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

Gene Gene SNPs miRNA Gene ontology Other IDs Protein Pathways Associated diseases
Entrez ID Entrez Gene ID - the GENE ID in NCBI Gene database.	51111
Gene name Gene Name - the full gene name approved by the HGNC.	Lysine methyltransferase 5B
Gene symbol Gene Symbol - the official gene symbol approved by the HGNC.	KMT5B
Synonyms (NCBI Gene) Gene synonyms aliases	CGI-85, CGI85, MRD51, SUV420H1
Chromosome Chromosome number	11
Chromosome location Chromosomal Location - indicates the cytogenetic location of the gene or region on the chromosome.	11q13.2
Summary Summary of gene provided in NCBI Entrez Gene.	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

Protein

UniProt ID

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

Show/Hide Causal Diseases (2)

Disease merge term	Disease name	dbSNP ID	References
Causal Diseases caused by PATHOGENIC or LIKELY PATHOGENIC variants from ClinVar only
Mental retardation	Intellectual disability, autosomal dominant 51	rs1555028154, rs1555023232, rs1555034768, rs1565240833, rs114727354, rs1590954686, rs1590956245	N/A
neural tube defect	Neural tube defect	rs114727354	N/A

Show/Hide Unknown Diseases (4)

Disease merge term	Disease name	Evidence	References	Source
Unknown Includes: (1) ClinVar NON-pathogenic variants (Uncertain, Benign, Conflicting, VUS), (2) GenCC associations, (3) GWAS associations, (4) CBGDA evidence-based associations. NOTE: Diseases with pathogenic evidence are excluded to avoid conflicts.
Alzheimer disease	Alzheimer's disease or family history of Alzheimer's disease	N/A	N/A	GWAS
autism spectrum disorder	Autism spectrum disorder	N/A	N/A	ClinVar
Breast Cancer	Breast cancer in childhood cancer survivors	N/A	N/A	GWAS
Neurodevelopmental Disorders	complex neurodevelopmental disorder	N/A	N/A	GenCC

Show/Hide Text Mining Associations (19)

Disease Name	Relationship Type	References
Associations from Text Mining Disease 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)