Gene Gene information from NCBI Gene database.
Entrez ID 10765
Gene name Lysine demethylase 5B
Gene symbol KDM5B
Synonyms (NCBI Gene)
CT31JARID1BMRT65PLU-1PLU1PPP1R98PUT1RBBP2H1ARBP2-H1
Chromosome 1
Chromosome location 1q32.1
Summary This gene encodes a lysine-specific histone demethylase that belongs to the jumonji/ARID domain-containing family of histone demethylases. The encoded protein is capable of demethylating tri-, di- and monomethylated lysine 4 of histone H3. This protein pl
SNPs SNP information provided by dbSNP.
7
SNP ID Visualize variation Clinical significance Consequence
rs375695605 G>A,C Pathogenic Coding sequence variant, missense variant
rs755833290 AA>-,AAA Likely-pathogenic Frameshift variant, coding sequence variant
rs1558478047 A>C Likely-pathogenic Stop gained, coding sequence variant
rs1558479778 G>- Pathogenic Frameshift variant, coding sequence variant
rs1558498928 G>A Likely-pathogenic Stop gained, coding sequence variant
miRNA miRNA information provided by mirtarbase database.
627
miRTarBase ID miRNA Experiments Reference
MIRT016728 hsa-miR-335-5p Microarray 18185580
MIRT020412 hsa-miR-29c-3p Sequencing 20371350
MIRT046553 hsa-let-7i-5p CLASH 23622248
MIRT038506 hsa-miR-296-3p CLASH 23622248
MIRT656976 hsa-miR-766-3p HITS-CLIP 23824327
Gene ontology (GO) Gene Ontology (GO) annotations describing the biological processes, molecular functions, and cellular components associated with a gene.
49
GO ID Ontology Definition Evidence Reference
GO:0000785 Component Chromatin IBA
GO:0003676 Function Nucleic acid binding EXP 20403335
GO:0003676 Function Nucleic acid binding IMP 20403335
GO:0003677 Function DNA binding IDA 15640446
GO:0003677 Function DNA binding IEA
Other IDs Other IDs provides unique identifiers for this gene in OMIM, HGNC, and Ensembl databases.
MIM HGNC e!Ensembl
605393 18039 ENSG00000117139
Protein Protein information from UniProt database.
UniProt ID Unique identifier for the protein in the UniProt database. Click to view detailed protein information.
Q9UGL1
Protein name Lysine-specific demethylase 5B (EC 1.14.11.67) (Cancer/testis antigen 31) (CT31) (Histone demethylase JARID1B) (Jumonji/ARID domain-containing protein 1B) (PLU-1) (Retinoblastoma-binding protein 2 homolog 1) (RBP2-H1) ([histone H3]-trimethyl-L-lysine(4) d
Protein function Histone demethylase that demethylates 'Lys-4' of histone H3, thereby playing a central role in histone code (PubMed:24952722, PubMed:27214403, PubMed:28262558). Does not demethylate histone H3 'Lys-9' or H3 'Lys-27'. Demethylates trimethylated,
PDB 2MA5 , 2MNY , 2MNZ , 5A1F , 5A3N , 5A3P , 5A3T , 5A3W , 5FPL , 5FPU , 5FUN , 5FUP , 5FV3 , 5FY4 , 5FY5 , 5FY9 , 5FYB , 5FYS , 5FYT , 5FYU , 5FYV , 5FYY , 5FYZ , 5FZ0 , 5FZ1 , 5FZ3 , 5FZ4 , 5FZ6 , 5FZ7 , 5FZ8 , 5FZ9 , 5FZA , 5FZB , 5FZC , 5FZD , 5FZE , 5FZF , 5FZG , 5FZH , 5FZI , 5FZK , 5FZL , 5FZM , 5LW9 , 5LWB , 6EIN , 6EIU , 6EIY , 6EJ0 , 6EJ1 , 6EK6
Family and domains

Pfam

Accession ID Position in sequence Description Type
PF02375 JmjN 33 66 jmjN domain Family
PF01388 ARID 99 183 ARID/BRIGHT DNA binding domain Domain
PF00628 PHD 311 359 PHD-finger Domain
PF02373 JmjC 486 602 JmjC domain, hydroxylase Domain
PF02928 zf-C5HC2 692 744 C5HC2 zinc finger Domain
PF08429 PLU-1 757 1088 PLU-1-like protein Family
PF00628 PHD 1178 1224 PHD-finger Domain
PF00628 PHD 1486 1538 PHD-finger Domain
Tissue specificity TISSUE SPECIFICITY: Ubiquitously expressed, with highest levels in testis. Down-regulated in melanoma and glioblastoma. Up-regulated in breast cancer (at protein level). {ECO:0000269|PubMed:10336460, ECO:0000269|PubMed:10616211, ECO:0000269|PubMed:1087866
Sequence
MEAATTLHPGPRPALPLGGPGPLGEFLPPPECPVFEPSWEEFADPFAFIHKIRPIAEQTG
ICKVRP
PPDWQPPFACDVDKLHFTPRIQRLNELEAQTRVKLNFLDQIAKYWELQGSTLKI
PHVERKILDLFQLNKLVAEEGGFAVVCKDRKWTKIATKMGFAPGKAVGSHIRGHYERILN
PYN
LFLSGDSLRCLQKPNLTTDTKDKEYKPHDIPQRQSVQPSETCPPARRAKRMRAEAMN
IKIEPEETTEARTHNLRRRMGCPTPKCENEKEMKSSIKQEPIERKDYIVENEKEKPKSRS
KKATNAVDLYVCLLCGSGNDEDRLLLCDGCDDSYHTFCLIPPLHDVPKGDWRCPKCLAQE
CSKPQEAFGFEQAARDYTLRTFGEMADAFKSDYFNMPVHMVPTELVEKEFWRLVSTIEED
VTVEYGADIASKEFGSGFPVRDGKIKLSPEEEEYLDSGWNLNNMPVMEQSVLAHITADIC
GMKLPWLYVGMCFSSFCWHIEDHWSYSINYLHWGEPKTWYGVPGYAAEQLENVMKKLAPE
LFVSQPDLLHQLVTIMNPNTLMTHEVPVYRTNQCAGEFVITFPRAYHSGFNQGFNFAEAV
NF
CTVDWLPLGRQCVEHYRLLHRYCVFSHDEMICKMASKADVLDVVVASTVQKDMAIMIE
DEKALRETVRKLGVIDSERMDFELLPDDERQCVKCKTTCFMSAISCSCKPGLLVCLHHVK
ELCSCPPYKYKLRYRYTLDDLYPM
MNALKLRAESYNEWALNVNEALEAKINKKKSLVSFK
ALIEESEMKKFPDNDLLRHLRLVTQDAEKCASVAQQLLNGKRQTRYRSGGGKSQNQLTVN
ELRQFVTQLYALPCVLSQTPLLKDLLNRVEDFQQHSQKLLSEETPSAAELQDLLDVSFEF
DVELPQLAEMRIRLEQARWLEEVQQACLDPSSLTLDDMRRLIDLGVGLAPYSAVEKAMAR
LQELLTVSEHWDDKAKSLLKARPRHSLNSLATAVKEIEEIPAYLPNGAALKDSVQRARDW
LQDVEGLQAGGRVPVLDTLIELVTRGRSIPVHLNSLPRLETLVAEVQAWKECAVNTFLTE
NSPYSLLE
VLCPRCDIGLLGLKRKQRKLKEPLPNGKKKSTKLESLSDLERALTESKETAS
AMATLGEARLREMEALQSLRLANEGKLLSPLQDVDIKICLCQKAPAAPMIQCELCRDAFH
TSCVAVPSISQGLRIWLCPHCRRS
EKPPLEKILPLLASLQRIRVRLPEGDALRYMIERTV
NWQHRAQQLLSSGNLKFVQDRVGSGLLYSRWQASAGQVSDTNKVSQPPGTTSFSLPDDWD
NRTSYLHSPFSTGRSCIPLHGVSPEVNELLMEAQLLQVSLPEIQELYQTLLAKPSPAQQT
DRSSPVRPSSEKNDCCRGKRDGINSLERKLKRRLEREGLSSERWERVKKMRTPKKKKIKL
SHPKDMNNFKLERERSYELVRSAETHSLPSDTSYSEQEDSEDEDAICPAVSCLQPEGDEV
DWVQCDGSCNQWFHQVCVGVSPEMAEKEDYICVRCTVK
DAPSRK
Sequence length 1544
Interactions View interactions
Pathways Pathway information has different metabolic/signaling pathways associated with genes.
  Reactome
    HDMs demethylate histones
TFAP2 (AP-2) family regulates transcription of cell cycle factors
Associated diseases Disease associations from ClinVar (causal & non-causal) and other databases (OMIM, Orphanet, GWAS, etc.).
40
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)
Causal Diseases associated with Pathogenic or Likely Pathogenic variants in ClinVar
Phenotype Name Clinical Significance dbSNP ID RCV Accession Evidence Score
Intellectual disability, autosomal recessive 65 Likely pathogenic; Pathogenic rs1287727763, rs2102232815, rs527951173, rs367833330, rs750775126, rs2527627635, rs2527627970, rs2527426205, rs2527411037, rs2527486492, rs2527565001, rs746837045, rs2527456144, rs1388990301, rs2527421668
View all (9 more)
RCV001542642
RCV001553744
RCV004698867
RCV005931967
RCV004067578
View all (19 more)
★★★★★
ClinVar: Pathogenic / Likely Pathogenic (≥5 Variants)
KDM5B-related disorder Likely pathogenic rs1287727763, rs1388990301, rs2527565074, rs2527411857, rs148131534 RCV004728767
RCV004550641
RCV004550605
RCV004552445
RCV004554159
★★★★★
ClinVar: Pathogenic / Likely Pathogenic (≥5 Variants)
Neurodevelopmental disorder Likely pathogenic; Pathogenic rs866525850 RCV006249811
★★★★☆
ClinVar: Pathogenic / Likely Pathogenic (<5 Variants)
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.
Phenotype Name Clinical Significance Source Evidence Score
Acute myeloid leukemia Benign; Likely benign ClinVar
★★☆☆☆
Found in Text Mining + Unknown/Other Associations
Adrenocortical carcinoma, hereditary Conflicting classifications of pathogenicity; Benign; Likely benign ClinVar
★★☆☆☆
Found in Text Mining + Unknown/Other Associations
ALZHEIMER DISEASE GWAS catalog
★★☆☆☆
Found in Text Mining + Unknown/Other Associations
Autism spectrum disorder Likely benign; Conflicting classifications of pathogenicity ClinVar
★★☆☆☆
Found in Text Mining + Unknown/Other Associations
Associations from Text Mining Disease associations identified through text mining
Disease Name Disease (Merged) Source PMID Relationship Type Evidence Score
Absence of septum pellucidum Absence Of Septum Pellucidum HPO_DG
★☆☆☆☆
Found in Text Mining only
Acute leukemia Leukemia BEFREE 25755704
★☆☆☆☆
Found in Text Mining only
Acute lymphocytic leukemia Lymphocytic Leukemia BEFREE 29565495
★☆☆☆☆
Found in Text Mining only
Acute monocytic leukemia Monocytic Leukemia BEFREE 29602065
★☆☆☆☆
Found in Text Mining only
Acute Undifferentiated Leukemia Leukemia BEFREE 26190263
★☆☆☆☆
Found in Text Mining only
Agenesis of Corpus Callosum Corpus callosum agenesis Pubtator 34573379 Associate
★☆☆☆☆
Found in Text Mining only
Astigmatism Astigmatism HPO_DG
★☆☆☆☆
Found in Text Mining only
Atrial Septal Defects Atrial Septal Defect HPO_DG
★☆☆☆☆
Found in Text Mining only
Autism Spectrum Disorder Autism Pubtator 28344757, 28720891, 34573379 Associate
★★☆☆☆
Found in Text Mining + Unknown/Other Associations
Autism Spectrum Disorders Autism Spectrum Disorder BEFREE 30217758, 30902578
★★☆☆☆
Found in Text Mining + Unknown/Other Associations