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

105

Show/Hide Causal Diseases (8)

Phenotype Name	Clinical Significance	dbSNP ID	RCV Accession
Causal Diseases associated with Pathogenic or Likely Pathogenic variants in ClinVar
Autistic behavior	Pathogenic	rs2153068015	RCV001526519
Intellectual disability	Pathogenic	rs2153054646, rs2153039995	RCV001375671 RCV001544500
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 RCV002226895 RCV002287764 RCV002463469 RCV002472198 RCV002505926 RCV002571629 RCV003223528 RCV003320012 RCV003484529 RCV003492908 RCV004547407 RCV000515806 RCV000515785 RCV000677412 RCV000678692 RCV000678693 RCV000825000 RCV000988587 RCV001253630 RCV001265542
KMT5B-related disorder	Likely pathogenic	rs2496321996	RCV004548982
Neural tube defect	Likely pathogenic; Pathogenic	rs114727354	RCV001526514
Neurodevelopmental delay	Likely pathogenic	rs1565214242	RCV002274354
Rare genetic intellectual disability	Likely pathogenic	rs2496189023	RCV001257000
See cases	Likely pathogenic	rs2153040709, rs2153041094	RCV001420321 RCV001420275

Show/Hide Unknown Diseases (11)

Phenotype Name	Clinical Significance	dbSNP ID	RCV Accession
Unknown Diseases with uncertain, conflicting, or no pathogenic evidence in ClinVar
Acute myeloid leukemia	Likely benign	rs138913197	RCV005933007
Autism spectrum disorder	Uncertain significance	rs1555028104	RCV001291377
Cervical cancer	Likely benign	rs138913197	RCV005933008
Colon adenocarcinoma	Likely benign	rs138913197	RCV005933006
Familial cancer of breast	Likely benign	rs138913197	RCV005933005
Global developmental delay	Uncertain significance	rs2496380382	RCV002463859
KMT5B-related neurodevelopmental disorder	Uncertain significance	rs201298002	RCV001249697
Language retardation	Uncertain significance	rs1057518998	RCV000415298
Lung cancer	Likely benign	rs138913197	RCV005933010
Schizophrenia	Uncertain significance	rs2495703428	RCV002463506
Thymoma	Likely benign	rs138913197	RCV005933009

Show/Hide Text Mining Associations (19)

Disease Name	Relationship Type	References
Associations from Text MiningDisease associations identified through Pubtator
Attention Deficit Disorder with Hyperactivity	Associate	37927187
Autism Spectrum Disorder	Associate	26235986, 35110736, 37366052
Autistic Disorder	Associate	35110736, 37927187
Brain Diseases	Associate	26235986
Breast Neoplasms	Associate	24953066
Developmental Disabilities	Associate	29276005, 31238879, 37927187
Fetal Alcohol Spectrum Disorders	Stimulate	35110736
Friedreich Ataxia	Associate	33028632
Growth Disorders	Associate	35110736
Hand Injuries	Associate	37927187
Hypertension	Associate	32410228
Intellectual Disability	Associate	26235986, 29276005, 37927187
Mental Disorders	Associate	26235986
Neoplasms	Associate	26586479
Neoplasms	Inhibit	36376321
Sarcoma	Inhibit	36376321
Schizophrenia	Associate	26235986
Simpson Golabi Behmel syndrome	Associate	29276005
Squamous Cell Carcinoma of Head and Neck	Associate	31795200

KMT5B (lysine methyltransferase 5B)