EuRBPDB

Basic Information
Cancer Related Information

Description

RBPome

PRI

Literatures

Expression

Transcripts

Gene Model

PPI

Gene Ontology

Description

Ensembl ID: ENSG00000156531 (Gene tree)
Gene ID: 84295
Gene Symbol: PHF6
Alias: KIAA1823|MGC14797|CENP-31|BFLS|BORJ
Full Name: PHD finger protein 6
Gene Type: protein_coding
Species: Homo_sapiens
Status: confidence
Strand: Plus strand
Length: 55,540 bases
Position: chrX:134,373,253-134,428,792
Accession: 18145
RBP type: non-canonical RBP
Summary: This gene is a member of the plant homeodomain (PHD)-like finger (PHF) family. It encodes a protein with two PHD-type zinc finger domains, indicating a potential role in transcriptional regulation, that localizes to the nucleolus. Mutations affecting the coding region of this gene or the splicing of the transcript have been associated with Borjeson-Forssman-Lehmann syndrome (BFLS), a disorder characterized by cognitive disability, epilepsy, hypogonadism, hypometabolism, obesity, swelling of subcutaneous tissue of the face, narrow palpebral fissures, and large ears. Alternate splicing results in multiple transcript variants, encoding different isoforms. [provided by RefSeq, Jun 2010]

RNA binding proteome (RBPome)

PID	Title	Method	Time	Author	Doi
30607034	Comprehensive identification of RNA protein interactions in any organism using orthogonal organic phase separation (OOPS)	OOPS & HEK293	2019 Jan 3	Queiroz RML	DOI: 10.1038/s41587-018-0001-2
30528433	The Human RNA-Binding Proteome and Its Dynamics during Translational Arrest	XRNAX & HEK293	2018 Dec 6	Trendel J	DOI: 10.1016/j.cell.2018.11.004
22658674	Insights into RNA biology from an atlas of mammalian mRNA-binding proteins	RIC & Hela	2012 May 31	Castello A	DOI: 10.1016/j.cell.2012.04.031
30528433	The Human RNA-Binding Proteome and Its Dynamics during Translational Arrest	XRNAX & Hela	2018 Dec 6	Trendel J	DOI: 10.1016/j.cell.2018.11.004
30352994	Discovery of RNA-binding proteins and characterization of their dynamic responses by enhanced RNA interactome capture	RIC & Jurkat	2018 Oct 23	Perez-Perri JI	DOI:10.1038/s41467-018-06557-8

Protein-RNA interaction（RNA-Binding Site）

Click here to download all RNA binding sites

Literatures on RNA binding capacity

PID	Title	Article	Time	Author	Doi
23229552	PHF6 regulates cell cycle progression by suppressing ribosomal RNA synthesis.	J Biol Chem	2013 Feb 1	Wang J	doi: 10.1074/jbc.M112.414839

Expression

Transcripts

Transcript ID	Name	Length	RefSeq ID	Protein ID	Length	RefSeq ID	UniportKB ID
ENST00000332070	PHF6-201	4759	-	ENSP00000329097	365 (aa)	-	Q8IWS0
ENST00000370799	PHF6-202	4186	-	ENSP00000359835	324 (aa)	-	Q5JRC6
ENST00000625464	PHF6-205	4434	-	ENSP00000487420	366 (aa)	-	A0A0D9SGE8
ENST00000370803	PHF6-204	4489	-	ENSP00000359839	365 (aa)	-	Q8IWS0
ENST00000370800	PHF6-203	1150	-	ENSP00000359836	312 (aa)	-	Q8IWS0

Gene Model

Click here to download ENSG00000156531's gene model file

Protein-Protein Interaction (PPI)

Clik here to download ENSG00000156531's network

* RBP PPI network refers to all genes directly bind to RBP

Gene Ontology

Go ID	Go_term	PubmedID	Evidence	Category
GO:0000122	negative regulation of transcription by RNA polymerase II	24554700.	IDA	Process
GO:0000777	condensed chromosome kinetochore	-	IEA	Component
GO:0001227	DNA-binding transcription repressor activity, RNA polymerase II-specific	24554700.	IDA	Function
GO:0001835	blastocyst hatching	-	IEA	Process
GO:0003723	RNA binding	22658674.	HDA	Function
GO:0005515	protein binding	22720776.	IPI	Function
GO:0005634	nucleus	-	IDA	Component
GO:0005654	nucleoplasm	22720776.	IDA	Component
GO:0005730	nucleolus	22720776.	IDA	Component
GO:0015631	tubulin binding	22720776.	IPI	Function
GO:0019899	enzyme binding	22720776.	IPI	Function
GO:0042393	histone binding	22720776.	IPI	Function
GO:0042826	histone deacetylase binding	22720776.	IPI	Function
GO:0043021	ribonucleoprotein complex binding	22720776.	IPI	Function
GO:0043565	sequence-specific DNA binding	24554700.	IDA	Function
GO:0046872	metal ion binding	-	IEA	Function
GO:0051219	phosphoprotein binding	22720776.	IPI	Function
GO:0097110	scaffold protein binding	22720776.	IPI	Function

Cancer associated literatures

PID	Title	Article	Time	Author	Doi
26561469	The potential role of PHF6 as an oncogene: a genotranscriptomic/proteomic meta-analysis.	Tumour Biol	2016 Apr	Hajjari M	doi: 10.1007/s13277-015-4250-0
21030981	PHF6 mutations in adult acute myeloid leukemia.	Leukemia	2011 Jan	Van Vlierberghe P	doi: 10.1038/leu.2010.247
24674452	Detection of an activated JAK3 variant and a Xq26.3 microdeletion causing loss of PHF6 and miR-424 expression in myelodysplastic syndromes by combined targeted next generation sequencing and SNP array analysis.	Pathol Res Pract	2014 Jun	Kunze K	doi: 10.1016/j.prp.2014.02.006
23229552	PHF6 regulates cell cycle progression by suppressing ribosomal RNA synthesis.	J Biol Chem	2013 Feb 1	Wang J	doi: 10.1074/jbc.M112.414839
20228800	PHF6 mutations in T-cell acute lymphoblastic leukemia.	Nat Genet	2010 Apr	Van Vlierberghe P	doi: 10.1038/ng.542
24895337	MicroRNA-128-3p is a novel oncomiR targeting PHF6 in T-cell acute lymphoblastic leukemia.	Haematologica	2014 Aug	Mets E	doi: 10.3324/haematol.2013.099515
20806366	T-cell acute lymphoblastic leukemia in association with Brjeson-Forssman-Lehmann syndrome due to a mutation in PHF6.	Pediatr Blood Cancer	2010 Oct	Chao MM	doi: 10.1002/pbc.22574.
25737277	A genome-scale in vivo loss-of-function screen identifies Phf6 as a lineage-specific regulator of leukemia cell growth.	Genes Dev	2015 Mar 1	Meacham CE	doi: 10.1101/gad.254151.114.

Expression in 33 cancers

Mutations

Cancer	Chr	Position	Mutation Type	dbSNP	Protein-change	Allele Freq
BLCA	chrX	134378068	Nonsense_Mutation	NA	E68*	0.3
BLCA	chrX	134425232	Missense_Mutation	novel	E334Q	0.24
BLCA	chrX	134425345	3'UTR	rs750464938		0.96
BLCA	chrX	134377739	Missense_Mutation	novel	A41G	0.4
BLCA	chrX	134393508	Missense_Mutation	novel	S83F	0.4
BLCA	chrX	134415076	Missense_Mutation	NA	D264H	0.38
BLCA	chrX	134425236	Missense_Mutation	novel	R335K	0.4
BLCA	chrX	134377756	Splice_Site	NA	X46_splice	0.49
BRCA	chrX	134413493	Missense_Mutation	NA	D141N	0.45
BRCA	chrX	134425214	Missense_Mutation	NA	N328Y	0.16
BRCA	chrX	134417387	Intron	rs779414328		0.22
BRCA	chrX	134425452	3'UTR	novel		0.08
CESC	chrX	134377598	5'UTR	novel		0.2
CESC	chrX	134417418	Intron	NA		0.42
CESC	chrX	134415106	Nonsense_Mutation	NA	R274*	0.1
CESC	chrX	134427358	3'UTR	novel		0.32
CESC	chrX	134426257	3'UTR	novel		0.12
CESC	chrX	134417290	Missense_Mutation	NA	R319Q	0.46
CESC	chrX	134428718	3'UTR	novel		0.09
CESC	chrX	134427466	3'UTR	novel		0.15
CESC	chrX	134428514	3'UTR	novel		0.36
CHOL	chrX	134426042	3'UTR	novel		0.26
COAD	chrX	134377736	Missense_Mutation	novel	A40V	0.46
COAD	chrX	134425416	3'UTR	novel		0.33
COAD	chrX	134413609	Silent	NA	T179T	0.33
COAD	chrX	134425416	3'UTR	novel		0.4
COAD	chrX	134425390	3'UTR	novel		0.26
COAD	chrX	134377661	Missense_Mutation	novel	R15H	0.38
COAD	chrX	134415225	Intron	rs201454923		0.07
ESCA	chrX	134427832	3'UTR	novel		0.43
ESCA	chrX	134427728	3'UTR	novel		0.13
ESCA	chrX	134426073	3'UTR	novel		0.15
ESCA	chrX	134426194	3'UTR	novel		0.38
GBM	chrX	134417300	Nonsense_Mutation	novel	Y322*	0.27
HNSC	chrX	134415070	Missense_Mutation	novel	D262N	0.41
HNSC	chrX	134393563	Silent	novel	R101R	0.92
KIRC	chrX	134417209	Missense_Mutation	NA	C292S	0.09
KIRC	chrX	134377583	5'UTR	novel		0.08
KIRC	chrX	134377616	5'UTR	novel		0.53
LAML	chrX	134425208	Missense_Mutation	novel	C326R	0.08
LAML	chrX	134413822	Splice_Site	NA	X196_splice	0.53
LAML	chrX	134393949	Nonsense_Mutation	NA	E139*	0.72
LAML	chrX	134377682	Frame_Shift_Ins	NA	*N23Kfs2**	0.83
LGG	chrX	134393944	Missense_Mutation	NA	N137S	0.06
LGG	chrX	134415225	Intron	rs201454923		0.38
LGG	chrX	134377620	Translation_Start_Site	NA	M1?	0.29
LIHC	chrX	134393929	Missense_Mutation	rs756384013	K132R	0.5
LUAD	chrX	134425204	Silent	NA	L324L	0.94
LUAD	chrX	134413935	Missense_Mutation	novel	A233G	0.44
LUAD	chrX	134415236	Intron	novel		0.86
LUAD	chrX	134413637	Nonsense_Mutation	novel	E189*	0.32
LUAD	chrX	134417290	Missense_Mutation	NA	R319L	0.21
LUAD	chrX	134393927	Missense_Mutation	NA	H131Q	0.19
LUSC	chrX	134417281	Missense_Mutation	novel	N316I	0.13
LUSC	chrX	134393562	Missense_Mutation	novel	R101K	0.21
LUSC	chrX	134415028	Missense_Mutation	NA	G248C	0.11
LUSC	chrX	134393581	Silent	novel	C107C	0.1
LUSC	chrX	134415070	Missense_Mutation	novel	D262H	0.11
OV	chrX	134425346	3'UTR	novel		0.03
OV	chrX	134415015	Splice_Site	NA	X244_splice	0.28
PAAD	chrX	134415226	Intron	rs369581215		0.07
READ	chrX	134425416	3'UTR	novel		0.19
SARC	chrX	134393590	Missense_Mutation	novel	H110Q	0.45
SARC	chrX	134427634	3'UTR	novel		0.1
SKCM	chrX	134413563	Missense_Mutation	NA	K164R	0.83
SKCM	chrX	134417394	Intron	novel		0.44
SKCM	chrX	134417222	Silent	NA	A296A	0.76
SKCM	chrX	134417237	Silent	NA	Y301Y	1
STAD	chrX	134425416	3'UTR	novel		0.38
STAD	chrX	134415123	Splice_Region	novel		0.13
STAD	chrX	134417289	Nonsense_Mutation	NA	R319*	0.1
STAD	chrX	134413584	Missense_Mutation	NA	N171I	0.48
THCA	chrX	134393537	Missense_Mutation	NA	G93C	0.08
THCA	chrX	134417318	Intron	novel		0.06
THYM	chrX	134426073	3'UTR	novel		0.33
UCEC	chrX	134413824	Missense_Mutation	NA	R196K	0.35
UCEC	chrX	134415211	Intron	novel		0.05
UCEC	chrX	134417231	Missense_Mutation	NA	K299N	0.13
UCEC	chrX	134413528	Missense_Mutation	novel	E152D	0.31
UCEC	chrX	134417227	Missense_Mutation	novel	V298A	0.21
UCEC	chrX	134428620	3'UTR	novel		0.41
UCEC	chrX	134393930	Missense_Mutation	NA	K132N	0.36
UCEC	chrX	134417357	Intron	novel		0.49
UCEC	chrX	134428480	3'UTR	novel		0.19
UCEC	chrX	134393949	Missense_Mutation	rs770811341	E139K	0.52
UCEC	chrX	134427624	3'UTR	novel		0.19
UCEC	chrX	134427864	3'UTR	novel		0.45
UCEC	chrX	134426038	3'UTR	novel		0.6
UCEC	chrX	134393508	Missense_Mutation	novel	S83F	0.25
UCEC	chrX	134425943	3'UTR	novel		0.29
UCEC	chrX	134428686	3'UTR	novel		0.12
UCEC	chrX	134426772	3'UTR	novel		0.46
UCEC	chrX	134426061	3'UTR	novel		0.2
UCEC	chrX	134413647	Missense_Mutation	novel	S192N	0.06
UCEC	chrX	134415072	Missense_Mutation	novel	D262E	0.09
UCEC	chrX	134417288	Silent	NA	S318S	0.2
UCEC	chrX	134427347	3'UTR	novel		0.48
UCEC	chrX	134393621	Nonsense_Mutation	novel	Q121delinsPNSLAGFKIY*	0.04
UCEC	chrX	134393607	Missense_Mutation	rs267606359	R116Q	0.13
UCEC	chrX	134377630	Missense_Mutation	novel	V5I	0.16
UCEC	chrX	134425419	3'UTR	novel		0.15
UCEC	chrX	134377622	Nonsense_Mutation	NA	S2*	0.42
UCEC	chrX	134427071	3'UTR	novel		0.15
UCEC	chrX	134413888	Frame_Shift_Ins	novel	*G218Wfs6**	0.38
UCEC	chrX	134415061	Nonsense_Mutation	novel	E259*	0.4
UCEC	chrX	134425819	3'UTR	novel		0.42
UCEC	chrX	134426830	3'UTR	novel		0.38
UCEC	chrX	134428608	3'UTR	novel		0.33
UCEC	chrX	134427203	3'UTR	novel		0.32
UCEC	chrX	134425416	3'UTR	novel		0.21
UCEC	chrX	134427797	3'UTR	novel		0.33
UCEC	chrX	134428175	3'UTR	novel		0.38
UCEC	chrX	134428280	3'UTR	novel		0.43
UCEC	chrX	134428749	3'UTR	novel		0.24
UCEC	chrX	134428101	3'UTR	novel		0.47
UCEC	chrX	134428524	3'UTR	novel		0.5
UCEC	chrX	134425403	3'UTR	novel		0.47
UCEC	chrX	134427460	3'UTR	novel		0.37
UCEC	chrX	134428635	3'UTR	novel		0.44
UCEC	chrX	134426684	3'UTR	novel		0.57
UCEC	chrX	134427408	3'UTR	novel		0.56
UCEC	chrX	134427923	3'UTR	novel		0.41
UCEC	chrX	134428165	3'UTR	novel		0.5
UCEC	chrX	134415215	Intron	novel		0.35
UCEC	chrX	134415225	Intron	rs201454923		0.28
UCEC	chrX	134413559	Missense_Mutation	rs199945885	R163C	0.41
UCEC	chrX	134415116	Missense_Mutation	novel	R277I	0.3
UCEC	chrX	134425425	3'UTR	novel		0.57
UCEC	chrX	134427136	3'UTR	novel		0.26
UCEC	chrX	134428603	3'UTR	novel		0.28
UCEC	chrX	134426459	3'UTR	novel		0.43
UCEC	chrX	134415072	Frame_Shift_Ins	NA	D264*	0.27
UCEC	chrX	134393908	Splice_Site	novel	X125_splice	0.2
UCEC	chrX	134378099	Missense_Mutation	rs767406620	T78M	0.43
UCEC	chrX	134428381	3'UTR	novel		0.32
UCEC	chrX	134426431	3'UTR	novel		0.37
UCEC	chrX	134415225	Intron	rs201454923		0.23
UCEC	chrX	134427736	3'UTR	novel		0.22
UCEC	chrX	134427063	3'UTR	novel		0.48
UCEC	chrX	134428556	3'UTR	novel		0.37
UCEC	chrX	134427950	3'UTR	novel		0.27
UCEC	chrX	134428363	3'UTR	novel		0.21
UCEC	chrX	134428549	3'UTR	novel		0.35
UCEC	chrX	134425531	3'UTR	novel		0.5
UCEC	chrX	134426557	3'UTR	novel		0.53
UCEC	chrX	134428595	3'UTR	novel		0.38
UCEC	chrX	134425271	Nonsense_Mutation	novel	R347*	0.04
UCEC	chrX	134417298	Missense_Mutation	novel	Y322D	0.57
UCEC	chrX	134393537	Missense_Mutation	novel	G93S	0.06
UCEC	chrX	134425247	Missense_Mutation	novel	D339N	0.05
UCEC	chrX	134427333	3'UTR	novel		0.11
UCEC	chrX	134426246	3'UTR	novel		0.36
UCEC	chrX	134426746	3'UTR	novel		0.16
UCEC	chrX	134427491	3'UTR	rs149825333		0.53
UCEC	chrX	134428555	3'UTR	novel		0.51
UCEC	chrX	134393621	Frame_Shift_Ins	novel	*Q121Pfs24**	0.07
UCEC	chrX	134417479	Intron	novel		0.33
UCEC	chrX	134426007	3'UTR	novel		0.43
UCEC	chrX	134426773	3'UTR	novel		0.15
UCEC	chrX	134413639	Missense_Mutation	NA	E189D	0.3
UCEC	chrX	134413498	Silent	novel	L142L	0.37
UCEC	chrX	134426092	3'UTR	novel		0.34
UCEC	chrX	134427634	3'UTR	novel		0.36
UCEC	chrX	134425447	3'UTR	novel		0.32
UCEC	chrX	134428101	3'UTR	novel		0.24
UCEC	chrX	134427010	3'UTR	novel		0.35
UCEC	chrX	134427896	3'UTR	novel		0.35
UCEC	chrX	134417348	Intron	rs756755647		0.19
UCEC	chrX	134413571	Missense_Mutation	novel	P167S	0.37
UCEC	chrX	134427584	3'UTR	novel		0.33
UCEC	chrX	134428401	3'UTR	novel		0.36
UCEC	chrX	134425360	3'UTR	novel		0.39
UCEC	chrX	134427828	3'UTR	novel		0.3

Copy Number Variations (CNVs)

Cancer	Type	Freq	Q-value
DLBC	AMP	0.0833	0.24013
KIRC	AMP	0.0303	0.12739
READ	AMP	0.1333	0.14805
TGCT	DEL	0.0667	0.08422
THCA	DEL	0	0.21991
UCS	DEL	0.3036	0.063955

Survival Analysis

Cancer	P-value	Q-value
KIRC	0.0067	Kaplan-Meier Survival Analysis
SARC	0.0032	Kaplan-Meier Survival Analysis
MESO	0.044	Kaplan-Meier Survival Analysis
ACC	0.001	Kaplan-Meier Survival Analysis
HNSC	0.0073	Kaplan-Meier Survival Analysis
SKCM	0.00031	Kaplan-Meier Survival Analysis
LUSC	0.014	Kaplan-Meier Survival Analysis
BRCA	0.014	Kaplan-Meier Survival Analysis
KIRP	0.0024	Kaplan-Meier Survival Analysis
PAAD	0.0017	Kaplan-Meier Survival Analysis
BLCA	0.025	Kaplan-Meier Survival Analysis
UCEC	0.0053	Kaplan-Meier Survival Analysis
GBM	0.0008	Kaplan-Meier Survival Analysis
LIHC	0.0012	Kaplan-Meier Survival Analysis
LGG	0.011	Kaplan-Meier Survival Analysis