SAP130

gene
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Also known as FLJ12761

Summary

SAP130 (Sin3A associated protein 130, HGNC:29813) is a protein-coding gene on chromosome 2q14.3, encoding Histone deacetylase complex subunit SAP130 (Q9H0E3). Acts as a transcriptional repressor.

SAP130 is a subunit of the histone deacetylase (see HDAC1; MIM 601241)-dependent SIN3A (MIM 607776) corepressor complex (Fleischer et al., 2003 [PubMed 12724404]).

Source: NCBI Gene 79595 — RefSeq curated summary.

At a glance

  • Clinical variants (ClinVar): 136 total — 1 likely-pathogenic
  • Druggable target: yes
  • MANE Select transcript: NM_001330301

Identifiers

Gene identifiers

FieldValue
HGNC IDHGNC:29813
Approved symbolSAP130
NameSin3A associated protein 130
Location2q14.3
Locus typegene with protein product
StatusApproved
AliasesFLJ12761
Ensembl geneENSG00000136715
Ensembl biotypeprotein_coding
OMIM609697
Entrez79595

Gene structure

Transcript identifiers

Ensembl transcripts: 36 — 36 protein_coding

ENST00000259234, ENST00000259235, ENST00000357702, ENST00000424298, ENST00000450957, ENST00000643581, ENST00000866430, ENST00000866431, ENST00000866432, ENST00000866433, ENST00000866434, ENST00000866435, ENST00000866436, ENST00000866437, ENST00000866438, ENST00000866439, ENST00000866440, ENST00000866441, ENST00000866442, ENST00000866443, ENST00000866444, ENST00000866445, ENST00000866446, ENST00000866447, ENST00000866448, ENST00000866449, ENST00000866450, ENST00000866451, ENST00000866452, ENST00000934352, ENST00000934353, ENST00000934354, ENST00000934355, ENST00000934356, ENST00000934357, ENST00000972237

RefSeq mRNA: 7 — MANE Select: NM_001330301 NM_001145928, NM_001330299, NM_001330300, NM_001330301, NM_001330302, NM_001330303, NM_024545

CCDS: CCDS2153, CCDS54397, CCDS82510, CCDS86881

Canonical transcript exons

ENST00000643581 — 21 exons

ExonStartEnd
ENSE00000925839127986785127986962
ENSE00000925842127989564127989866
ENSE00000925843127993187127993308
ENSE00001206113127977985127978089
ENSE00001621408128010269128010393
ENSE00001627566127942424127942537
ENSE00001660862127949869127949994
ENSE00001664915128017680128017915
ENSE00001677145128013030128013154
ENSE00001682582127999741127999845
ENSE00001683324128016389128016547
ENSE00001708529128014803128014914
ENSE00001720134127945456127945559
ENSE00001732040127954986127955344
ENSE00001738051128027940128028059
ENSE00001740238128000056128000146
ENSE00001740960127950160127950408
ENSE00001747504127996350127996491
ENSE00001774386128000307128000454
ENSE00003650801128026181128026298
ENSE00003903745127941222127942164

Expression profiles

Bgee: expression breadth ubiquitous, 263 present calls, max score 93.92.

FANTOM5 (CAGE): breadth ubiquitous, TPM avg 15.3209 / max 154.5431, expressed in 1802 samples.

FANTOM5 promoters (4 alternative TSS)

Promoter IDTPM avgSamples expressed
305878.92471752
305883.92391577
305862.02751269
305890.4448218

Top tissues by expression

282 total, by Bgee expression score (0-100, higher = more expressed):

TissueAnatomy IDExpression scoreQuality
spermCL:000001993.92gold quality
male germ cellCL:000001592.71gold quality
adult organismUBERON:000702392.62gold quality
left testisUBERON:000453391.49gold quality
right testisUBERON:000453491.24gold quality
testisUBERON:000047390.53gold quality
cortical plateUBERON:000534388.24gold quality
secondary oocyteCL:000065587.52gold quality
male germ line stem cell (sensu Vertebrata) in testisCL:0000089 ∩ UBERON:000047387.02gold quality
ventricular zoneUBERON:000305386.06gold quality
ganglionic eminenceUBERON:000402386.05gold quality
stromal cell of endometriumCL:000225585.55gold quality
esophagus squamous epitheliumUBERON:000692084.65gold quality
primordial germ cell in gonadCL:0000670 ∩ UBERON:000099184.44gold quality
popliteal arteryUBERON:000225083.92gold quality
tibial arteryUBERON:000761083.91gold quality
embryoUBERON:000092283.38gold quality
granulocyteCL:000009483.04gold quality
islet of LangerhansUBERON:000000682.95gold quality
aortaUBERON:000094782.77gold quality
gastrocnemiusUBERON:000138882.62gold quality
epithelium of esophagusUBERON:000197682.61gold quality
adenohypophysisUBERON:000219682.58gold quality
pituitary glandUBERON:000000782.27gold quality
skin of legUBERON:000151182.27gold quality
muscle of legUBERON:000138382.18gold quality
descending thoracic aortaUBERON:000234582.11gold quality
bloodUBERON:000017882.06gold quality
gingival epitheliumUBERON:000194981.99gold quality
mucosa of transverse colonUBERON:000499181.62gold quality

Single-cell (SCXA)

Detected in 1 experiment(s), a significant marker in 1.

ExperimentMarker?Max mean expression
E-ANND-3yes4.74

Regulation

Is transcription factor: yes

Downstream targets (CollecTRI)

1 targets.

TargetRegulation
IFNB1Unknown

miRNA regulators (miRDB)

51 targeting SAP130, top 30 by miRDB confidence (max_score; target_count = how many genes the miRNA targets in total — lower means more specific):

miRNAMax scoreAvg scoremiRNA target_count
HSA-MIR-4692100.0067.322066
HSA-MIR-574-5P100.0066.01989
HSA-MIR-451499.9967.101870
HSA-MIR-314899.9775.066478
HSA-MIR-589-3P99.9169.622088
HSA-MIR-548D-3P99.8770.674362
HSA-MIR-30A-3P99.8769.742928
HSA-MIR-30D-3P99.8769.922917
HSA-MIR-30E-3P99.8769.682942
HSA-MIR-548BB-3P99.8670.584354
HSA-MIR-548AC99.8470.774351
HSA-MIR-548H-3P99.8470.804349
HSA-MIR-548Z99.8470.804349
HSA-MIR-6756-5P99.8267.972466
HSA-MIR-3681-5P99.8266.88387
HSA-MIR-674599.7465.331321
HSA-MIR-6766-5P99.6867.702325
HSA-MIR-6849-5P99.6466.00352
HSA-MIR-425-5P99.5967.67900
HSA-MIR-891B99.5969.811083
HSA-MIR-24-3P99.5969.971934
HSA-MIR-516B-5P99.5666.331495
HSA-MIR-6716-5P99.5668.621244
HSA-MIR-363-5P99.4664.511015
HSA-MIR-150-3P99.4370.51920
HSA-MIR-3614-5P99.3065.25837
HSA-MIR-548V99.2969.471157
HSA-MIR-6719-3P99.2967.781387
HSA-MIR-642A-3P99.2367.671258
HSA-MIR-642B-3P99.2367.671258

Literature-anchored findings (GeneRIF, showing 2)

  • the TGFbeta pathway activation leads to recruitment of a KLF14-mSin3A-HDAC2 repressor complex to the TGFbetaRII promoter, as well as the remodeling of chromatin to increase histone marks that associate with transcriptional silencing. (PMID:19088080)
  • Ambiguity about Splicing Factor 3b Subunit 3 (SF3B3) and Sin3A Associated Protein 130 (SAP130). (PMID:33800128)

Cross-species orthologs

5 orthologs

OrganismSymbolGene ID
danio_reriosap130aENSDARG00000056924
danio_reriosap130bENSDARG00000079352
mus_musculusSap130ENSMUSG00000024260
rattus_norvegicusSap130ENSRNOG00000016773
drosophila_melanogasterSap130FBGN0262714

Protein

Protein identifiers

Histone deacetylase complex subunit SAP130Q9H0E3 (reviewed: Q9H0E3)

Alternative names: 130 kDa Sin3-associated polypeptide, Sin3-associated polypeptide p130

All UniProt accessions (5): A0A2R8YDB8, C9J683, C9JTJ5, Q9H0E3, H7BXF5

UniProt curated annotations — full annotation on UniProt →

Function. Acts as a transcriptional repressor. 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.

Subunit / interactions. Component of a mSin3A corepressor complex that contains SIN3A, SAP130, SUDS3/SAP45, ARID4B/SAP180, HDAC1 and HDAC2. Interacts (released by dead or dying cells) with CLEC4E.

Subcellular location. Nucleus.

Tissue specificity. Expressed in various cancer cell ines.

Post-translational modifications. Acetylated. Sumoylated with SUMO1.

Domain organisation. The N-terminus may interact with a transcriptional coactivator. The C-terminus may interact with HDAC-dependent and HDAC-independent corepressors.

Similarity. Belongs to the SAP130 family.

Isoforms (3)

UniProt IDNamesCanonical?
Q9H0E3-11yes
Q9H0E3-22
Q9H0E3-33

RefSeq proteins (7): NP_001139400, NP_001317228, NP_001317229, NP_001317230, NP_001317231, NP_001317232, NP_078821 (=MANE)

Domains & families (InterPro)

IDNameType
IPR024137His_deAcase_cplx_SAP130Family
IPR031963SAP130_CDomain

Pfam: PF16014

UniProt features (23 total): modified residue 7, region of interest 6, compositionally biased region 4, cross-link 3, splice variant 2, chain 1

Structure

Experimental structures (PDB)

0 structures.

Predicted structure (AlphaFold)

ModelpLDDTFraction very-high
AF-Q9H0E3-F145.330.08

Functional residue map

Curated UniProt residues grouped by drug-discovery relevance — catalytic, ligand-binding, modification, and mutation-validated positions. Source: UniProtKB sequence features.

Post-translational modifications (10): 232, 355, 442, 465, 855, 856, 875, 785, 864, 869

Function

Pathways and Gene Ontology

Reactome pathways

7 pathways

IDPathway
R-HSA-3214847HATs acetylate histones
R-HSA-427413NoRC negatively regulates rRNA expression
R-HSA-212165Epigenetic regulation of gene expression
R-HSA-3247509Chromatin modifying enzymes
R-HSA-4839726Chromatin organization
R-HSA-5250941Negative epigenetic regulation of rRNA expression
R-HSA-74160Gene expression (Transcription)

MSigDB gene sets: 130 (showing top): GSE18804_BRAIN_VS_COLON_TUMORAL_MACROPHAGE_DN, GSE18804_SPLEEN_MACROPHAGE_VS_TUMORAL_MACROPHAGE_UP, RNGTGGGC_UNKNOWN, GOBP_REGULATION_OF_CELLULAR_RESPONSE_TO_GROWTH_FACTOR_STIMULUS, PAX4_01, NAGY_STAGA_COMPONENTS_HUMAN, GCM_GSPT1, BOYAULT_LIVER_CANCER_SUBCLASS_G2, GGGTGGRR_PAX4_03, GOBP_NEGATIVE_REGULATION_OF_MULTICELLULAR_ORGANISMAL_PROCESS, GOBP_REGULATION_OF_TRANSMEMBRANE_RECEPTOR_PROTEIN_SERINE_THREONINE_KINASE_SIGNALING_PATHWAY, GOBP_RESPONSE_TO_TRANSFORMING_GROWTH_FACTOR_BETA, ZIC1_01, GCM_NUMA1, GOBP_MAINTENANCE_OF_CELL_NUMBER

GO Biological Process (8): negative regulation of transcription by RNA polymerase II (GO:0000122), negative regulation of cell migration (GO:0030336), negative regulation of transforming growth factor beta receptor signaling pathway (GO:0030512), negative regulation of stem cell population maintenance (GO:1902455), positive regulation of stem cell population maintenance (GO:1902459), in utero embryonic development (GO:0001701), embryonic placenta development (GO:0001892), regulation of DNA-templated transcription (GO:0006355)

GO Molecular Function (0):

GO Cellular Component (3): nucleus (GO:0005634), nuclear speck (GO:0016607), Sin3-type complex (GO:0070822)

Reactome top-level categories

Rollup of top-5 pathways:

CategoryPathways
Chromatin modifying enzymes1
Negative epigenetic regulation of rRNA expression1
Gene expression (Transcription)1
Chromatin organization1
Epigenetic regulation of gene expression1

GO top-level categories

Rollup of top GO terms by namespace:

CategoryTerms
stem cell population maintenance2
regulation of stem cell population maintenance2
regulation of transcription by RNA polymerase II1
transcription by RNA polymerase II1
negative regulation of DNA-templated transcription1
cell migration1
regulation of cell migration1
negative regulation of cell motility1
transforming growth factor beta receptor signaling pathway1
regulation of transforming growth factor beta receptor signaling pathway1
negative regulation of transmembrane receptor protein serine/threonine kinase signaling pathway1
negative regulation of developmental process1
negative regulation of multicellular organismal process1
positive regulation of developmental process1
positive regulation of multicellular organismal process1
chordate embryonic development1
in utero embryonic development1
placenta development1
embryonic organ development1
DNA-templated transcription1
regulation of gene expression1
regulation of RNA biosynthetic process1
intracellular membrane-bounded organelle1
nuclear ribonucleoprotein granule1
histone deacetylase complex1
nuclear chromosome1
chromatin1

Protein interactions and networks

STRING

1485 interactions, top by confidence (×1000):

Protein AProtein BPartner UniProtScore
SAP130CLEC4EQ9ULY5708
SAP130OR52W1Q6IF63606
SAP130MSANTD1Q6ZTZ1570
SAP130SAP30LQ9HAJ7514
SAP130TADA2BQ86TJ2512
SAP130CLEC7AQ9BXN2497
SAP130CATSPER3Q86XQ3490
SAP130OR52B2Q96RD2482
SAP130CNGA4Q8IV77470
SAP130TAF10Q12962459
SAP130SNUPNO95149451
SAP130SUDS3Q9H7L9445
SAP130SAP30O75446434
SAP130BRMS1LQ5PSV4414
SAP130DMP1Q13316414

IntAct

109 interactions, top by confidence:

ABTypeScore
HDAC2KDM1Apsi-mi:“MI:0914”(association)0.890
HDAC1CDK2AP1psi-mi:“MI:0914”(association)0.840
RBBP7CDK2AP1psi-mi:“MI:0914”(association)0.840
HDAC1TNRC18psi-mi:“MI:0914”(association)0.790
RBBP4CDK2AP1psi-mi:“MI:0914”(association)0.790
HDAC1ZNF609psi-mi:“MI:0914”(association)0.730
RBBP7HAT1psi-mi:“MI:0914”(association)0.730
NFICNFIBpsi-mi:“MI:2364”(proximity)0.690
FOXK2DVL2psi-mi:“MI:0914”(association)0.640
SINHCAFTNRC18psi-mi:“MI:0914”(association)0.640
ZNF704SAP30psi-mi:“MI:0914”(association)0.640
ILF3ADARpsi-mi:“MI:0914”(association)0.640
SIN3BTNRC18psi-mi:“MI:0914”(association)0.530
FHL2CNOT1psi-mi:“MI:0914”(association)0.530
RBBP4TNRC18psi-mi:“MI:0914”(association)0.530
RBBP7SMARCA5psi-mi:“MI:0914”(association)0.530
RBBP7EPOPpsi-mi:“MI:0914”(association)0.530
SAP30TNRC18psi-mi:“MI:0914”(association)0.530
DAXXTNRC18psi-mi:“MI:0914”(association)0.530

BioGRID (248): SAP130 (Affinity Capture-Western), SAP130 (Affinity Capture-Western), CUL4B (Affinity Capture-Western), DDB1 (Affinity Capture-Western), SAP130 (Co-fractionation), SAP130 (Affinity Capture-MS), SAP130 (Affinity Capture-MS), SAP130 (Co-fractionation), SIN3A (Co-fractionation), SAP130 (Affinity Capture-Western), SAP130 (Reconstituted Complex), SAP130 (Proximity Label-MS), SAP130 (Affinity Capture-MS), SAP130 (Affinity Capture-MS), SAP130 (Affinity Capture-MS)

ESM2 similar proteins: A0JME2, A2AUY4, D3ZKB9, D4A666, E1B7L7, F1QZ88, F6NSX9, F8VPJ6, P59759, P78364, Q08CM4, Q0IHV2, Q15723, Q2IBE6, Q2IBF7, Q2QLB3, Q3TUF7, Q4G0F8, Q5DTH5, Q5U4Q0, Q5ZIE8, Q5ZM88, Q63HK5, Q641Z1, Q6P4L9, Q6P4R8, Q6PIJ4, Q6ZPK0, Q6ZSZ6, Q6ZU65, Q76L83, Q7ZUK7, Q7ZUV7, Q80WC1, Q8AYC1, Q8BZ32, Q8C966, Q8CGV9, Q8CHP6, Q8NDX5

Diamond homologs: Q5F3U0, Q5M7C3, Q6DDH6, Q8BIH0, Q9H0E3

SIGNOR signaling

0 interactions.

Enriched among interaction partners

Reactome pathways and GO biological processes over-represented among this gene’s 119 IntAct physical interaction partners (hypergeometric vs the genome-wide background, BH-FDR, gene-set size 15–500, ranked by fold). A functional readout of the neighbourhood — distinct from this gene’s own memberships above, and biased toward well-studied / hub proteins, so read it as themes rather than proof.

Reactome pathways:

PathwayPartnersFoldFDR
Regulation of TP53 Activity through Acetylation632.6×1e-05
Deactivation of the beta-catenin transactivating complex513.9×1e-03
Regulation of PTEN gene transcription612.8×6e-04
HDACs deacetylate histones710.0×6e-04
Negative Regulation of CDH1 Gene Transcription710.0×6e-04
TCF dependent signaling in response to WNT79.8×6e-04
Potential therapeutics for SARS79.5×6e-04
Transcriptional regulation by RUNX158.7×7e-03

GO biological processes:

GO termPartnersFoldFDR
negative regulation of stem cell population maintenance961.0×2e-12
positive regulation of stem cell population maintenance1030.4×1e-10
negative regulation of transforming growth factor beta receptor signaling pathway913.8×2e-06
somatic stem cell population maintenance613.2×4e-04
negative regulation of cell migration109.9×8e-06
DNA replication68.8×4e-03
transcription by RNA polymerase II127.5×8e-06
chromatin remodeling117.1×4e-05

Disease & clinical

Clinical variants and AI predictions

ClinVar

136 variants total. Per-class counts are floors (≥ shown; pagination cap):

ClassificationCount (floor)
Pathogenic0
Likely pathogenic1
Uncertain significance112
Likely benign2
Benign0

Top pathogenic / likely-pathogenic (1)

Variant IDHGVSClassification
808800NM_001330301.2(SAP130):c.181C>T (p.Gln61Ter)Likely pathogenic

SpliceAI

0 predictions. Top by Δscore:

AlphaMissense

6808 scored. Top likely-pathogenic:

VariantProtein changeam_pathogenicity
2:127942067:A:GL1029P1.000
2:127942076:A:TV1026D1.000
2:127942119:C:GA1012P1.000
2:127942130:T:GQ1008P1.000
2:127942142:A:GL1004P1.000
2:127942147:A:CC1002W1.000
2:127942150:C:AR1001S1.000
2:127942150:C:GR1001S1.000
2:127942151:C:AR1001M1.000
2:127942151:C:GR1001T1.000
2:127942153:C:AQ1000H1.000
2:127942153:C:GQ1000H1.000
2:127942154:T:GQ1000P1.000
2:127942159:A:CN998K1.000
2:127942159:A:TN998K1.000
2:127942163:C:TG997E1.000
2:127942164:C:GG997R1.000
2:127942164:C:TG997R1.000
2:127942431:A:GL994P1.000
2:127942497:A:GL972P1.000
2:127942506:A:GL969P1.000
2:127945457:A:GL958P1.000
2:127945481:A:GL950P1.000
2:127945492:C:AW946C1.000
2:127945492:C:GW946C1.000
2:127945493:C:GW946S1.000
2:127945494:A:GW946R1.000
2:127945494:A:TW946R1.000
2:127945496:C:TG945D1.000
2:127945497:C:GG945R1.000

dbSNP variants (sampled 300 via entrez): RS1000029976 (2:127975425 T>C), RS1000110688 (2:128016658 C>T), RS1000129196 (2:128022778 C>T), RS1000150497 (2:128020163 T>A,C), RS1000182219 (2:128019831 A>C,T), RS1000224546 (2:128022446 T>C), RS1000246311 (2:127979784 G>A), RS1000254962 (2:127945013 T>G), RS1000257930 (2:127982116 G>A,T), RS1000367822 (2:127945809 T>C), RS1000377873 (2:127974526 A>C), RS1000388147 (2:127988448 A>C,T), RS1000418017 (2:127945567 C>G,T), RS1000429761 (2:128014154 A>G), RS1000461461 (2:128016858 C>T)

Disease associations

OMIM: gene MIM:609697 | disease phenotypes:

GenCC curated gene-disease

Mondo (0):

Orphanet (0):

HPO phenotypes

0 total (0 of 0 shown, HPO-id order):

GWAS associations

0 associations (top):

Drugs & pharmacology

Drug and pharmacology data

Is drug target: yes

ChEMBL targets (2): CHEMBL1229012 (SINGLE PROTEIN), CHEMBL3885592 (PROTEIN COMPLEX)

PharmGKB: 1 entry (VIP=true, CPIC=false)

CTD chemical–gene interactions

32 total (human), top 30 by PubMed support.

ChemicalActions (top 5)PubMed papers
sodium arseniteincreases abundance, increases expression2
Benzo(a)pyreneaffects methylation, decreases methylation2
Particulate Matterdecreases expression, increases abundance, affects expression2
aristolochic acid Idecreases expression1
FR900359affects phosphorylation1
TAK-243decreases sumoylation1
dicrotophosincreases expression1
triphenyl phosphateaffects expression1
trichostatin Aaffects expression1
cobaltous chlorideincreases expression1
benzo(e)pyrenedecreases methylation1
aflatoxin B2decreases methylation1
beta-methylcholineaffects expression1
di-n-butylphosphoric acidaffects expression1
CGP 52608increases reaction, affects binding1
Acetaminophenincreases expression1
Air Pollutantsdecreases expression, increases abundance1
Arsenicincreases abundance, increases expression1
Vehicle Emissionsaffects expression, increases abundance1
Cadmiumdecreases expression, increases abundance1
Caffeineincreases phosphorylation1
Carbamazepineaffects expression1
Enzyme Inhibitorsdecreases activity, increases O-linked glycosylation1
Ivermectindecreases expression1
Methapyrilenedecreases methylation1
Dronabinolincreases expression1
Tobacco Smoke Pollutionincreases expression1
Urethaneincreases expression1
Cyclosporineincreases expression1
Aflatoxin B1decreases methylation1

ChEMBL screening assays

4 unique, capped per target: 4 binding

Representative assays (with source publication via chembl_document):

Assay IDTypeDescriptionSource paper
CHEMBL1226396BindingBinding affinity to SAP130 in human HeLa cells at 2 uM by LC-MS/MS analysisSpliceostatin A targets SF3b and inhibits both splicing and nuclear retention of pre-mRNA. — Nat Chem Biol

Clinical trials (associated diseases)

0 trials via MONDO — disease-level, not drug-specific.

No linked Atlas pages yet — the cross-entity mesh grows as the corpus expands.