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GeneBe

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): 13:21140118-21149097

Links

ENSG00000150459NCBI:10284OMIM:602949HGNC:10530Uniprot:O00422AlphaFoldGenCCjaxSfariGnomADPubmedClinVar

Phenotypes

GenCC

Source: genCC

No genCC data.

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the SAP18 gene.

  • Inborn genetic diseases (4 variants)

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
4
clinvar
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 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)2532950
13-21140568-G-A not specified Uncertain significance (Nov 06, 2023)3157782
13-21140578-A-G not specified Uncertain significance (Dec 19, 2022)2353375
13-21140585-G-T not specified Uncertain significance (Sep 27, 2021)2252498
13-21140586-C-A not specified Uncertain significance (Nov 30, 2021)2408627

GnomAD

Source: gnomAD

GeneTypeBio TypeTranscript Coding Exons Length
SAP18protein_codingprotein_codingENST00000382533 48569
pLI Probability
LOF Intolerant
pRec Probability
LOF Recessive
Individuals with
no LOFs
Individuals with
Homozygous LOFs
Individuals with
Heterozygous LOFs
Defined p
0.08300.8761257061401257470.000163
Z-Score Observed Expected Observed/Expected Mutation Rate Total Possible in Transcript
Missense0.768801020.7860.000005081107
Missense in Polyphen720.6380.33917261
Synonymous-1.905338.11.390.00000186338
Loss of Function1.7438.480.3544.29e-795

LoF frequencies by population

EthnicitySum of pLOFs p
African & African-American0.00009730.0000908
Ashkenazi Jewish0.000.00
East Asian0.000.00
Finnish0.000.00
European (Non-Finnish)0.0001630.000149
Middle Eastern0.000.00
South Asian0.0007970.000719
Other0.000.00

dbNSFP

Source: dbNSFP

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

AllRecessiveDominant
MendelianMediumMediumMedium
Primary ImmunodeficiencyMediumMediumMedium
CancerMediumMediumMedium

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