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

Gene Gene miRNA Gene ontology Other IDs Protein Pathways Associated diseases
Entrez ID Entrez Gene ID - the GENE ID in NCBI Gene database.	5253
Gene name Gene Name - the full gene name approved by the HGNC.	PHD finger protein 2
Gene symbol Gene Symbol - the official gene symbol approved by the HGNC.	PHF2
Synonyms (NCBI Gene) Gene synonyms aliases	CENP-35, GRC5, JHDM1E, KDM7C
Chromosome Chromosome number	9
Chromosome location Chromosomal Location - indicates the cytogenetic location of the gene or region on the chromosome.	9q22.31
Summary Summary of gene provided in NCBI Entrez Gene.	This gene encodes a protein which contains a zinc finger-like PHD (plant homeodomain) finger, distinct from other classes of zinc finger motifs, and a hydrophobic and highly conserved domain. The PHD finger shows the typical Cys4-His-Cys3 arrangement. PHD

Show/Hide all(193)

miRTarBase ID	miRNA	Experiments
MIRT1230900	hsa-miR-1207-5p	CLIP-seq
MIRT1230901	hsa-miR-1253	CLIP-seq
MIRT1230902	hsa-miR-18a	CLIP-seq
MIRT1230903	hsa-miR-18b	CLIP-seq
MIRT1230904	hsa-miR-1909	CLIP-seq
MIRT1230905	hsa-miR-198	CLIP-seq
MIRT1230906	hsa-miR-2053	CLIP-seq
MIRT1230907	hsa-miR-214	CLIP-seq
MIRT1230908	hsa-miR-2964a-5p	CLIP-seq
MIRT1230909	hsa-miR-302a	CLIP-seq
MIRT1230910	hsa-miR-302b	CLIP-seq
MIRT1230911	hsa-miR-302c	CLIP-seq
MIRT1230912	hsa-miR-302d	CLIP-seq
MIRT1230913	hsa-miR-302e	CLIP-seq
MIRT1230914	hsa-miR-3065-5p	CLIP-seq
MIRT1230915	hsa-miR-31	CLIP-seq
MIRT1230916	hsa-miR-3121-3p	CLIP-seq
MIRT1230917	hsa-miR-3124-5p	CLIP-seq
MIRT1230918	hsa-miR-3148	CLIP-seq
MIRT1230919	hsa-miR-3184	CLIP-seq
MIRT1230920	hsa-miR-3185	CLIP-seq
MIRT1230921	hsa-miR-342-5p	CLIP-seq
MIRT1230922	hsa-miR-345	CLIP-seq
MIRT1230923	hsa-miR-3613-3p	CLIP-seq
MIRT1230924	hsa-miR-361-3p	CLIP-seq
MIRT1230925	hsa-miR-3619-5p	CLIP-seq
MIRT1230926	hsa-miR-3713	CLIP-seq
MIRT1230927	hsa-miR-372	CLIP-seq
MIRT1230928	hsa-miR-373	CLIP-seq
MIRT1230929	hsa-miR-378g	CLIP-seq
MIRT1230930	hsa-miR-3925-3p	CLIP-seq
MIRT1230931	hsa-miR-410	CLIP-seq
MIRT1230932	hsa-miR-421	CLIP-seq
MIRT1230933	hsa-miR-423-5p	CLIP-seq
MIRT1230934	hsa-miR-4251	CLIP-seq
MIRT1230935	hsa-miR-4261	CLIP-seq
MIRT1230936	hsa-miR-4283	CLIP-seq
MIRT1230937	hsa-miR-4307	CLIP-seq
MIRT1230938	hsa-miR-4312	CLIP-seq
MIRT1230939	hsa-miR-4422	CLIP-seq
MIRT1230940	hsa-miR-4435	CLIP-seq
MIRT1230941	hsa-miR-4436b-3p	CLIP-seq
MIRT1230942	hsa-miR-4437	CLIP-seq
MIRT1230943	hsa-miR-4457	CLIP-seq
MIRT1230944	hsa-miR-4496	CLIP-seq
MIRT1230945	hsa-miR-4506	CLIP-seq
MIRT1230946	hsa-miR-4508	CLIP-seq
MIRT1230947	hsa-miR-4511	CLIP-seq
MIRT1230948	hsa-miR-4530	CLIP-seq
MIRT1230949	hsa-miR-4664-5p	CLIP-seq
MIRT1230950	hsa-miR-4674	CLIP-seq
MIRT1230951	hsa-miR-4680-5p	CLIP-seq
MIRT1230952	hsa-miR-4696	CLIP-seq
MIRT1230953	hsa-miR-4698	CLIP-seq
MIRT1230954	hsa-miR-4711-3p	CLIP-seq
MIRT1230955	hsa-miR-4711-5p	CLIP-seq
MIRT1230956	hsa-miR-4735-3p	CLIP-seq
MIRT1230957	hsa-miR-4760-5p	CLIP-seq
MIRT1230958	hsa-miR-4761-5p	CLIP-seq
MIRT1230959	hsa-miR-4763-3p	CLIP-seq
MIRT1230960	hsa-miR-4766-5p	CLIP-seq
MIRT1230961	hsa-miR-4787-5p	CLIP-seq
MIRT1230962	hsa-miR-485-3p	CLIP-seq
MIRT1230963	hsa-miR-487a	CLIP-seq
MIRT1230964	hsa-miR-512-5p	CLIP-seq
MIRT1230965	hsa-miR-513b	CLIP-seq
MIRT1230966	hsa-miR-515-5p	CLIP-seq
MIRT1230967	hsa-miR-520a-3p	CLIP-seq
MIRT1230968	hsa-miR-520a-5p	CLIP-seq
MIRT1230969	hsa-miR-520b	CLIP-seq
MIRT1230970	hsa-miR-520c-3p	CLIP-seq
MIRT1230971	hsa-miR-520d-3p	CLIP-seq
MIRT1230972	hsa-miR-520e	CLIP-seq
MIRT1230973	hsa-miR-520f	CLIP-seq
MIRT1230974	hsa-miR-525-5p	CLIP-seq
MIRT1230975	hsa-miR-545	CLIP-seq
MIRT1230976	hsa-miR-548ae	CLIP-seq
MIRT1230977	hsa-miR-548aj	CLIP-seq
MIRT1230978	hsa-miR-548am	CLIP-seq
MIRT1230979	hsa-miR-548p	CLIP-seq
MIRT1230980	hsa-miR-548x	CLIP-seq
MIRT1230981	hsa-miR-569	CLIP-seq
MIRT1230982	hsa-miR-574-5p	CLIP-seq
MIRT1230983	hsa-miR-615-5p	CLIP-seq
MIRT1230984	hsa-miR-618	CLIP-seq
MIRT1230985	hsa-miR-624	CLIP-seq
MIRT1230986	hsa-miR-628-3p	CLIP-seq
MIRT1230987	hsa-miR-644	CLIP-seq
MIRT1230988	hsa-miR-647	CLIP-seq
MIRT1230989	hsa-miR-663b	CLIP-seq
MIRT1230990	hsa-miR-744	CLIP-seq
MIRT1230991	hsa-miR-759	CLIP-seq
MIRT1230992	hsa-miR-761	CLIP-seq
MIRT1230993	hsa-miR-766	CLIP-seq
MIRT1552298	hsa-miR-1261	CLIP-seq
MIRT1552299	hsa-miR-3681	CLIP-seq
MIRT1552300	hsa-miR-4753-5p	CLIP-seq
MIRT2067794	hsa-miR-106a	CLIP-seq
MIRT2067795	hsa-miR-106b	CLIP-seq
MIRT1230900	hsa-miR-1207-5p	CLIP-seq
MIRT2067796	hsa-miR-1343	CLIP-seq
MIRT2067797	hsa-miR-17	CLIP-seq
MIRT1230902	hsa-miR-18a	CLIP-seq
MIRT1230903	hsa-miR-18b	CLIP-seq
MIRT2067798	hsa-miR-1913	CLIP-seq
MIRT2067799	hsa-miR-20a	CLIP-seq
MIRT2067800	hsa-miR-20b	CLIP-seq
MIRT2067801	hsa-miR-22	CLIP-seq
MIRT2067802	hsa-miR-3120-3p	CLIP-seq
MIRT1230917	hsa-miR-3124-5p	CLIP-seq
MIRT2067803	hsa-miR-3181	CLIP-seq
MIRT2067804	hsa-miR-3192	CLIP-seq
MIRT2067805	hsa-miR-324-3p	CLIP-seq
MIRT2067806	hsa-miR-3609	CLIP-seq
MIRT1230924	hsa-miR-361-3p	CLIP-seq
MIRT1230935	hsa-miR-4261	CLIP-seq
MIRT1230936	hsa-miR-4283	CLIP-seq
MIRT1230937	hsa-miR-4307	CLIP-seq
MIRT2067807	hsa-miR-4313	CLIP-seq
MIRT1230941	hsa-miR-4436b-3p	CLIP-seq
MIRT1230943	hsa-miR-4457	CLIP-seq
MIRT1230946	hsa-miR-4508	CLIP-seq
MIRT2067808	hsa-miR-4719	CLIP-seq
MIRT1230956	hsa-miR-4735-3p	CLIP-seq
MIRT1230958	hsa-miR-4761-5p	CLIP-seq
MIRT1230959	hsa-miR-4763-3p	CLIP-seq
MIRT1230961	hsa-miR-4787-5p	CLIP-seq
MIRT2067809	hsa-miR-4796-3p	CLIP-seq
MIRT1230965	hsa-miR-513b	CLIP-seq
MIRT2067810	hsa-miR-519d	CLIP-seq
MIRT1230976	hsa-miR-548ae	CLIP-seq
MIRT2067811	hsa-miR-548ah	CLIP-seq
MIRT1230977	hsa-miR-548aj	CLIP-seq
MIRT1230978	hsa-miR-548am	CLIP-seq
MIRT1230980	hsa-miR-548x	CLIP-seq
MIRT1230983	hsa-miR-615-5p	CLIP-seq
MIRT1230985	hsa-miR-624	CLIP-seq
MIRT1230986	hsa-miR-628-3p	CLIP-seq
MIRT1230990	hsa-miR-744	CLIP-seq
MIRT2067812	hsa-miR-93	CLIP-seq
MIRT2067794	hsa-miR-106a	CLIP-seq
MIRT2067795	hsa-miR-106b	CLIP-seq
MIRT2295248	hsa-miR-1228	CLIP-seq
MIRT2295249	hsa-miR-1291	CLIP-seq
MIRT2067797	hsa-miR-17	CLIP-seq
MIRT2067799	hsa-miR-20a	CLIP-seq
MIRT2067800	hsa-miR-20b	CLIP-seq
MIRT1230907	hsa-miR-214	CLIP-seq
MIRT2295250	hsa-miR-2861	CLIP-seq
MIRT2295251	hsa-miR-3173-5p	CLIP-seq
MIRT1230922	hsa-miR-345	CLIP-seq
MIRT2067806	hsa-miR-3609	CLIP-seq
MIRT1230923	hsa-miR-3613-3p	CLIP-seq
MIRT1230925	hsa-miR-3619-5p	CLIP-seq
MIRT2295252	hsa-miR-4291	CLIP-seq
MIRT1230937	hsa-miR-4307	CLIP-seq
MIRT1230940	hsa-miR-4435	CLIP-seq
MIRT2295253	hsa-miR-4493	CLIP-seq
MIRT2295254	hsa-miR-4667-3p	CLIP-seq
MIRT2295255	hsa-miR-4667-5p	CLIP-seq
MIRT2295256	hsa-miR-4700-5p	CLIP-seq
MIRT2295257	hsa-miR-4705	CLIP-seq
MIRT2067809	hsa-miR-4796-3p	CLIP-seq
MIRT1230964	hsa-miR-512-5p	CLIP-seq
MIRT2067810	hsa-miR-519d	CLIP-seq
MIRT1230975	hsa-miR-545	CLIP-seq
MIRT1230976	hsa-miR-548ae	CLIP-seq
MIRT2067811	hsa-miR-548ah	CLIP-seq
MIRT1230977	hsa-miR-548aj	CLIP-seq
MIRT1230978	hsa-miR-548am	CLIP-seq
MIRT1230979	hsa-miR-548p	CLIP-seq
MIRT1230980	hsa-miR-548x	CLIP-seq
MIRT2295258	hsa-miR-558	CLIP-seq
MIRT2295259	hsa-miR-574-3p	CLIP-seq
MIRT1230989	hsa-miR-663b	CLIP-seq
MIRT1230992	hsa-miR-761	CLIP-seq
MIRT2295260	hsa-miR-922	CLIP-seq
MIRT2067812	hsa-miR-93	CLIP-seq
MIRT2067794	hsa-miR-106a	CLIP-seq
MIRT2067795	hsa-miR-106b	CLIP-seq
MIRT1552298	hsa-miR-1261	CLIP-seq
MIRT2067797	hsa-miR-17	CLIP-seq
MIRT2067799	hsa-miR-20a	CLIP-seq
MIRT2067800	hsa-miR-20b	CLIP-seq
MIRT2295250	hsa-miR-2861	CLIP-seq
MIRT2067806	hsa-miR-3609	CLIP-seq
MIRT1552299	hsa-miR-3681	CLIP-seq
MIRT2295253	hsa-miR-4493	CLIP-seq
MIRT1552300	hsa-miR-4753-5p	CLIP-seq
MIRT2067809	hsa-miR-4796-3p	CLIP-seq
MIRT2067810	hsa-miR-519d	CLIP-seq
MIRT2067811	hsa-miR-548ah	CLIP-seq
MIRT2067812	hsa-miR-93	CLIP-seq

Show/Hide all(36)

GO ID	Ontology	Definition	Evidence	Reference
GO:0000775	Component	Chromosome, centromeric region	IEA
GO:0000776	Component	Kinetochore	IDA	20813266
GO:0000776	Component	Kinetochore	IEA
GO:0001889	Process	Liver development	TAS	21532585
GO:0003712	Function	Transcription coregulator activity	IBA
GO:0003713	Function	Transcription coactivator activity	IDA	21532585
GO:0005506	Function	Iron ion binding	IDA	21167174
GO:0005506	Function	Iron ion binding	IEA
GO:0005515	Function	Protein binding	IPI	21532585, 30021884, 35271311
GO:0005634	Component	Nucleus	IEA
GO:0005634	Component	Nucleus	TAS	10051327
GO:0005654	Component	Nucleoplasm	IDA
GO:0005654	Component	Nucleoplasm	TAS
GO:0005694	Component	Chromosome	IEA
GO:0005730	Component	Nucleolus	IDA	20129925
GO:0005730	Component	Nucleolus	IEA
GO:0006325	Process	Chromatin organization	IEA
GO:0006338	Process	Chromatin remodeling	IBA
GO:0006357	Process	Regulation of transcription by RNA polymerase II	IBA
GO:0006482	Process	Protein demethylation	IDA	21532585
GO:0008270	Function	Zinc ion binding	IDA	20129925
GO:0008270	Function	Zinc ion binding	IEA
GO:0016491	Function	Oxidoreductase activity	IEA
GO:0032452	Function	Histone demethylase activity	IBA
GO:0032454	Function	Histone H3K9 demethylase activity	IDA	21532585
GO:0032454	Function	Histone H3K9 demethylase activity	IEA
GO:0035575	Function	Histone H4K20 demethylase activity	IEA
GO:0035575	Function	Histone H4K20 demethylase activity	ISS
GO:0045815	Process	Transcription initiation-coupled chromatin remodeling	IEA
GO:0045815	Process	Transcription initiation-coupled chromatin remodeling	ISS
GO:0045893	Process	Positive regulation of DNA-templated transcription	IEA
GO:0046872	Function	Metal ion binding	IEA
GO:0051213	Function	Dioxygenase activity	IEA
GO:0061188	Process	Negative regulation of rDNA heterochromatin formation	IEA
GO:0061188	Process	Negative regulation of rDNA heterochromatin formation	IMP	20129925
GO:0140002	Function	Histone H3K4me3 reader activity	IDA	20129925, 21167174

MIM	HGNC	e!Ensembl
604351	8920	ENSG00000197724

Protein

UniProt ID

O75151

Protein name

Lysine-specific demethylase PHF2 (EC 1.14.11.-) (GRC5) (PHD finger protein 2)

Protein function

Lysine demethylase that demethylates both histones and non-histone proteins (PubMed:20129925, PubMed:21167174, PubMed:21532585). Enzymatically inactive by itself, and becomes active following phosphorylation by PKA: forms a complex with ARID5B a

PDB

3KQI , 3PTR , 3PU3 , 3PU8 , 3PUA , 3PUS , 7M10 , 8F8Y , 8F8Z

Family and domains

Pfam

Accession	ID	Position in sequence	Description	Type
PF00628	PHD	7 → 56	PHD-finger	Domain
PF02373	JmjC	236 → 336	JmjC domain, hydroxylase	Domain
PF17811	JHD	340 → 443	Jumonji helical domain	Domain

Tissue specificity

TISSUE SPECIFICITY: Widely expressed, including in liver (at protein level). {ECO:0000269|PubMed:21532585}.

Sequence

MATVPVYCVCRLPYDVTRFMIECDACKDWFHGSCVGVEEEEAPDIDIYHCPNCEKTHGKS
TLKKKRTWHKHGPGQAPDVKPVQNGSQLFIKELRSRTFPSAEDVVARVPGSQLTLGYMEE
HGFTEPILVPKKDGLGLAVPAPTFYVSDVENYVGPERSVDVTDVTKQKDCKMKLKEFVDY
YYSTNRKRVLNVTNLEFSDTRMSSFVEPPDIVKKLSWVENYWPDDALLAKPKVTKYCLIC
VKDSYTDFHIDSGGASAWYHVLKGEKTFYLIRPASANISLYERWRSASNHSEMFFADQVD
KCYKCIVKQGQTLFIPSGWIYATLTPVDCLAFAGHFLHSLSVEMQMRAYEVERRLKLGSL
TQFPNFETACWYMGKHLLEAFKGSHKSGKQLPPHLVQGAKILNGAFRSWTKKQALAEHED
ELPEHFKPSQLIKDLAKEIRLSENASKAVRPEVNTVASSDEVCDGDREKEEPPSPIEATP
PQSLLEKVSKKKTPKTVKMPKPSKIPKPPKPPKPPRPPKTLKLKDGGKKKGKKSRESASP
TIPNLDLLEAHTKEALTKMEPPKKGKATKSVLSVPNKDVVHMQNDVERLEIREQTKSKSE
AKWKYKNSKPDSLLKMEEEQKLEKSPLAGNKDNKFSFSFSNKKLLGSKALRPPTSPGVFG
ALQNFKEDKPKPVRDEYEYVSDDGELKIDEFPIRRKKNAPKRDLSFLLDKKAVLPTPVTK
PKLDSAAYKSDDSSDEGSLHIDTDTKPGRNARVKKESGSSAAGILDLLQASEEVGALEYN
PSSQPPASPSTQEAIQGMLSMANLQASDSCLQTTWGAGQAKGSSLAAHGARKNGGGSGKS
AGKRLLKRAAKNSVDLDDYEEEQDHLDACFKDSDYVYPSLESDEDNPIFKSRSKKRKGSD
DAPYSPTARVGPSVPRQDRPVREGTRVASIETGLAAAAAKLSQQEEQKSKKKKSAKRKLT
PNTTSPSTSTSISAGTTSTSTTPASTTPASTTPASTSTASSQASQEGSSPEPPPESHSSS
LADHEYTAAGTFTGAQAGRTSQPMAPGVFLTQRRPSASSPNNNTAAKGKRTKKGMATAKQ
RLGKILKIHRNGKLLL

Sequence length

1096

Interactions

View interactions

	Reactome
			HDMs demethylate histones

Show/Hide Unknown Diseases (6)

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.
Diabetes	Childhood onset type 2 diabetes	N/A	N/A	GWAS
Insomnia	Insomnia	N/A	N/A	GWAS
Irritable Bowel Syndrome	Irritable bowel syndrome	N/A	N/A	GWAS
Metabolic Syndrome	Metabolic syndrome	N/A	N/A	GWAS
Neuroticism	Neuroticism	N/A	N/A	GWAS
Schizophrenia	Schizophrenia	N/A	N/A	GWAS

Show/Hide Text Mining Associations (17)

Disease Name	Relationship Type	References
Associations from Text Mining Disease associations identified through Pubtator
Anodontia	Associate	27744626
Anxiety Disorders	Associate	34741163
Breast Neoplasms	Associate	18990233
Carcinogenesis	Associate	27744626
Carcinoma Hepatocellular	Associate	31214616, 37828054
Colorectal Neoplasms	Associate	27744626
Depressive Disorder	Associate	30718454
Irritable Bowel Syndrome	Associate	34741163
Leukemia	Associate	28994305
Leukemia B Cell	Associate	28994305
Leukemia Lymphocytic Chronic B Cell	Associate	32051441
Lung Neoplasms	Associate	36872368
Nasopharyngeal Carcinoma	Associate	37352861
Neoplasm Metastasis	Associate	36872368
Neoplasms	Associate	27744626, 36872368
Neoplasms	Inhibit	35729160, 37352861, 37828054
Osteosarcoma	Associate	35729160

PHF2 (PHD finger protein 2)