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

Gene Gene information from NCBI Gene database. Gene miRNA Gene ontology Other IDs Protein Associated diseases
Entrez ID	23469
Gene name	PHD finger protein 3
Gene symbol	PHF3
Synonyms (NCBI Gene)	-
Chromosome	6
Chromosome location	6q12
Summary	This gene encodes a member of a PHD finger-containing gene family. This gene may function as a transcription factor and may be involved in glioblastomas development. Alternative splicing results in multiple transcript variants. [provided by RefSeq, Mar 20

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Show/Hide all (137)

miRTarBase ID	miRNA	Experiments	Reference
MIRT019971	hsa-miR-375	Microarray	20215506
MIRT020337	hsa-miR-130b-3p	Sequencing	20371350
MIRT027369	hsa-miR-101-3p	Sequencing	20371350
MIRT051438	hsa-let-7e-5p	CLASH	23622248
MIRT655151	hsa-miR-4530	HITS-CLIP	23824327
MIRT655152	hsa-miR-338-3p	HITS-CLIP	23824327
MIRT655150	hsa-miR-5088-3p	HITS-CLIP	23824327
MIRT655149	hsa-miR-766-3p	HITS-CLIP	23824327
MIRT655148	hsa-miR-3925-3p	HITS-CLIP	23824327
MIRT655147	hsa-miR-4287	HITS-CLIP	23824327
MIRT655146	hsa-miR-4685-3p	HITS-CLIP	23824327
MIRT655145	hsa-miR-6845-3p	HITS-CLIP	23824327
MIRT655144	hsa-miR-4427	HITS-CLIP	23824327
MIRT655143	hsa-miR-5187-3p	HITS-CLIP	23824327
MIRT655142	hsa-miR-4680-3p	HITS-CLIP	23824327
MIRT655141	hsa-miR-942-5p	HITS-CLIP	23824327
MIRT655140	hsa-miR-4691-5p	HITS-CLIP	23824327
MIRT655139	hsa-miR-6792-3p	HITS-CLIP	23824327
MIRT655137	hsa-miR-6749-3p	HITS-CLIP	23824327
MIRT655138	hsa-miR-6873-3p	HITS-CLIP	23824327
MIRT655136	hsa-miR-670-3p	HITS-CLIP	23824327
MIRT655135	hsa-miR-1238-3p	HITS-CLIP	23824327
MIRT655134	hsa-miR-4768-5p	HITS-CLIP	23824327
MIRT655133	hsa-miR-6833-3p	HITS-CLIP	23824327
MIRT027369	hsa-miR-101-3p	PAR-CLIP	20371350
MIRT027369	hsa-miR-101-3p	PAR-CLIP	20371350
MIRT566435	hsa-miR-144-3p	PAR-CLIP	20371350
MIRT566434	hsa-miR-582-5p	PAR-CLIP	20371350
MIRT566433	hsa-miR-548p	PAR-CLIP	20371350
MIRT566432	hsa-miR-545-5p	PAR-CLIP	20371350
MIRT655151	hsa-miR-4530	HITS-CLIP	23824327
MIRT655152	hsa-miR-338-3p	HITS-CLIP	23824327
MIRT655150	hsa-miR-5088-3p	HITS-CLIP	23824327
MIRT655149	hsa-miR-766-3p	HITS-CLIP	23824327
MIRT655148	hsa-miR-3925-3p	HITS-CLIP	23824327
MIRT655147	hsa-miR-4287	HITS-CLIP	23824327
MIRT655146	hsa-miR-4685-3p	HITS-CLIP	23824327
MIRT655145	hsa-miR-6845-3p	HITS-CLIP	23824327
MIRT655144	hsa-miR-4427	HITS-CLIP	23824327
MIRT655143	hsa-miR-5187-3p	HITS-CLIP	23824327
MIRT655142	hsa-miR-4680-3p	HITS-CLIP	23824327
MIRT655141	hsa-miR-942-5p	HITS-CLIP	23824327
MIRT655140	hsa-miR-4691-5p	HITS-CLIP	23824327
MIRT655139	hsa-miR-6792-3p	HITS-CLIP	23824327
MIRT655137	hsa-miR-6749-3p	HITS-CLIP	23824327
MIRT655138	hsa-miR-6873-3p	HITS-CLIP	23824327
MIRT655136	hsa-miR-670-3p	HITS-CLIP	23824327
MIRT655135	hsa-miR-1238-3p	HITS-CLIP	23824327
MIRT655134	hsa-miR-4768-5p	HITS-CLIP	23824327
MIRT655133	hsa-miR-6833-3p	HITS-CLIP	23824327
MIRT027369	hsa-miR-101-3p	PAR-CLIP	20371350
MIRT027369	hsa-miR-101-3p	PAR-CLIP	20371350
MIRT566435	hsa-miR-144-3p	PAR-CLIP	20371350
MIRT566434	hsa-miR-582-5p	PAR-CLIP	20371350
MIRT566433	hsa-miR-548p	PAR-CLIP	20371350
MIRT566432	hsa-miR-545-5p	PAR-CLIP	20371350
MIRT1231088	hsa-miR-1297	CLIP-seq
MIRT1231089	hsa-miR-140-3p	CLIP-seq
MIRT1231090	hsa-miR-1587	CLIP-seq
MIRT1231091	hsa-miR-183	CLIP-seq
MIRT1231092	hsa-miR-26a	CLIP-seq
MIRT1231093	hsa-miR-26b	CLIP-seq
MIRT1231094	hsa-miR-3189-3p	CLIP-seq
MIRT1231095	hsa-miR-320a	CLIP-seq
MIRT1231096	hsa-miR-320b	CLIP-seq
MIRT1231097	hsa-miR-320c	CLIP-seq
MIRT1231098	hsa-miR-320d	CLIP-seq
MIRT1231099	hsa-miR-3613-3p	CLIP-seq
MIRT1231100	hsa-miR-3646	CLIP-seq
MIRT1231101	hsa-miR-3647-3p	CLIP-seq
MIRT1231102	hsa-miR-3662	CLIP-seq
MIRT1231103	hsa-miR-3920	CLIP-seq
MIRT1231104	hsa-miR-4272	CLIP-seq
MIRT1231105	hsa-miR-4282	CLIP-seq
MIRT1231106	hsa-miR-4426	CLIP-seq
MIRT1231107	hsa-miR-4429	CLIP-seq
MIRT1231108	hsa-miR-4465	CLIP-seq
MIRT1231109	hsa-miR-4647	CLIP-seq
MIRT1231110	hsa-miR-4662b	CLIP-seq
MIRT1231111	hsa-miR-4674	CLIP-seq
MIRT1231112	hsa-miR-4690-5p	CLIP-seq
MIRT1231113	hsa-miR-4709-3p	CLIP-seq
MIRT1231114	hsa-miR-4720-3p	CLIP-seq
MIRT1231115	hsa-miR-4742-5p	CLIP-seq
MIRT1231116	hsa-miR-4762-3p	CLIP-seq
MIRT1231117	hsa-miR-548a-3p	CLIP-seq
MIRT1231118	hsa-miR-548ae	CLIP-seq
MIRT1231119	hsa-miR-548aj	CLIP-seq
MIRT1231120	hsa-miR-548am	CLIP-seq
MIRT1231121	hsa-miR-548c-3p	CLIP-seq
MIRT1231122	hsa-miR-548e	CLIP-seq
MIRT1231123	hsa-miR-548f	CLIP-seq
MIRT1231124	hsa-miR-548x	CLIP-seq
MIRT1231125	hsa-miR-590-3p	CLIP-seq
MIRT1231126	hsa-miR-635	CLIP-seq
MIRT1231127	hsa-miR-767-3p	CLIP-seq
MIRT1231088	hsa-miR-1297	CLIP-seq
MIRT2067818	hsa-miR-139-5p	CLIP-seq
MIRT2067819	hsa-miR-224	CLIP-seq
MIRT1231092	hsa-miR-26a	CLIP-seq
MIRT1231093	hsa-miR-26b	CLIP-seq
MIRT2067820	hsa-miR-377	CLIP-seq
MIRT2067821	hsa-miR-4268	CLIP-seq
MIRT2067822	hsa-miR-4448	CLIP-seq
MIRT1231108	hsa-miR-4465	CLIP-seq
MIRT1231112	hsa-miR-4690-5p	CLIP-seq
MIRT1231115	hsa-miR-4742-5p	CLIP-seq
MIRT2067823	hsa-miR-498	CLIP-seq
MIRT1231088	hsa-miR-1297	CLIP-seq
MIRT2295274	hsa-miR-142-5p	CLIP-seq
MIRT2295275	hsa-miR-181a	CLIP-seq
MIRT2295276	hsa-miR-181b	CLIP-seq
MIRT2295277	hsa-miR-181c	CLIP-seq
MIRT2295278	hsa-miR-181d	CLIP-seq
MIRT2067819	hsa-miR-224	CLIP-seq
MIRT1231092	hsa-miR-26a	CLIP-seq
MIRT1231093	hsa-miR-26b	CLIP-seq
MIRT2295279	hsa-miR-3125	CLIP-seq
MIRT2295280	hsa-miR-340	CLIP-seq
MIRT1231099	hsa-miR-3613-3p	CLIP-seq
MIRT1231100	hsa-miR-3646	CLIP-seq
MIRT2067820	hsa-miR-377	CLIP-seq
MIRT2295281	hsa-miR-3916	CLIP-seq
MIRT2295282	hsa-miR-410	CLIP-seq
MIRT2295283	hsa-miR-4262	CLIP-seq
MIRT1231108	hsa-miR-4465	CLIP-seq
MIRT2295284	hsa-miR-4528	CLIP-seq
MIRT2067823	hsa-miR-498	CLIP-seq
MIRT1231117	hsa-miR-548a-3p	CLIP-seq
MIRT1231118	hsa-miR-548ae	CLIP-seq
MIRT1231119	hsa-miR-548aj	CLIP-seq
MIRT1231120	hsa-miR-548am	CLIP-seq
MIRT1231122	hsa-miR-548e	CLIP-seq
MIRT1231123	hsa-miR-548f	CLIP-seq
MIRT1231124	hsa-miR-548x	CLIP-seq
MIRT1231127	hsa-miR-767-3p	CLIP-seq
MIRT2295285	hsa-miR-877	CLIP-seq

Show/Hide all (5)

GO ID	Ontology	Definition	Evidence
GO:0005634	Component	Nucleus	IBA
GO:0006351	Process	DNA-templated transcription	IEA
GO:0006357	Process	Regulation of transcription by RNA polymerase II	IBA
GO:0008270	Function	Zinc ion binding	IEA
GO:0046872	Function	Metal ion binding	IEA

MIM	HGNC	e!Ensembl
607789	8921	ENSG00000118482

Q92576

Protein name

PHD finger protein 3

PDB

2DME , 6IC8 , 6IC9 , 6Q2V , 6Q5Y

Family and domains

Pfam

Accession	ID	Position in sequence	Description	Type
PF00628	PHD	719 → 772	PHD-finger	Domain
PF07500	TFIIS_M	925 → 1038	Transcription factor S-II (TFIIS), central domain	Domain
PF07744	SPOC	1199 → 1349	SPOC domain	Domain

Tissue specificity

TISSUE SPECIFICITY: Ubiquitous. Expression is significantly reduced or lost in glioblastomas, glioblastoma cell lines, anaplastic astrocytomas, and astrocytomas. {ECO:0000269|PubMed:11856869}.

Sequence

MDIVDTFNHLIPTEHLDDALFLGSNLENEVCEDFSASQNVLEDSLKNMLSDKDPMLGSAS
NQFCLPVLDSNDPNFQMPCSTVVGLDDIMDEGVVKESGNDTIDEEELILPNRNLRDKVEE
NSVRSPRKSPRLMAQEQVRSLRQSTIAKRSNAAPLSNTKKASGKTVSTAKAGVKQPERSQ
VKEEVCMSLKPEYHKENRRCSRNSGQIEVVPEVSVSSSHSSVSSCLEMKDEDGLDSKHKC
NNPGEIDVPSHELNCSLLSETCVTIGEKKNEALMECKAKPVGSPLFKFSDKEEHEQNDSI
SGKTGETVVEEMIATRKVEQDSKETVKLSHEDDHILEDAGSSDISSDAACTNPNKTENSL
VGLPSCVDEVTECNLELKDTMGIADKTENTLERNKIEPLGYCEDAESNRQLESTEFNKSN
LEVVDTSTFGPESNILENAICDVPDQNSKQLNAIESTKIESHETANLQDDRNSQSSSVSY
LESKSVKSKHTKPVIHSKQNMTTDAPKKIVAAKYEVIHSKTKVNVKSVKRNTDVPESQQN
FHRPVKVRKKQIDKEPKIQSCNSGVKSVKNQAHSVLKKTLQDQTLVQIFKPLTHSLSDKS
HAHPGCLKEPHHPAQTGHVSHSSQKQCHKPQQQAPAMKTNSHVKEELEHPGVEHFKEEDK
LKLKKPEKNLQPRQRRSSKSFSLDEPPLFIPDNIATIRREGSDHSSSFESKYMWTPSKQC
GFCKKPHGNRFMVGCGRCDDWFHGDCVGLSLSQAQQMGEEDKEYVCVKCCAEEDKKTEIL
DPDTLENQATVEFHSGDKTMECEKLGLSKHTTNDRTKYIDDTVKHKVKILKRESGEGRNS
SDCRDNEIKKWQLAPLRKMGQPVLPRRSSEEKSEKIPKESTTVTCTGEKASKPGTHEKQE
MKKKKVEKGVLNVHPAASASKPSADQIRQSVRHSLKDILMKRLTDSNLKVPEEKAAKVAT
KIEKELFSFFRDTDAKYKNKYRSLMFNLKDPKNNILFKKVLKGEVTPDHLIRMSPEELAS
KELAAWRRRENRHTIEMIEKEQREVERRPITKITHKGEIEIESDAPMKEQEAAMEIQEPA
ANKSLEKPEGSEKQKEEVDSMSKDTTSQHRQHLFDLNCKICIGRMAPPVDDLSPKKVKVV
VGVARKHSDNEAESIADALSSTSNILASEFFEEEKQESPKSTFSPAPRPEMPGTVEVEST
FLARLNFIWKGFINMPSVAKFVTKAYPVSGSPEYLTEDLPDSIQVGGRISPQTVWDYVEK
IKASGTKEICVVRFTPVTEEDQISYTLLFAYFSSRKRYGVAANNMKQVKDMYLIPLGATD
KIPHPLVPFDGPGLELHRPNLLLGLIIRQKLKRQHSACASTSHIAETPESAPPIALPPDK
KSKIEVSTEEAPEEENDFFNSFTTVLHKQRNKPQQNLQEDLPTAVEPLMEVTKQEPPKPL
RFLPGVLIGWENQPTTLELANKPLPVDDILQSLLGTTGQVYDQAQSVMEQNTVKEIPFLN
EQTNSKIEKTDNVEVTDGENKEIKVKVDNISESTDKSAEIETSVVGSSSISAGSLTSLSL
RGKPPDVSTEAFLTNLSIQSKQEETVESKEKTLKRQLQEDQENNLQDNQTSNSSPCRSNV
GKGNIDGNVSCSENLVANTARSPQFINLKRDPRQAAGRSQPVTTSESKDGDSCRNGEKHM
LPGLSHNKEHLTEQINVEEKLCSAEKNSCVQQSDNLKVAQNSPSVENIQTSQAEQAKPLQ
EDILMQNIETVHPFRRGSAVATSHFEVGNTCPSEFPSKSITFTSRSTSPRTSTNFSPMRP
QQPNLQHLKSSPPGFPFPGPPNFPPQSMFGFPPHLPPPLLPPPGFGFAQNPMVPWPPVVH
LPGQPQRMMGPLSQASRYIGPQNFYQVKDIRRPERRHSDPWGRQDQQQLDRPFNRGKGDR
QRFYSDSHHLKRERHEKEWEQESERHRRRDRSQDKDRDRKSREEGHKDKERARLSHGDRG
TDGKASRDSRNVDKKPDKPKSEDYEKDKEREKSKHREGEKDRDRYHKDRDHTDRTKSKR

Sequence length

2039

Interactions

View interactions

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)

Show/Hide Unknown Diseases (19)

Phenotype Name	Clinical Significance	Source	Evidence Score
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.
ALZHEIMER DISEASE	—	GWAS catalog	★★★★★ ★★☆☆☆ Found in Text Mining + Unknown/Other Associations
ASTIGMATISM	—	Disgenet	★★★★★ ★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Autism spectrum disorder	Likely benign	ClinVar	★★★★★ ★★☆☆☆ Found in Text Mining + Unknown/Other Associations
AUTOSOMAL RECESSIVE RETINITIS PIGMENTOSA	—	Disgenet	★★★★★ ★★☆☆☆ Found in Text Mining + Unknown/Other Associations
DYSCHROMATOPSIA	—	Disgenet	★★★★★ ★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Hepatocellular carcinoma	Uncertain significance; Benign	ClinVar	★★★★★ ★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Intellectual disability	Uncertain significance	ClinVar Disgenet	★★★★★ ★★★☆☆ Reported in Unknown/Other Associations (≥2 sources)
MAJOR DEPRESSIVE DISORDER	—	GWAS catalog	★★★★★ ★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Neurodevelopmental delay	Uncertain significance	ClinVar	★★★★★ ★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Neurodevelopmental disorder	Uncertain significance	ClinVar	★★★★★ ★★☆☆☆ Found in Text Mining + Unknown/Other Associations
NEURODEVELOPMENTAL DISORDERS	—	Disgenet	★★★★★ ★★☆☆☆ Found in Text Mining + Unknown/Other Associations
PHF3-related disorder	Uncertain significance; Benign; Likely benign	ClinVar	★★★★★ ★★☆☆☆ Found in Text Mining + Unknown/Other Associations
RETINITIS PIGMENTOSA	—	Disgenet	★★★★★ ★★☆☆☆ Found in Text Mining + Unknown/Other Associations
RETINITIS PIGMENTOSA 25	—	Disgenet	★★★★★ ★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Sarcoma	Benign	ClinVar	★★★★★ ★★☆☆☆ Found in Text Mining + Unknown/Other Associations
SCHIZOPHRENIA	—	GWAS catalog	★★★★★ ★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Thymoma	Benign	ClinVar	★★★★★ ★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Thyroid cancer, nonmedullary, 1	Benign	ClinVar	★★★★★ ★★☆☆☆ Found in Text Mining + Unknown/Other Associations
TOURETTE SYNDROME	—	GWAS catalog	★★★★★ ★★☆☆☆ Found in Text Mining + Unknown/Other Associations

Show/Hide Text Mining Associations (11)

Disease Name	Disease (Merged)	Source	PMID	Relationship Type	Evidence Score
Associations from Text Mining Disease associations identified through text mining
Astrocytoma	Astrocytoma	BEFREE	11856869		★★★★★ ★☆☆☆☆ Found in Text Mining only
Carcinoma Pancreatic Ductal	Pancreatic ductal carcinoma	Pubtator	32696980	Associate	★★★★★ ★☆☆☆☆ Found in Text Mining only
Glioblastoma	Glioblastoma	BEFREE	11464277, 11856869		★★★★★ ★☆☆☆☆ Found in Text Mining only
Glioblastoma	Glioblastoma	LHGDN	11856869, 15906353		★★★★★ ★☆☆☆☆ Found in Text Mining only
Glioblastoma Multiforme	Glioblastoma	BEFREE	11464277, 11856869		★★★★★ ★☆☆☆☆ Found in Text Mining only
Major Depressive Disorder	Mental Depression	GWASCAT_DG	30571770		★★★★★ ★★☆☆☆ Found in Text Mining + Unknown/Other Associations
obsolete Rod-cone dystrophy	Rod-cone dystrophy	CLINVAR_DG			★★★★★ ★☆☆☆☆ Found in Text Mining only
Retinal Dystrophies	Retinal Dystrophy	CLINVAR_DG	26872967		★★★★★ ★☆☆☆☆ Found in Text Mining only
Retinitis Pigmentosa	Retinitis Pigmentosa	CLINVAR_DG	29550188, 30718709		★★★★★ ★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Retinitis Pigmentosa 25	Retinitis Pigmentosa	CLINVAR_DG	18976725, 20375346, 20537394, 21069908, 24474277, 26161267, 26261414		★★★★★ ★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Unipolar Depression	Mental Depression	GWASCAT_DG	30571770		★★★★★ ★☆☆☆☆ Found in Text Mining only

PHF3 (PHD finger protein 3)