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SETD1B SET domain containing 1B, histone lysine methyltransferase [ Homo sapiens (human) ]

Gene ID: 23067, updated on 13-Apr-2024

Summary

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Official Symbol
SETD1Bprovided by HGNC
Official Full Name
SET domain containing 1B, histone lysine methyltransferaseprovided by HGNC
Primary source
HGNC:HGNC:29187
See related
Ensembl:ENSG00000139718 MIM:611055; AllianceGenome:HGNC:29187
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
KMT2G; Set1B; IDDSELD
Summary
SET1B is a component of a histone methyltransferase complex that produces trimethylated histone H3 at Lys4 (Lee et al., 2007 [PubMed 17355966]).[supplied by OMIM, Mar 2008]
Expression
Ubiquitous expression in endometrium (RPKM 7.9), spleen (RPKM 6.1) and 25 other tissues See more
Orthologs
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Genomic context

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See SETD1B in Genome Data Viewer
Location:
12q24.31
Exon count:
20
Annotation release Status Assembly Chr Location
RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 12 NC_000012.12 (121790155..121832656)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 12 NC_060936.1 (121800295..121829318)
105.20220307 previous assembly GRCh37.p13 (GCF_000001405.25) 12 NC_000012.11 (122241915..122270562)

Chromosome 12 - NC_000012.12Genomic Context describing neighboring genes Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr12:122101860-122102399 Neighboring gene uncharacterized LOC105370034 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr12:122109697-122110623 Neighboring gene MORN repeat containing 3 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr12:122124874-122125860 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 7181 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 4984 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 4985 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 4986 Neighboring gene transmembrane protein 120B Neighboring gene H3K4me1 hESC enhancer GRCh37_chr12:122165743-122166363 Neighboring gene H3K27ac hESC enhancer GRCh37_chr12:122194907-122195407 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr12:122204395-122204898 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr12:122207988-122208500 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 4987 Neighboring gene Sharpr-MPRA regulatory region 8824 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr12:122216872-122217390 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr12:122217391-122217909 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 7182 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 7183 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 4988 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr12:122227166-122227882 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 7184 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 7185 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr12:122230665-122231496 Neighboring gene H3K27ac hESC enhancer GRCh37_chr12:122231502-122232042 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr12:122232583-122233123 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 7187 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr12:122236367-122236906 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr12:122235825-122236366 Neighboring gene H3K27ac hESC enhancer GRCh37_chr12:122236907-122237446 Neighboring gene H3K27ac hESC enhancer GRCh37_chr12:122237447-122237986 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 4992 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 4993 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 7188 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 7189 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 7190 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 4994 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 4996 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 4995 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 4997 Neighboring gene long intergenic non-protein coding RNA 1089 Neighboring gene ras homolog family member F, filopodia associated Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr12:122248237-122249046 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr12:122249091-122249703 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 4998 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 4999 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr12:122252006-122252512 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr12:122276754-122277424 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 5000 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr12:122278096-122278765 Neighboring gene MED14-independent group 3 enhancer GRCh37_chr12:122293687-122294886 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr12:122297907-122298424 Neighboring gene H3K27ac hESC enhancer GRCh37_chr12:122298425-122298941 Neighboring gene Sharpr-MPRA regulatory region 2080 Neighboring gene 4-hydroxyphenylpyruvate dioxygenase Neighboring gene Sharpr-MPRA regulatory region 2229 Neighboring gene transcript inducer of AURKA lysosomal degradation Neighboring gene OCT4-NANOG-H3K27ac hESC enhancer GRCh37_chr12:122326353-122326966 Neighboring gene OCT4-NANOG-H3K27ac hESC enhancer GRCh37_chr12:122326967-122327580 Neighboring gene proteasome 26S subunit, non-ATPase 9 Neighboring gene RNA, U7 small nuclear 170 pseudogene

Genomic regions, transcripts, and products

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Go to nucleotide: Graphics FASTA GenBank

Expression

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  • 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

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Related articles in PubMed

  1. SETD1B-Related Neurodevelopmental Disorder. Adam MP, et al. , 1993. PMID 36173874
  2. Delineating the molecular and phenotypic spectrum of the SETD1B-related syndrome. Weerts MJA, et al. Genet Med, 2021 Nov. PMID 34345025, Free PMC Article
  3. SETD1B-associated neurodevelopmental disorder. Roston A, et al. J Med Genet, 2021 Mar. PMID 32546566
  4. A genome-wide DNA methylation signature for SETD1B-related syndrome. Krzyzewska IM, et al. Clin Epigenetics, 2019 Nov 4. PMID 31685013, Free PMC Article
  5. A novel de novo frameshift variant in SETD1B causes epilepsy. Den K, et al. J Hum Genet, 2019 Aug. PMID 31110234

See all (58) citations in PubMed

GeneRIFs: Gene References Into Functions

What's a GeneRIF?
  1. Phenotypic spectrum of SETD1B-related disorder: Myoclonic absence seizures and concurrent intellectual disability - Insights from two cases.
    Title: Phenotypic spectrum of SETD1B-related disorder: Myoclonic absence seizures and concurrent intellectual disability - Insights from two cases.
  2. Molecular insight into the SETD1A/B N-terminal region and its interaction with WDR82.
    Title: Molecular insight into the SETD1A/B N-terminal region and its interaction with WDR82.
  3. Delineating the molecular and phenotypic spectrum of the SETD1B-related syndrome.
    Title: Delineating the molecular and phenotypic spectrum of the SETD1B-related syndrome.
  4. SETD1B-associated neurodevelopmental disorder.
    Title: SETD1B-associated neurodevelopmental disorder.
  5. Study identify a specific hypermethylation signature associated with loss of function mutations in the SETD1B gene which may be used as an epigenetic marker supporting the diagnosis of syndromic SETD1B-related diseases.
    Title: A genome-wide DNA methylation signature for SETD1B-related syndrome.
  6. Results show that SETD1B is the most frequently mutated gene along with TP53 in primary hepatic neuroendocrine tumors (PHNETs). A biological analysis suggests that one of the three SETD1B mutants, A1054del, promotes cell proliferation, migration and invasion compared to wild-type SETD1B. Our work unveils that SETD1B A1054del mutant is functional in PHNET and implicates this gene on PHNET pathogenesis.
    Title: SET domain containing 1B gene is mutated in primary hepatic neuroendocrine tumors.
  7. we report a first epilepsy patient with a frameshift variant in SETD1B, emphasizing a possible pathomechanistic association of SETD1B abnormality with neurodevelopmental delay with epilepsy.
    Title: A novel de novo frameshift variant in SETD1B causes epilepsy.
  8. the results demonstrated that SETD1B is essential in the progression of hepatocellular carcinoma and may be used as a potential prognostic marker and therapeutic target in hepatocellular carcinoma.
    Title: High‑level SETD1B gene expression is associated with unfavorable prognosis in hepatocellular carcinoma.
  9. SETD1B aberration is likely to be the core defect in 12q24.3 deletion syndrome.
    Title: De novo variants in SETD1B are associated with intellectual disability, epilepsy and autism.
  10. KMT2G levels were higher in metastatic clear cell renal cell carcinomas and may be a good marker for discriminating metastatic tumors from non-metastatic tumors.
    Title: Expression and clinical significance of COMPASS family of histone methyltransferases in clear cell renal cell carcinoma.
Submit: New GeneRIF Correction See all GeneRIFs (14)

Phenotypes

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Find tests for this gene in the NIH Genetic Testing Registry (GTR)

Review eQTL and phenotype association data in this region using PheGenI

EBI GWAS Catalog

Description
A genome- and phenome-wide association study to identify genetic variants influencing platelet count and volume and their pleiotropic effects.
EBI GWAS Catalog

Variation

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See variants in ClinVar

See studies and variants in dbVar

See Variation Viewer (GRCh37.p13)

See Variation Viewer (GRCh38)

Genotypes

HIV-1 interactions

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Replication interactions

Interaction Pubs
Knockdown of SET domain containing 1B (SETD1B) by siRNA inhibits the early stages of HIV-1 replication in 293T cells infected with VSV-G pseudotyped HIV-1 PubMed

Go to the HIV-1, Human Interaction Database

Pathways from PubChem

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Interactions

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Products Interactant Other Gene Complex Source Pubs Description

General gene information

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Markers

Homology

Clone Names

  • FLJ20803, KIAA1076

Gene Ontology Provided by GOA

Function Evidence Code Pubs
enables RNA binding IEA
Inferred from Electronic Annotation
more info
  
enables histone H3 methyltransferase activity TAS
Traceable Author Statement
more info
  
contributes_to histone H3K4 methyltransferase activity IDA
Inferred from Direct Assay
more info
 PubMed 
enables histone H3K4 monomethyltransferase activity IEA
Inferred from Electronic Annotation
more info
  
enables histone H3K4 trimethyltransferase activity IEA
Inferred from Electronic Annotation
more info
  
enables protein binding IPI
Inferred from Physical Interaction
more info
 PubMed 
Process Evidence Code Pubs
involved_in chromatin remodeling IEA
Inferred from Electronic Annotation
more info
  
involved_in methylation IEA
Inferred from Electronic Annotation
more info
  
Component Evidence Code Pubs
part_of Set1C/COMPASS complex IBA
Inferred from Biological aspect of Ancestor
more info
  
part_of Set1C/COMPASS complex IDA
Inferred from Direct Assay
more info
 PubMed 
part_of Set1C/COMPASS complex IPI
Inferred from Physical Interaction
more info
 PubMed 
located_in chromosome IEA
Inferred from Electronic Annotation
more info
  
located_in cytoplasm IDA
Inferred from Direct Assay
more info
 PubMed 
part_of histone methyltransferase complex IDA
Inferred from Direct Assay
more info
 PubMed 
located_in nuclear speck IEA
Inferred from Electronic Annotation
more info
  
located_in nucleoplasm IDA
Inferred from Direct Assay
more info
  
located_in nucleoplasm TAS
Traceable Author Statement
more info
  
located_in nucleus IDA
Inferred from Direct Assay
more info
 PubMed 

General protein information

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Preferred Names
histone-lysine N-methyltransferase SETD1B
Names
SET domain-containing protein 1B
lysine N-methyltransferase 2G
NP_001340274.1
XP_024304666.1
XP_047284508.1
XP_047284509.1
XP_054227457.1
XP_054227458.1

NCBI Reference Sequences (RefSeq)

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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.

mRNA and Protein(s)

  1. NM_001353345.2 → NP_001340274.1  histone-lysine N-methyltransferase SETD1B

    Status: REVIEWED

    Source sequence(s)
    AC079360, AC084018
    Consensus CDS
    CCDS86338.1
    UniProtKB/Swiss-Prot
    F6MFW1, Q9UPS6
    Related
    ENSP00000474253.1, ENST00000604567.6
    Conserved Domains (5) summary
    smart00317
    Location:1834 → 1949
    SET; SET (Su(var)3-9, Enhancer-of-zeste, Trithorax) domain
    smart00508
    Location:1950 → 1966
    PostSET; Cysteine-rich motif following a subset of SET domains
    cd12549
    Location:101 → 193
    RRM_Set1B; RNA recognition motif in vertebrate histone-lysine N-methyltransferase Setd1B (Set1B)
    pfam11764
    Location:1679 → 1821
    N-SET; COMPASS (Complex proteins associated with Set1p) component N
    cl25865
    Location:1237 → 1308
    Trypan_PARP; Procyclic acidic repetitive protein (PARP)

RefSeqs of Annotated Genomes: GCF_000001405.40-RS_2023_10

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

Reference GRCh38.p14 Primary Assembly

Genomic

  1. NC_000012.12 Reference GRCh38.p14 Primary Assembly

    Range
    121790155..121832656
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_047428553.1 → XP_047284509.1  histone-lysine N-methyltransferase SETD1B isoform X1

    UniProtKB/Swiss-Prot
    F6MFW1, Q9UPS6

  2. XM_024448898.2 → XP_024304666.1  histone-lysine N-methyltransferase SETD1B isoform X1

    UniProtKB/Swiss-Prot
    F6MFW1, Q9UPS6
    Conserved Domains (5) summary
    smart00317
    Location:1834 → 1949
    SET; SET (Su(var)3-9, Enhancer-of-zeste, Trithorax) domain
    smart00508
    Location:1950 → 1966
    PostSET; Cysteine-rich motif following a subset of SET domains
    cd12549
    Location:101 → 193
    RRM_Set1B; RNA recognition motif in vertebrate histone-lysine N-methyltransferase Setd1B (Set1B)
    pfam11764
    Location:1679 → 1821
    N-SET; COMPASS (Complex proteins associated with Set1p) component N
    cl25865
    Location:1237 → 1308
    Trypan_PARP; Procyclic acidic repetitive protein (PARP)

  3. XM_047428552.1 → XP_047284508.1  histone-lysine N-methyltransferase SETD1B isoform X1

    UniProtKB/Swiss-Prot
    F6MFW1, Q9UPS6
    Related
    ENSP00000481531.1, ENST00000619791.1

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060936.1 Alternate T2T-CHM13v2.0

    Range
    121800295..121829318
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_054371482.1 → XP_054227457.1  histone-lysine N-methyltransferase SETD1B isoform X1

    UniProtKB/Swiss-Prot
    F6MFW1, Q9UPS6

  2. XM_054371483.1 → XP_054227458.1  histone-lysine N-methyltransferase SETD1B isoform X1

    UniProtKB/Swiss-Prot
    F6MFW1, Q9UPS6

Suppressed Reference Sequence(s)

The following Reference Sequences have been suppressed. Explain

  1. NM_015048.1: Suppressed sequence

    Description
    NM_015048.1: This RefSeq was removed because currently there is insufficient support for the transcript and the protein.
Nucleotide Protein
Heading Accession and Version
Protein Accession Links
GenPept Link UniProtKB Link
Q9UPS6.3 GenPept UniProtKB/Swiss-Prot:Q9UPS6

Gene LinkOut

The following LinkOut resources are supplied by external providers. These providers are responsible for maintaining the links.

Chemical Information
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