Gene Gene information from NCBI Gene database.
Entrez ID 6418
Gene name SET nuclear proto-oncogene
Gene symbol SET
Synonyms (NCBI Gene)
2PP2AI2PP2AIGAADIPP2A2MRD58PHAPIITAF-ITAF-IBETA
Chromosome 9
Chromosome location 9q34.11
Summary The protein encoded by this gene inhibits acetylation of nucleosomes, especially histone H4, by histone acetylases (HAT). This inhibition is most likely accomplished by masking histone lysines from being acetylated, and the consequence is to silence HAT-d
SNPs SNP information provided by dbSNP.
8
SNP ID Visualize variation Clinical significance Consequence
rs1554776342 ACAG>- Pathogenic Coding sequence variant, frameshift variant
rs1554776500 T>G Pathogenic Coding sequence variant, missense variant
rs1554776933 ->TA Pathogenic Coding sequence variant, frameshift variant
rs1554776938 CTT>- Pathogenic Inframe indel, coding sequence variant, stop gained
rs1564360978 C>T Pathogenic Missense variant, coding sequence variant
miRNA miRNA information provided by mirtarbase database.
1168
miRTarBase ID miRNA Experiments Reference
MIRT001112 hsa-miR-199b-5p qRT-PCR 19900756
MIRT001112 hsa-miR-199b-5p Western blot 19900756
MIRT001112 hsa-miR-199b-5p qRT-PCR 19900756
MIRT001112 hsa-miR-199b-5p Western blot 19900756
MIRT001112 hsa-miR-199b-5p Luciferase reporter assay 19900756
Transcription factors Transcription factors information provided by TRRUST V2 database.
1
Transcription factor Regulation Reference
SERTAD1 Activation 20570897
Gene ontology (GO) Gene Ontology (GO) annotations describing the biological processes, molecular functions, and cellular components associated with a gene.
31
GO ID Ontology Definition Evidence Reference
GO:0000785 Component Chromatin IBA
GO:0003677 Function DNA binding IEA
GO:0003682 Function Chromatin binding IBA
GO:0004864 Function Protein phosphatase inhibitor activity TAS 8626647
GO:0005515 Function Protein binding IPI 11909973, 12628186, 16189514, 17245428, 17309103, 17318177, 19343227, 20195357, 21988832, 23195690, 24983498, 25416956, 31515488, 32296183, 32814053, 33961781, 35271311
Other IDs Other IDs provides unique identifiers for this gene in OMIM, HGNC, and Ensembl databases.
MIM HGNC e!Ensembl
600960 10760 ENSG00000119335
Protein Protein information from UniProt database.
UniProt ID Unique identifier for the protein in the UniProt database. Click to view detailed protein information.
Q01105
Protein name Protein SET (HLA-DR-associated protein II) (Inhibitor of granzyme A-activated DNase) (IGAAD) (PHAPII) (Phosphatase 2A inhibitor I2PP2A) (I-2PP2A) (Template-activating factor I) (TAF-I)
Protein function Multitasking protein, involved in apoptosis, transcription, nucleosome assembly and histone chaperoning. Isoform 2 anti-apoptotic activity is mediated by inhibition of the GZMA-activated DNase, NME1. In the course of cytotoxic T-lymphocyte (CTL)
PDB 2E50 , 7MTO
Family and domains

Pfam

Accession ID Position in sequence Description Type
PF00956 NAP 88 236 Nucleosome assembly protein (NAP) Family
Tissue specificity TISSUE SPECIFICITY: Widely expressed. Low levels in quiescent cells during serum starvation, contact inhibition or differentiation. Highly expressed in Wilms' tumor.
Sequence
MAPKRQSPLPPQKKKPRPPPALGPEETSASAGLPKKGEKEQQEAIEHIDEVQNEIDRLNE
QASEEILKVEQKYNKLRQPFFQKRSELIAKIPNFWVTTFVNHPQVSALLGEEDEEALHYL
TRVEVTEFEDIKSGYRIDFYFDENPYFENKVLSKEFHLNESGDPSSKSTEIKWKSGKDLT
KRSSQTQNKASRKRQHEEPESFFTWFTDHSDAGADELGEVIKDDIWPNPLQYYLVP
DMDD
EEGEGEEDDDDDEEEEGLEDIDEEGDEDEGEEDEDDDEGEEGEEDEGEDD
Sequence length 290
Interactions View interactions
Pathways Pathway information has different metabolic/signaling pathways associated with genes.
  Reactome
    Condensation of Prophase Chromosomes
HuR (ELAVL1) binds and stabilizes mRNA
Associated diseases Disease associations from ClinVar (causal & non-causal) and other databases (OMIM, Orphanet, GWAS, etc.).
10
Evidence Score: ★☆☆☆☆  Gene-disease association found in Text Mining only ★★☆☆☆  Found in Text Mining and Unknown/Other Associations ★★★☆☆  Reported in Unknown/Other Associations across ≥2 Sources ★★★★☆  ClinVar: Pathogenic/Likely Pathogenic (<5 Variants) ★★★★★  ClinVar: Pathogenic/Likely Pathogenic (≥5 Variants)
Causal Diseases associated with Pathogenic or Likely Pathogenic variants in ClinVar
Phenotype Name Clinical Significance dbSNP ID RCV Accession Evidence Score
Global developmental delay Likely pathogenic; Pathogenic rs1554776342 RCV001526660
★★★★☆
ClinVar: Pathogenic / Likely Pathogenic (<5 Variants)
Intellectual disability Likely pathogenic; Pathogenic rs1554776342 RCV003106006
★★★★☆
ClinVar: Pathogenic / Likely Pathogenic (<5 Variants)
Intellectual disability, autosomal dominant 58 Pathogenic; Likely pathogenic rs764645296, rs2490433063, rs2523226839, rs2490430337, rs1554776342, rs1554776500, rs1564360978, rs1554776933, rs1554776938, rs1589460606, rs1589457762, rs1861628072, rs1861593395, rs1861625938 RCV001849903
RCV003224941
RCV003233437
RCV004595087
RCV000678248
View all (9 more)
★★★★★
ClinVar: Pathogenic / Likely Pathogenic (≥5 Variants)
SET-related disorder Likely pathogenic; Pathogenic rs1554776342 RCV003325969
★★★★☆
ClinVar: Pathogenic / Likely Pathogenic (<5 Variants)
Unknown / Other Associations ClinVar entries with uncertain/conflicting evidence, and associations from other databases (OMIM, Orphanet, GWAS, etc.) where the gene is not established as causal.
Phenotype Name Clinical Significance Source Evidence Score
AUTOSOMAL DOMINANT NON-SYNDROMIC INTELLECTUAL DISABILITY CTD, Disgenet, Orphanet
CTD, Disgenet, Orphanet
CTD, Disgenet, Orphanet
★★☆☆☆
Found in Text Mining + Unknown/Other Associations
Dysgerminoma other ClinVar
★★☆☆☆
Found in Text Mining + Unknown/Other Associations
Gastric cancer Likely benign ClinVar
★★☆☆☆
Found in Text Mining + Unknown/Other Associations
Hepatocellular carcinoma other ClinVar
★★☆☆☆
Found in Text Mining + Unknown/Other Associations
Associations from Text Mining Disease associations identified through text mining
Disease Name Disease (Merged) Source PMID Relationship Type Evidence Score
Acute leukemia Leukemia BEFREE 22677993
★☆☆☆☆
Found in Text Mining only
Acute lymphocytic leukemia Lymphocytic Leukemia BEFREE 30125757, 30669574
★☆☆☆☆
Found in Text Mining only
Acute Promyelocytic Leukemia Promyelocytic Leukemia BEFREE 23338687, 24430359, 24454695
★☆☆☆☆
Found in Text Mining only
Acute Undifferentiated Leukemia Leukemia BEFREE 1384675, 15239126, 15750928, 17233820, 17569777, 17620317, 20682390, 7753797, 8131851, 8294483, 8895527
★☆☆☆☆
Found in Text Mining only
Adenocarcinoma of large intestine Colorectal Cancer BEFREE 21725597
★☆☆☆☆
Found in Text Mining only
Adenocarcinoma of lung (disorder) Lung adenocarcinoma BEFREE 31176779
★☆☆☆☆
Found in Text Mining only
Adult Acute Lymphocytic Leukemia Lymphocytic Leukemia BEFREE 30125757, 30669574
★☆☆☆☆
Found in Text Mining only
Adult Medulloblastoma Medulloblastoma BEFREE 30224541
★☆☆☆☆
Found in Text Mining only
Age related macular degeneration Age-related macular degeneration BEFREE 27771146
★☆☆☆☆
Found in Text Mining only
Alveolar Soft Part Sarcoma Alveolar Sarcoma BEFREE 24621013
★☆☆☆☆
Found in Text Mining only