Gene Gene information from NCBI Gene database.
Entrez ID 5927
Gene name Lysine demethylase 5A
Gene symbol KDM5A
Synonyms (NCBI Gene)
NEDEHCRBBP-2RBBP2RBP2
Chromosome 12
Chromosome location 12p13.33
Summary This gene encodes a member of the Jumonji, AT-rich interactive domain 1 (JARID1) histone demethylase protein family. The encoded protein plays a role in gene regulation through the histone code by specifically demethylating lysine 4 of histone H3. The enc
miRNA miRNA information provided by mirtarbase database.
778
miRTarBase ID miRNA Experiments Reference
MIRT017637 hsa-miR-335-5p Microarray 18185580
MIRT623483 hsa-miR-548ae-3p HITS-CLIP 23824327
MIRT623482 hsa-miR-548ah-3p HITS-CLIP 23824327
MIRT623481 hsa-miR-548aj-3p HITS-CLIP 23824327
MIRT623480 hsa-miR-548am-3p HITS-CLIP 23824327
Gene ontology (GO) Gene Ontology (GO) annotations describing the biological processes, molecular functions, and cellular components associated with a gene.
41
GO ID Ontology Definition Evidence Reference
GO:0000122 Process Negative regulation of transcription by RNA polymerase II IEA
GO:0000785 Component Chromatin IBA
GO:0000976 Function Transcription cis-regulatory region binding IMP 18270511
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
180202 9886 ENSG00000073614
Protein Protein information from UniProt database.
UniProt ID Unique identifier for the protein in the UniProt database. Click to view detailed protein information.
P29375
Protein name Lysine-specific demethylase 5A (EC 1.14.11.67) (Histone demethylase JARID1A) (Jumonji/ARID domain-containing protein 1A) (Retinoblastoma-binding protein 2) (RBBP-2) ([histone H3]-trimethyl-L-lysine(4) demethylase 5A)
Protein function Histone demethylase that specifically demethylates 'Lys-4' of histone H3, thereby playing a central role in histone code. Does not demethylate histone H3 'Lys-9', H3 'Lys-27', H3 'Lys-36', H3 'Lys-79' or H4 'Lys-20'. Demethylates trimethylated a
PDB 2JXJ , 2KGG , 2KGI , 3GL6 , 5C11 , 5CEH , 5E6H , 5ISL , 5IVB , 5IVC , 5IVE , 5IVF , 5IVJ , 5IVV , 5IVY , 5IW0 , 5IWF , 5K4L , 5V9P , 5V9T , 6BGU , 6BGV , 6BGW , 6BGX , 6BGY , 6BGZ , 6BH0 , 6BH1 , 6BH2 , 6BH3 , 6BH4 , 6BH5 , 6DQ4 , 6DQ5 , 6DQ6 , 6DQ7 , 6DQ8 , 6DQ9 , 6DQA , 6DQB , 6DQC , 6DQD , 6DQE , 6DQF , 7KLO , 7KLR
Family and domains

Pfam

Accession ID Position in sequence Description Type
PF02375 JmjN 20 53 jmjN domain Family
PF01388 ARID 86 170 ARID/BRIGHT DNA binding domain Domain
PF00628 PHD 295 343 PHD-finger Domain
PF02373 JmjC 470 586 JmjC domain, hydroxylase Domain
PF02928 zf-C5HC2 676 728 C5HC2 zinc finger Domain
PF08429 PLU-1 741 1072 PLU-1-like protein Family
PF00628 PHD 1163 1218 PHD-finger Domain
Sequence
MAGVGPGGYAAEFVPPPECPVFEPSWEEFTDPLSFIGRIRPLAEKTGICKIRPPKDWQPP
FACEVKSFRFTPRVQRLNELEAMTRVRLDFLDQLAKFWELQGSTLKIPVVERKILDLYAL
SKIVASKGGFEMVTKEKKWSKVGSRLGYLPGKGTGSLLKSHYERILYPYE
LFQSGVSLMG
VQMPNLDLKEKVEPEVLSTDTQTSPEPGTRMNILPKRTRRVKTQSESGDVSRNTELKKLQ
IFGAGPKVVGLAMGTKDKEDEVTRRRKVTNRSDAFNMQMRQRKGTLSVNFVDLYVCMFCG
RGNNEDKLLLCDGCDDSYHTFCLIPPLPDVPKGDWRCPKCVAE
ECSKPREAFGFEQAVRE
YTLQSFGEMADNFKSDYFNMPVHMVPTELVEKEFWRLVSSIEEDVIVEYGADISSKDFGS
GFPVKDGRRKILPEEEEYALSGWNLNNMPVLEQSVLAHINVDISGMKVPWLYVGMCFSSF
CWHIEDHWSYSINYLHWGEPKTWYGVPSHAAEQLEEVMRELAPELFESQPDLLHQLVTIM
NPNVLMEHGVPVYRTNQCAGEFVVTFPRAYHSGFNQGYNFAEAVNF
CTADWLPIGRQCVN
HYRRLRRHCVFSHEELIFKMAADPECLDVGLAAMVCKELTLMTEEETRLRESVVQMGVLM
SEEEVFELVPDDERQCSACRTTCFLSALTCSCNPERLVCLYHPTDLCPCPMQKKCLRYRY
PLEDLPSL
LYGVKVRAQSYDTWVSRVTEALSANFNHKKDLIELRVMLEDAEDRKYPENDL
FRKLRDAVKEAETCASVAQLLLSKKQKHRQSPDSGRTRTKLTVEELKAFVQQLFSLPCVI
SQARQVKNLLDDVEEFHERAQEAMMDETPDSSKLQMLIDMGSSLYVELPELPRLKQELQQ
ARWLDEVRLTLSDPQQVTLDVMKKLIDSGVGLAPHHAVEKAMAELQELLTVSERWEEKAK
VCLQARPRHSVASLESIVNEAKNIPAFLPNVLSLKEALQKAREWTAKVEAIQSGSNYAYL
EQLESLSAKGRPIPVRLEALPQVESQVAAARAWRERTGRTFLKKNSSHTLLQ
VLSPRTDI
GVYGSGKNRRKKVKELIEKEKEKDLDLEPLSDLEEGLEETRDTAMVVAVFKEREQKEIEA
MHSLRAANLAKMTMVDRIEEVKFCICRKTASGFMLQCELCKDWFHNSCVPLPKSSSQKKG
SSWQAKEVKFLCPLCMRS
RRPRLETILSLLVSLQKLPVRLPEGEALQCLTERAMSWQDRA
RQALATDELSSALAKLSVLSQRMVEQAAREKTEKIISAELQKAAANPDLQGHLPSFQQSA
FNRVVSSVSSSPRQTMDYDDEETDSDEDIRETYGYDMKDTASVKSSSSLEPNLFCDEEIP
IKSEEVVTHMWTAPSFCAEHAYSSASKSCSQGSSTPRKQPRKSPLVPRSLEPPVLELSPG
AKAQLEELMMVGDLLEVSLDETQHIWRILQATHPPSEDRFLHIMEDDSMEEKPLKVKGKD
SSEKKRKRKLEKVEQLFGEGKQKSKELKKMDKPRKKKLKLGADKSKELNKLAKKLAKEEE
RKKKKEKAAAAKVELVKESTEKKREKKVLDIPSKYDWSGAEESDDENAVCAAQNCQRPCK
DKVDWVQCDGGCDEWFHQVCVGVSPEMAENEDYICINCAKKQGPVSPGPAPPPSFIMSYK
LPMEDLKETS
Sequence length 1690
Interactions View interactions
Pathways Pathway information has different metabolic/signaling pathways associated with genes.
  Reactome
    HDMs demethylate histones
Associated diseases Disease associations from ClinVar (causal & non-causal) and other databases (OMIM, Orphanet, GWAS, etc.).
23
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
El Hayek-Chahrour neurodevelopmental disorder Pathogenic rs2498247383, rs2498285184 RCV004544250
RCV004544251
★★★★☆
ClinVar: Pathogenic / Likely Pathogenic (<5 Variants)
Intellectual disability Likely pathogenic rs1356405952, rs1943362366 RCV003225001
RCV003225002
★★★★☆
ClinVar: Pathogenic / Likely Pathogenic (<5 Variants)
Seizure Likely pathogenic rs1356405952, rs1943362366 RCV003225001
RCV003225002
★★★★☆
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 Likely benign ClinVar
★★☆☆☆
Found in Text Mining + Unknown/Other Associations
ANKYLOSING SPONDYLITIS Disgenet
★★☆☆☆
Found in Text Mining + Unknown/Other Associations
Colon adenocarcinoma Likely benign ClinVar
★★☆☆☆
Found in Text Mining + Unknown/Other Associations
CONGENITAL HEART DISEASE ClinGen, Disgenet
ClinGen, Disgenet
★★☆☆☆
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
Acute leukemia Leukemia BEFREE 16419055
★☆☆☆☆
Found in Text Mining only
Acute lymphocytic leukemia Lymphocytic Leukemia BEFREE 27008505
★☆☆☆☆
Found in Text Mining only
Acute Megakaryocytic Leukemias Megakaryocytic Leukemia BEFREE 23531517, 31698461
★☆☆☆☆
Found in Text Mining only
Acute monocytic leukemia Monocytic Leukemia BEFREE 29602065
★☆☆☆☆
Found in Text Mining only
Adult Acute Lymphocytic Leukemia Lymphocytic Leukemia BEFREE 27008505
★☆☆☆☆
Found in Text Mining only
Ankylosing spondylitis Ankylosing Spondylitis BEFREE 21562575, 24069348
★★☆☆☆
Found in Text Mining + Unknown/Other Associations
Arrhythmogenic Right Ventricular Dysplasia Arrhythmogenic right ventricular cardiomyopathy BEFREE 28665611
★☆☆☆☆
Found in Text Mining only
Autism Spectrum Disorder Autism Pubtator 37992166 Associate
★☆☆☆☆
Found in Text Mining only
Autism Spectrum Disorders Autism Spectrum Disorder BEFREE 30902578
★☆☆☆☆
Found in Text Mining only
Breast Carcinoma Breast Carcinoma BEFREE 23266085, 29028222, 30149757, 30650517
★☆☆☆☆
Found in Text Mining only