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

Gene ID: 55209, updated on 26-Oct-2022

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; AllianceGenome:HGNC:25566
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
MRD23; SETD5A
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
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Try the new Transcript table

Genomic context

See SETD5 in Genome Data Viewer
Location:
3p25.3
Exon count:
31
Annotation release Status Assembly Chr Location
110 current GRCh38.p14 (GCF_000001405.40) 3 NC_000003.12 (9397615..9478154)
110 current T2T-CHM13v2.0 (GCF_009914755.1) 3 NC_060927.1 (9389553..9470070)
105.20220307 previous assembly GRCh37.p13 (GCF_000001405.25) 3 NC_000003.11 (9439299..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 Sharpr-MPRA regulatory region 11896 Neighboring gene THUMP domain containing 3 Neighboring gene Sharpr-MPRA regulatory region 15302 Neighboring gene LHFPL tetraspan subfamily member 4 Neighboring gene uncharacterized LOC105376949

Genomic regions, transcripts, and products

Bibliography

GeneRIFs: Gene References Into Functions

What's a GeneRIF?

Phenotypes

Associated conditions

Description Tests
Intellectual disability-facial dysmorphism syndrome due to SETD5 haploinsufficiency
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 PubChem

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
enables histone H3K36 methyltransferase activity ISS
Inferred from Sequence or Structural Similarity
more info
 
enables histone H3K9 methyltransferase activity ISS
Inferred from Sequence or Structural Similarity
more info
 
enables methylated histone binding IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
enables transcription corepressor activity IEA
Inferred from Electronic Annotation
more info
 
Process Evidence Code Pubs
involved_in chromatin organization IEA
Inferred from Electronic Annotation
more info
 
involved_in cognition ISS
Inferred from Sequence or Structural Similarity
more info
 
involved_in histone modification IEA
Inferred from Electronic Annotation
more info
 
involved_in methylation IEA
Inferred from Electronic Annotation
more info
 
involved_in negative regulation of transcription by RNA polymerase III IEA
Inferred from Electronic Annotation
more info
 
involved_in regulation of DNA-templated transcription IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
involved_in regulation of DNA-templated transcription elongation ISS
Inferred from Sequence or Structural Similarity
more info
 
involved_in regulation of chromatin organization ISS
Inferred from Sequence or Structural Similarity
more info
 
involved_in regulation of histone acetylation IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
involved_in regulation of synapse assembly ISS
Inferred from Sequence or Structural Similarity
more info
 
Component Evidence Code Pubs
part_of Rpd3L-Expanded complex IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
part_of Set3 complex IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
located_in euchromatin ISS
Inferred from Sequence or Structural Similarity
more info
 
located_in nucleoplasm IDA
Inferred from Direct Assay
more info
 
located_in 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_011532224.1
XP_011532230.1
XP_011532235.1
XP_016862260.1
XP_016862263.1
XP_047304422.1
XP_047304423.1
XP_047304424.1
XP_047304425.1
XP_047304426.1
XP_047304427.1
XP_047304428.1
XP_047304429.1
XP_047304430.1
XP_047304431.1
XP_047304432.1
XP_047304433.1
XP_047304434.1
XP_047304435.1
XP_047304436.1
XP_047304437.1
XP_047304438.1
XP_047304439.1
XP_047304440.1
XP_047304441.1
XP_047304442.1
XP_047304443.1
XP_047304444.1
XP_047304445.1
XP_047304446.1
XP_047304447.1
XP_047304448.1
XP_047304449.1
XP_047304450.1
XP_047304451.1
XP_047304452.1
XP_047304453.1
XP_047304454.1
XP_047304455.1
XP_047304456.1
XP_047304457.1
XP_047304458.1
XP_047304459.1
XP_047304460.1
XP_047304461.1
XP_047304462.1
XP_047304463.1
XP_047304464.1

NCBI Reference Sequences (RefSeq)

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_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, Q9NVI9
    Related
    ENSP00000385852.2, ENST00000402198.7
    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
    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
    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 110 details...Open this link in a new tab

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

Reference GRCh38.p14 Primary Assembly

Genomic

  1. NC_000003.12 Reference GRCh38.p14 Primary Assembly

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

mRNA and Protein(s)

  1. XM_047448468.1XP_047304424.1  histone-lysine N-methyltransferase SETD5 isoform X1

  2. XM_047448473.1XP_047304429.1  histone-lysine N-methyltransferase SETD5 isoform X2

  3. XM_047448482.1XP_047304438.1  histone-lysine N-methyltransferase SETD5 isoform X7

    UniProtKB/TrEMBL
    A0A804HKJ9
  4. XM_047448487.1XP_047304443.1  histone-lysine N-methyltransferase SETD5 isoform X12

    UniProtKB/TrEMBL
    E7EWN3
  5. XM_047448489.1XP_047304445.1  histone-lysine N-methyltransferase SETD5 isoform X13

  6. XM_047448496.1XP_047304452.1  histone-lysine N-methyltransferase SETD5 isoform X18

    UniProtKB/Swiss-Prot
    Q9NVI9
  7. XM_047448474.1XP_047304430.1  histone-lysine N-methyltransferase SETD5 isoform X2

  8. XM_047448481.1XP_047304437.1  histone-lysine N-methyltransferase SETD5 isoform X7

    UniProtKB/TrEMBL
    A0A804HKJ9
  9. XM_047448479.1XP_047304435.1  histone-lysine N-methyltransferase SETD5 isoform X6

  10. XM_047448488.1XP_047304444.1  histone-lysine N-methyltransferase SETD5 isoform X12

    UniProtKB/TrEMBL
    E7EWN3
  11. XM_047448490.1XP_047304446.1  histone-lysine N-methyltransferase SETD5 isoform X13

  12. XM_047448497.1XP_047304453.1  histone-lysine N-methyltransferase SETD5 isoform X18

    UniProtKB/Swiss-Prot
    Q9NVI9
  13. XM_047448466.1XP_047304422.1  histone-lysine N-methyltransferase SETD5 isoform X1

  14. XM_047448477.1XP_047304433.1  histone-lysine N-methyltransferase SETD5 isoform X4

  15. XM_047448483.1XP_047304439.1  histone-lysine N-methyltransferase SETD5 isoform X9

  16. XM_047448478.1XP_047304434.1  histone-lysine N-methyltransferase SETD5 isoform X5

  17. XM_047448486.1XP_047304442.1  histone-lysine N-methyltransferase SETD5 isoform X11

  18. XM_047448485.1XP_047304441.1  histone-lysine N-methyltransferase SETD5 isoform X10

  19. XM_047448495.1XP_047304451.1  histone-lysine N-methyltransferase SETD5 isoform X17

  20. XM_047448476.1XP_047304432.1  histone-lysine N-methyltransferase SETD5 isoform X3

  21. XM_011533922.2XP_011532224.1  histone-lysine N-methyltransferase SETD5 isoform X2

    See identical proteins and their annotated locations for XP_011532224.1

    Conserved Domains (3) summary
    PLN02217
    Location:13531460
    PLN02217; probable pectinesterase/pectinesterase inhibitor
    COG5644
    Location:466686
    COG5644; U3 small nucleolar RNA-associated protein 14 [Function unknown]
    cd19181
    Location:298447
    SET_SETD5; SET domain (including post-SET domain) found in SET domain-containing protein 5 (SETD5) and similar proteins
  22. XM_047448480.1XP_047304436.1  histone-lysine N-methyltransferase SETD5 isoform X7

    UniProtKB/TrEMBL
    A0A804HKJ9
    Related
    ENSP00000507956.1, ENST00000682536.1
  23. XM_017006771.2XP_016862260.1  histone-lysine N-methyltransferase SETD5 isoform X6

    Conserved Domains (3) summary
    PLN02217
    Location:13401447
    PLN02217; probable pectinesterase/pectinesterase inhibitor
    COG5644
    Location:453673
    COG5644; U3 small nucleolar RNA-associated protein 14 [Function unknown]
    cd19181
    Location:285434
    SET_SETD5; SET domain (including post-SET domain) found in SET domain-containing protein 5 (SETD5) and similar proteins
  24. XM_005265301.2XP_005265358.1  histone-lysine N-methyltransferase SETD5 isoform X12

    UniProtKB/TrEMBL
    E7EWN3
    Related
    ENSP00000384114.1, ENST00000407969.5
    Conserved Domains (3) summary
    PLN02217
    Location:13211428
    PLN02217; probable pectinesterase/pectinesterase inhibitor
    COG5644
    Location:453673
    COG5644; U3 small nucleolar RNA-associated protein 14 [Function unknown]
    cd19181
    Location:285434
    SET_SETD5; SET domain (including post-SET domain) found in SET domain-containing protein 5 (SETD5) and similar proteins
  25. XM_011533928.2XP_011532230.1  histone-lysine N-methyltransferase SETD5 isoform X8

    Conserved Domains (3) summary
    PLN02217
    Location:13341441
    PLN02217; probable pectinesterase/pectinesterase inhibitor
    COG5644
    Location:447667
    COG5644; U3 small nucleolar RNA-associated protein 14 [Function unknown]
    cd19181
    Location:279428
    SET_SETD5; SET domain (including post-SET domain) found in SET domain-containing protein 5 (SETD5) and similar proteins
  26. XM_047448492.1XP_047304448.1  histone-lysine N-methyltransferase SETD5 isoform X15

  27. XM_017006774.2XP_016862263.1  histone-lysine N-methyltransferase SETD5 isoform X13

    Conserved Domains (3) summary
    PLN02217
    Location:13211428
    PLN02217; probable pectinesterase/pectinesterase inhibitor
    COG5644
    Location:434654
    COG5644; U3 small nucleolar RNA-associated protein 14 [Function unknown]
    cd19181
    Location:266415
    SET_SETD5; SET domain (including post-SET domain) found in SET domain-containing protein 5 (SETD5) and similar proteins
  28. XM_047448500.1XP_047304456.1  histone-lysine N-methyltransferase SETD5 isoform X22

  29. XM_047448501.1XP_047304457.1  histone-lysine N-methyltransferase SETD5 isoform X23

  30. XM_047448503.1XP_047304459.1  histone-lysine N-methyltransferase SETD5 isoform X25

  31. XM_047448504.1XP_047304460.1  histone-lysine N-methyltransferase SETD5 isoform X26

  32. XM_047448502.1XP_047304458.1  histone-lysine N-methyltransferase SETD5 isoform X24

  33. XM_047448505.1XP_047304461.1  histone-lysine N-methyltransferase SETD5 isoform X27

  34. XM_047448506.1XP_047304462.1  histone-lysine N-methyltransferase SETD5 isoform X28

    Related
    ENSP00000507953.1, ENST00000684055.1
  35. XM_047448507.1XP_047304463.1  histone-lysine N-methyltransferase SETD5 isoform X29

  36. XM_047448508.1XP_047304464.1  histone-lysine N-methyltransferase SETD5 isoform X30

  37. XM_047448491.1XP_047304447.1  histone-lysine N-methyltransferase SETD5 isoform X14

  38. XM_047448470.1XP_047304426.1  histone-lysine N-methyltransferase SETD5 isoform X1

  39. XM_047448469.1XP_047304425.1  histone-lysine N-methyltransferase SETD5 isoform X1

  40. XM_047448484.1XP_047304440.1  histone-lysine N-methyltransferase SETD5 isoform X10

  41. XM_047448494.1XP_047304450.1  histone-lysine N-methyltransferase SETD5 isoform X16

  42. XM_047448498.1XP_047304454.1  histone-lysine N-methyltransferase SETD5 isoform X19

  43. XM_047448472.1XP_047304428.1  histone-lysine N-methyltransferase SETD5 isoform X1

  44. XM_047448475.1XP_047304431.1  histone-lysine N-methyltransferase SETD5 isoform X2

  45. XM_047448467.1XP_047304423.1  histone-lysine N-methyltransferase SETD5 isoform X1

  46. XM_047448493.1XP_047304449.1  histone-lysine N-methyltransferase SETD5 isoform X15

  47. XM_047448471.1XP_047304427.1  histone-lysine N-methyltransferase SETD5 isoform X1

  48. XM_047448499.1XP_047304455.1  histone-lysine N-methyltransferase SETD5 isoform X20

  49. XM_011533933.2XP_011532235.1  histone-lysine N-methyltransferase SETD5 isoform X21

    See identical proteins and their annotated locations for XP_011532235.1

    Conserved Domains (3) summary
    PLN02217
    Location:12101317
    PLN02217; probable pectinesterase/pectinesterase inhibitor
    COG5644
    Location:323543
    COG5644; U3 small nucleolar RNA-associated protein 14 [Function unknown]
    cd19181
    Location:155304
    SET_SETD5; SET domain (including post-SET domain) found in SET domain-containing protein 5 (SETD5) and similar proteins

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060927.1 Alternate T2T-CHM13v2.0

    Range
    9389553..9470070
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

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.