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KMT5B lysine methyltransferase 5B [ Homo sapiens (human) ]

Gene ID: 51111, updated on 7-Apr-2024

Summary

Official Symbol
KMT5Bprovided by HGNC
Official Full Name
lysine methyltransferase 5Bprovided by HGNC
Primary source
HGNC:HGNC:24283
See related
Ensembl:ENSG00000110066 MIM:610881; AllianceGenome:HGNC:24283
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
CGI85; MRD51; CGI-85; SUV420H1
Summary
This gene encodes a protein that contains a SET domain. SET domains appear to be protein-protein interaction domains that mediate interactions with a family of proteins that display similarity with dual-specificity phosphatases (dsPTPases). The function of this gene has not been determined. Several alternatively spliced transcript variants encoding different isoforms have been found for this gene. [provided by RefSeq, Jul 2014]
Expression
Ubiquitous expression in thyroid (RPKM 12.1), endometrium (RPKM 8.7) and 25 other tissues See more
Orthologs
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Genomic context

See KMT5B in Genome Data Viewer
Location:
11q13.2
Exon count:
14
Annotation release Status Assembly Chr Location
RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 11 NC_000011.10 (68154863..68213648, complement)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 11 NC_060935.1 (68158479..68217261, complement)
105.20220307 previous assembly GRCh37.p13 (GCF_000001405.25) 11 NC_000011.9 (67922330..67981115, complement)

Chromosome 11 - NC_000011.10Genomic Context describing neighboring genes Neighboring gene T cell immune regulator 1, ATPase H+ transporting V0 subunit a3 Neighboring gene H3K27ac hESC enhancer GRCh37_chr11:67834020-67834520 Neighboring gene choline kinase alpha Neighboring gene ReSE screen-validated silencer GRCh37_chr11:67850572-67850749 Neighboring gene ReSE screen-validated silencer GRCh37_chr11:67861600-67861729 Neighboring gene ReSE screen-validated silencer GRCh37_chr11:67870988-67871188 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 5130 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr11:67886638-67887154 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 5131 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 5132 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 3658 Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr11:67888828-67889593 Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr11:67889594-67890360 Neighboring gene CHKA divergent transcript Neighboring gene ReSE screen-validated silencer GRCh37_chr11:67907579-67907779 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 3661 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 3662 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr11:67981441-67982143 Neighboring gene Sharpr-MPRA regulatory region 2086 Neighboring gene MPRA-validated peak1319 silencer Neighboring gene P300/CBP strongly-dependent group 1 enhancer GRCh37_chr11:68034746-68035945 Neighboring gene H3K27ac hESC enhancer GRCh37_chr11:68039550-68040404 Neighboring gene uncharacterized LOC105369363 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 3666 Neighboring gene chromosome 11 open reading frame 24 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 5133 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 5134

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
Intellectual disability, autosomal dominant 51
MedGen: C4540474 OMIM: 617788 GeneReviews: Not available
Compare labs

Copy number response

Description
Copy number response
Haploinsufficency

Sufficient evidence for dosage pathogenicity (Last evaluated 2023-06-13)

ClinGen Genome Curation PagePubMed
Triplosensitivity

No evidence available (Last evaluated 2023-06-13)

ClinGen Genome Curation Page

EBI GWAS Catalog

Description
Loci associated with N-glycosylation of human immunoglobulin G show pleiotropy with autoimmune diseases and haematological cancers.
EBI GWAS Catalog

HIV-1 interactions

Replication interactions

Interaction Pubs
Knockdown of suppressor of variegation 4-20 homolog 1 (SUV420H1) by siRNA inhibits HIV-1 replication in HeLa-derived TZM-bl cells PubMed

Go to the HIV-1, Human Interaction Database

Pathways from PubChem

Interactions

Products Interactant Other Gene Complex Source Pubs Description

General gene information

Markers

Clone Names

  • MGC703, MGC21161, MGC118906, MGC118909

Gene Ontology Provided by GOA

Function Evidence Code Pubs
enables S-adenosyl-L-methionine binding ISS
Inferred from Sequence or Structural Similarity
more info
 
enables chromatin binding IDA
Inferred from Direct Assay
more info
PubMed 
enables histone H4 methyltransferase activity TAS
Traceable Author Statement
more info
 
enables histone H4K20 methyltransferase activity IBA
Inferred from Biological aspect of Ancestor
more info
 
enables histone H4K20 methyltransferase activity IDA
Inferred from Direct Assay
more info
PubMed 
enables histone H4K20 methyltransferase activity IMP
Inferred from Mutant Phenotype
more info
PubMed 
enables histone H4K20 monomethyltransferase activity IEA
Inferred from Electronic Annotation
more info
 
enables histone H4K20me methyltransferase activity IEA
Inferred from Electronic Annotation
more info
 
enables histone methyltransferase activity IDA
Inferred from Direct Assay
more info
PubMed 
enables metal ion binding 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 repair 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 muscle organ development IEA
Inferred from Electronic Annotation
more info
 
involved_in positive regulation of double-strand break repair via nonhomologous end joining IMP
Inferred from Mutant Phenotype
more info
PubMed 
involved_in positive regulation of isotype switching ISS
Inferred from Sequence or Structural Similarity
more info
 
Component Evidence Code Pubs
located_in condensed chromosome, centromeric region IEA
Inferred from Electronic Annotation
more info
 
located_in nucleoplasm IDA
Inferred from Direct Assay
more info
 
located_in nucleoplasm TAS
Traceable Author Statement
more info
 
is_active_in nucleus IBA
Inferred from Biological aspect of Ancestor
more info
 

General protein information

Preferred Names
histone-lysine N-methyltransferase KMT5B
Names
[histone H4]-N-methyl-L-lysine20 N-methyltransferase KMT5B
[histone H4]-lysine20 N-methyltransferase KMT5B
histone-lysine N-methyltransferase SUV420H1
lysine (K)-specific methyltransferase 5B
lysine N-methyltransferase 5B
lysine-specific methyltransferase 5B
su(var)4-20 homolog 1
suppressor of variegation 4-20 homolog 1
NP_001287836.1
NP_001287837.1
NP_001287838.1
NP_001350495.1
NP_001356353.1
NP_001356354.1
NP_001356355.1
NP_001356356.1
NP_001356357.1
NP_001356358.1
NP_001356359.1
NP_001356360.1
NP_001356361.1
NP_001356362.1
NP_057112.3
NP_060105.3
XP_005274092.2
XP_005274093.2
XP_006718644.1
XP_011543394.1
XP_024304338.1
XP_047283027.1
XP_047283028.1
XP_047283029.1
XP_054225022.1
XP_054225023.1
XP_054225024.1
XP_054225025.1
XP_054225026.1
XP_054225027.1
XP_054225028.1
XP_054225029.1

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_052873.1 RefSeqGene

    Range
    5477..63910
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. NM_001300907.1NP_001287836.1  histone-lysine N-methyltransferase KMT5B isoform 3

    See identical proteins and their annotated locations for NP_001287836.1

    Status: REVIEWED

    Description
    Transcript Variant: This variant (3) contains an alternate exon and uses a downstream start codon compared to variant 1. The resulting isoform (3) is shorter at the N-terminus compared to isoform 1.
    Source sequence(s)
    AP002992, BC108304
    Consensus CDS
    CCDS91518.1
    UniProtKB/TrEMBL
    A0A8V8TQB9
    Conserved Domains (1) summary
    smart00317
    Location:31142
    SET; SET (Su(var)3-9, Enhancer-of-zeste, Trithorax) domain
  2. NM_001300908.2NP_001287837.1  histone-lysine N-methyltransferase KMT5B isoform 4

    Status: REVIEWED

    Description
    Transcript Variant: This variant (4) uses an alternate first exon and an alternate splice junction at the 5' end of an exon, and uses a downstream start codon compared to variant 1. The resulting isoform (4) is shorter at the N-terminus compared to isoform 1.
    Source sequence(s)
    AK314336, AP002992, CR997801
    Conserved Domains (1) summary
    pfam00856
    Location:2168
    SET; SET domain
  3. NM_001300909.2NP_001287838.1  histone-lysine N-methyltransferase KMT5B isoform 5

    Status: REVIEWED

    Description
    Transcript Variant: This variant (5) uses an alternate first exon, lacks an alternate in-frame exon, and differs in the 3' UTR and coding sequence compared to variant 1. The resulting isoform (5) has a shorter and distinct C-terminus and lacks an alternate internal segment compared to isoform 1.
    Source sequence(s)
    AK299201, AP002992, BC002522, CR997801, KC877427
    Consensus CDS
    CCDS76444.1
    UniProtKB/TrEMBL
    B7WNX0, B7Z5N2
    Related
    ENSP00000384724.2, ENST00000402185.6
    Conserved Domains (1) summary
    smart00317
    Location:180291
    SET; SET (Su(var)3-9, Enhancer-of-zeste, Trithorax) domain
  4. NM_001363566.2NP_001350495.1  histone-lysine N-methyltransferase KMT5B isoform 6

    Status: REVIEWED

    Source sequence(s)
    AP002992, KC877427
    Consensus CDS
    CCDS86221.1
    UniProtKB/TrEMBL
    B5MCB3, B7Z5N2
    Related
    ENSP00000385005.1, ENST00000402789.5
    Conserved Domains (1) summary
    cd19184
    Location:192335
    SET_KMT5B; SET domain (including post-SET domain) found in histone-lysine N-methyltransferase 5B (KMT5B) and similar proteins
  5. NM_001369424.1NP_001356353.1  histone-lysine N-methyltransferase KMT5B isoform 7

    Status: REVIEWED

    Source sequence(s)
    AP002992, KC877427
    Related
    ENST00000700525.1
    Conserved Domains (1) summary
    smart00317
    Location:31142
    SET; SET (Su(var)3-9, Enhancer-of-zeste, Trithorax) domain
  6. NM_001369425.1NP_001356354.1  histone-lysine N-methyltransferase KMT5B isoform 8

    Status: REVIEWED

    Source sequence(s)
    AP002992
    Consensus CDS
    CCDS91519.1
    UniProtKB/TrEMBL
    B7Z5N2, C9JFG1
    Related
    ENSP00000403233.2, ENST00000458496.2
    Conserved Domains (1) summary
    smart00317
    Location:132243
    SET; SET (Su(var)3-9, Enhancer-of-zeste, Trithorax) domain
  7. NM_001369426.1NP_001356355.1  histone-lysine N-methyltransferase KMT5B isoform 1

    Status: REVIEWED

    Source sequence(s)
    AP002992, KC877427
    Consensus CDS
    CCDS31623.1
    UniProtKB/Swiss-Prot
    A0A0A0MT19, B7WNX7, Q3SX56, Q4FZB7, Q4V775, Q6P150, Q96E44, Q9BUL0, Q9H022, Q9H2K3, Q9NXV3, Q9Y393
    Conserved Domains (1) summary
    cd19184
    Location:192335
    SET_KMT5B; SET domain (including post-SET domain) found in histone-lysine N-methyltransferase 5B (KMT5B) and similar proteins
  8. NM_001369427.1NP_001356356.1  histone-lysine N-methyltransferase KMT5B isoform 2

    Status: REVIEWED

    Source sequence(s)
    AP002992, KC877427
    Consensus CDS
    CCDS44660.1
    UniProtKB/TrEMBL
    B7Z5N2
    Related
    ENSP00000385640.1, ENST00000405515.5
    Conserved Domains (1) summary
    smart00317
    Location:203314
    SET; SET (Su(var)3-9, Enhancer-of-zeste, Trithorax) domain
  9. NM_001369428.1NP_001356357.1  histone-lysine N-methyltransferase KMT5B isoform 3

    Status: REVIEWED

    Source sequence(s)
    AP002992, KC877427
    Consensus CDS
    CCDS91518.1
    UniProtKB/TrEMBL
    A0A8V8TQB9
    Conserved Domains (1) summary
    smart00317
    Location:31142
    SET; SET (Su(var)3-9, Enhancer-of-zeste, Trithorax) domain
  10. NM_001369429.1NP_001356358.1  histone-lysine N-methyltransferase KMT5B isoform 3

    Status: REVIEWED

    Source sequence(s)
    AP002992, KC877427
    Consensus CDS
    CCDS91518.1
    UniProtKB/TrEMBL
    A0A8V8TQB9
    Related
    ENSP00000515030.1, ENST00000700523.1
    Conserved Domains (1) summary
    smart00317
    Location:31142
    SET; SET (Su(var)3-9, Enhancer-of-zeste, Trithorax) domain
  11. NM_001369430.1NP_001356359.1  histone-lysine N-methyltransferase KMT5B isoform 3

    Status: REVIEWED

    Source sequence(s)
    AP002992
    Consensus CDS
    CCDS91518.1
    UniProtKB/TrEMBL
    A0A8V8TQB9
    Conserved Domains (1) summary
    smart00317
    Location:31142
    SET; SET (Su(var)3-9, Enhancer-of-zeste, Trithorax) domain
  12. NM_001369431.1NP_001356360.1  histone-lysine N-methyltransferase KMT5B isoform 3

    Status: REVIEWED

    Source sequence(s)
    AP002992, KC877427
    Consensus CDS
    CCDS91518.1
    UniProtKB/TrEMBL
    A0A8V8TQB9
    Conserved Domains (1) summary
    smart00317
    Location:31142
    SET; SET (Su(var)3-9, Enhancer-of-zeste, Trithorax) domain
  13. NM_001369432.1NP_001356361.1  histone-lysine N-methyltransferase KMT5B isoform 3

    Status: REVIEWED

    Source sequence(s)
    AP002992, KC877427
    Consensus CDS
    CCDS91518.1
    UniProtKB/TrEMBL
    A0A8V8TQB9
    Conserved Domains (1) summary
    smart00317
    Location:31142
    SET; SET (Su(var)3-9, Enhancer-of-zeste, Trithorax) domain
  14. NM_001369433.1NP_001356362.1  histone-lysine N-methyltransferase KMT5B isoform 3

    Status: REVIEWED

    Source sequence(s)
    AP002992, KC877427
    Consensus CDS
    CCDS91518.1
    UniProtKB/TrEMBL
    A0A8V8TQB9
    Conserved Domains (1) summary
    smart00317
    Location:31142
    SET; SET (Su(var)3-9, Enhancer-of-zeste, Trithorax) domain
  15. NM_016028.4NP_057112.3  histone-lysine N-methyltransferase KMT5B isoform 2

    See identical proteins and their annotated locations for NP_057112.3

    Status: REVIEWED

    Description
    Transcript Variant: This variant (2) has an alternate 3' exon and utilizes an upstream stop codon, compared to variant 1. The resulting isoform (2) is shorter and has a distinct C-terminus compared to isoform 1.
    Source sequence(s)
    BC002522, BM152996
    Consensus CDS
    CCDS44660.1
    UniProtKB/TrEMBL
    B7Z5N2
    Related
    ENSP00000385965.2, ENST00000401547.6
    Conserved Domains (1) summary
    smart00317
    Location:203314
    SET; SET (Su(var)3-9, Enhancer-of-zeste, Trithorax) domain
  16. NM_017635.5NP_060105.3  histone-lysine N-methyltransferase KMT5B isoform 1

    See identical proteins and their annotated locations for NP_060105.3

    Status: REVIEWED

    Description
    Transcript Variant: This variant (1) encodes the longest isoform (1).
    Source sequence(s)
    AP002992, BC099714, BC108304
    Consensus CDS
    CCDS31623.1
    UniProtKB/Swiss-Prot
    A0A0A0MT19, B7WNX7, Q3SX56, Q4FZB7, Q4V775, Q6P150, Q96E44, Q9BUL0, Q9H022, Q9H2K3, Q9NXV3, Q9Y393
    Related
    ENSP00000305899.4, ENST00000304363.9
    Conserved Domains (1) summary
    cd19184
    Location:192335
    SET_KMT5B; SET domain (including post-SET domain) found in histone-lysine N-methyltransferase 5B (KMT5B) and similar proteins

RNA

  1. NR_161378.1 RNA Sequence

    Status: REVIEWED

    Source sequence(s)
    AP002992, KC877427
  2. NR_161379.1 RNA Sequence

    Status: REVIEWED

    Source sequence(s)
    AP002992, KC877427
  3. NR_161380.1 RNA Sequence

    Status: REVIEWED

    Source sequence(s)
    AP002992, KC877427

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_000011.10 Reference GRCh38.p14 Primary Assembly

    Range
    68154863..68213648 complement
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_047427072.1XP_047283028.1  histone-lysine N-methyltransferase KMT5B isoform X4

  2. XM_011545092.4XP_011543394.1  histone-lysine N-methyltransferase KMT5B isoform X3

    UniProtKB/TrEMBL
    C9J6S5
    Related
    ENSP00000406377.2, ENST00000453170.6
    Conserved Domains (1) summary
    smart00317
    Location:132243
    SET; SET (Su(var)3-9, Enhancer-of-zeste, Trithorax) domain
  3. XM_005274036.5XP_005274093.2  histone-lysine N-methyltransferase KMT5B isoform X2

    See identical proteins and their annotated locations for XP_005274093.2

    Conserved Domains (1) summary
    smart00317
    Location:180291
    SET; SET (Su(var)3-9, Enhancer-of-zeste, Trithorax) domain
  4. XM_005274035.5XP_005274092.2  histone-lysine N-methyltransferase KMT5B isoform X1

    See identical proteins and their annotated locations for XP_005274092.2

    UniProtKB/Swiss-Prot
    A0A0A0MT19, B7WNX7, Q3SX56, Q4FZB7, Q4V775, Q6P150, Q96E44, Q9BUL0, Q9H022, Q9H2K3, Q9NXV3, Q9Y393
    Conserved Domains (1) summary
    cd19184
    Location:192335
    SET_KMT5B; SET domain (including post-SET domain) found in histone-lysine N-methyltransferase 5B (KMT5B) and similar proteins
  5. XM_006718581.2XP_006718644.1  histone-lysine N-methyltransferase KMT5B isoform X2

    See identical proteins and their annotated locations for XP_006718644.1

    Conserved Domains (1) summary
    smart00317
    Location:180291
    SET; SET (Su(var)3-9, Enhancer-of-zeste, Trithorax) domain
  6. XM_047427071.1XP_047283027.1  histone-lysine N-methyltransferase KMT5B isoform X1

    UniProtKB/Swiss-Prot
    A0A0A0MT19, B7WNX7, Q3SX56, Q4FZB7, Q4V775, Q6P150, Q96E44, Q9BUL0, Q9H022, Q9H2K3, Q9NXV3, Q9Y393
  7. XM_047427073.1XP_047283029.1  histone-lysine N-methyltransferase KMT5B isoform X5

  8. XM_024448570.2XP_024304338.1  histone-lysine N-methyltransferase KMT5B isoform X5

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060935.1 Alternate T2T-CHM13v2.0

    Range
    68158479..68217261 complement
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_054369052.1XP_054225027.1  histone-lysine N-methyltransferase KMT5B isoform X4

  2. XM_054369051.1XP_054225026.1  histone-lysine N-methyltransferase KMT5B isoform X3

    UniProtKB/TrEMBL
    C9J6S5
  3. XM_054369049.1XP_054225024.1  histone-lysine N-methyltransferase KMT5B isoform X2

  4. XM_054369047.1XP_054225022.1  histone-lysine N-methyltransferase KMT5B isoform X1

    UniProtKB/Swiss-Prot
    A0A0A0MT19, B7WNX7, Q3SX56, Q4FZB7, Q4V775, Q6P150, Q96E44, Q9BUL0, Q9H022, Q9H2K3, Q9NXV3, Q9Y393
  5. XM_054369050.1XP_054225025.1  histone-lysine N-methyltransferase KMT5B isoform X2

  6. XM_054369048.1XP_054225023.1  histone-lysine N-methyltransferase KMT5B isoform X1

    UniProtKB/Swiss-Prot
    A0A0A0MT19, B7WNX7, Q3SX56, Q4FZB7, Q4V775, Q6P150, Q96E44, Q9BUL0, Q9H022, Q9H2K3, Q9NXV3, Q9Y393
  7. XM_054369053.1XP_054225028.1  histone-lysine N-methyltransferase KMT5B isoform X5

  8. XM_054369054.1XP_054225029.1  histone-lysine N-methyltransferase KMT5B isoform X5