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    SETD5 SET domain containing 5 [ Homo sapiens (human) ]

    Gene ID: 55209, updated on 15-Jun-2019

    Summary

    Official Symbol
    SETD5provided by HGNC
    Official Full Name
    SET domain containing 5provided by HGNC
    Primary source
    HGNC:HGNC:25566
    See related
    Ensembl:ENSG00000168137 MIM:615743
    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
    Summary
    This function of this gene has yet to be determined but based on sequence similarity to other SET domain proteins it may function as a histone methyltransferase. Mutations in this gene have been associated with an autosomal dominant form of intellectual disability. Alternative splicing results in multiple transcript variants encoding different isoforms. [provided by RefSeq, Jul 2017]
    Expression
    Ubiquitous expression in brain (RPKM 9.1), thyroid (RPKM 9.1) and 25 other tissues See more
    Orthologs

    Genomic context

    See SETD5 in Genome Data Viewer
    Location:
    3p25.3
    Exon count:
    36
    Annotation release Status Assembly Chr Location
    109 current GRCh38.p12 (GCF_000001405.38) 3 NC_000003.12 (9397700..9478154)
    105 previous assembly GRCh37.p13 (GCF_000001405.25) 3 NC_000003.11 (9439384..9519838)

    Chromosome 3 - NC_000003.12Genomic Context describing neighboring genes Neighboring gene SLIT-ROBO Rho GTPase activating protein 3 Neighboring gene phosphoglycerate mutase 1 pseudogene 4 Neighboring gene THUMPD3 antisense RNA 1 Neighboring gene THUMP domain containing 3 Neighboring gene LHFPL tetraspan subfamily member 4 Neighboring gene uncharacterized LOC105376949

    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
    Mental retardation, autosomal dominant 23
    MedGen: C3810406 OMIM: 615761 GeneReviews: Not available
    Compare labs

    Copy number response

    Description
    Copy number response
    Triplosensitivity

    No evidence available (Last evaluated (2014-11-06)

    ClinGen Genome Curation Page
    Haploinsufficency

    Sufficient evidence for dosage pathogenicity (Last evaluated (2014-11-06)

    ClinGen Genome Curation PagePubMed

    Pathways from BioSystems

    • 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...

    Interactions

    Products Interactant Other Gene Complex Source Pubs Description

    General gene information

    Markers

    Homology

    Clone Names

    • FLJ10707, KIAA1757, DKFZp686J18276

    Gene Ontology Provided by GOA

    Function Evidence Code Pubs
    histone methyltransferase activity (H3-K9 specific) ISS
    Inferred from Sequence or Structural Similarity
    more info
     
    Process Evidence Code Pubs
    covalent chromatin modification ISS
    Inferred from Sequence or Structural Similarity
    more info
     
    histone H3-K9 methylation IEA
    Inferred from Electronic Annotation
    more info
     
    regulation of chromatin organization ISS
    Inferred from Sequence or Structural Similarity
    more info
     
    regulation of histone acetylation ISS
    Inferred from Sequence or Structural Similarity
    more info
     
    Component Evidence Code Pubs
    colocalizes_with Cdc73/Paf1 complex ISS
    Inferred from Sequence or Structural Similarity
    more info
     
    nucleoplasm IDA
    Inferred from Direct Assay
    more info
     
    nucleus ISS
    Inferred from Sequence or Structural Similarity
    more info
     

    General protein information

    Preferred Names
    histone-lysine N-methyltransferase SETD5
    Names
    SET domain-containing protein 5
    NP_001073986.1
    NP_001278972.1
    NP_001336380.1
    XP_005265358.1
    XP_005265360.1
    XP_011532222.1
    XP_011532223.1
    XP_011532224.1
    XP_011532229.1
    XP_011532230.1
    XP_011532232.1
    XP_011532234.1
    XP_011532235.1
    XP_016862256.1
    XP_016862257.1
    XP_016862259.1
    XP_016862260.1
    XP_016862261.1
    XP_016862262.1
    XP_016862263.1
    XP_016862264.1
    XP_016862265.1
    XP_016862266.1
    XP_016862267.1
    XP_016862268.1
    XP_016862269.1
    XP_016862271.1
    XP_016862272.1
    XP_016862273.1
    XP_016862274.1
    XP_016862275.1
    XP_024309388.1
    XP_024309389.1

    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_034132.1 RefSeqGene

      Range
      5001..85455
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. NM_001080517.2NP_001073986.1  histone-lysine N-methyltransferase SETD5 isoform 1

      See identical proteins and their annotated locations for NP_001073986.1

      Status: REVIEWED

      Description
      Transcript Variant: This variant (1) encodes the longer isoform (1).
      Source sequence(s)
      AB051544, AC018506, AI243838, AK092046, AW021954, CR627408, DB275141
      Consensus CDS
      CCDS46741.1
      UniProtKB/Swiss-Prot
      Q9C0A6
      Related
      ENSP00000385852.1, ENST00000402198.5
      Conserved Domains (1) summary
      smart00317
      Location:286395
      SET; SET (Su(var)3-9, Enhancer-of-zeste, Trithorax) domain
    2. NM_001292043.2NP_001278972.1  histone-lysine N-methyltransferase SETD5 isoform 2

      See identical proteins and their annotated locations for NP_001278972.1

      Status: REVIEWED

      Description
      Transcript Variant: This variant (2) contains an alternate 5' exon structure and initiates translation at a downstream start codon, compared to variant 1. The encoded protein (isoform 2) has a shorter N-terminus, compared to isoform 1. Variants 2 and 3 both encode the same isoform (2).
      Source sequence(s)
      AB051544, AC018506, AI243838, AK092046, AW021954, CR627408, DB275141
      Consensus CDS
      CCDS74892.1
      UniProtKB/Swiss-Prot
      Q9C0A6
      Related
      ENSP00000302028.6, ENST00000302463.10
      Conserved Domains (2) summary
      smart00317
      Location:188297
      SET; SET (Su(var)3-9, Enhancer-of-zeste, Trithorax) domain
      cl27032
      Location:336556
      Utp14; Utp14 protein
    3. NM_001349451.2NP_001336380.1  histone-lysine N-methyltransferase SETD5 isoform 2

      Status: REVIEWED

      Description
      Transcript Variant: This variant (3) contains an alternate 5' exon structure and initiates translation at a downstream start codon, compared to variant 1. The encoded protein (isoform 2) has a shorter N-terminus, compared to isoform 1. Variants 2 and 3 both encode the same isoform (2).
      Source sequence(s)
      AC018506
      Consensus CDS
      CCDS74892.1
      Conserved Domains (2) summary
      smart00317
      Location:188297
      SET; SET (Su(var)3-9, Enhancer-of-zeste, Trithorax) domain
      cl27032
      Location:336556
      Utp14; Utp14 protein

    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
      9397615..9478154
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_017006770.1XP_016862259.1  histone-lysine N-methyltransferase SETD5 isoform X4

      Conserved Domains (1) summary
      smart00317
      Location:325434
      SET; SET (Su(var)3-9, Enhancer-of-zeste, Trithorax) domain
    2. XM_017006772.1XP_016862261.1  histone-lysine N-methyltransferase SETD5 isoform X8

      Conserved Domains (1) summary
      smart00317
      Location:312421
      SET; SET (Su(var)3-9, Enhancer-of-zeste, Trithorax) domain
    3. XM_017006773.1XP_016862262.1  histone-lysine N-methyltransferase SETD5 isoform X9

    4. XM_017006775.1XP_016862264.1  histone-lysine N-methyltransferase SETD5 isoform X13

    5. XM_017006767.1XP_016862256.1  histone-lysine N-methyltransferase SETD5 isoform X1

      Conserved Domains (1) summary
      smart00317
      Location:325434
      SET; SET (Su(var)3-9, Enhancer-of-zeste, Trithorax) domain
    6. XM_011533920.1XP_011532222.1  histone-lysine N-methyltransferase SETD5 isoform X1

      See identical proteins and their annotated locations for XP_011532222.1

      Conserved Domains (1) summary
      smart00317
      Location:325434
      SET; SET (Su(var)3-9, Enhancer-of-zeste, Trithorax) domain
    7. XM_024453620.1XP_024309388.1  histone-lysine N-methyltransferase SETD5 isoform X3

      Conserved Domains (2) summary
      smart00317
      Location:312421
      SET; SET (Su(var)3-9, Enhancer-of-zeste, Trithorax) domain
      cl27032
      Location:460680
      Utp14; Utp14 protein
    8. XM_017006783.1XP_016862272.1  histone-lysine N-methyltransferase SETD5 isoform X19

    9. XM_011533927.1XP_011532229.1  histone-lysine N-methyltransferase SETD5 isoform X5

      Conserved Domains (1) summary
      smart00317
      Location:306415
      SET; SET (Su(var)3-9, Enhancer-of-zeste, Trithorax) domain
    10. XM_011533930.1XP_011532232.1  histone-lysine N-methyltransferase SETD5 isoform X12

      Conserved Domains (1) summary
      smart00317
      Location:280389
      SET; SET (Su(var)3-9, Enhancer-of-zeste, Trithorax) domain
    11. XM_005265303.1XP_005265360.1  histone-lysine N-methyltransferase SETD5 isoform X14

      Conserved Domains (1) summary
      smart00317
      Location:267376
      SET; SET (Su(var)3-9, Enhancer-of-zeste, Trithorax) domain
    12. XM_017006776.1XP_016862265.1  histone-lysine N-methyltransferase SETD5 isoform X16

      Conserved Domains (1) summary
      smart00317
      Location:188297
      SET; SET (Su(var)3-9, Enhancer-of-zeste, Trithorax) domain
    13. XM_017006779.1XP_016862268.1  histone-lysine N-methyltransferase SETD5 isoform X17

      Conserved Domains (1) summary
      smart00317
      Location:175284
      SET; SET (Su(var)3-9, Enhancer-of-zeste, Trithorax) domain
    14. XM_017006778.1XP_016862267.1  histone-lysine N-methyltransferase SETD5 isoform X16

      Conserved Domains (1) summary
      smart00317
      Location:188297
      SET; SET (Su(var)3-9, Enhancer-of-zeste, Trithorax) domain
    15. XM_017006780.1XP_016862269.1  histone-lysine N-methyltransferase SETD5 isoform X17

      Conserved Domains (1) summary
      smart00317
      Location:175284
      SET; SET (Su(var)3-9, Enhancer-of-zeste, Trithorax) domain
    16. XM_017006777.1XP_016862266.1  histone-lysine N-methyltransferase SETD5 isoform X16

      Conserved Domains (1) summary
      smart00317
      Location:188297
      SET; SET (Su(var)3-9, Enhancer-of-zeste, Trithorax) domain
    17. XM_011533932.1XP_011532234.1  histone-lysine N-methyltransferase SETD5 isoform X17

      See identical proteins and their annotated locations for XP_011532234.1

      Conserved Domains (1) summary
      smart00317
      Location:175284
      SET; SET (Su(var)3-9, Enhancer-of-zeste, Trithorax) domain
    18. XM_017006782.1XP_016862271.1  histone-lysine N-methyltransferase SETD5 isoform X18

      Conserved Domains (1) summary
      smart00317
      Location:325434
      SET; SET (Su(var)3-9, Enhancer-of-zeste, Trithorax) domain
    19. XM_017006784.1XP_016862273.1  histone-lysine N-methyltransferase SETD5 isoform X20

      Conserved Domains (1) summary
      smart00317
      Location:325434
      SET; SET (Su(var)3-9, Enhancer-of-zeste, Trithorax) domain
    20. XM_017006785.1XP_016862274.1  histone-lysine N-methyltransferase SETD5 isoform X21

    21. XM_017006786.1XP_016862275.1  histone-lysine N-methyltransferase SETD5 isoform X22

    22. XM_011533922.1XP_011532224.1  histone-lysine N-methyltransferase SETD5 isoform X2

      See identical proteins and their annotated locations for XP_011532224.1

      Conserved Domains (1) summary
      smart00317
      Location:318427
      SET; SET (Su(var)3-9, Enhancer-of-zeste, Trithorax) domain
    23. XM_017006771.1XP_016862260.1  histone-lysine N-methyltransferase SETD5 isoform X6

    24. XM_005265301.1XP_005265358.1  histone-lysine N-methyltransferase SETD5 isoform X10

      UniProtKB/TrEMBL
      E7EWN3
      Related
      ENSP00000384114.1, ENST00000407969.5
      Conserved Domains (1) summary
      smart00317
      Location:305414
      SET; SET (Su(var)3-9, Enhancer-of-zeste, Trithorax) domain
    25. XM_011533928.1XP_011532230.1  histone-lysine N-methyltransferase SETD5 isoform X7

      Conserved Domains (1) summary
      smart00317
      Location:299408
      SET; SET (Su(var)3-9, Enhancer-of-zeste, Trithorax) domain
    26. XM_017006774.1XP_016862263.1  histone-lysine N-methyltransferase SETD5 isoform X11

    27. XM_011533921.2XP_011532223.1  histone-lysine N-methyltransferase SETD5 isoform X1

      See identical proteins and their annotated locations for XP_011532223.1

      Conserved Domains (1) summary
      smart00317
      Location:325434
      SET; SET (Su(var)3-9, Enhancer-of-zeste, Trithorax) domain
    28. XM_017006768.2XP_016862257.1  histone-lysine N-methyltransferase SETD5 isoform X2

      Conserved Domains (1) summary
      smart00317
      Location:318427
      SET; SET (Su(var)3-9, Enhancer-of-zeste, Trithorax) domain
    29. XM_011533933.1XP_011532235.1  histone-lysine N-methyltransferase SETD5 isoform X17

      See identical proteins and their annotated locations for XP_011532235.1

      Conserved Domains (1) summary
      smart00317
      Location:175284
      SET; SET (Su(var)3-9, Enhancer-of-zeste, Trithorax) domain
    30. XM_024453621.1XP_024309389.1  histone-lysine N-methyltransferase SETD5 isoform X15

      Conserved Domains (3) summary
      smart00317
      Location:204313
      SET; SET (Su(var)3-9, Enhancer-of-zeste, Trithorax) domain
      cl27032
      Location:352572
      Utp14; Utp14 protein
      cl27601
      Location:12391346
      Pectinesterase

    RNA

    1. XR_001740195.2 RNA Sequence

    Suppressed Reference Sequence(s)

    The following Reference Sequences have been suppressed. Explain

    1. NM_018187.2: Suppressed sequence

      Description
      NM_018187.2: This RefSeq was suppressed temporarily based on the calculation that the annotated protein was shorter than a protein or proteins from a putative ortholog.
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