Menu
GeneBe

SAP30

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

Basic information

Region (hg38): 4:173369968-173377532

Links

ENSG00000164105NCBI:8819OMIM:603378HGNC:10532Uniprot:O75446AlphaFoldGenCCjaxSfariGnomADPubmedClinVar

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
clinvar
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 not specified Uncertain significance (May 01, 2022)2390403
4-173371244-C-T not specified Uncertain significance (Feb 28, 2023)2469379
4-173371346-C-T not specified Uncertain significance (Jan 08, 2024)3157784
4-173371354-G-A not specified Uncertain significance (Feb 27, 2024)3157785
4-173371378-C-G not specified Uncertain significance (Sep 17, 2021)2344204
4-173373504-G-C not specified Uncertain significance (Dec 16, 2023)3157786
4-173373997-T-C not specified Uncertain significance (Jul 19, 2023)2612572
4-173374006-G-A not specified Uncertain significance (Jun 16, 2023)2588788
4-173377251-C-T not specified Uncertain significance (Jan 31, 2024)3157787
4-173377260-A-G not specified Uncertain significance (Sep 14, 2022)2312313
4-173377313-A-G not specified Uncertain significance (Apr 28, 2022)2400721

GnomAD

Source: gnomAD

GeneTypeBio TypeTranscript Coding Exons Length
SAP30protein_codingprotein_codingENST00000296504 47564
pLI Probability
LOF Intolerant
pRec Probability
LOF Recessive
Individuals with
no LOFs
Individuals with
Homozygous LOFs
Individuals with
Heterozygous LOFs
Defined p
0.3100.674125662071256690.0000279
Z-Score Observed Expected Observed/Expected Mutation Rate Total Possible in Transcript
Missense0.885771020.7540.000004491401
Missense in Polyphen2549.1320.50883653
Synonymous-0.04554140.61.010.00000184441
Loss of Function2.0228.290.2414.23e-7106

LoF frequencies by population

EthnicitySum of pLOFs p
African & African-American0.000.00
Ashkenazi Jewish0.000.00
East Asian0.000.00
Finnish0.000.00
European (Non-Finnish)0.00005700.0000528
Middle Eastern0.000.00
South Asian0.00003290.0000327
Other0.000.00

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

AllRecessiveDominant
MendelianMediumMediumMedium
Primary ImmunodeficiencyMediumMediumMedium
CancerMediumMediumMedium

Mouse Genome Informatics

Gene name
Sap30
Phenotype

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