SIN3B
SIN3 transcription regulator family member B, the group of EMSY complex|SIN3 histone deacetylase complex subunits
Basic information
Region (hg38): 19:16829398-16880353
Links
Phenotypes
GenCC
Source:
- SIN3A-related intellectual disability syndrome due to a point mutation (Supportive), mode of inheritance: AD
- syndromic intellectual disability (Limited), mode of inheritance: AD
ClinVar
This is a list of variants' phenotypes submitted to
- not_specified (138 variants)
- not_provided (89 variants)
- SIN3B-related_disorder (23 variants)
- Neurodevelopmental_disorder (1 variants)
- SIN3B-related_neurodevelopmental_disorder (1 variants)
- SIN3B-associated_disorder (1 variants)
Variants pathogenicity by type
Statistics on ClinVar variants can assist in determining whether a specific variant type in the SIN3B gene is commonly pathogenic or not. These statistics are base on transcript: NM_001297595.2. Only rare variants are included in the table.
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.
| Effect | PathogenicP | Likely pathogenicLP | VUSVUS | Likely benignLB | BenignB | Sum |
|---|---|---|---|---|---|---|
| synonymous | 18 | 18 | ||||
| missense | 194 | 204 | ||||
| nonsense | 1 | |||||
| start loss | 0 | |||||
| frameshift | 1 | |||||
| splice donor/acceptor (+/-2bp) | 1 | |||||
| Total | 0 | 1 | 196 | 27 | 1 |
Loading clinvar variants...
GnomAD
Source:
| Gene | Type | Bio Type | Transcript | Coding Exons | Length |
|---|---|---|---|---|---|
| SIN3B | protein_coding | protein_coding | ENST00000379803 | 20 | 50954 |
| pLI Probability LOF Intolerant | pRec Probability LOF Recessive | Individuals with no LOFs | Individuals with Homozygous LOFs | Individuals with Heterozygous LOFs | Defined | p |
|---|---|---|---|---|---|---|
| 1.00 | 0.0000117 | 125741 | 0 | 7 | 125748 | 0.0000278 |
| Z-Score | Observed | Expected | Observed/Expected | Mutation Rate | Total Possible in Transcript | |
|---|---|---|---|---|---|---|
| Missense | 3.87 | 454 | 752 | 0.603 | 0.0000525 | 7619 |
| Missense in Polyphen | 44 | 176.97 | 0.24863 | 1813 | ||
| Synonymous | 0.175 | 321 | 325 | 0.988 | 0.0000247 | 2253 |
| Loss of Function | 6.18 | 5 | 54.0 | 0.0927 | 0.00000240 | 629 |
LoF frequencies by population
| Ethnicity | Sum of pLOFs | p |
|---|---|---|
| African & African-American | 0.0000301 | 0.0000301 |
| Ashkenazi Jewish | 0.00 | 0.00 |
| East Asian | 0.00 | 0.00 |
| Finnish | 0.0000959 | 0.0000924 |
| European (Non-Finnish) | 0.0000355 | 0.0000352 |
| Middle Eastern | 0.00 | 0.00 |
| South Asian | 0.00 | 0.00 |
| Other | 0.00 | 0.00 |
dbNSFP
Source:
- Function
- FUNCTION: Acts as a transcriptional repressor. Interacts with MXI1 to repress MYC responsive genes and antagonize MYC oncogenic activities. Interacts with MAD-MAX heterodimers by binding to MAD. The heterodimer then represses transcription by tethering SIN3B to DNA. Also forms a complex with FOXK1 which represses transcription. With FOXK1, regulates cell cycle progression probably by repressing cell cycle inhibitor genes expression. {ECO:0000250|UniProtKB:Q62141}.;
- Pathway
- NoRC negatively regulates rRNA expression;Negative epigenetic regulation of rRNA expression;Epigenetic regulation of gene expression;Gene expression (Transcription);mets affect on macrophage differentiation;Generic Transcription Pathway;Regulation of lipid metabolism by Peroxisome proliferator-activated receptor alpha (PPARalpha);Metabolism of lipids;RNA Polymerase II Transcription;RUNX1 regulates genes involved in megakaryocyte differentiation and platelet function;Metabolism;Transcriptional regulation by RUNX1;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
- 0.117
Intolerance Scores
- loftool
- 0.233
- rvis_EVS
- -1.37
- rvis_percentile_EVS
- 4.51
Haploinsufficiency Scores
- pHI
- 0.338
- hipred
- Y
- hipred_score
- 0.745
- ghis
- 0.582
Essentials
- essential_gene_CRISPR
- N
- essential_gene_CRISPR2
- N
- essential_gene_gene_trap
- N
- gene_indispensability_pred
- E
- gene_indispensability_score
- 0.944
Gene Damage Prediction
| All | Recessive | Dominant | |
|---|---|---|---|
| Mendelian | Medium | Medium | Medium |
| Primary Immunodeficiency | Medium | Medium | Medium |
| Cancer | Medium | Medium | Medium |
Mouse Genome Informatics
- Gene name
- Sin3b
- Phenotype
- growth/size/body region phenotype; cellular phenotype; immune system phenotype; liver/biliary system phenotype; mortality/aging (the observable characteristics related to the ability of a mammalian organism to live and age that are manifested throughout development and life span); normal phenotype; hematopoietic system phenotype; skeleton phenotype;
Zebrafish Information Network
- Gene name
- sin3b
- Affected structure
- whole organism
- Phenotype tag
- abnormal
- Phenotype quality
- decreased behavioural activity
Gene ontology
- Biological process
- negative regulation of transcription by RNA polymerase II;histone deacetylation;regulation of lipid metabolic process
- Cellular component
- chromatin;X chromosome;Y chromosome;XY body;nucleus;nucleoplasm;cytoplasm;Sin3 complex;autosome
- Molecular function
- chromatin binding;transcription corepressor activity;histone deacetylase activity;protein binding