Huntington's disease (HD), a neurodegenerative disorder characterized by loss of striatal neurons, is caused by an expansion of a polyglutamine tract in the HD protein huntingtin. This gene encodes a protein belonging to a class of huntingtin interacting proteins characterized by WW motifs. This protein is a histone methyltransferase that is specific for lysine-36 of histone H3... See more...

Aliases for SETD2 Gene

Aliases for SETD2 Gene

  • SET Domain Containing 2, Histone Lysine Methyltransferase 2 3 5
  • HIF-1 2 3 4
  • KMT3A 2 3 4
  • HYPB 2 3 4
  • Histone-Lysine N-Methyltransferase SETD2 3 4
  • Protein-Lysine N-Methyltransferase SETD2 3 4
  • Huntingtin-Interacting Protein B 3 4
  • Lysine N-Methyltransferase 3A 3 4
  • Huntingtin Yeast Partner B 3 4
  • SET Domain Containing 2 2 3
  • KIAA1732 2 4
  • P231HBP 3 4
  • HIP-1 3 4
  • SET2 3 4
  • Huntingtin Interacting Protein 1 3
  • Huntingtin-Interacting Protein 1 4
  • SET Domain-Containing Protein 2 4
  • EC 2.1.1.359 4
  • EC 2.1.1.43 51
  • EC 2.1.1.- 4
  • FLJ23184 2
  • HSPC069 3
  • HBP231 3
  • SETD2 5
  • HSET2 4
  • HIF1 4
  • LLS 3

External Ids for SETD2 Gene

Summaries for SETD2 Gene

Entrez Gene Summary for SETD2 Gene

  • Huntington's disease (HD), a neurodegenerative disorder characterized by loss of striatal neurons, is caused by an expansion of a polyglutamine tract in the HD protein huntingtin. This gene encodes a protein belonging to a class of huntingtin interacting proteins characterized by WW motifs. This protein is a histone methyltransferase that is specific for lysine-36 of histone H3, and methylation of this residue is associated with active chromatin. This protein also contains a novel transcriptional activation domain and has been found associated with hyperphosphorylated RNA polymerase II. [provided by RefSeq, Aug 2008]

GeneCards Summary for SETD2 Gene

SETD2 (SET Domain Containing 2, Histone Lysine Methyltransferase) is a Protein Coding gene. Diseases associated with SETD2 include Luscan-Lumish Syndrome and Sotos Syndrome 1. Among its related pathways are Lysine degradation and PKMTs methylate histone lysines. Gene Ontology (GO) annotations related to this gene include histone-lysine N-methyltransferase activity. An important paralog of this gene is KMT2C.

UniProtKB/Swiss-Prot Summary for SETD2 Gene

  • Histone methyltransferase that specifically trimethylates 'Lys-36' of histone H3 (H3K36me3) using dimethylated 'Lys-36' (H3K36me2) as substrate (PubMed:16118227, PubMed:19141475, PubMed:21526191, PubMed:21792193, PubMed:23043551, PubMed:27474439). It is capable of trimethylating unmethylated H3K36 (H3K36me0) in vitro (PubMed:19332550). Represents the main enzyme generating H3K36me3, a specific tag for epigenetic transcriptional activation (By similarity). Plays a role in chromatin structure modulation during elongation by coordinating recruitment of the FACT complex and by interacting with hyperphosphorylated POLR2A (PubMed:23325844). Acts as a key regulator of DNA mismatch repair in G1 and early S phase by generating H3K36me3, a mark required to recruit MSH6 subunit of the MutS alpha complex: early recruitment of the MutS alpha complex to chromatin to be replicated allows a quick identification of mismatch DNA to initiate the mismatch repair reaction (PubMed:23622243). Required for DNA double-strand break repair in response to DNA damage: acts by mediating formation of H3K36me3, promoting recruitment of RAD51 and DNA repair via homologous recombination (HR) (PubMed:24843002). Acts as a tumor suppressor (PubMed:24509477). H3K36me3 also plays an essential role in the maintenance of a heterochromatic state, by recruiting DNA methyltransferase DNMT3A (PubMed:27317772). H3K36me3 is also enhanced in intron-containing genes, suggesting that SETD2 recruitment is enhanced by splicing and that splicing is coupled to recruitment of elongating RNA polymerase (PubMed:21792193). Required during angiogenesis (By similarity). Required for endoderm development by promoting embryonic stem cell differentiation toward endoderm: acts by mediating formation of H3K36me3 in distal promoter regions of FGFR3, leading to regulate transcription initiation of FGFR3 (By similarity). In addition to histones, also mediates methylation of other proteins, such as tubulins and STAT1 (PubMed:27518565, PubMed:28753426). Trimethylates 'Lys-40' of alpha-tubulins such as TUBA1B (alpha-TubK40me3); alpha-TubK40me3 is required for normal mitosis and cytokinesis and may be a specific tag in cytoskeletal remodeling (PubMed:27518565). Involved in interferon-alpha-induced antiviral defense by mediating both monomethylation of STAT1 at 'Lys-525' and catalyzing H3K36me3 on promoters of some interferon-stimulated genes (ISGs) to activate gene transcription (PubMed:28753426).
  • (Microbial infection) Recruited to the promoters of adenovirus 12 E1A gene in case of infection, possibly leading to regulate its expression.

Gene Wiki entry for SETD2 Gene

No data available for CIViC Summary , Tocris Summary , PharmGKB "VIP" Summary , Rfam classification and piRNA Summary for SETD2 Gene

Genomics for SETD2 Gene

GeneHancer (GH) Regulatory Elements Pubs

Promoters and enhancers for SETD2 Gene
- Elite GeneHancer and/or Elite GeneHancer-gene association Download GeneHancer data from 2017 publication | Request up-to-date GeneHancer data (full dataset)

GeneHancers around SETD2 on the GeneHancer Hub at the UCSC Golden Path

Cistromic (ChIP-Seq) regulation report from SPP (The Signaling Pathways Project) for SETD2

Top Transcription factor binding sites by QIAGEN in the SETD2 gene promoter:
  • AP-4
  • ARP-1
  • FOXO4
  • NRSF form 1
  • NRSF form 2
  • Pax-4a
  • Sox9
  • Sp1
  • SREBP-1a
  • SREBP-1b

Genomic Locations for SETD2 Gene

Genomic Locations for SETD2 Gene
chr3:47,016,408-47,164,113
(GRCh38/hg38)
Size:
147,706 bases
Orientation:
Minus strand
chr3:47,057,898-47,205,467
(GRCh37/hg19)
Size:
147,570 bases
Orientation:
Minus strand

Genomic View for SETD2 Gene

Genes around SETD2 on UCSC Golden Path with GeneCards custom track

Cytogenetic band:
SETD2 Gene in genomic location: bands according to Ensembl, locations according to GeneLoc (and/or Entrez Gene and/or Ensembl if different)
Genomic Location for SETD2 Gene
GeneLoc Logo Genomic Neighborhood Exon StructureGene Density

RefSeq DNA sequence for SETD2 Gene

Proteins for SETD2 Gene

  • Protein details for SETD2 Gene (UniProtKB/Swiss-Prot)

    Protein Symbol:
    Q9BYW2-SETD2_HUMAN
    Recommended name:
    Histone-lysine N-methyltransferase SETD2
    Protein Accession:
    Q9BYW2
    Secondary Accessions:
    • O75397
    • O75405
    • Q17RW8
    • Q5BKS9
    • Q5QGN2
    • Q69YI5
    • Q6IN64
    • Q6ZN53
    • Q6ZS25
    • Q8N3R0
    • Q8TCN0
    • Q9C0D1
    • Q9H696
    • Q9NZW9

    Protein attributes for SETD2 Gene

    Size:
    2564 amino acids
    Molecular mass:
    287597 Da
    Quaternary structure:
    • Specifically interacts with hyperphosphorylated C-terminal domain (CTD) of RNA polymerase II large subunit (POLR2A): binds to CTD heptad repeats doubly phosphorylated on 'Ser-2' and 'Ser-5' of each heptad (PubMed:16118227, PubMed:16314571). Interacts with HTT (PubMed:11461154, PubMed:9700202, PubMed:10958656). Interacts with IWS1 (PubMed:19141475). Interacts with p53/TP53; leading to regulate p53/TP53 target genes (PubMed:18585004). Component of a complex with HNRNPL (PubMed:19332550). Interacts with TUBA1A; the interaction is independent on alpha-tubulin acetylation on 'Lys-40' (PubMed:27518565). Interacts with STAT1 (PubMed:28753426).
    SequenceCaution:
    • Sequence=AAF29041.1; Type=Frameshift; Evidence={ECO:0000305}; Sequence=AAH72440.1; Type=Erroneous termination; Note=Truncated C-terminus.; Evidence={ECO:0000305}; Sequence=AAI17163.1; Type=Erroneous initiation; Note=Truncated N-terminus.; Evidence={ECO:0000305}; Sequence=AAI17165.1; Type=Erroneous initiation; Note=Truncated N-terminus.; Evidence={ECO:0000305}; Sequence=AAT77612.1; Type=Erroneous initiation; Note=Truncated N-terminus.; Evidence={ECO:0000305}; Sequence=AAT77613.1; Type=Erroneous initiation; Note=Truncated N-terminus.; Evidence={ECO:0000305}; Sequence=BAB15367.1; Type=Erroneous initiation; Note=Truncated N-terminus.; Evidence={ECO:0000305}; Sequence=BAB15367.1; Type=Miscellaneous discrepancy; Note=Contaminating sequence. Potential poly-A sequence.; Evidence={ECO:0000305}; Sequence=BAC87131.1; Type=Erroneous initiation; Note=Truncated N-terminus.; Evidence={ECO:0000305}; Sequence=CAC28349.1; Type=Erroneous termination; Note=Truncated C-terminus.; Evidence={ECO:0000305}; Sequence=CAD38601.2; Type=Erroneous initiation; Note=Truncated N-terminus.; Evidence={ECO:0000305};

    Three dimensional structures from OCA and Proteopedia for SETD2 Gene

    Alternative splice isoforms for SETD2 Gene

    UniProtKB/Swiss-Prot:

neXtProt entry for SETD2 Gene

Selected DME Specific Peptides for SETD2 Gene

Q9BYW2:
  • NHSCEPN
  • RFMNHSC

Post-translational modifications for SETD2 Gene

Domains & Families for SETD2 Gene

Gene Families for SETD2 Gene

HGNC:
Human Protein Atlas (HPA):
  • Cancer-related genes
  • Disease related genes
  • Enzymes
  • Plasma proteins
  • Potential drug targets
  • Predicted intracellular proteins

Protein Domains for SETD2 Gene

InterPro:
Blocks:
  • Nuclear protein SET
ProtoNet:

Suggested Antigen Peptide Sequences for SETD2 Gene

GenScript: Design optimal peptide antigens:
  • p231HBP (SETD2_HUMAN)

Graphical View of Domain Structure for InterPro Entry

Q9BYW2

UniProtKB/Swiss-Prot:

SETD2_HUMAN :
  • The low charge region mediates the transcriptional activation activity.
  • Belongs to the class V-like SAM-binding methyltransferase superfamily. Histone-lysine methyltransferase family. SET2 subfamily.
Domain:
  • The low charge region mediates the transcriptional activation activity.
  • The catalytic SET domain binds histone H3 (PubMed:27474439, PubMed:28256625). It is also able to bind oncogenic histone H3 K36M/I found in a number of cancer types, in which histone H3 'Lys-36' is replaced by a Met or an Ile residue. When binding the oncogenic variant histone H3 K36M/I, the SET domain undergoes dramatic conformational change to accommodate the histone H3 peptide, leading to sequester and inhibit SETD2 activity and block global H3K36 methylation (PubMed:27474439, PubMed:28256625).
Family:
  • Belongs to the class V-like SAM-binding methyltransferase superfamily. Histone-lysine methyltransferase family. SET2 subfamily.
genes like me logo Genes that share domains with SETD2: view

Function for SETD2 Gene

Molecular function for SETD2 Gene

UniProtKB/Swiss-Prot Function:
Histone methyltransferase that specifically trimethylates 'Lys-36' of histone H3 (H3K36me3) using dimethylated 'Lys-36' (H3K36me2) as substrate (PubMed:16118227, PubMed:19141475, PubMed:21526191, PubMed:21792193, PubMed:23043551, PubMed:27474439). It is capable of trimethylating unmethylated H3K36 (H3K36me0) in vitro (PubMed:19332550). Represents the main enzyme generating H3K36me3, a specific tag for epigenetic transcriptional activation (By similarity). Plays a role in chromatin structure modulation during elongation by coordinating recruitment of the FACT complex and by interacting with hyperphosphorylated POLR2A (PubMed:23325844). Acts as a key regulator of DNA mismatch repair in G1 and early S phase by generating H3K36me3, a mark required to recruit MSH6 subunit of the MutS alpha complex: early recruitment of the MutS alpha complex to chromatin to be replicated allows a quick identification of mismatch DNA to initiate the mismatch repair reaction (PubMed:23622243). Required for DNA double-strand break repair in response to DNA damage: acts by mediating formation of H3K36me3, promoting recruitment of RAD51 and DNA repair via homologous recombination (HR) (PubMed:24843002). Acts as a tumor suppressor (PubMed:24509477). H3K36me3 also plays an essential role in the maintenance of a heterochromatic state, by recruiting DNA methyltransferase DNMT3A (PubMed:27317772). H3K36me3 is also enhanced in intron-containing genes, suggesting that SETD2 recruitment is enhanced by splicing and that splicing is coupled to recruitment of elongating RNA polymerase (PubMed:21792193). Required during angiogenesis (By similarity). Required for endoderm development by promoting embryonic stem cell differentiation toward endoderm: acts by mediating formation of H3K36me3 in distal promoter regions of FGFR3, leading to regulate transcription initiation of FGFR3 (By similarity). In addition to histones, also mediates methylation of other proteins, such as tubulins and STAT1 (PubMed:27518565, PubMed:28753426). Trimethylates 'Lys-40' of alpha-tubulins such as TUBA1B (alpha-TubK40me3); alpha-TubK40me3 is required for normal mitosis and cytokinesis and may be a specific tag in cytoskeletal remodeling (PubMed:27518565). Involved in interferon-alpha-induced antiviral defense by mediating both monomethylation of STAT1 at 'Lys-525' and catalyzing H3K36me3 on promoters of some interferon-stimulated genes (ISGs) to activate gene transcription (PubMed:28753426).
UniProtKB/Swiss-Prot Function:
(Microbial infection) Recruited to the promoters of adenovirus 12 E1A gene in case of infection, possibly leading to regulate its expression.
UniProtKB/Swiss-Prot CatalyticActivity:
Reaction=L-lysyl(36)-[histone H3] + 3 S-adenosyl-L-methionine = 3 H(+) + N(6),N(6),N(6)-trimethyl-L-lysyl(36)-[histone H3] + 3 S-adenosyl-L-homocysteine; Xref=Rhea:RHEA:60324, Rhea:RHEA-COMP:9785, Rhea:RHEA-COMP:15536, ChEBI:CHEBI:15378, ChEBI:CHEBI:29969, ChEBI:CHEBI:57856, ChEBI:CHEBI:59789, ChEBI:CHEBI:61961; EC=2.1.1.359; Evidence={ECO:0000269|PubMed:19332550, ECO:0000269|PubMed:23043551, ECO:0000269|PubMed:27474439};.
UniProtKB/Swiss-Prot CatalyticActivity:
Reaction=L-lysyl-[protein] + S-adenosyl-L-methionine = H(+) + N(6)-methyl-L-lysyl-[protein] + S-adenosyl-L-homocysteine; Xref=Rhea:RHEA:51736, Rhea:RHEA-COMP:9752, Rhea:RHEA-COMP:13053, ChEBI:CHEBI:15378, ChEBI:CHEBI:29969, ChEBI:CHEBI:57856, ChEBI:CHEBI:59789, ChEBI:CHEBI:61929; Evidence={ECO:0000269|PubMed:23043551, ECO:0000269|PubMed:28753426};.
UniProtKB/Swiss-Prot CatalyticActivity:
Reaction=L-lysyl-[protein] + 3 S-adenosyl-L-methionine = 3 H(+) + N(6),N(6),N(6)-trimethyl-L-lysyl-[protein] + 3 S-adenosyl-L-homocysteine; Xref=Rhea:RHEA:54192, Rhea:RHEA-COMP:9752, Rhea:RHEA-COMP:13826, ChEBI:CHEBI:15378, ChEBI:CHEBI:29969, ChEBI:CHEBI:57856, ChEBI:CHEBI:59789, ChEBI:CHEBI:61961; Evidence={ECO:0000269|PubMed:27518565};.
UniProtKB/Swiss-Prot BiophysicochemicalProperties:
Kinetic parameters: KM=1.21 uM for S-adenosyl-L-methionine {ECO:0000269|PubMed:23043551}; KM=0.42 uM for histone H3 {ECO:0000269|PubMed:23043551}; Note=Kcat is 0.14 min(-1). {ECO:0000269|PubMed:23043551};
UniProtKB/Swiss-Prot EnzymeRegulation:
Specifically inhibited by sinefungin derivatives. N-propyl sinefungin (Pr-SNF) interacts preferentially with SETD2.

Enzyme Numbers (IUBMB) for SETD2 Gene

Phenotypes From GWAS Catalog for SETD2 Gene

Gene Ontology (GO) - Molecular Function for SETD2 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0005515 protein binding IEA,IPI 17500595
GO:0008168 methyltransferase activity IEA --
GO:0016279 protein-lysine N-methyltransferase activity IDA 28753426
GO:0016740 transferase activity IEA --
GO:0018024 histone-lysine N-methyltransferase activity IEA,TAS --
genes like me logo Genes that share ontologies with SETD2: view
genes like me logo Genes that share phenotypes with SETD2: view

Human Phenotype Ontology for SETD2 Gene

HPO Id HPO Name Alternative Ids Definition Synonyms

Animal Models for SETD2 Gene

MGI Knock Outs for SETD2:
  • Setd2 Setd2<tm1b(NCOM)Mfgc>
  • Setd2 Setd2<tm1Zhch>

Animal Model Products

CRISPR Products

Inhibitory RNA Products

  • Search GeneCopoeia for shRNA, lentivirus and/or AAV clone products for SETD2

No data available for Transcription Factor Targets and HOMER Transcription for SETD2 Gene

Localization for SETD2 Gene

Subcellular locations from UniProtKB/Swiss-Prot for SETD2 Gene

Nucleus. Chromosome.

Subcellular locations from

COMPARTMENTS
Extracellular space Cytosol Plasma membrane Cytoskeleton Lysosome Endosome Peroxisome ER Golgi Apparatus Nucleus Mitochondrion 0 1 2 3 4 5 Confidence
COMPARTMENTS Subcellular localization image for SETD2 gene
Compartment Confidence
nucleus 5
cytosol 3
plasma membrane 2
extracellular 2
cytoskeleton 2
mitochondrion 2
peroxisome 1
endoplasmic reticulum 1
endosome 1
lysosome 1
golgi apparatus 1

Subcellular locations from the

Human Protein Atlas (HPA)
  • Cytosol (2)
  • Nuclear speckles (2)
See all subcellular structures

Gene Ontology (GO) - Cellular Components for SETD2 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0005634 nucleus IEA,ISS --
GO:0005654 nucleoplasm TAS --
GO:0005694 chromosome ISS --
genes like me logo Genes that share ontologies with SETD2: view

Pathways & Interactions for SETD2 Gene

genes like me logo Genes that share pathways with SETD2: view

Pathways by source for SETD2 Gene

1 Cell Signaling Technology pathway for SETD2 Gene
1 GeneTex pathway for SETD2 Gene

SIGNOR curated interactions for SETD2 Gene

Activates:

Gene Ontology (GO) - Biological Process for SETD2 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0001525 angiogenesis IEA --
GO:0001570 vasculogenesis IEA --
GO:0001763 morphogenesis of a branching structure IEA --
GO:0001843 neural tube closure IEA --
GO:0002376 immune system process IEA --
genes like me logo Genes that share ontologies with SETD2: view

Drugs & Compounds for SETD2 Gene

(57) Drugs for SETD2 Gene - From: HMDB and Novoseek

Name Status Disease Links Group Role Mechanism of Action Clinical Trials
D-Lysine Approved, Experimental Nutra Agonist, Full agonist 0
s-adenosylhomocysteine Experimental Pharma 0

(41) Additional Compounds for SETD2 Gene - From: Novoseek and HMDB

Name Synonyms Role CAS Number PubChem IDs PubMed IDs
s-adenosylmethionine
  • (3S)-5'-[(3-amino-3-Carboxypropyl)methylsulfonio]-5'-deoxyadenosine, inner salt
  • [1-(Adenin-9-yl)-1,5-dideoxy-beta-D-ribofuranos-5-yl][(3S)-3-amino-3-carboxypropyl](methyl)sulfonium
  • Acylcarnitine
  • AdoMet
  • S-(5'-Deoxyadenosin-5'-yl)-L-methionine
485-80-3
genes like me logo Genes that share compounds with SETD2: view

Transcripts for SETD2 Gene

mRNA/cDNA for SETD2 Gene

3 REFSEQ mRNAs :
26 NCBI additional mRNA sequence :
9 Ensembl transcripts including schematic representations, and UCSC links to gene/alias where relevant :

CRISPR Products

Inhibitory RNA Products

  • Search GeneCopoeia for shRNA, lentivirus and/or AAV clone products for SETD2

Alternative Splicing Database (ASD) splice patterns (SP) for SETD2 Gene

ExUns: 1a · 1b · 1c ^ 2 ^ 3 ^ 4 ^ 5 ^ 6 ^ 7 ^ 8a · 8b ^ 9a · 9b ^ 10 ^ 11a · 11b · 11c · 11d ^ 12 ^ 13 ^ 14 ^ 15 ^ 16 ^ 17 ^ 18a · 18b ^
SP1: - - - - -
SP2: - - - - - -
SP3: - - - - - -
SP4: - - - -
SP5: - - -
SP6: - - - -
SP7: - - -
SP8:
SP9:

ExUns: 19a · 19b ^ 20 ^ 21a · 21b ^ 22 ^ 23 ^ 24 ^ 25
SP1:
SP2:
SP3:
SP4: - -
SP5:
SP6:
SP7:
SP8:
SP9:

Relevant External Links for SETD2 Gene

GeneLoc Exon Structure for
SETD2

Expression for SETD2 Gene

mRNA expression in normal human tissues from GTEx, Illumina, BioGPS, and SAGE for SETD2 Gene

mRNA expression in embryonic tissues and stem cells from LifeMap Discovery

Protein differential expression in normal tissues from HIPED for SETD2 Gene

This gene is overexpressed in Serum (21.6), Bone marrow mesenchymal stem cell (19.9), and Cervix (7.7).

Integrated Proteomics: protein expression in normal tissues and cell lines from ProteomicsDB, MaxQB, and MOPED for SETD2 Gene



Transcriptomic regulation report from SPP (The Signaling Pathways Project) for SETD2

SOURCE GeneReport for Unigene cluster for SETD2 Gene:

Hs.517941

mRNA Expression by UniProt/SwissProt for SETD2 Gene:

Q9BYW2-SETD2_HUMAN
Tissue specificity: Ubiquitously expressed.

Evidence on tissue expression from TISSUES for SETD2 Gene

  • Nervous system(4.8)
  • Liver(4.6)
  • Intestine(4.6)
  • Blood(4.6)
  • Lung(3.8)
  • Kidney(3.2)
  • Skin(3.2)
  • Muscle(3.1)
  • Heart(3)
  • Spleen(2.9)
  • Bone marrow(2.7)
  • Lymph node(2.5)
  • Thyroid gland(2.3)
  • Stomach(2.2)

Phenotype-based relationships between genes and organs from Gene ORGANizer for SETD2 Gene

Germ Layers:
  • ectoderm
  • endoderm
  • mesoderm
Systems:
  • cardiovascular
  • digestive
  • endocrine
  • immune
  • integumentary
  • nervous
  • reproductive
  • respiratory
  • skeletal muscle
  • skeleton
  • urinary
Regions:
Head and neck:
  • brain
  • cerebellum
  • chin
  • cranial nerve
  • ear
  • eye
  • eyelid
  • face
  • forehead
  • head
  • jaw
  • mandible
  • maxilla
  • meninges
  • middle ear
  • mouth
  • neck
  • nose
  • outer ear
  • scalp
  • skull
  • tooth
Thorax:
  • chest wall
  • clavicle
  • heart
  • heart valve
  • lung
  • rib
  • rib cage
  • scapula
  • sternum
Abdomen:
  • adrenal gland
  • intestine
  • kidney
  • pancreas
  • small intestine
Pelvis:
  • fallopian tube
  • ovary
  • pelvis
  • penis
  • prostate
  • testicle
  • uterus
  • vagina
  • vas deferens
  • vulva
Limb:
  • ankle
  • arm
  • digit
  • elbow
  • femur
  • fibula
  • finger
  • foot
  • forearm
  • hand
  • hip
  • humerus
  • knee
  • lower limb
  • nail
  • radius
  • shin
  • shoulder
  • thigh
  • tibia
  • toe
  • ulna
  • upper limb
  • wrist
General:
  • blood
  • blood vessel
  • hair
  • peripheral nerve
  • peripheral nervous system
  • skin
  • spinal column
  • spinal cord
  • sweat gland
  • vertebrae
genes like me logo Genes that share expression patterns with SETD2: view

No data available for mRNA differential expression in normal tissues and Protein tissue co-expression partners for SETD2 Gene

Orthologs for SETD2 Gene

This gene was present in the common ancestor of animals and fungi.

Orthologs for SETD2 Gene

Organism Taxonomy Gene Similarity Type Details
Chimpanzee
(Pan troglodytes)
Mammalia SETD2 30 31
  • 99.59 (n)
OneToOne
Dog
(Canis familiaris)
Mammalia SETD2 30 31
  • 92.44 (n)
OneToOne
Cow
(Bos Taurus)
Mammalia SETD2 30 31
  • 90.64 (n)
OneToOne
Mouse
(Mus musculus)
Mammalia Setd2 30 17 31
  • 87.27 (n)
OneToOne
Rat
(Rattus norvegicus)
Mammalia Setd2 30
  • 86.93 (n)
Oppossum
(Monodelphis domestica)
Mammalia SETD2 31
  • 74 (a)
OneToOne
Chicken
(Gallus gallus)
Aves SETD2 30 31
  • 67.84 (n)
OneToOne
Lizard
(Anolis carolinensis)
Reptilia SETD2 31
  • 60 (a)
OneToOne
Tropical Clawed Frog
(Silurana tropicalis)
Amphibia LOC100492810 30
  • 64.62 (n)
Str.16666 30
African clawed frog
(Xenopus laevis)
Amphibia Xl.26109 30
Zebrafish
(Danio rerio)
Actinopterygii setd2 30 31
  • 58.44 (n)
OneToOne
wufb97h09 30
Fruit Fly
(Drosophila melanogaster)
Insecta Set2 31
  • 20 (a)
ManyToMany
Worm
(Caenorhabditis elegans)
Secernentea met-1 31
  • 24 (a)
OneToOne
Baker's yeast
(Saccharomyces cerevisiae)
Saccharomycetes SET2 31 33
  • 26 (a)
OneToMany
Sea Squirt
(Ciona savignyi)
Ascidiacea -- 31
  • 53 (a)
OneToOne
Species where no ortholog for SETD2 was found in the sources mined by GeneCards:
  • A. gosspyii yeast (Eremothecium gossypii)
  • Actinobacteria (Mycobacterium tuberculosis)
  • African malaria mosquito (Anopheles gambiae)
  • Alicante grape (Vitis vinifera)
  • Alpha proteobacteria (Wolbachia pipientis)
  • Amoeba (Dictyostelium discoideum)
  • Archea (Pyrococcus horikoshii)
  • Barley (Hordeum vulgare)
  • Beta proteobacteria (Neisseria meningitidis)
  • Bread mold (Neurospora crassa)
  • Chromalveolata (Phytophthora infestans)
  • Common water flea (Daphnia pulex)
  • Corn (Zea mays)
  • E. coli (Escherichia coli)
  • Filamentous fungi (Aspergillus nidulans)
  • Firmicute Bacteria (Streptococcus pneumoniae)
  • Fission Yeast (Schizosaccharomyces pombe)
  • Green Algae (Chlamydomonas reinhardtii)
  • Honey Bee (Apis mellifera)
  • K. Lactis Yeast (Kluyveromyces lactis)
  • Loblloly Pine (Pinus taeda)
  • Malaria Parasite (Plasmodium falciparum)
  • Medicago Trunc (Medicago Truncatula)
  • Moss (Physcomitrella patens)
  • Orangutan (Pongo pygmaeus)
  • Pig (Sus scrofa)
  • Platypus (Ornithorhynchus anatinus)
  • Rainbow Trout (Oncorhynchus mykiss)
  • Rice (Oryza sativa)
  • Rice Blast Fungus (Magnaporthe grisea)
  • Schistosome Parasite (Schistosoma mansoni)
  • Sea Anemone (Nematostella vectensis)
  • Sea Vase (Ciona intestinalis)
  • Sea Urchin (Strongylocentrotus purpuratus)
  • Sorghum (Sorghum bicolor)
  • Soybean (Glycine max)
  • Stem Rust Fungus (Puccinia graminis)
  • Sugarcane (Saccharum officinarum)
  • Thale Cress (Arabidopsis thaliana)
  • Tomato (Lycopersicon esculentum)
  • Toxoplasmosis (Toxoplasma gondii)
  • Trichoplax (Trichoplax adhaerens)
  • Wheat (Triticum aestivum)

Evolution for SETD2 Gene

ENSEMBL:
Gene Tree for SETD2 (if available)
TreeFam:
Gene Tree for SETD2 (if available)
Aminode:
Evolutionary constrained regions (ECRs) for SETD2: view image

Paralogs for SETD2 Gene

(2) SIMAP similar genes for SETD2 Gene using alignment to 5 proteins:

  • SETD2_HUMAN
  • C9JG86_HUMAN
  • H7BXT4_HUMAN
  • H7BZ93_HUMAN
  • H7C3H4_HUMAN
genes like me logo Genes that share paralogs with SETD2: view

Variants for SETD2 Gene

Sequence variations, with clinical significance, from ClinVar and Humsavar, with links to dbSNP for SETD2 Gene

SNP ID Clinical significance and condition Chr 03 pos Variation AA Info Type
624022 Likely Pathogenic: not provided 47,123,345(-) CAG/C NONSENSE,NON_CODING_TRANSCRIPT_VARIANT
641456 Uncertain Significance: Luscan-lumish syndrome 47,120,867(-) T/A MISSENSE_VARIANT,NON_CODING_TRANSCRIPT_VARIANT
642342 Likely Benign: Luscan-lumish syndrome 47,163,923(-) A/T INITIATIOR_CODON_VARIANT,MISSENSE_VARIANT,NON_CODING_TRANSCRIPT_VARIANT,FIVE_PRIME_UTR_VARIANT
642782 Uncertain Significance: Luscan-lumish syndrome 47,057,355(-) G/T MISSENSE_VARIANT,NON_CODING_TRANSCRIPT_VARIANT
644892 Uncertain Significance: Luscan-lumish syndrome 47,046,577(-) AATCTGTTGC/A NON_CODING_TRANSCRIPT_VARIANT,INFRAME_DELETION

Additional dbSNP identifiers (rs#s) for SETD2 Gene

Structural Variations from Database of Genomic Variants (DGV) for SETD2 Gene

Variant ID Type Subtype PubMed ID
esv2725239 CNV deletion 23290073
esv3568733 CNV loss 25503493
esv3596073 CNV loss 21293372
nsv1002970 CNV gain 25217958
nsv1007714 CNV gain 25217958
nsv3801 CNV deletion 18451855
nsv428417 CNV loss 18775914
nsv590210 CNV loss 21841781
nsv590211 CNV gain 21841781
nsv997261 CNV gain 25217958

Variation tolerance for SETD2 Gene

Residual Variation Intolerance Score: 1.12% of all genes are more intolerant (likely to be disease-causing)
Gene Damage Index Score: 15.02; 96.86% of all genes are more intolerant (likely to be disease-causing)

Additional Variant Information for SETD2 Gene

Human Gene Mutation Database (HGMD)
SETD2
SNPedia medical, phenotypic, and genealogical associations of SNPs for
SETD2

SNP Genotyping and Copy Number Assay Products

No data available for Polymorphic Variants from UniProtKB/Swiss-Prot for SETD2 Gene

Disorders for SETD2 Gene

MalaCards: The human disease database

(39) MalaCards diseases for SETD2 Gene - From: UniProtKB/Swiss-Prot, OMIM, ClinVar, GTR, Orphanet, DISEASES, Novoseek, and GeneCards

- elite association - COSMIC cancer census association via MalaCards
Search SETD2 in MalaCards View complete list of genes associated with diseases

UniProtKB/Swiss-Prot

SETD2_HUMAN
  • Renal cell carcinoma (RCC) [MIM:144700]: Renal cell carcinoma is a heterogeneous group of sporadic or hereditary carcinoma derived from cells of the proximal renal tubular epithelium. It is subclassified into clear cell renal carcinoma (non-papillary carcinoma), papillary renal cell carcinoma, chromophobe renal cell carcinoma, collecting duct carcinoma with medullary carcinoma of the kidney, and unclassified renal cell carcinoma. Clear cell renal cell carcinoma is the most common subtype. {ECO:0000269 PubMed:20054297, ECO:0000269 PubMed:23622243, ECO:0000269 PubMed:23792563, ECO:0000269 PubMed:25728682}. Note=The disease may be caused by mutations affecting the gene represented in this entry. Defects of SETD2 are associated with loss of DNA methylation at non-promoter regions (PubMed:23792563). SETD2 defects lead to aberrant and reduced nucleosome compaction and chromatin association of key replication proteins, such as MCM7 and DNA polymerase delta, leading to hinder replication fork progression and prevent loading of RAD51 homologous recombination repair factor at DNA breaks (PubMed:25728682). {ECO:0000269 PubMed:23792563, ECO:0000269 PubMed:25728682}.
  • Luscan-Lumish syndrome (LLS) [MIM:616831]: An autosomal dominant syndrome with a variable phenotype. Clinical features include macrocephaly, distinctive facial appearance, postnatal overgrowth, various degrees of learning difficulties, autism spectrum disorder, and intellectual disability. {ECO:0000269 PubMed:23160955, ECO:0000269 PubMed:24852293, ECO:0000269 PubMed:26084711, ECO:0000269 PubMed:27317772}. Note=The disease may be caused by mutations affecting the gene represented in this entry.
  • Leukemia, acute lymphoblastic (ALL) [MIM:613065]: A subtype of acute leukemia, a cancer of the white blood cells. ALL is a malignant disease of bone marrow and the most common malignancy diagnosed in children. The malignant cells are lymphoid precursor cells (lymphoblasts) that are arrested in an early stage of development. The lymphoblasts replace the normal marrow elements, resulting in a marked decrease in the production of normal blood cells. Consequently, anemia, thrombocytopenia, and neutropenia occur to varying degrees. The lymphoblasts also proliferate in organs other than the marrow, particularly the liver, spleen, and lymphnodes. {ECO:0000269 PubMed:24509477, ECO:0000269 PubMed:24662245}. Note=The disease may be caused by mutations affecting distinct genetic loci, including the gene represented in this entry.
  • Leukemia, acute myelogenous (AML) [MIM:601626]: A subtype of acute leukemia, a cancer of the white blood cells. AML is a malignant disease of bone marrow characterized by maturational arrest of hematopoietic precursors at an early stage of development. Clonal expansion of myeloid blasts occurs in bone marrow, blood, and other tissue. Myelogenous leukemias develop from changes in cells that normally produce neutrophils, basophils, eosinophils and monocytes. {ECO:0000269 PubMed:16314571, ECO:0000269 PubMed:24509477}. Note=The disease may be caused by mutations affecting distinct genetic loci, including the gene represented in this entry.

Additional Disease Information for SETD2

Genetic Association Database
(GAD)
Human Genome Epidemiology Navigator
(HuGE)
ATLAS of Genetics and Cytogenetics in Oncology and Haematology
Open Targets Platform
genes like me logo Genes that share disorders with SETD2: view

No data available for Genatlas for SETD2 Gene

Publications for SETD2 Gene

  1. Identification and characterization of a novel human histone H3 lysine 36-specific methyltransferase. (PMID: 16118227) Sun XJ … Chen Z (The Journal of biological chemistry 2005) 2 3 4
  2. Identification of the full-length huntingtin- interacting protein p231HBP/HYPB as a DNA-binding factor. (PMID: 11461154) Rega S … Pützer BM (Molecular and cellular neurosciences 2001) 2 3 4
  3. Molecular basis for the role of oncogenic histone mutations in modulating H3K36 methylation. (PMID: 28256625) Zhang Y … Jia S (Scientific reports 2017) 3 4
  4. Methyltransferase SETD2-Mediated Methylation of STAT1 Is Critical for Interferon Antiviral Activity. (PMID: 28753426) Chen K … Cao X (Cell 2017) 3 4
  5. Dual Chromatin and Cytoskeletal Remodeling by SETD2. (PMID: 27518565) Park IY … Walker CL (Cell 2016) 3 4

Products for SETD2 Gene

  • Signalway ELISA kits for SETD2
  • Signalway Proteins for SETD2

Sources for SETD2 Gene