ||
| 13-21140568-G-A | not specified | Uncertain significance (Nov 06, 2023) | ||
| 13-21140578-A-G | not specified | Uncertain significance (Mar 11, 2025) | ||
| 13-21140585-G-T | not specified | Uncertain significance (Sep 27, 2021) | ||
| 13-21140586-C-A | not specified | Uncertain significance (Nov 30, 2021) | ||
| 13-21140586-C-T | not specified | Uncertain significance (Feb 12, 2025) | ||
| 13-21140599-G-A | not specified | Uncertain significance (Mar 05, 2025) | ||
| 13-21140664-C-T | not specified | Uncertain significance (Sep 03, 2024) |
GnomAD
Source:
| Gene | Type | Bio Type | Transcript | Coding Exons | Length |
|---|---|---|---|---|---|
| SAP18 | protein_coding | protein_coding | ENST00000382533 | 4 | 8569 |
| pLI Probability LOF Intolerant | pRec Probability LOF Recessive | Individuals with no LOFs | Individuals with Homozygous LOFs | Individuals with Heterozygous LOFs | Defined | p |
|---|---|---|---|---|---|---|
| 0.0830 | 0.876 | 125706 | 1 | 40 | 125747 | 0.000163 |
| Z-Score | Observed | Expected | Observed/Expected | Mutation Rate | Total Possible in Transcript | |
|---|---|---|---|---|---|---|
| Missense | 0.768 | 80 | 102 | 0.786 | 0.00000508 | 1107 |
| Missense in Polyphen | 7 | 20.638 | 0.33917 | 261 | ||
| Synonymous | -1.90 | 53 | 38.1 | 1.39 | 0.00000186 | 338 |
| Loss of Function | 1.74 | 3 | 8.48 | 0.354 | 4.29e-7 | 95 |
LoF frequencies by population
| Ethnicity | Sum of pLOFs | p |
|---|---|---|
| African & African-American | 0.0000973 | 0.0000908 |
| Ashkenazi Jewish | 0.00 | 0.00 |
| East Asian | 0.00 | 0.00 |
| Finnish | 0.00 | 0.00 |
| European (Non-Finnish) | 0.000163 | 0.000149 |
| Middle Eastern | 0.00 | 0.00 |
| South Asian | 0.000797 | 0.000719 |
| Other | 0.00 | 0.00 |
dbNSFP
Source:
- Function
- FUNCTION: Component of the SIN3-repressing complex. Enhances the ability of SIN3-HDAC1-mediated transcriptional repression. When tethered to the promoter, it can direct the formation of a repressive complex to core histone proteins. Auxiliary component of the splicing-dependent multiprotein exon junction complex (EJC) deposited at splice junction on mRNAs. The EJC is a dynamic structure consisting of core proteins and several peripheral nuclear and cytoplasmic associated factors that join the complex only transiently either during EJC assembly or during subsequent mRNA metabolism. Component of the ASAP and PSAP complexes which bind RNA in a sequence-independent manner and are proposed to be recruited to the EJC prior to or during the splicing process and to regulate specific excision of introns in specific transcription subsets. The ASAP complex can inhibit mRNA processing during in vitro splicing reactions. The ASAP complex promotes apoptosis and is disassembled after induction of apoptosis. Involved in the splicing modulation of BCL2L1/Bcl-X (and probably other apoptotic genes); specifically inhibits the formation of proapoptotic isoforms such as Bcl-X(S); the activity is different from the established EJC assembly and function. {ECO:0000269|PubMed:12665594, ECO:0000269|PubMed:20966198, ECO:0000269|PubMed:22203037, ECO:0000269|PubMed:9150135}.;
- Pathway
- mRNA surveillance pathway - Homo sapiens (human);RNA transport - Homo sapiens (human);HH-Ncore;Hedgehog Signaling Pathway;NoRC negatively regulates rRNA expression;Negative epigenetic regulation of rRNA expression;Epigenetic regulation of gene expression;Gene expression (Transcription);HDACs deacetylate histones;Chromatin modifying enzymes;Chromatin organization;Regulation of Telomerase;Signaling events mediated by HDAC Class I;Hedgehog signaling events mediated by Gli proteins;Regulation of nuclear SMAD2/3 signaling
(Consensus)
Recessive Scores
- pRec
- 0.149
Intolerance Scores
- loftool
- 0.388
- rvis_EVS
- -0.12
- rvis_percentile_EVS
- 44.54
Haploinsufficiency Scores
- pHI
- 0.448
- hipred
- Y
- hipred_score
- 0.681
- ghis
- 0.648
Essentials
- essential_gene_CRISPR
- E
- essential_gene_CRISPR2
- E
- essential_gene_gene_trap
- E
- gene_indispensability_pred
- E
- gene_indispensability_score
- 0.998
Gene Damage Prediction
| All | Recessive | Dominant | |
|---|---|---|---|
| Mendelian | Medium | Medium | Medium |
| Primary Immunodeficiency | Medium | Medium | Medium |
| Cancer | Medium | Medium | Medium |
Mouse Genome Informatics
- Gene name
- Sap18
- Phenotype
Gene ontology
- Biological process
- regulation of alternative mRNA splicing, via spliceosome;regulation of transcription by RNA polymerase II;mRNA processing;RNA splicing;histone deacetylation;positive regulation of apoptotic process;negative regulation of mRNA splicing, via spliceosome;negative regulation of nucleic acid-templated transcription
- Cellular component
- histone deacetylase complex;nucleoplasm;cytosol;nuclear body;nuclear speck;exon-exon junction complex;ASAP complex
- Molecular function
- transcription corepressor activity;RNA binding;histone deacetylase activity;protein binding