Gene Details | GeDiPNet - Complete Gene Info, Disease Associations & Pathways

Gene Gene information from NCBI Gene database. Gene SNPs miRNA Gene ontology Other IDs Protein Pathways Associated diseases
Entrez ID	51111
Gene name	Lysine methyltransferase 5B
Gene symbol	KMT5B
Synonyms (NCBI Gene)	CGI-85CGI85MRD51SUV420H1
Chromosome	11
Chromosome location	11q13.2
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 o

Show/Hide all (13)

SNP ID	Visualize variation	Clinical significance	Consequence
rs114727354	G>A,T	Benign, likely-pathogenic	Non coding transcript variant, 5 prime UTR variant, coding sequence variant, synonymous variant, stop gained
rs878853164	C>A	Likely-pathogenic	Stop gained, genic downstream transcript variant, coding sequence variant
rs1555023232	CT>-	Pathogenic	Coding sequence variant, frameshift variant, genic downstream transcript variant
rs1555027828	A>C	Likely-pathogenic	Coding sequence variant, non coding transcript variant, missense variant, 5 prime UTR variant
rs1555028154	A>-	Pathogenic	5 prime UTR variant, coding sequence variant, intron variant, non coding transcript variant, frameshift variant
rs1555028206	G>A	Pathogenic	Stop gained, 5 prime UTR variant, coding sequence variant, intron variant, non coding transcript variant
rs1555034768	G>-	Pathogenic	5 prime UTR variant, coding sequence variant, intron variant, non coding transcript variant, frameshift variant
rs1565212298	G>A	Likely-pathogenic	Coding sequence variant, stop gained, genic downstream transcript variant
rs1565226034	T>C	Likely-pathogenic	5 prime UTR variant, coding sequence variant, missense variant, intron variant, non coding transcript variant
rs1565240833	G>-	Pathogenic	5 prime UTR variant, coding sequence variant, intron variant, non coding transcript variant, frameshift variant
rs1590954686	G>A	Pathogenic	5 prime UTR variant, coding sequence variant, stop gained, non coding transcript variant
rs1590955042	T>C	Likely-pathogenic	5 prime UTR variant, splice acceptor variant, non coding transcript variant
rs1590956245	ATTTT>-	Pathogenic	Non coding transcript variant, 5 prime UTR variant, coding sequence variant, frameshift variant, intron variant

Show/Hide all (17)

miRTarBase ID	miRNA	Experiments	Reference
MIRT534014	hsa-miR-106a-5p	PAR-CLIP	22012620
MIRT534013	hsa-miR-20b-5p	PAR-CLIP	22012620
MIRT534012	hsa-miR-519d-3p	PAR-CLIP	22012620
MIRT534011	hsa-miR-17-5p	PAR-CLIP	22012620
MIRT534010	hsa-miR-526b-3p	PAR-CLIP	22012620
MIRT028080	hsa-miR-93-5p	PAR-CLIP	22012620
MIRT534009	hsa-miR-106b-5p	PAR-CLIP	22012620
MIRT534008	hsa-miR-20a-5p	PAR-CLIP	22012620
MIRT534007	hsa-miR-3609	PAR-CLIP	22012620
MIRT534006	hsa-miR-548ah-5p	PAR-CLIP	22012620
MIRT534005	hsa-miR-4796-3p	PAR-CLIP	22012620
MIRT534004	hsa-miR-889-3p	PAR-CLIP	22012620
MIRT534003	hsa-miR-502-5p	PAR-CLIP	22012620
MIRT534002	hsa-miR-5585-3p	PAR-CLIP	22012620
MIRT726407	hsa-miR-92a-3p	HITS-CLIP	22473208
MIRT726406	hsa-miR-92b-3p	HITS-CLIP	22473208
MIRT028330	hsa-miR-32-5p	HITS-CLIP	22473208

Show/Hide all (42)

GO ID	Ontology	Definition	Evidence	Reference
GO:0000779	Component	Condensed chromosome, centromeric region	IEA
GO:0001650	Component	Fibrillar center	IDA
GO:0003682	Function	Chromatin binding	IDA	28114273
GO:0003682	Function	Chromatin binding	IEA
GO:0005515	Function	Protein binding	IPI	19074285, 32296183
GO:0005634	Component	Nucleus	IBA
GO:0005634	Component	Nucleus	IEA
GO:0005654	Component	Nucleoplasm	IDA
GO:0005654	Component	Nucleoplasm	TAS
GO:0005694	Component	Chromosome	IEA
GO:0005730	Component	Nucleolus	IDA
GO:0005813	Component	Centrosome	IDA
GO:0005886	Component	Plasma membrane	IDA
GO:0005929	Component	Cilium	IDA
GO:0006281	Process	DNA repair	IEA
GO:0006281	Process	DNA repair	IMP	28114273
GO:0006325	Process	Chromatin organization	IEA
GO:0006338	Process	Chromatin remodeling	IEA
GO:0007517	Process	Muscle organ development	IEA
GO:0008168	Function	Methyltransferase activity	IEA
GO:0015630	Component	Microtubule cytoskeleton	IDA
GO:0016740	Function	Transferase activity	IEA
GO:0032259	Process	Methylation	IEA
GO:0036064	Component	Ciliary basal body	IDA
GO:0036464	Component	Cytoplasmic ribonucleoprotein granule	IDA
GO:0042054	Function	Histone methyltransferase activity	IDA	17707234
GO:0042799	Function	Histone H4K20 methyltransferase activity	IBA
GO:0042799	Function	Histone H4K20 methyltransferase activity	IDA	24396869
GO:0042799	Function	Histone H4K20 methyltransferase activity	IEA
GO:0042799	Function	Histone H4K20 methyltransferase activity	IMP	28114273
GO:0045171	Component	Intercellular bridge	IDA
GO:0045830	Process	Positive regulation of isotype switching	IEA
GO:0045830	Process	Positive regulation of isotype switching	ISS
GO:0046872	Function	Metal ion binding	IEA
GO:0072686	Component	Mitotic spindle	IDA
GO:0140939	Function	Histone H4 methyltransferase activity	TAS
GO:0140941	Function	Histone H4K20me methyltransferase activity	IEA
GO:0140944	Function	Histone H4K20 monomethyltransferase activity	IEA
GO:1904047	Function	S-adenosyl-L-methionine binding	IEA
GO:1904047	Function	S-adenosyl-L-methionine binding	ISS
GO:2001034	Process	Positive regulation of double-strand break repair via nonhomologous end joining	IEA
GO:2001034	Process	Positive regulation of double-strand break repair via nonhomologous end joining	IMP	28114273

MIM	HGNC	e!Ensembl
610881	24283	ENSG00000110066

Q4FZB7

Protein name

Histone-lysine N-methyltransferase KMT5B (Lysine N-methyltransferase 5B) (Lysine-specific methyltransferase 5B) (Suppressor of variegation 4-20 homolog 1) (Su(var)4-20 homolog 1) (Suv4-20h1) ([histone H4]-N-methyl-L-lysine20 N-methyltransferase KMT5B) (EC

Protein function

Histone methyltransferase that specifically methylates monomethylated 'Lys-20' (H4K20me1) and dimethylated 'Lys-20' (H4K20me2) of histone H4 to produce respectively dimethylated 'Lys-20' (H4K20me2) and trimethylated 'Lys-20' (H4K20me3) and thus

PDB

3S8P , 5CPR , 5WBV , 7YRD , 7YRG , 8JHF , 8JHG , 8T68 , 8T9F , 8T9H

Family and domains

Pfam

Accession	ID	Position in sequence	Description	Type
PF00856	SET	137 → 308	SET domain	Family

Sequence

MKWLGESKNMVVNGRRNGGKLSNDHQQNQSKLQHTGKDTLKAGKNAVERRSNRCNGNSGF
EGQSRYVPSSGMSAKELCENDDLATSLVLDPYLGFQTHKMNTSAFPSRSSRHFSKSDSFS
HNNPVRFRPIKGRQEELKEVIERFKKDEHLEKAFKCLTSGEWARHYFLNKNKMQEKLFKE
HVFIYLRMFATDSGFEILPCNRYSSEQNGAKIVATKEWKRNDKIELLVGCIAELSEIEEN
MLLRHGENDFSVMYSTRKNCAQLWLGPAAFINHDCRPNCKFVSTGRDTACVKALRDIEPG
EEISCYYGDGFFGENNEFCECYTCERRGTGAFKSRVGLPAPAPVINSKYGLRETDKRLNR
LKKLGDSSKNSDSQSVSSNTDADTTQEKNNATSNRKSSVGVKKNSKSRTLTRQSMSRIPA
SSNSTSSKLTHINNSRVPKKLKKPAKPLLSKIKLRNHCKRLEQKNASRKLEMGNLVLKEP
KVVLYKNLPIKKDKEPEGPAQAAVASGCLTRHAAREHRQNPVRGAHSQGESSPCTYITRR
SVRTRTNLKEASDIKLEPNTLNGYKSSVTEPCPDSGEQLQPAPVLQEEELAHETAQKGEA
KCHKSDTGMSKKKSRQGKLVKQFAKIEESTPVHDSPGKDDAVPDLMGPHSDQGEHSGTVG
VPVSYTDCAPSPVGCSVVTSDSFKTKDSFRTAKSKKKRRITRYDAQLILENNSGIPKLTL
RRRHDSSSKTNDQENDGMNSSKISIKLSKDHDNDNNLYVAKLNNGFNSGSGSSSTKLKIQ
LKRDEENRGSYTEGLHENGVCCSDPLSLLESRMEVDDYSQYEEESTDDSSSSEGDEEEDD
YDDDFEDDFIPLPPAKRLRLIVGKDSIDIDISSRRREDQSLRLNA

Sequence length

885

Interactions

View interactions

	KEGG		Reactome
	Lysine degradation Metabolic pathways		PKMTs methylate histone lysines

Evidence Score: ★☆☆☆☆ Gene-disease association found in Text Mining only ★★☆☆☆ Found in Text Mining and Unknown/Other Associations ★★★☆☆ Reported in Unknown/Other Associations across ≥2 Sources ★★★★☆ ClinVar: Pathogenic/Likely Pathogenic (<5 Variants) ★★★★★ ClinVar: Pathogenic/Likely Pathogenic (≥5 Variants)

Show/Hide Causal Diseases (7)

Phenotype Name	Clinical Significance	dbSNP ID	RCV Accession	Evidence Score
Causal Diseases associated with Pathogenic or Likely Pathogenic variants in ClinVar
Autistic behavior	Pathogenic	rs2153068015	RCV001526519	★★★★★ ★★★★☆ ClinVar: Pathogenic / Likely Pathogenic (<5 Variants)
Intellectual disability	Pathogenic	rs2153054646, rs2153039995	RCV001375671 RCV001544500	★★★★★ ★★★★☆ ClinVar: Pathogenic / Likely Pathogenic (<5 Variants)
Intellectual disability, autosomal dominant 51	Pathogenic; Likely pathogenic	rs2153052073, rs2153055850, rs2153039957, rs2153052061, rs2153052371, rs2153040748, rs2496205950, rs767378835, rs2496380553, rs2495306873, rs2495592225, rs2496380462, rs1859424641, rs2496210221, rs2496195646 View all (10 more)	RCV001788544 RCV001788545 RCV003314009 RCV001787310 RCV001809216 View all (20 more)	★★★★★ ★★★★★ ClinVar: Pathogenic / Likely Pathogenic (≥5 Variants)
KMT5B-related disorder	Likely pathogenic	rs2496321996	RCV004548982	★★★★★ ★★★★☆ ClinVar: Pathogenic / Likely Pathogenic (<5 Variants)
Neural tube defect	Likely pathogenic; Pathogenic	rs114727354	RCV001526514	★★★★★ ★★★★☆ ClinVar: Pathogenic / Likely Pathogenic (<5 Variants)
Neurodevelopmental delay	Likely pathogenic	rs1565214242	RCV002274354	★★★★★ ★★★★☆ ClinVar: Pathogenic / Likely Pathogenic (<5 Variants)
Rare genetic intellectual disability	Likely pathogenic	rs2496189023	RCV001257000	★★★★★ ★★★★☆ ClinVar: Pathogenic / Likely Pathogenic (<5 Variants)

Show/Hide Unknown Diseases (21)

Phenotype Name	Clinical Significance	Source	Evidence Score
Unknown / Other Associations ClinVar entries with uncertain/conflicting evidence, and associations from other databases (OMIM, Orphanet, GWAS, etc.) where the gene is not established as causal.
Acute myeloid leukemia	Likely benign	ClinVar	★★★★★ ★★☆☆☆ Found in Text Mining + Unknown/Other Associations
ALZHEIMER DISEASE	—	GWAS catalog	★★★★★ ★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Autism spectrum disorder	Uncertain significance	ClinVar	★★★★★ ★★☆☆☆ Found in Text Mining + Unknown/Other Associations
AUTISM SPECTRUM DISORDERS	—	Disgenet	★★★★★ ★★☆☆☆ Found in Text Mining + Unknown/Other Associations
BREAST CARCINOMA	—	GWAS catalog	★★★★★ ★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Cervical cancer	Likely benign	ClinVar	★★★★★ ★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Colon adenocarcinoma	Likely benign	ClinVar	★★★★★ ★★☆☆☆ Found in Text Mining + Unknown/Other Associations
COMPLEX NEURODEVELOPMENTAL DISORDER	—	ClinGen, GWAS catalog	★★★★★ ★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Familial cancer of breast	Likely benign	ClinVar	★★★★★ ★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Global developmental delay	Uncertain significance	ClinVar Disgenet	★★★★★ ★★★☆☆ Reported in Unknown/Other Associations (≥2 sources)
GOUT	—	GWAS catalog	★★★★★ ★★☆☆☆ Found in Text Mining + Unknown/Other Associations
INTELLECTUAL DEVELOPMENTAL DISORDER, AUTOSOMAL DOMINANT 51	—	Disgenet, HPO Disgenet, HPO	★★★★★ ★★☆☆☆ Found in Text Mining + Unknown/Other Associations
INTELLECTUAL DISABILITY-HYPOTONIA-FACIAL DYSMORPHISM-MACROCEPHALY SYNDROME	—	Orphanet	★★★★★ ★★☆☆☆ Found in Text Mining + Unknown/Other Associations
KMT5B-related neurodevelopmental disorder	Uncertain significance	ClinVar	★★★★★ ★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Language retardation	Uncertain significance	ClinVar	★★★★★ ★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Lung cancer	Likely benign	ClinVar	★★★★★ ★★☆☆☆ Found in Text Mining + Unknown/Other Associations
NEURAL TUBE DEFECTS	—	Disgenet	★★★★★ ★★☆☆☆ Found in Text Mining + Unknown/Other Associations
NEURODEVELOPMENTAL DISORDERS	—	CTD, Disgenet CTD, Disgenet	★★★★★ ★★☆☆☆ Found in Text Mining + Unknown/Other Associations
NON-SPECIFIC SYNDROMIC INTELLECTUAL DISABILITY	—	Disgenet	★★★★★ ★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Schizophrenia	Uncertain significance	ClinVar Disgenet	★★★★★ ★★★☆☆ Reported in Unknown/Other Associations (≥2 sources)
Thymoma	Likely benign	ClinVar	★★★★★ ★★☆☆☆ Found in Text Mining + Unknown/Other Associations

Show/Hide Text Mining Associations (32)

Disease Name	Disease (Merged)	Source	PMID	Relationship Type	Evidence Score
Associations from Text Mining Disease associations identified through text mining
Attention Deficit Disorder with Hyperactivity	Attention deficit hyperactivity disorder	Pubtator	37927187	Associate	★★★★★ ★☆☆☆☆ Found in Text Mining only
Autism Spectrum Disorder	Autism	Pubtator	26235986, 35110736, 37366052	Associate	★★★★★ ★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Autism Spectrum Disorders	Autism Spectrum Disorder	BEFREE	26235986		★★★★★ ★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Autistic behavior	Autism	HPO_DG			★★★★★ ★★★★☆ ClinVar: Pathogenic / Likely Pathogenic (<5 Variants)
Autistic Disorder	Autism	Pubtator	35110736, 37927187	Associate	★★★★★ ★☆☆☆☆ Found in Text Mining only
Brain Diseases	Brain disease	Pubtator	26235986	Associate	★★★★★ ★☆☆☆☆ Found in Text Mining only
Breast Carcinoma	Breast Carcinoma	GWASCAT_DG	29059430		★★★★★ ★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Breast Neoplasms	Breast neoplasm	Pubtator	24953066	Associate	★★★★★ ★☆☆☆☆ Found in Text Mining only
Chronic Lymphocytic Leukemia	Lymphocytic Leukemia	BEFREE	28833505		★★★★★ ★☆☆☆☆ Found in Text Mining only
Cryptorchidism	Cryptorchidism	HPO_DG			★★★★★ ★☆☆☆☆ Found in Text Mining only
Developmental Disabilities	Development Disorder	BEFREE	29276005		★★★★★ ★☆☆☆☆ Found in Text Mining only
Developmental Disabilities	Developmental disability	Pubtator	29276005, 31238879, 37927187	Associate	★★★★★ ★☆☆☆☆ Found in Text Mining only
Dysmorphic features	Dysmorphic Features	CLINVAR_DG	15145825, 22495306, 22542183, 23665959, 25363760, 28135719, 28191889		★★★★★ ★☆☆☆☆ Found in Text Mining only
Global developmental delay	Developmental Delay	HPO_DG			★★★★★ ★★★☆☆ Reported in Unknown/Other Associations (≥2 sources)
Growth Disorders	Growth disorder	Pubtator	35110736	Associate	★★★★★ ★☆☆☆☆ Found in Text Mining only
Hypertension	Hypertension	Pubtator	32410228	Associate	★★★★★ ★☆☆☆☆ Found in Text Mining only
Intellectual Disability	Intellectual developmental disorder	Pubtator	26235986, 29276005, 37927187	Associate	★★★★★ ★★★★☆ ClinVar: Pathogenic / Likely Pathogenic (<5 Variants)
Intellectual Disability	Mental retardation	BEFREE	29276005		★★★★★ ★★★★☆ ClinVar: Pathogenic / Likely Pathogenic (<5 Variants)
Intellectual Disability	Mental retardation	HPO_DG			★★★★★ ★★★★☆ ClinVar: Pathogenic / Likely Pathogenic (<5 Variants)
leukemia	Leukemia	BEFREE	29616094		★★★★★ ★☆☆☆☆ Found in Text Mining only
Malignant Childhood Neoplasm	Malignant Neoplasm	GWASCAT_DG	29059430		★★★★★ ★☆☆☆☆ Found in Text Mining only
Malignant Neoplasms	Malignant Neoplasm	BEFREE	26586479, 31255706		★★★★★ ★☆☆☆☆ Found in Text Mining only
MENTAL RETARDATION, AUTOSOMAL DOMINANT 51	Mental retardation	GENOMICS_ENGLAND_DG	25363768, 28191889		★★★★★ ★☆☆☆☆ Found in Text Mining only
MENTAL RETARDATION, AUTOSOMAL DOMINANT 51	Mental retardation	UNIPROT_DG	28191889, 29276005		★★★★★ ★☆☆☆☆ Found in Text Mining only
MENTAL RETARDATION, AUTOSOMAL DOMINANT 51	Mental retardation	CLINVAR_DG	29276005		★★★★★ ★☆☆☆☆ Found in Text Mining only
Moderate intellectual disability	Mental retardation	CLINVAR_DG			★★★★★ ★☆☆☆☆ Found in Text Mining only
Myeloid Leukemia, Chronic	Myeloid Leukemia	BEFREE	29616094		★★★★★ ★☆☆☆☆ Found in Text Mining only
Neurodevelopmental Disorders	Neurodevelopmental Disorders	CTD_human_DG	28191889		★★★★★ ★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Pervasive Development Disorder	Autism spectrum disorder	BEFREE	26235986		★★★★★ ★☆☆☆☆ Found in Text Mining only
Sarcoma	Sarcoma	Pubtator	36376321	Inhibit	★★★★★ ★☆☆☆☆ Found in Text Mining only
Schizophrenia	Schizophrenia	Pubtator	26235986	Associate	★★★★★ ★★★☆☆ Reported in Unknown/Other Associations (≥2 sources)
Squamous Cell Carcinoma of Head and Neck	Squamous cell carcinoma	Pubtator	31795200	Associate	★★★★★ ★☆☆☆☆ Found in Text Mining only

KMT5B (lysine methyltransferase 5B)