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    SETD1A SET domain containing 1A, histone lysine methyltransferase [ Homo sapiens (human) ]

    Gene ID: 9739, updated on 2-Nov-2024

    Summary

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    Official Symbol
    SETD1Aprovided by HGNC
    Official Full Name
    SET domain containing 1A, histone lysine methyltransferaseprovided by HGNC
    Primary source
    HGNC:HGNC:29010
    See related
    Ensembl:ENSG00000099381 MIM:611052; AllianceGenome:HGNC:29010
    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
    Set1; EPEDD; EPEO2; KMT2F; Set1A; NEDSID
    Summary
    The protein encoded by this gene is a component of a histone methyltransferase (HMT) complex that produces mono-, di-, and trimethylated histone H3 at Lys4. Trimethylation of histone H3 at lysine 4 (H3K4me3) is a chromatin modification known to generally mark the transcription start sites of active genes. The protein contains SET domains, a RNA recognition motif domain and is a member of the class V-like SAM-binding methyltransferase superfamily. [provided by RefSeq, Dec 2016]
    Expression
    Ubiquitous expression in testis (RPKM 10.6), bone marrow (RPKM 6.2) and 25 other tissues See more
    Orthologs
    mouse all
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    Genomic context

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    See SETD1A in Genome Data Viewer
    Location:
    16p11.2
    Exon count:
    23
    Annotation release Status Assembly Chr Location
    RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 16 NC_000016.10 (30957754..30984664)
    RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 16 NC_060940.1 (31344075..31372106)
    RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 16 NC_000016.9 (30969075..30995985)

    Chromosome 16 - NC_000016.10Genomic Context describing neighboring genes Neighboring gene H3K27ac hESC enhancers GRCh37_chr16:30932963-30933931 and GRCh37_chr16:30933932-30934899 Neighboring gene FBXL19 antisense RNA 1 Neighboring gene F-box and leucine rich repeat protein 19 Neighboring gene Sharpr-MPRA regulatory region 7559 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 7401 Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr16:30953885-30954827 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 7402 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 7403 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr16:30960708-30961226 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 10740 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr16:30961745-30962262 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr16:30964322-30964887 Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr16:30968383-30969146 Neighboring gene ORAI calcium release-activated calcium modulator 3 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 7405 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 7406 Neighboring gene ReSE screen-validated silencer GRCh37_chr16:30974870-30975017 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr16:30995997-30996509 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr16:30999355-30999854 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr16:31001361-31002004 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr16:31002005-31002648 Neighboring gene hydroxy-delta-5-steroid dehydrogenase, 3 beta- and steroid delta-isomerase 7 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 10742 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 10743 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 7407 Neighboring gene syntaxin 1B Neighboring gene H3K4me1 hESC enhancer GRCh37_chr16:31011808-31012308 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr16:31012309-31012809

    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 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. SETD1A regulates transcriptional pause release of heme biosynthesis genes in leukemia. Hoshii T, et al. Cell Rep, 2022 Nov 29. PMID 36450243, Free PMC Article
    2. Histone methyltransferase SETD1A participates in lung cancer progression. Du M, et al. Thorac Cancer, 2021 Aug. PMID 34219384, Free PMC Article
    3. The H3K4 methyltransferase SETD1A is required for proliferation of non-small cell lung cancer cells by promoting S-phase progression. Kang JY, et al. Biochem Biophys Res Commun, 2021 Jul 5. PMID 34023776
    4. Rare loss-of-function variants in SETD1A are associated with schizophrenia and developmental disorders. Singh T, et al. Nat Neurosci, 2016 Apr. PMID 26974950, Free PMC Article
    5. Diverse roles of WDR5-RbBP5-ASH2L-DPY30 (WRAD) complex in the functions of the SET1 histone methyltransferase family. Ali A, et al. J Biosci, 2017 Mar. PMID 28229975

    See all (139) citations in PubMed

    GeneRIFs: Gene References Into Functions

    What's a GeneRIF?
    1. BOD1L mediates chromatin binding and non-canonical function of H3K4 methyltransferase SETD1A.
      Title: BOD1L mediates chromatin binding and non-canonical function of H3K4 methyltransferase SETD1A.
    2. SETD1A variant-associated psychosis: A systematic review of the clinical literature and description of two new cases.
      Title: SETD1A variant-associated psychosis: A systematic review of the clinical literature and description of two new cases.
    3. In Vivo and In Vitro Characterization of the RNA Binding Capacity of SETD1A (KMT2F).
      Title: In Vivo and In Vitro Characterization of the RNA Binding Capacity of SETD1A (KMT2F).
    4. Epigenotype-genotype-phenotype correlations in SETD1A and SETD2 chromatin disorders.
      Title: Epigenotype-genotype-phenotype correlations in SETD1A and SETD2 chromatin disorders.
    5. SETD1A function in leukemia is mediated through interaction with mitotic regulators BuGZ/BUB3.
      Title: SETD1A function in leukemia is mediated through interaction with mitotic regulators BuGZ/BUB3.
    6. SETD1A drives stemness by reprogramming the epigenetic landscape in hepatocellular carcinoma stem cells.
      Title: SETD1A drives stemness by reprogramming the epigenetic landscape in hepatocellular carcinoma stem cells.
    7. 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.
    8. SETD1A regulates transcriptional pause release of heme biosynthesis genes in leukemia.
      Title: SETD1A regulates transcriptional pause release of heme biosynthesis genes in leukemia.
    9. Loss-of-function variants in the schizophrenia risk gene SETD1A alter neuronal network activity in human neurons through the cAMP/PKA pathway.
      Title: Loss-of-function variants in the schizophrenia risk gene SETD1A alter neuronal network activity in human neurons through the cAMP/PKA pathway.
    10. Novel missense SETD1A variants in Japanese patients with schizophrenia: Resequencing and association analysis.
      Title: Novel missense SETD1A variants in Japanese patients with schizophrenia: Resequencing and association analysis.
    Submit: New GeneRIF Correction See all GeneRIFs (59)

    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

    Associated conditions

    Description Tests
    Epilepsy, early-onset, with or without developmental delay
    MedGen: C5882670 OMIM: 618832 GeneReviews: Not available
    		Compare labs
    Neurodevelopmental disorder with speech impairment and dysmorphic facies
    MedGen: C5436699 OMIM: 619056 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

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

    ClinGen Genome Curation PagePubMed

    Variation

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    See Variation Viewer (GRCh37.p13)

    HIV-1 interactions

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    Protein interactions

    Protein Gene Interaction Pubs
    Tat tat Three components (Setd1A, CXXC1, WDR5) of the Set1 histone methyltransferase complex are identified to interact with HIV-1 Tat in Jurkat cell 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

    • KIAA0339

    Gene Ontology Provided by GOA

    Function Evidence Code Pubs
    enables RNA binding IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    enables RNA polymerase II-specific DNA-binding transcription factor binding IPI
    Inferred from Physical Interaction
    more info
    		 PubMed 
    enables beta-catenin binding IPI
    Inferred from Physical Interaction
    more info
    		 PubMed 
    enables histone H3K4 methyltransferase activity IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    enables 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 DNA damage response IEA
    Inferred from Electronic Annotation
    more info
    		  
    involved_in brain development IMP
    Inferred from Mutant Phenotype
    more info
    		 PubMed 
    involved_in chromatin remodeling IEA
    Inferred from Electronic Annotation
    more info
    		  
    involved_in methylation IEA
    Inferred from Electronic Annotation
    more info
    		  
    involved_in regulation of chromatin organization IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    involved_in regulation of hematopoietic stem cell differentiation IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    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 
    part_of Set1C/COMPASS complex TAS
    Traceable Author Statement
    more info
    		 PubMed 
    located_in chromatin IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    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 IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    located_in nucleoplasm TAS
    Traceable Author Statement
    more info
    		  
    located_in nucleus IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    located_in nucleus IMP
    Inferred from Mutant Phenotype
    more info
    		 PubMed 

    General protein information

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    Preferred Names
    histone-lysine N-methyltransferase SETD1A
    Names
    SET domain-containing protein 1A
    hSET1A
    lysine N-methyltransferase 2F
    set1/Ash2 histone methyltransferase complex subunit SET1
    NP_055527.1
    XP_005255780.1
    XP_006721169.1
    XP_016879398.1
    XP_024306267.1
    XP_047290918.1
    XP_047290919.1
    XP_047290920.1
    XP_054170479.1
    XP_054170480.1
    XP_054170481.1
    XP_054170482.1
    XP_054170483.1
    XP_054170484.1
    XP_054170485.1

    NCBI Reference Sequences (RefSeq)

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    NEW Try the new Transcript table

    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_052948.1 RefSeqGene

      Range
      5461..32371
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. NM_014712.3 → NP_055527.1  histone-lysine N-methyltransferase SETD1A

      See identical proteins and their annotated locations for NP_055527.1

      Status: REVIEWED

      Source sequence(s)
      AB002337, BC027450
      Consensus CDS
      CCDS32435.1
      UniProtKB/Swiss-Prot
      A0A804HLA6, A6NP62, O15047, Q6PIF3, Q8TAJ6
      Related
      ENSP00000262519.8, ENST00000262519.14
      Conserved Domains (5) summary
      smart00317
      Location:1568 → 1691
      SET; SET (Su(var)3-9, Enhancer-of-zeste, Trithorax) domain
      smart00508
      Location:1691 → 1707
      PostSET; Cysteine-rich motif following a subset of SET domains
      cd12548
      Location:92 → 186
      RRM_Set1A; RNA recognition motif in vertebrate histone-lysine N-methyltransferase Setd1A (Set1A)
      pfam11764
      Location:1425 → 1562
      N-SET; COMPASS (Complex proteins associated with Set1p) component N
      cl26247
      Location:1070 → 1130
      DNA_pol3_delta2; DNA polymerase III, delta subunit

    RefSeqs of Annotated Genomes: GCF_000001405.40-RS_2024_08

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

    Reference GRCh38.p14 Primary Assembly

    Genomic

    1. NC_000016.10 Reference GRCh38.p14 Primary Assembly

      Range
      30957754..30984664
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_017023909.2 → XP_016879398.1  histone-lysine N-methyltransferase SETD1A isoform X1

      UniProtKB/Swiss-Prot
      A0A804HLA6, A6NP62, O15047, Q6PIF3, Q8TAJ6
      Conserved Domains (5) summary
      smart00317
      Location:1568 → 1691
      SET; SET (Su(var)3-9, Enhancer-of-zeste, Trithorax) domain
      smart00508
      Location:1691 → 1707
      PostSET; Cysteine-rich motif following a subset of SET domains
      cd12548
      Location:92 → 186
      RRM_Set1A; RNA recognition motif in vertebrate histone-lysine N-methyltransferase Setd1A (Set1A)
      pfam11764
      Location:1425 → 1562
      N-SET; COMPASS (Complex proteins associated with Set1p) component N
      cl26247
      Location:1070 → 1130
      DNA_pol3_delta2; DNA polymerase III, delta subunit

    2. XM_005255723.1 → XP_005255780.1  histone-lysine N-methyltransferase SETD1A isoform X1

      See identical proteins and their annotated locations for XP_005255780.1

      UniProtKB/Swiss-Prot
      A0A804HLA6, A6NP62, O15047, Q6PIF3, Q8TAJ6
      Related
      ENSP00000507683.1, ENST00000684162.1
      Conserved Domains (5) summary
      smart00317
      Location:1568 → 1691
      SET; SET (Su(var)3-9, Enhancer-of-zeste, Trithorax) domain
      smart00508
      Location:1691 → 1707
      PostSET; Cysteine-rich motif following a subset of SET domains
      cd12548
      Location:92 → 186
      RRM_Set1A; RNA recognition motif in vertebrate histone-lysine N-methyltransferase Setd1A (Set1A)
      pfam11764
      Location:1425 → 1562
      N-SET; COMPASS (Complex proteins associated with Set1p) component N
      cl26247
      Location:1070 → 1130
      DNA_pol3_delta2; DNA polymerase III, delta subunit

    3. XM_047434964.1 → XP_047290920.1  histone-lysine N-methyltransferase SETD1A isoform X2

    4. XM_047434962.1 → XP_047290918.1  histone-lysine N-methyltransferase SETD1A isoform X1

      UniProtKB/Swiss-Prot
      A0A804HLA6, A6NP62, O15047, Q6PIF3, Q8TAJ6

    5. XM_006721106.4 → XP_006721169.1  histone-lysine N-methyltransferase SETD1A isoform X1

      See identical proteins and their annotated locations for XP_006721169.1

      UniProtKB/Swiss-Prot
      A0A804HLA6, A6NP62, O15047, Q6PIF3, Q8TAJ6
      Conserved Domains (5) summary
      smart00317
      Location:1568 → 1691
      SET; SET (Su(var)3-9, Enhancer-of-zeste, Trithorax) domain
      smart00508
      Location:1691 → 1707
      PostSET; Cysteine-rich motif following a subset of SET domains
      cd12548
      Location:92 → 186
      RRM_Set1A; RNA recognition motif in vertebrate histone-lysine N-methyltransferase Setd1A (Set1A)
      pfam11764
      Location:1425 → 1562
      N-SET; COMPASS (Complex proteins associated with Set1p) component N
      cl26247
      Location:1070 → 1130
      DNA_pol3_delta2; DNA polymerase III, delta subunit

    6. XM_024450499.2 → XP_024306267.1  histone-lysine N-methyltransferase SETD1A isoform X1

      UniProtKB/Swiss-Prot
      A0A804HLA6, A6NP62, O15047, Q6PIF3, Q8TAJ6
      Conserved Domains (5) summary
      smart00317
      Location:1568 → 1691
      SET; SET (Su(var)3-9, Enhancer-of-zeste, Trithorax) domain
      smart00508
      Location:1691 → 1707
      PostSET; Cysteine-rich motif following a subset of SET domains
      cd12548
      Location:92 → 186
      RRM_Set1A; RNA recognition motif in vertebrate histone-lysine N-methyltransferase Setd1A (Set1A)
      pfam11764
      Location:1425 → 1562
      N-SET; COMPASS (Complex proteins associated with Set1p) component N
      cl26247
      Location:1070 → 1130
      DNA_pol3_delta2; DNA polymerase III, delta subunit

    7. XM_047434963.1 → XP_047290919.1  histone-lysine N-methyltransferase SETD1A isoform X1

      UniProtKB/Swiss-Prot
      A0A804HLA6, A6NP62, O15047, Q6PIF3, Q8TAJ6

    Alternate T2T-CHM13v2.0

    Genomic

    1. NC_060940.1 Alternate T2T-CHM13v2.0

      Range
      31344075..31372106
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_054314504.1 → XP_054170479.1  histone-lysine N-methyltransferase SETD1A isoform X1

      UniProtKB/Swiss-Prot
      A0A804HLA6, A6NP62, O15047, Q6PIF3, Q8TAJ6

    2. XM_054314510.1 → XP_054170485.1  histone-lysine N-methyltransferase SETD1A isoform X2

    3. XM_054314506.1 → XP_054170481.1  histone-lysine N-methyltransferase SETD1A isoform X1

      UniProtKB/Swiss-Prot
      A0A804HLA6, A6NP62, O15047, Q6PIF3, Q8TAJ6

    4. XM_054314508.1 → XP_054170483.1  histone-lysine N-methyltransferase SETD1A isoform X1

      UniProtKB/Swiss-Prot
      A0A804HLA6, A6NP62, O15047, Q6PIF3, Q8TAJ6

    5. XM_054314507.1 → XP_054170482.1  histone-lysine N-methyltransferase SETD1A isoform X1

      UniProtKB/Swiss-Prot
      A0A804HLA6, A6NP62, O15047, Q6PIF3, Q8TAJ6

    6. XM_054314505.1 → XP_054170480.1  histone-lysine N-methyltransferase SETD1A isoform X1

      UniProtKB/Swiss-Prot
      A0A804HLA6, A6NP62, O15047, Q6PIF3, Q8TAJ6

    7. XM_054314509.1 → XP_054170484.1  histone-lysine N-methyltransferase SETD1A isoform X1

      UniProtKB/Swiss-Prot
      A0A804HLA6, A6NP62, O15047, Q6PIF3, Q8TAJ6
    Nucleotide Protein
    Heading Accession and Version
    Protein Accession Links
    GenPept Link UniProtKB Link
    O15047.3 GenPept UniProtKB/Swiss-Prot:O15047

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