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

ENSG00000150459

∙ NCBI:10284 ∙ OMIM:602949 ∙ HGNC:10530 ∙ Uniprot:O00422 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

Phenotypes

GenCC

Source: genCC

No genCC data.

ClinVar

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

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			5 clinvar			5
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	5	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	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

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: 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

	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