SAP30
Sin3A associated protein 30, the group of SIN3 histone deacetylase complex subunits
Basic information
Region (hg38): 4:173369968-173377532
Links
Phenotypes
GenCC
Source:
No genCC data.
ClinVar
This is a list of variants' phenotypes submitted to
- 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:
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:
- 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
- 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