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SETD2 SET domain containing 2, histone lysine methyltransferase [ Homo sapiens (human) ]

Gene ID: 29072, updated on 15-Jun-2019

Summary

Official Symbol
SETD2provided by HGNC
Official Full Name
SET domain containing 2, histone lysine methyltransferaseprovided by HGNC
Primary source
HGNC:HGNC:18420
See related
Ensembl:ENSG00000181555 MIM:612778
Gene type
protein coding
RefSeq status
REVIEWED
Organism
Homo sapiens
Lineage
Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Primates; Haplorrhini; Catarrhini; Hominidae; Homo
Also known as
LLS; HYPB; SET2; HIF-1; HIP-1; KMT3A; HBP231; HSPC069; p231HBP
Summary
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]
Expression
Ubiquitous expression in bone marrow (RPKM 11.9), testis (RPKM 11.0) and 25 other tissues See more
Orthologs

Genomic context

See SETD2 in Genome Data Viewer
Location:
3p21.31
Exon count:
26
Annotation release Status Assembly Chr Location
109 current GRCh38.p12 (GCF_000001405.38) 3 NC_000003.12 (47016408..47164037, complement)
105 previous assembly GRCh37.p13 (GCF_000001405.25) 3 NC_000003.11 (47057898..47205467, complement)

Chromosome 3 - NC_000003.12Genomic Context describing neighboring genes Neighboring gene coiled-coil domain containing 12 Neighboring gene neurobeachin like 2 Neighboring gene neurotrophin receptor associated death domain, pseudogene Neighboring gene mitochondrial ribosomal protein L57 pseudogene 3 Neighboring gene KIF9 antisense RNA 1 Neighboring gene small nucleolar RNA, C/D box 13 pseudogene 3 Neighboring gene kinesin family member 9 Neighboring gene small nucleolar RNA, C/D box 13J

Genomic regions, transcripts, and products

Expression

  • Project title: HPA RNA-seq normal tissues
  • Description: RNA-seq was performed of tissue samples from 95 human individuals representing 27 different tissues in order to determine tissue-specificity of all protein-coding genes
  • BioProject: PRJEB4337
  • Publication: PMID 24309898
  • Analysis date: Wed Apr 4 07:08:55 2018

Bibliography

GeneRIFs: Gene References Into FunctionsWhat's a GeneRIF?

Phenotypes

Associated conditions

Description Tests
Luscan-lumish syndrome
MedGen: C4085873 OMIM: 616831 GeneReviews: Not available
Compare labs

Copy number response

Description
Copy number response
Triplosensitivity

No evidence available (Last evaluated (2018-02-28)

ClinGen Genome Curation Page
Haploinsufficency

Some evidence for dosage pathogenicity (Last evaluated (2018-02-28)

ClinGen Genome Curation PagePubMed

NHGRI GWAS Catalog

Description
Discovery and refinement of loci associated with lipid levels.
NHGRI GWA Catalog

Pathways from BioSystems

  • Chromatin modifying enzymes, organism-specific biosystem (from REACTOME)
    Chromatin modifying enzymes, organism-specific biosystemEukaryotic DNA is associated with histone proteins and organized into a complex nucleoprotein structure called chromatin. This structure decreases the accessibility of DNA but also helps to protect i...
  • Chromatin organization, organism-specific biosystem (from REACTOME)
    Chromatin organization, organism-specific biosystemChromatin organization refers to the composition and conformation of complexes between DNA, protein and RNA. It is determined by processes that result in the specification, formation or maintenance o...
  • Histone Modifications, organism-specific biosystem (from WikiPathways)
    Histone Modifications, organism-specific biosystemHistones can undergo many post-translational modifications that are involved in transcription regulation. This pathway provides an overview of various modifications for histones H3 and H4 and the en...
  • Lysine degradation, organism-specific biosystem (from KEGG)
    Lysine degradation, organism-specific biosystem
    Lysine degradation
  • Lysine degradation, conserved biosystem (from KEGG)
    Lysine degradation, conserved biosystem
    Lysine degradation
  • Mesodermal Commitment Pathway, organism-specific biosystem (from WikiPathways)
    Mesodermal Commitment Pathway, organism-specific biosystemModel depicting mesodermal specification based on the literature and highly enriched gene expression profiles via comparison across dozens of independent induced and embryonic pluripotent stem cell l...
  • PKMTs methylate histone lysines, organism-specific biosystem (from REACTOME)
    PKMTs methylate histone lysines, organism-specific biosystemLysine methyltransferases (KMTs) and arginine methyltransferases (RMTs) have a common mechanism of catalysis. Both families transfer a methyl group from a common donor, S-adenosyl-L-methionine (SAM),...
  • Pathways Affected in Adenoid Cystic Carcinoma, organism-specific biosystem (from WikiPathways)
    Pathways Affected in Adenoid Cystic Carcinoma, organism-specific biosystemProtein pathways altered by mutations in adenoid cystic carcinoma. Pathways include epigentic modification, DNA damage checkpoint signals, MYB/MYC signalling pathway, FGF/IGF/PI3K signalling, and not...

Interactions

Products Interactant Other Gene Complex Source Pubs Description

General gene information

Markers

Homology

Clone Names

  • FLJ16420, FLJ22472, FLJ23184, FLJ45883, FLJ46217, KIAA1732

Gene Ontology Provided by GOA

Function Evidence Code Pubs
alpha-tubulin binding IDA
Inferred from Direct Assay
more info
PubMed 
histone methyltransferase activity (H3-K36 specific) IDA
Inferred from Direct Assay
more info
PubMed 
histone-lysine N-methyltransferase activity IDA
Inferred from Direct Assay
more info
PubMed 
histone-lysine N-methyltransferase activity IMP
Inferred from Mutant Phenotype
more info
PubMed 
histone-lysine N-methyltransferase activity TAS
Traceable Author Statement
more info
 
metal ion binding IEA
Inferred from Electronic Annotation
more info
 
protein binding IPI
Inferred from Physical Interaction
more info
PubMed 
protein-lysine N-methyltransferase activity IDA
Inferred from Direct Assay
more info
PubMed 
Process Evidence Code Pubs
angiogenesis IEA
Inferred from Electronic Annotation
more info
 
cell migration involved in vasculogenesis IEA
Inferred from Electronic Annotation
more info
 
coronary vasculature morphogenesis IEA
Inferred from Electronic Annotation
more info
 
defense response to virus IDA
Inferred from Direct Assay
more info
PubMed 
embryonic cranial skeleton morphogenesis IEA
Inferred from Electronic Annotation
more info
 
embryonic placenta morphogenesis IEA
Inferred from Electronic Annotation
more info
 
endodermal cell differentiation ISS
Inferred from Sequence or Structural Similarity
more info
 
forebrain development IEA
Inferred from Electronic Annotation
more info
 
histone H3-K36 dimethylation IDA
Inferred from Direct Assay
more info
PubMed 
histone H3-K36 trimethylation IDA
Inferred from Direct Assay
more info
PubMed 
histone H3-K36 trimethylation IMP
Inferred from Mutant Phenotype
more info
PubMed 
mesoderm morphogenesis IEA
Inferred from Electronic Annotation
more info
 
microtubule cytoskeleton organization involved in mitosis IDA
Inferred from Direct Assay
more info
PubMed 
mismatch repair IMP
Inferred from Mutant Phenotype
more info
PubMed 
morphogenesis of a branching structure IEA
Inferred from Electronic Annotation
more info
 
neural tube closure IEA
Inferred from Electronic Annotation
more info
 
nucleosome organization IMP
Inferred from Mutant Phenotype
more info
PubMed 
peptidyl-lysine monomethylation IDA
Inferred from Direct Assay
more info
PubMed 
peptidyl-lysine trimethylation IDA
Inferred from Direct Assay
more info
PubMed 
pericardium development IEA
Inferred from Electronic Annotation
more info
 
positive regulation of interferon-alpha production IDA
Inferred from Direct Assay
more info
PubMed 
regulation of cytokinesis IDA
Inferred from Direct Assay
more info
PubMed 
regulation of double-strand break repair via homologous recombination IDA
Inferred from Direct Assay
more info
PubMed 
regulation of mRNA export from nucleus IMP
Inferred from Mutant Phenotype
more info
PubMed 
regulation of protein localization to chromatin IDA
Inferred from Direct Assay
more info
PubMed 
regulation of transcription, DNA-templated IEA
Inferred from Electronic Annotation
more info
 
response to type I interferon IDA
Inferred from Direct Assay
more info
PubMed 
stem cell development IEA
Inferred from Electronic Annotation
more info
 
stem cell differentiation ISS
Inferred from Sequence or Structural Similarity
more info
 
transcription elongation from RNA polymerase II promoter IMP
Inferred from Mutant Phenotype
more info
PubMed 
Component Evidence Code Pubs
chromosome ISS
Inferred from Sequence or Structural Similarity
more info
 
nucleoplasm TAS
Traceable Author Statement
more info
 
nucleus ISS
Inferred from Sequence or Structural Similarity
more info
 

General protein information

Preferred Names
histone-lysine N-methyltransferase SETD2
Names
SET domain containing 2
huntingtin interacting protein 1
huntingtin yeast partner B
huntingtin-interacting protein B
lysine N-methyltransferase 3A
protein-lysine N-methyltransferase SETD2
NP_001336299.1
NP_054878.5
XP_011531934.1
XP_011531936.1
XP_024309255.1
XP_024309256.1
XP_024309257.1

NCBI Reference Sequences (RefSeq)

RefSeqs maintained independently of Annotated Genomes

These reference sequences exist independently of genome builds. Explain

These reference sequences are curated independently of the genome annotation cycle, so their versions may not match the RefSeq versions in the current genome build. Identify version mismatches by comparing the version of the RefSeq in this section to the one reported in Genomic regions, transcripts, and products above.

Genomic

  1. NG_032091.1 RefSeqGene

    Range
    5001..152570
    Download
    GenBank, FASTA, Sequence Viewer (Graphics), LRG_775

mRNA and Protein(s)

  1. NM_001349370.2NP_001336299.1  histone-lysine N-methyltransferase SETD2 isoform 2

    Status: REVIEWED

    Description
    Transcript Variant: This variant (2) differs in the 5' UTR and coding sequence compared to variant 1. The resulting isoform (2) is shorter at the N-terminus compared to isoform 1.
    Source sequence(s)
    AC094020, AC127430
    Conserved Domains (6) summary
    pfam05279
    Location:18962079
    Asp-B-Hydro_N; Aspartyl beta-hydroxylase N-terminal region
    smart00570
    Location:14511505
    AWS; associated with SET domains
    smart00317
    Location:15061629
    SET; SET (Su(var)3-9, Enhancer-of-zeste, Trithorax) domain
    smart00508
    Location:16301646
    PostSET; Cysteine-rich motif following a subset of SET domains
    pfam00397
    Location:23472376
    WW; WW domain
    pfam08236
    Location:24252512
    SRI; SRI (Set2 Rpb1 interacting) domain
  2. NM_014159.6NP_054878.5  histone-lysine N-methyltransferase SETD2 isoform 1

    See identical proteins and their annotated locations for NP_054878.5

    Status: REVIEWED

    Description
    Transcript Variant: This variant (1) encodes the longer isoform (1).
    Source sequence(s)
    AI671342, AK127782, AY576987, BC117162, BX649110, DA800082
    Consensus CDS
    CCDS2749.2
    UniProtKB/Swiss-Prot
    Q9BYW2
    Related
    ENSP00000386759.3, ENST00000409792.3
    Conserved Domains (6) summary
    pfam05279
    Location:19402123
    Asp-B-Hydro_N; Aspartyl beta-hydroxylase N-terminal region
    smart00570
    Location:14951549
    AWS; associated with SET domains
    smart00317
    Location:15501673
    SET; SET (Su(var)3-9, Enhancer-of-zeste, Trithorax) domain
    smart00508
    Location:16741690
    PostSET; Cysteine-rich motif following a subset of SET domains
    pfam00397
    Location:23912420
    WW; WW domain
    pfam08236
    Location:24692548
    SRI; SRI (Set2 Rpb1 interacting) domain

RNA

  1. NR_146158.1 RNA Sequence

    Status: REVIEWED

    Description
    Transcript Variant: This variant (3) contains an alternate exon compared to variant 1. This variant is represented as non-coding because the use of the 5'-most expected translational start codon renders the transcript a candidate for nonsense-mediated mRNA decay (NMD).
    Source sequence(s)
    AC094020, AC127430, AI671342

RefSeqs of Annotated Genomes: Homo sapiens Annotation Release 109

The following sections contain reference sequences that belong to a specific genome build. Explain

Reference GRCh38.p13 Primary Assembly

Genomic

  1. NC_000003.12 Reference GRCh38.p13 Primary Assembly

    Range
    47016408..47164113 complement
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_011533632.3XP_011531934.1  histone-lysine N-methyltransferase SETD2 isoform X4

    Conserved Domains (6) summary
    pfam05279
    Location:19482131
    Asp-B-Hydro_N; Aspartyl beta-hydroxylase N-terminal region
    smart00570
    Location:15031557
    AWS; associated with SET domains
    smart00317
    Location:15581681
    SET; SET (Su(var)3-9, Enhancer-of-zeste, Trithorax) domain
    smart00508
    Location:16821698
    PostSET; Cysteine-rich motif following a subset of SET domains
    pfam00397
    Location:23992428
    WW; WW domain
    pfam08236
    Location:24772556
    SRI; SRI (Set2 Rpb1 interacting) domain
  2. XM_011533634.1XP_011531936.1  histone-lysine N-methyltransferase SETD2 isoform X2

    Conserved Domains (6) summary
    pfam05279
    Location:18962079
    Asp-B-Hydro_N; Aspartyl beta-hydroxylase N-terminal region
    smart00570
    Location:14511505
    AWS; associated with SET domains
    smart00317
    Location:15061629
    SET; SET (Su(var)3-9, Enhancer-of-zeste, Trithorax) domain
    smart00508
    Location:16301646
    PostSET; Cysteine-rich motif following a subset of SET domains
    pfam00397
    Location:23472376
    WW; WW domain
    pfam08236
    Location:24252512
    SRI; SRI (Set2 Rpb1 interacting) domain
  3. XM_024453488.1XP_024309256.1  histone-lysine N-methyltransferase SETD2 isoform X3

    Conserved Domains (5) summary
    pfam05279
    Location:17961979
    Asp-B-Hydro_N; Aspartyl beta-hydroxylase N-terminal region
    smart00570
    Location:14511505
    AWS; associated with SET domains
    smart00508
    Location:15301546
    PostSET; Cysteine-rich motif following a subset of SET domains
    pfam00397
    Location:22472276
    WW; WW domain
    pfam08236
    Location:23252412
    SRI; SRI (Set2 Rpb1 interacting) domain
  4. XM_024453487.1XP_024309255.1  histone-lysine N-methyltransferase SETD2 isoform X1

    Conserved Domains (6) summary
    pfam05279
    Location:18512034
    Asp-B-Hydro_N; Aspartyl beta-hydroxylase N-terminal region
    smart00570
    Location:14511505
    AWS; associated with SET domains
    smart00317
    Location:15061629
    SET; SET (Su(var)3-9, Enhancer-of-zeste, Trithorax) domain
    smart00508
    Location:16301646
    PostSET; Cysteine-rich motif following a subset of SET domains
    pfam00397
    Location:23022331
    WW; WW domain
    pfam08236
    Location:23802467
    SRI; SRI (Set2 Rpb1 interacting) domain
  5. XM_024453489.1XP_024309257.1  histone-lysine N-methyltransferase SETD2 isoform X5

    Conserved Domains (2) summary
    smart00570
    Location:14511505
    AWS; associated with SET domains
    smart00317
    Location:15061595
    SET; SET (Su(var)3-9, Enhancer-of-zeste, Trithorax) domain

RNA

  1. XR_001740131.2 RNA Sequence

  2. XR_002959515.1 RNA Sequence

  3. XR_002959510.1 RNA Sequence

    Related
    ENST00000330022.11
  4. XR_002959511.1 RNA Sequence

    Related
    ENST00000431180.5
  5. XR_002959512.1 RNA Sequence

  6. XR_002959513.1 RNA Sequence

  7. XR_002959516.1 RNA Sequence

  8. XR_002959517.1 RNA Sequence

  9. XR_002959514.1 RNA Sequence

Suppressed Reference Sequence(s)

The following Reference Sequences have been suppressed. Explain

  1. NM_012271.1: Suppressed sequence

    Description
    NM_012271.1: This RefSeq was permanently suppressed because it is a nonsense-mediated mRNA decay (NMD) candidate.
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