SUDS3
protein-codingSDS3 homolog, SIN3A corepressor complex component, the group of SIN3 histone deacetylase complex subunits
Gene summary
SDS3 is a subunit of the histone deacetylase (see HDAC1; MIM 601241)-dependent SIN3A (MIM 607776) corepressor complex (Fleischer et al., 2003 [PubMed 12724404]).[supplied by OMIM, Mar 2008]
MANE transcript
Inheritance
ClinVar variants
Top phenotype
gnomAD constraint
Max pathogenic AF
Genomic locus
External References & Databases
Transcript & Mutation Effects
hg38 • Region Span ~41.5 kbGenCC Phenotypes & Disease Associations
Curated gene-disease validity assertions and inheritance patterns
No GenCC data available for this gene.
ClinVar Associated Diseases & Phenotypes
Reported disease conditions connected to SUDS3 variants in ClinVar
ClinVar Variants & Pathogenicity by Type
Statistics based on transcript NM_022491.3. Only rare variants are included.
We include only reliable ClinVar variants with their consequences to MANE Select, MANE Plus Clinical transcripts, or transcripts with TSL equal to 1. Click a count to filter the variants table below.
Slight differences between displayed counts and ClinVar may occur due to a different transcript/consequence chosen by our variant effect predictor, or because we classify Benign/Likely benign as Likely benign and Pathogenic/Likely pathogenic as Likely pathogenic.
| Effect | PathogenicP | Likely pathogenicLP | VUS | Likely benignLB | BenignB | Sum |
|---|---|---|---|---|---|---|
| synonymous | 2 | 2 | ||||
| missense | 25 | 25 | ||||
| nonsense | 0 | |||||
| start loss | 0 | |||||
| frameshift | 0 | |||||
| splice donor/acceptor (+/-2bp) | 2 | 2 | ||||
| Total | 0 | 0 | 27 | 2 | 0 | 29 |
Transcript Catalog
Annotated transcript isoforms across RefSeq and Ensembl databases
| Transcript ID | Source | Protein ID | Coding Exons | MANE Status |
|---|---|---|---|---|
| RefSeq | NP_071936.2 | 12 | MANE Select | |
| Ensembl | ENSP00000443988.1 | 12 | MANE Select | |
| Ensembl | ENSP00000529574.1 | 11 | Standard | |
| Ensembl | ENSP00000529574.1 | 11 | Standard |
Model Organisms & Knockout Phenotypes
Observed phenotypic effects in mouse and zebrafish models
| Gene / Model | Organism | Observed Phenotype |
|---|---|---|
| suds3 | Danio rerio | Structure: head Quality: decreased size abnormal |
Gene Ontology (GO) Annotations & Pathways
Biological processes, molecular functions, cellular components and pathways
Pathways ConsensusPathDB
- NoRC negatively regulates rRNA expression
- Negative epigenetic regulation of rRNA expression
- Epigenetic regulation of gene expression
- Gene expression (Transcription)
- Post-translational protein modification
Biological Process
- negative regulation of transcription by RNA polymerase II
- apoptotic process
- histone deacetylation
- substantia nigra development
- positive regulation of apoptotic process
Molecular Function
- histone deacetylase activity
- protein binding
- enzyme binding
- histone deacetylase binding
Cellular Component
- nucleus
- nucleoplasm
- cytosol
- Sin3 complex
- nuclear body
gnomAD Constraint
Source:
- Gene type
- protein_coding
- Transcript type
- protein_coding
- Transcript
- ENST00000543473
- Coding exons
- 12
- Length
- 41656
- Individuals with no LoFs
- 124627
- Homozygous LoFs
- 0
- Heterozygous LoFs
- 11
- Defined
- 124638
- p
- 0.0000441
| Z-Score | Observed | Expected | Observed/Expected | Mutation Rate | Total Possible | |
|---|---|---|---|---|---|---|
| Missense | 1.94 | 96 | 167 | 0.576 | 0.00000867 | 2129 |
| Missense (PolyPhen) | 21 | 50.448 | 0.41627 | 644 | ||
| Synonymous | 1.22 | 49 | 61.1 | 0.801 | 0.00000313 | 572 |
| Loss of Function | 2.82 | 8 | 22.4 | 0.357 | 0.00000113 | 276 |
Population LoF Frequency
| Population | CAF | p-value | Status |
|---|---|---|---|
| African | 0.000071 | 0.000065 | rare |
| Latino/Admixed American | 0 | 0.0 | absent |
| Ashkenazi Jewish | 0 | 0.0 | absent |
| East Asian | 0.000056 | 0.000056 | rare |
| Finnish | 0.000046 | 0.000046 | rare |
| European (Non-Finnish) | 0.000045 | 0.000044 | rare |
| South Asian | 0.00011 | 0.000098 | rare |
| Other | 0 | 0.0 | absent |
dbNSFP Gene Annotations
Source:
- Function
- FUNCTION: Regulatory protein which represses transcription and augments histone deacetylase activity of HDAC1. May have a potential role in tumor suppressor pathways through regulation of apoptosis. May function in the assembly and/or enzymatic activity of the mSin3A corepressor complex or in mediating interactions between the complex and other regulatory complexes. {ECO:0000269|PubMed:12724404, ECO:0000269|PubMed:21239494}.;
Recessive Scores
- pRec
- 0.109
Intolerance Scores
- LoFtool
- 0.572
- RVIS EVS
- -0.23
- RVIS percentile EVS
- 36.86
Essentials
- Essential (CRISPR)
- E
- Essential (CRISPR2)
- E
- Essential (gene trap)
- E
- Indispensability pred.
- E
- Indispensability score
- 0.870
Gene Damage Prediction
| All | Recessive | Dominant | |
|---|---|---|---|
| Mendelian | Medium | Medium | Medium |
| Primary Immunodeficiency | Medium | Medium | Medium |
| Cancer | Medium | Medium | Medium |