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GeneE
26 sources retrieved Β· Most recent: April 2026 Β· Index updated 14 days ago
β“˜GeneE is for informational purposes only. It is not a substitute for professional medical advice, diagnosis, or treatment.
SETD2
SET domain containing 2, histone lysine methyltransferase
Chromosome 3 Β· 3p21.31
NCBI Gene: 29072Ensembl: ENSG00000181555.22HGNC: HGNC:18420UniProt: A0A1W2PPX9
214PubMed Papers
26Diseases
0Drugs
68Pathogenic Variants
FUNCTIONAL ROLE
DNA RepairHighly ConstrainedHub GeneTranscription FactorTumor Suppressor
RESEARCH IMPACT
TrendingVariant-Rich
CLINICAL
OMIM Disease Gene
DATA QUALITY
βœ“ Experimental GO Evidenceβœ“ Swiss-Prot Reviewed
protein bindingprotein-lysine N-methyltransferase activityalpha-tubulin bindinghistone H3K36 methyltransferase activityLuscan-Lumish syndromeclear cell renal carcinomaPleural MesotheliomaIntellectual disability
✦AI Summary

SETD2 is a histone H3K36 trimethyltransferase that catalyzes H3K36me3, a critical mark of active transcription 1. As a component of the RNA polymerase II elongation machinery, SETD2 is recruited to transcribed genes where it suppresses cryptic transcription, regulates splicing, and provides binding sites for transcription elongation factors 1. During stimulation-responsive transcription, H3.3S31 phosphorylation directly engages SETD2, facilitating rapid gene induction by ejecting the elongation corepressor ZMYND11 2. SETD2 functions as a tumor suppressor across multiple cancer types. In clear cell renal cell carcinoma (ccRCC), SETD2 mutations correlate with widespread DNA hypomethylation and aggressive disease phenotypes 3. SETD2 loss promotes ferroptosis sensitivity through H3K36me3-mediated regulation of ferrochelatase transcription and ferroptosis-related pathways 4. In pancreatic ductal adenocarcinoma, SETD2 loss unleashes BMP2 signaling via ectopic H3K27Ac gain, reshaping the tumor microenvironment toward lipid-rich cancer-associated fibroblasts that metabolically support tumor progression 5. Clinical genomic analysis identified SETD2 mutations as associated with reduced metastatic potential in immunotherapy-treated lung adenocarcinoma 6. SETD2 mutations occur recurrently in malignant pleural mesothelioma, often through gene fusions and splice alterations 7, highlighting its broad significance as a chr3-regulating tumor suppressor.

Sources cited
1
SETD2 catalyzes H3K36me3 deposition during transcription elongation; structural basis of SETD2 recruitment to RNA polymerase II machinery
PMID: 39666822
2
H3.3S31 phosphorylation engages SETD2 at stimulation-induced genes to promote rapid transcription by ejecting ZMYND11
PMID: 32699416
3
SETD2 mutations in ccRCC associated with widespread DNA hypomethylation and aggressive disease phenotypes
PMID: 23792563
4
SETD2 knockdown promotes ferroptosis sensitivity in ccRCC through H3K36me3 regulation of ferrochelatase and ferroptosis pathways
PMID: 37604811
5
SETD2 loss in pancreatic cancer unleashes BMP2 signaling via ectopic H3K27Ac, driving lipid-laden CAF differentiation that metabolically supports tumor progression
PMID: 38579725
6
SETD2 mutations associated with lower metastatic potential in immunotherapy-treated lung adenocarcinoma
PMID: 39506116
7
SETD2 is significantly mutated in malignant pleural mesothelioma through gene fusions and splice alterations
PMID: 26928227
Disease Associationsβ“˜26
Luscan-Lumish syndromeOpen Targets
0.77Strong
clear cell renal carcinomaOpen Targets
0.60Moderate
Pleural MesotheliomaOpen Targets
0.57Moderate
Intellectual disabilityOpen Targets
0.56Moderate
intellectual developmental disorder, autosomal dominant 70Open Targets
0.53Moderate
neurodegenerative diseaseOpen Targets
0.53Moderate
genetic disorderOpen Targets
0.53Moderate
lung adenocarcinomaOpen Targets
0.50Moderate
chronic lymphocytic leukemiaOpen Targets
0.49Moderate
acute lymphoblastic leukemiaOpen Targets
0.49Moderate
renal cell carcinomaOpen Targets
0.48Moderate
melanomaOpen Targets
0.45Moderate
Rabin-Pappas syndromeOpen Targets
0.44Moderate
non-small cell lung carcinomaOpen Targets
0.44Moderate
pancreatic neuroendocrine tumorOpen Targets
0.44Moderate
cutaneous melanomaOpen Targets
0.42Moderate
SETD2-related neurodevelopmental disorder without or with macrocephaly/overgrowthOpen Targets
0.40Weak
kidney neoplasmOpen Targets
0.38Weak
hemangioblastomaOpen Targets
0.38Weak
acute myeloid leukemiaOpen Targets
0.37Weak
Intellectual developmental disorder, autosomal dominant 70UniProt
Leukemia, acute lymphoblasticUniProt
Leukemia, acute myelogenousUniProt
Luscan-Lumish syndromeUniProt
Rabin-Pappas syndromeUniProt
Renal cell carcinomaUniProt
Pathogenic Variants68
NM_014159.7(SETD2):c.2303_2304del (p.Val768fs)Pathogenic
not provided
β˜…β˜…β˜†β˜†2025β†’ Residue 768
NM_014159.7(SETD2):c.4792C>T (p.Arg1598Ter)Pathogenic
Luscan-Lumish syndrome|not provided|Neoplasm
β˜…β˜…β˜†β˜†2025β†’ Residue 1598
NM_014159.7(SETD2):c.1289_1290del (p.Asp429_Ser430insTer)Pathogenic
not provided|Luscan-Lumish syndrome|Inborn genetic diseases
β˜…β˜…β˜†β˜†2024β†’ Residue 429
NM_014159.7(SETD2):c.5218C>T (p.Arg1740Trp)Pathogenic
not provided|Luscan-Lumish syndrome;Corpus callosum, agenesis of;Cerebellar vermis hypoplasia|Luscan-Lumish syndrome|SETD2-related disorder|Inborn genetic diseases|Congenital cerebellar hypoplasia|Rabin-Pappas syndrome|SETD2 associated neurodevelopmental disorder with multiple congenital anomalies
β˜…β˜…β˜†β˜†2024β†’ Residue 1740
NM_014159.7(SETD2):c.4457_4460delAGAAPathogenic
Inborn genetic diseases|not provided|Neoplasm
β˜…β˜…β˜†β˜†2023
NM_014159.7(SETD2):c.913dup (p.Thr305fs)Likely pathogenic
SETD2-related disorder|Luscan-Lumish syndrome
β˜…β˜…β˜†β˜†2023β†’ Residue 305
NM_014159.7(SETD2):c.5152G>A (p.Glu1718Lys)Likely pathogenic
not provided|See cases
β˜…β˜…β˜†β˜†2022β†’ Residue 1718
NM_014159.7(SETD2):c.4486C>T (p.Arg1496Ter)Pathogenic
not provided
β˜…β˜†β˜†β˜†2025β†’ Residue 1496
NM_014159.7(SETD2):c.4449_4452delAGAA (p.Lys1486fs)Pathogenic
Luscan-Lumish syndrome
β˜…β˜†β˜†β˜†2025β†’ Residue 1486
NM_014159.7(SETD2):c.6190_6191dup (p.Asp2064fs)Likely pathogenic
SETD2-related disorder
β˜…β˜†β˜†β˜†2025β†’ Residue 2064
NM_014159.7(SETD2):c.5278-1G>APathogenic
not provided
β˜…β˜†β˜†β˜†2025
NM_014159.7(SETD2):c.4814A>G (p.Tyr1605Cys)Likely pathogenic
not provided
β˜…β˜†β˜†β˜†2025β†’ Residue 1605
NM_014159.7(SETD2):c.5189_5190del (p.Leu1729_Ser1730insTer)Pathogenic
Luscan-Lumish syndrome
β˜…β˜†β˜†β˜†2025β†’ Residue 1729
NM_014159.7(SETD2):c.1858C>T (p.Arg620Ter)Likely pathogenic
SETD2-related disorder
β˜…β˜†β˜†β˜†2025β†’ Residue 620
NM_014159.7(SETD2):c.5142+2T>GLikely pathogenic
Luscan-Lumish syndrome
β˜…β˜†β˜†β˜†2025
NM_014159.7(SETD2):c.4712C>T (p.Pro1571Leu)Likely pathogenic
not provided
β˜…β˜†β˜†β˜†2024β†’ Residue 1571
NM_014159.7(SETD2):c.6284dup (p.Asp2096fs)Pathogenic
Luscan-Lumish syndrome
β˜…β˜†β˜†β˜†2024β†’ Residue 2096
NM_014159.7(SETD2):c.7350+1G>APathogenic
Inborn genetic diseases
β˜…β˜†β˜†β˜†2024
NM_014159.7(SETD2):c.6148C>T (p.Gln2050Ter)Pathogenic
Luscan-Lumish syndrome
β˜…β˜†β˜†β˜†2024β†’ Residue 2050
NM_014159.7(SETD2):c.5123G>C (p.Arg1708Pro)Likely pathogenic
Luscan-Lumish syndrome
β˜…β˜†β˜†β˜†2024β†’ Residue 1708
View on ClinVar β†—
Related Genes
POLR2BProtein interaction100%H3C1Protein interaction100%KDM5CProtein interaction100%H2BC4Protein interaction99%KDM5AProtein interaction99%UTYProtein interaction99%
Tissue Expression6 tissues
Bone Marrow
100%
Ovary
45%
Lung
41%
Liver
34%
Brain
32%
Heart
31%
Gene Interaction Network
Click a node to explore
SETD2POLR2BH3C1KDM5CH2BC4KDM5AUTY
PROTEIN STRUCTURE
Preparing viewer…
PDB5JLB Β· 1.50 Γ… Β· X-ray
View on RCSB β†—
Constraintβ“˜
LOEUFβ“˜
0.18Highly Constrained
pLIβ“˜
1.00Intolerant
Observed/Expected LoF0.13 [0.09–0.18]
RankingsWhere SETD2 stands among ~20K protein-coding genes
  • #1,941of 20,598
    Most Researched214 Β· top 10%
  • #1,063of 5,498
    Most Pathogenic Variants68 Β· top quartile
  • #321of 17,882
    Most Constrained (LOEUF)0.18 Β· top 5%
Genes detectedSETD2
Sources retrieved26 papers
Response timeβ€”
πŸ“„ Sources
26β–Ό
1
Tumor cell-intrinsic epigenetic dysregulation shapes cancer-associated fibroblasts heterogeneity to metabolically support pancreatic cancer.
PMID: 38579725
Cancer Cell Β· 2024
1.00
2
Automated real-world data integration improves cancer outcome prediction.
PMID: 39506116
Nature Β· 2024
0.90
3
Knockdown of SETD2 promotes erastin-induced ferroptosis in ccRCC.
PMID: 37604811
Cell Death Dis Β· 2023
0.80
4
SETD2 Restricts Prostate Cancer Metastasis by Integrating EZH2 and AMPK Signaling Pathways.
PMID: 32619406
Cancer Cell Β· 2020
0.76
5
Histone H3.3 phosphorylation amplifies stimulation-induced transcription.
PMID: 32699416
Nature Β· 2020
0.70