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GeneE
25 sources retrieved Β· Most recent: April 2026 Β· Index updated 14 days ago
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SIN3A
SIN3 transcription regulator family member A
Chromosome 15 Β· 15q24.2
NCBI Gene: 25942Ensembl: ENSG00000169375.18HGNC: HGNC:19353UniProt: Q96ST3
371PubMed Papers
21Diseases
0Drugs
107Pathogenic Variants
FUNCTIONAL ROLE
Highly ConstrainedHub GeneTranscription Factor
RESEARCH IMPACT
Highly StudiedTrendingVariant-Rich
CLINICAL
OMIM Disease Gene
DATA QUALITY
βœ“ Experimental GO Evidenceβœ“ Swiss-Prot Reviewed
type I interferon-mediated signaling pathwayheterochromatin formationtranscription regulator inhibitor activitynegative regulation of protein localization to nucleus15q24 microdeletion syndromeSIN3A-related intellectual disability syndromechromosome 15q24 deletion syndromesyndromic intellectual disability
✦AI Summary

SIN3A is a transcriptional corepressor that functions primarily through histone deacetylation and chr15 remodeling 1. It mediates transcriptional repression by interacting with histone deacetylase complexes and associates with multiple regulatory proteins to suppress gene expression 1. In circulating tumor cell clusters, SIN3A binding sites are hypomethylated, correlating with enhanced stemness and metastatic potential 2. Disease relevance of SIN3A dysfunction is increasingly recognized. Loss of SIN3A in alveolar type 2 cells triggers p53-dependent cellular senescence and spontaneous progressive pulmonary fibrosis in mice, identifying senescence as a key pathogenic mechanism 3. Conversely, SIN3A overexpression demonstrates therapeutic potential in pulmonary arterial hypertension by preventing BMPR2 promoter methylation through downregulation of methyltransferases (DNMT1, EZH2) and upregulation of demethylase TET1, with adeno-associated virus-mediated SIN3A delivery attenuating pulmonary vascular remodeling in preclinical models 4. Additionally, SIN3A participates in repressive complexes containing MECP2 and HDAC1 that regulate neuroinflammation through PU.1 motif targeting, with therapeutic implications for neurodegenerative diseases 5. These findings position SIN3A as a critical epigenetic regulator with context-dependent roles in disease pathogenesis and potential as a therapeutic target across multiple organ systems.

Sources cited
1
Loss of Sin3a in alveolar type 2 cells causes p53-dependent cellular senescence and progressive pulmonary fibrosis
PMID: 32991815
2
SIN3A overexpression upregulates BMPR2 by preventing promoter methylation and reduces pulmonary hypertension pathology in vivo
PMID: 34078089
3
SIN3A binding sites are hypomethylated in circulating tumor cell clusters, associated with stemness and metastatic potential
PMID: 30633912
4
SIN3A mediates transcriptional repression through interaction with histone deacetylase and corepressor complexes
PMID: 10508514
5
SIN3A participates in MECP2/HDAC1-containing repressive complexes that regulate neuroinflammation through PU.1 motif targeting
PMID: 37642942
Disease Associationsβ“˜21
15q24 microdeletion syndromeOpen Targets
0.75Strong
SIN3A-related intellectual disability syndromeOpen Targets
0.62Moderate
chromosome 15q24 deletion syndromeOpen Targets
0.57Moderate
syndromic intellectual disabilityOpen Targets
0.55Moderate
genetic disorderOpen Targets
0.54Moderate
neurodegenerative diseaseOpen Targets
0.43Moderate
Burkitts lymphomaOpen Targets
0.37Weak
autismOpen Targets
0.37Weak
Rett syndromeOpen Targets
0.37Weak
non-Hodgkins lymphomaOpen Targets
0.33Weak
Intellectual disabilityOpen Targets
0.27Weak
Neurodevelopmental disorderOpen Targets
0.27Weak
type 2 diabetes mellitusOpen Targets
0.15Weak
Rare genetic intellectual disabilityOpen Targets
0.11Weak
breast cancerOpen Targets
0.10Weak
autism spectrum disorderOpen Targets
0.09Suggestive
allergic rhinitisOpen Targets
0.07Suggestive
colorectal carcinomaOpen Targets
0.07Suggestive
nonpapillary renal cell carcinomaOpen Targets
0.06Suggestive
diabetes mellitusOpen Targets
0.06Suggestive
Witteveen-Kolk syndromeUniProt
Pathogenic Variants107
NM_001145358.2(SIN3A):c.2353_2356del (p.Gln785fs)Pathogenic
not provided|SIN3A-related intellectual disability syndrome due to a point mutation
β˜…β˜…β˜†β˜†2026β†’ Residue 785
NM_001145358.2(SIN3A):c.2764C>T (p.Arg922Ter)Pathogenic
not provided|SIN3A-related intellectual disability syndrome due to a point mutation
β˜…β˜…β˜†β˜†2025β†’ Residue 922
NM_001145358.2(SIN3A):c.2844_2847del (p.Lys948fs)Pathogenic
not provided|SIN3A-related intellectual disability syndrome due to a point mutation
β˜…β˜…β˜†β˜†2025β†’ Residue 948
NM_001145358.2(SIN3A):c.3314dup (p.Tyr1105Ter)Pathogenic
Inborn genetic diseases|SIN3A-related intellectual disability syndrome due to a point mutation
β˜…β˜…β˜†β˜†2025β†’ Residue 1105
NM_001145358.2(SIN3A):c.1609C>T (p.Arg537Ter)Pathogenic
not provided
β˜…β˜…β˜†β˜†2024β†’ Residue 537
NM_001145358.2(SIN3A):c.2689C>T (p.Arg897Ter)Pathogenic
not provided
β˜…β˜…β˜†β˜†2024β†’ Residue 897
NM_001145358.2(SIN3A):c.2152C>T (p.Arg718Ter)Pathogenic
not provided|SIN3A-related intellectual disability syndrome due to a point mutation|Intellectual disability|SIN3A-related disorder|Gastric cancer
β˜…β˜…β˜†β˜†2024β†’ Residue 718
NM_001145358.2(SIN3A):c.1411C>T (p.Arg471Ter)Pathogenic
SIN3A-related intellectual disability syndrome|not provided|SIN3A-related intellectual disability syndrome due to a point mutation
β˜…β˜…β˜†β˜†2024β†’ Residue 471
NM_001145358.2(SIN3A):c.1657C>T (p.Arg553Ter)Pathogenic
Inborn genetic diseases|not provided|SIN3A-related intellectual disability syndrome
β˜…β˜…β˜†β˜†2023β†’ Residue 553
NM_001145358.2(SIN3A):c.2809_2810del (p.Lys937fs)Pathogenic
not provided|SIN3A-related intellectual disability syndrome due to a point mutation
β˜…β˜…β˜†β˜†2021β†’ Residue 937
NM_001145358.2(SIN3A):c.2803C>T (p.Arg935Ter)Pathogenic
SIN3A-related intellectual disability syndrome due to a point mutation
β˜…β˜…β˜†β˜†2021β†’ Residue 935
NM_001145358.2(SIN3A):c.473+2T>APathogenic
SIN3A-related intellectual disability syndrome due to a point mutation
β˜…β˜†β˜†β˜†2025
NM_001145358.2(SIN3A):c.640del (p.His214fs)Pathogenic
not provided
β˜…β˜†β˜†β˜†2025β†’ Residue 214
NM_001145358.2(SIN3A):c.1909C>T (p.Gln637Ter)Pathogenic
not provided
β˜…β˜†β˜†β˜†2025β†’ Residue 637
NM_001145358.2(SIN3A):c.1620_1693dup (p.Tyr565delinsTrpAlaLeuLeuTrpArgTer)Pathogenic
not provided
β˜…β˜†β˜†β˜†2025β†’ Residue 565
NM_001145358.2(SIN3A):c.3418C>T (p.Arg1140Ter)Pathogenic
SIN3A-related intellectual disability syndrome due to a point mutation
β˜…β˜†β˜†β˜†2025β†’ Residue 1140
NM_001145358.2(SIN3A):c.2242delinsCCTCATTGAG (p.Ser748delinsProHisTer)Pathogenic
SIN3A-related intellectual disability syndrome
β˜…β˜†β˜†β˜†2025β†’ Residue 748
NM_001145358.2(SIN3A):c.971_974dup (p.Lys326fs)Pathogenic
not provided
β˜…β˜†β˜†β˜†2025β†’ Residue 326
NM_001145358.2(SIN3A):c.1541T>A (p.Leu514Ter)Pathogenic
not provided
β˜…β˜†β˜†β˜†2025β†’ Residue 514
NM_001145358.2(SIN3A):c.2945del (p.Ser982fs)Pathogenic
not provided
β˜…β˜†β˜†β˜†2025β†’ Residue 982
View on ClinVar β†—
Related Genes
RUNX1T1Protein interaction100%MXI1Protein interaction100%SKIProtein interaction100%ZBTB7AProtein interaction100%SAP25Protein interaction100%EMSYProtein interaction100%
Tissue Expression6 tissues
Bone Marrow
100%
Brain
69%
Ovary
69%
Lung
54%
Heart
50%
Liver
36%
Gene Interaction Network
Click a node to explore
SIN3ARUNX1T1MXI1SKIZBTB7ASAP25EMSY
PROTEIN STRUCTURE
Preparing viewer…
AlphaFoldAI-predicted Β· UniProt Q96ST3
View on AlphaFold β†—
Constraintβ“˜
LOEUFβ“˜
0.14Highly Constrained
pLIβ“˜
1.00Intolerant
Observed/Expected LoF0.08 [0.05–0.14]
RankingsWhere SIN3A stands among ~20K protein-coding genes
  • #823of 20,598
    Most Researched371 Β· top 5%
  • #724of 5,498
    Most Pathogenic Variants107 Β· top quartile
  • #168of 17,882
    Most Constrained (LOEUF)0.14 Β· top 1%
Genes detectedSIN3A
Sources retrieved25 papers
Response timeβ€”
πŸ“„ Sources
25β–Ό
1
Senescence of Alveolar Type 2 Cells Drives Progressive Pulmonary Fibrosis.
PMID: 32991815
Am J Respir Crit Care Med Β· 2021
1.00
2
Regulation of the Methylation and Expression Levels of the BMPR2 Gene by SIN3a as a Novel Therapeutic Mechanism in Pulmonary Arterial Hypertension.
PMID: 34078089
Circulation Β· 2021
0.90
3
Circulating Tumor Cell Clustering Shapes DNA Methylation to Enable Metastasis Seeding.
PMID: 30633912
Cell Β· 2019
0.80
4
Neutrophil cell surface receptors and their intracellular signal transduction pathways.
PMID: 23994464
Int Immunopharmacol Β· 2013
0.70
5
Understanding the role of ten-eleven translocation family proteins in kidney diseases.
PMID: 39377353
Biochem Soc Trans Β· 2024
0.68