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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:O75446AlphaFoldGenCCjaxSfariGnomADPubmed

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)link
4-173371244-C-T Inborn genetic diseases Uncertain significance (Feb 28, 2023)link
4-173371378-C-G Inborn genetic diseases Uncertain significance (Sep 17, 2021)link
4-173373997-T-C Inborn genetic diseases Uncertain significance (Jul 19, 2023)link
4-173374006-G-A Inborn genetic diseases Uncertain significance (Jun 16, 2023)link
4-173377260-A-G Inborn genetic diseases Uncertain significance (Sep 14, 2022)link
4-173377313-A-G Inborn genetic diseases Uncertain significance (Apr 28, 2022)link

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