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

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 (4 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.

Variant type	Pathogenic	Likely pathogenic	VUS	Likely benign	Benign	Sum
synonymous						0
missense			4			4
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice variant						0
non coding						0
Total	0	0	4	0	0

Variants in SAP30

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

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