SAP30

Sin3A associated protein 30, the group of SIN3 histone deacetylase complex subunits

Basic information

Region (hg38): 4:173369968-173377532

Links

ENSG00000164105 ∙ NCBI:8819 ∙ OMIM:603378 ∙ HGNC:10532 ∙ Uniprot:O75446 ∙ 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 SAP30 gene.

• Inborn genetic diseases (7 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the SAP30 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			7			7
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	7	0	0

Variants in SAP30

This is a list of pathogenic ClinVar variants found in the SAP30 region.

You can filter this list by clicking the number of variants in the Variants pathogenicity by type table.

Position	Type	Phenotype	Significance	ClinVar
4-173371198-C-T		Inborn genetic diseases	Uncertain significance (May 01, 2022)
4-173371244-C-T		Inborn genetic diseases	Uncertain significance (Feb 28, 2023)
4-173371378-C-G		Inborn genetic diseases	Uncertain significance (Sep 17, 2021)
4-173373997-T-C		Inborn genetic diseases	Uncertain significance (Jul 19, 2023)
4-173374006-G-A		Inborn genetic diseases	Uncertain significance (Jun 16, 2023)
4-173377260-A-G		Inborn genetic diseases	Uncertain significance (Sep 14, 2022)
4-173377313-A-G		Inborn genetic diseases	Uncertain significance (Apr 28, 2022)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
SAP30	protein_coding	protein_coding	ENST00000296504	4	7564

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.310	0.674	125662	0	7	125669	0.0000279

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.885	77	102	0.754	0.00000449	1401
Missense in Polyphen		25	49.132	0.50883		653
Synonymous	-0.0455	41	40.6	1.01	0.00000184	441
Loss of Function	2.02	2	8.29	0.241	4.23e-7	106

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.00	0.00
Ashkenazi Jewish	0.00	0.00
East Asian	0.00	0.00
Finnish	0.00	0.00
European (Non-Finnish)	0.0000570	0.0000528
Middle Eastern	0.00	0.00
South Asian	0.0000329	0.0000327
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Involved in the functional recruitment of the Sin3- histone deacetylase complex (HDAC) to a specific subset of N-CoR corepressor complexes. Capable of transcription repression by N- CoR. Active in deacetylating core histone octamers (when in a complex) but inactive in deacetylating nucleosomal histones. {ECO:0000250|UniProtKB:O88574, ECO:0000269|PubMed:9651585}.
• Pathway: Retinoblastoma (RB) in Cancer;Notch Signaling Pathway;Notch;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: 0.112

Intolerance Scores

• loftool: 0.510
• rvis_EVS: 0.06
• rvis_percentile_EVS: 58

Haploinsufficiency Scores

• pHI: 0.229
• hipred: Y
• hipred_score: 0.640
• ghis: 0.579

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.914

Gene Damage Prediction

	All	Recessive	Dominant
Mendelian	Medium	Medium	Medium
Primary Immunodeficiency	Medium	Medium	Medium
Cancer	Medium	Medium	Medium

Mouse Genome Informatics

• Gene name: Sap30

Gene ontology

• Biological process: negative regulation of transcription by RNA polymerase II;regulation of transcription, DNA-templated;histone deacetylation;skeletal muscle cell differentiation
• Cellular component: histone deacetylase complex;nucleoplasm
• Molecular function: DNA binding;transcription corepressor activity;histone deacetylase activity;protein binding;metal ion binding