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

Gene ID: 55209, updated on 1-Aug-2020

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
109.20200522 current GRCh38.p13 (GCF_000001405.39) 3 NC_000003.12 (9397615..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 Functions

What'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

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-K36 specific) ISS
Inferred from Sequence or Structural Similarity
more info
 
histone methyltransferase activity (H3-K9 specific) ISS
Inferred from Sequence or Structural Similarity
more info
 
Process Evidence Code Pubs
cognition ISS
Inferred from Sequence or Structural Similarity
more info
 
covalent chromatin modification ISS
Inferred from Sequence or Structural Similarity
more info
 
histone H3-K36 trimethylation ISS
Inferred from Sequence or Structural Similarity
more info
 
histone H3-K9 methylation IEA
Inferred from Electronic Annotation
more info
 
regulation of DNA-templated transcription, elongation ISS
Inferred from Sequence or Structural Similarity
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
 
regulation of synapse assembly 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
 
nuclear euchromatin 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
    4916..85455
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. NM_001080517.3NP_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, CR627408
    Consensus CDS
    CCDS46741.1
    UniProtKB/Swiss-Prot
    Q9C0A6
    Related
    ENSP00000385852.1, ENST00000402198.6
    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
    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 109.20200522

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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