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GeneE
10 sources retrieved Β· Most recent: April 2026 Β· Index updated 15 days ago
β“˜GeneE is for informational purposes only. It is not a substitute for professional medical advice, diagnosis, or treatment.
KMT5B
lysine methyltransferase 5B
Chromosome 11 Β· 11q13.2
NCBI Gene: 51111Ensembl: ENSG00000110066.16HGNC: HGNC:24283UniProt: A0A8V8TQB9
58PubMed Papers
21Diseases
0Drugs
71Pathogenic Variants
FUNCTIONAL ROLE
DNA RepairHighly ConstrainedTranscription Factor
RESEARCH IMPACT
Variant-Rich
CLINICAL
OMIM Disease Gene
DATA QUALITY
βœ“ Experimental GO Evidenceβœ“ Swiss-Prot Reviewed
chromatin bindingprotein bindinghistone methyltransferase activityhistone H4K20 methyltransferase activityintellectual disability, autosomal dominant 51genetic disorderIntellectual disabilitycomplex neurodevelopmental disorder
✦AI Summary

KMT5B is a histone methyltransferase that catalyzes methylation of histone H4 lysine 20, specifically converting H4K20me1 to H4K20me2 and H4K20me2 to H4K20me3 1. The resulting H4K20me3 mark functions as an epigenetic tag for transcriptional repression, particularly in pericentric heterochromatin where KMT5B establishes constitutive heterochromatin 2. KMT5B facilitates TP53BP1 recruitment and DNA repair through non-homologous end-joining by catalyzing H4K20 methylation 1. Beyond DNA repair, KMT5B regulates neuronal development and myogenesis 3. KMT5B localizes to mitotic spindle microtubules, linking it to cellular proliferation biology 4. Pathogenic KMT5B variants cause neurodevelopmental disorder characterized by global developmental delay, macrocephaly, autism spectrum disorder, hypotonia, and congenital heart defects 56. Loss of KMT5B function impairs neuronal dendritic complexity and accelerates neural progenitor cell migration 6. In cancer, KMT5B overexpression mediates H4K20me3-dependent silencing of inflammatory genes in persister cells, promoting drug tolerance 7, while mutant p53 upregulates KMT5B to confer chemoresistance in nasopharyngeal carcinoma 8.

Sources cited
1
KMT5B catalyzes di- and trimethylation of H4K20 and facilitates TP53BP1 foci formation in NHEJ-directed DNA repair
PMID: 28114273
2
KMT5B methylates H4K20me1 and H4K20me2 and functions in constitutive heterochromatin establishment
PMID: 24396869
3
KMT5B plays a role in myogenesis by regulating target gene expression
PMID: 23720823
4
KMT5B haploinsufficiency causes neurodevelopmental disorder with developmental delay, macrocephaly, autism, hypotonia, and congenital heart defects
PMID: 36897941
5
KMT5B loss-of-function impairs neuronal dendritic complexity and accelerates neural progenitor cell migration
PMID: 35331928
6
KMT5B localizes to mitotic spindle microtubules and is enriched among ASD risk genes associated with tubulin biology
PMID: 37366052
7
KMT5B overexpression mediates H4K20me3-dependent silencing of inflammatory genes in persister cancer cells
PMID: 39476057
8
Mutant p53 upregulates KMT5B to confer 5-FU chemoresistance in nasopharyngeal carcinoma
PMID: 40316196
Disease Associationsβ“˜21
intellectual disability, autosomal dominant 51Open Targets
0.79Strong
genetic disorderOpen Targets
0.52Moderate
Intellectual disabilityOpen Targets
0.43Moderate
complex neurodevelopmental disorderOpen Targets
0.37Weak
Autistic behaviorOpen Targets
0.34Weak
neural tube defectOpen Targets
0.34Weak
autism spectrum disorderOpen Targets
0.33Weak
poisoningOpen Targets
0.32Weak
Neurodevelopmental delayOpen Targets
0.27Weak
Alzheimer diseaseOpen Targets
0.26Weak
Rare genetic intellectual disabilityOpen Targets
0.26Weak
Global developmental delayOpen Targets
0.12Weak
schizophreniaOpen Targets
0.11Weak
intellectual disability with language impairmentOpen Targets
0.11Weak
Abnormal erythrocyte morphologyOpen Targets
0.10Suggestive
neoplasmOpen Targets
0.08Suggestive
head and neck squamous cell carcinomaOpen Targets
0.08Suggestive
glioblastoma multiformeOpen Targets
0.08Suggestive
sarcomaOpen Targets
0.05Suggestive
cancerOpen Targets
0.04Suggestive
Intellectual developmental disorder, autosomal dominant 51UniProt
Pathogenic Variants71
NM_017635.5(KMT5B):c.780_781del (p.Ala261fs)Pathogenic
Inborn genetic diseases|not provided
β˜…β˜…β˜†β˜†2025β†’ Residue 261
NM_017635.5(KMT5B):c.840+1_840+5delPathogenic
Intellectual disability, autosomal dominant 51|not provided
β˜…β˜…β˜†β˜†2025
NM_017635.5(KMT5B):c.2347C>T (p.Arg783Ter)Pathogenic
Intellectual disability, autosomal dominant 51|not provided
β˜…β˜…β˜†β˜†2025β†’ Residue 783
NM_017635.5(KMT5B):c.856C>T (p.Arg286Ter)Pathogenic
Intellectual disability, autosomal dominant 51|not provided
β˜…β˜…β˜†β˜†2024β†’ Residue 286
NM_017635.5(KMT5B):c.2422_2425del (p.Leu808fs)Pathogenic
not provided|Intellectual disability, autosomal dominant 51
β˜…β˜…β˜†β˜†2024β†’ Residue 808
NM_017635.5(KMT5B):c.234_235del (p.Cys78_Glu79delinsTer)Pathogenic
Autistic behavior|not provided
β˜…β˜…β˜†β˜†2024β†’ Residue 78
NM_017635.5(KMT5B):c.725del (p.Leu242fs)Pathogenic
Intellectual disability, autosomal dominant 51|not provided
β˜…β˜…β˜†β˜†2024β†’ Residue 242
NM_017635.5(KMT5B):c.2434C>T (p.Arg812Ter)Likely pathogenic
not provided|Inborn genetic diseases
β˜…β˜…β˜†β˜†2024β†’ Residue 812
NM_017635.5(KMT5B):c.1183C>T (p.Arg395Ter)Pathogenic
Intellectual disability, autosomal dominant 51
β˜…β˜…β˜†β˜†2023β†’ Residue 395
NM_017635.5(KMT5B):c.668_672del (p.Lys223fs)Pathogenic
Intellectual disability, autosomal dominant 51
β˜…β˜…β˜†β˜†2021β†’ Residue 223
NM_017635.5(KMT5B):c.559C>T (p.Arg187Ter)Pathogenic
Intellectual disability, autosomal dominant 51|Neural tube defect
β˜…β˜…β˜†β˜†2019β†’ Residue 187
NM_017635.5(KMT5B):c.977+2T>ALikely pathogenic
Intellectual disability, autosomal dominant 51
β˜…β˜†β˜†β˜†2026
NM_017635.5(KMT5B):c.290del (p.Thr97fs)Pathogenic
not provided
β˜…β˜†β˜†β˜†2025β†’ Residue 97
NM_017635.5(KMT5B):c.1208del (p.Lys403fs)Pathogenic
Intellectual disability, autosomal dominant 51
β˜…β˜†β˜†β˜†2025β†’ Residue 403
NM_017635.5(KMT5B):c.329C>G (p.Ser110Ter)Pathogenic
Intellectual disability, autosomal dominant 51
β˜…β˜†β˜†β˜†2025β†’ Residue 110
NM_017635.5(KMT5B):c.590T>C (p.Ile197Thr)Likely pathogenic
Intellectual disability, autosomal dominant 51
β˜…β˜†β˜†β˜†2025β†’ Residue 197
NM_017635.5(KMT5B):c.933C>A (p.Phe311Leu)Likely pathogenic
Intellectual disability, autosomal dominant 51
β˜…β˜†β˜†β˜†2025β†’ Residue 311
NM_017635.5(KMT5B):c.978-1G>TLikely pathogenic
Inborn genetic diseases
β˜…β˜†β˜†β˜†2025
NM_017635.5(KMT5B):c.921T>A (p.Tyr307Ter)Pathogenic
Intellectual disability, autosomal dominant 51
β˜…β˜†β˜†β˜†2025β†’ Residue 307
NM_017635.5(KMT5B):c.1423_1424del (p.Leu475fs)Likely pathogenic
Intellectual disability, autosomal dominant 51
β˜…β˜†β˜†β˜†2025β†’ Residue 475
View on ClinVar β†—
Related Genes
KMT5CShared pathway100%KMT5AProtein interaction100%PRMT5Protein interaction100%CBX1Protein interaction94%DNMT1Protein interaction93%H4C6Protein interaction91%
Tissue Expression6 tissues
Ovary
100%
Heart
91%
Liver
87%
Brain
70%
Bone Marrow
62%
Lung
62%
Gene Interaction Network
Click a node to explore
KMT5BKMT5CKMT5APRMT5CBX1DNMT1H4C6
PROTEIN STRUCTURE
Preparing viewer…
PDB3S8P Β· 1.85 Γ… Β· X-ray
View on RCSB β†—
Constraintβ“˜
LOEUFβ“˜
0.19Highly Constrained
pLIβ“˜
1.00Intolerant
Observed/Expected LoF0.11 [0.06–0.19]
RankingsWhere KMT5B stands among ~20K protein-coding genes
  • #7,886of 20,598
    Most Researched58
  • #1,029of 5,498
    Most Pathogenic Variants71 Β· top quartile
  • #395of 17,882
    Most Constrained (LOEUF)0.19 Β· top 5%
Genes detectedKMT5B
Sources retrieved10 papers
Response timeβ€”
πŸ“„ Sources
10β–Ό
1
Targeted sequencing identifies 91 neurodevelopmental-disorder risk genes with autism and developmental-disability biases.
PMID: 28191889
Nat Genet Β· 2017
1.00
2
Autism genes converge on asynchronous development of shared neuron classes.
PMID: 35110736
Nature Β· 2022
0.90
3
Histone Lysine Methylases and Demethylases in the Landscape of Human Developmental Disorders.
PMID: 29276005
Am J Hum Genet Β· 2018
0.80
4
Mechanism of KMT5B haploinsufficiency in neurodevelopment in humans and mice.
PMID: 36897941
Sci Adv Β· 2023
0.70
5
Loss-of-function of KMT5B leads to neurodevelopmental disorder and impairs neuronal development and neurogenesis.
PMID: 35331928
J Genet Genomics Β· 2022
0.60