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

Gene ID: 9739, updated on 5-May-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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Location:
16p11.2
Exon count:
23
Annotation release Status Assembly Chr Location
RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 16 NC_000016.10 (30957754..30984664)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 16 NC_060940.1 (31344075..31372106)
105.20220307 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

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. Loss-of-function variants in the schizophrenia risk gene SETD1A alter neuronal network activity in human neurons through the cAMP/PKA pathway. Wang S, et al. Cell Rep, 2022 May 3. PMID 35508131, Free PMC Article
  3. Novel missense SETD1A variants in Japanese patients with schizophrenia: Resequencing and association analysis. Morikawa R, et al. Psychiatry Res, 2022 Apr. PMID 35235885
  4. Histone methyltransferase SETD1A participates in lung cancer progression. Du M, et al. Thorac Cancer, 2021 Aug. PMID 34219384, Free PMC Article
  5. 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

See all (123) citations in PubMed

GeneRIFs: Gene References Into Functions

What's a GeneRIF?
  1. 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.
  2. 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).
  3. Epigenotype-genotype-phenotype correlations in SETD1A and SETD2 chromatin disorders.
    Title: Epigenotype-genotype-phenotype correlations in SETD1A and SETD2 chromatin disorders.
  4. 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.
  5. 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.
  6. 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.
  7. SETD1A regulates transcriptional pause release of heme biosynthesis genes in leukemia.
    Title: SETD1A regulates transcriptional pause release of heme biosynthesis genes in leukemia.
  8. 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.
  9. 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.
  10. Cell type-specific mechanism of Setd1a heterozygosity in schizophrenia pathogenesis.
    Title: Cell type-specific mechanism of Setd1a heterozygosity in schizophrenia pathogenesis.
Submit: New GeneRIF Correction See all GeneRIFs (58)

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: C5394228 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 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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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 
part_of 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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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_2023_10

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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