PHF3

Summary

PHF3 (PHD finger protein 3, HGNC:8921) is a protein-coding gene on chromosome 6q12, encoding PHD finger protein 3 (Q92576).

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.

Source: NCBI Gene 23469 — RefSeq curated summary.

At a glance

• GWAS associations: 3
• Clinical variants (ClinVar): 339 total — 2 pathogenic, 5 likely-pathogenic
• Phenotypes (HPO): 1
• Dosage sensitivity (ClinGen): haploinsufficiency little evidence, triplosensitivity no evidence
• MANE Select transcript: NM_001370348

Identifiers

Gene identifiers

Field	Value
HGNC ID	HGNC:8921
Approved symbol	PHF3
Name	PHD finger protein 3
Location	6q12
Locus type	gene with protein product
Status	Approved
Ensembl gene	ENSG00000118482
Ensembl biotype	protein_coding
OMIM	607789
Entrez	23469

Gene structure

Transcript identifiers

Ensembl transcripts: 17 — 14 protein_coding, 2 protein_coding_CDS_not_defined, 1 nonsense_mediated_decay

ENST00000262043, ENST00000393387, ENST00000420043, ENST00000481385, ENST00000494284, ENST00000503248, ENST00000505138, ENST00000506783, ENST00000509330, ENST00000509876, ENST00000514822, ENST00000515594, ENST00000903919, ENST00000935699, ENST00000935700, ENST00000935701, ENST00000935702

RefSeq mRNA: 6 — MANE Select: NM_001370348 NM_001290259, NM_001290260, NM_001370348, NM_001370349, NM_001370350, NM_015153

CCDS: CCDS4966, CCDS78155

Canonical transcript exons

ENST00000262043 — 16 exons

Exon	Start	End
ENSE00000000288	63635802	63636150
ENSE00000757689	63646527	63646795
ENSE00000757767	63711586	63726011
ENSE00003465187	63698449	63698605
ENSE00003468018	63698223	63698367
ENSE00003487126	63684129	63685911
ENSE00003492192	63702508	63702639
ENSE00003498516	63694581	63694764
ENSE00003531855	63706729	63706876
ENSE00003550828	63703536	63703671
ENSE00003577370	63691737	63692043
ENSE00003588652	63680000	63680161
ENSE00003590204	63709151	63709240
ENSE00003600773	63711167	63711362
ENSE00003603205	63700350	63700466
ENSE00003691663	63706029	63706224

Expression profiles

Bgee: expression breadth ubiquitous, 303 present calls, max score 98.83.

FANTOM5 (CAGE): breadth ubiquitous, TPM avg 36.4496 / max 1139.7572, expressed in 1799 samples.

FANTOM5 promoters (4 alternative TSS)

Promoter ID	TPM avg	Samples expressed
68398	21.1917	1715
68395	15.2275	1747
68399	0.0255	5
204039	0.0049	2

Top tissues by expression

303 total, by Bgee expression score (0-100, higher = more expressed):

Tissue	Anatomy ID	Expression score	Quality
tendon of biceps brachii	UBERON:0008188	98.83	gold quality
calcaneal tendon	UBERON:0003701	98.31	gold quality
tendon	UBERON:0000043	98.20	gold quality
adrenal tissue	UBERON:0018303	96.83	gold quality
germinal epithelium of ovary	UBERON:0001304	96.65	gold quality
tibia	UBERON:0000979	96.22	gold quality
endothelial cell	CL:0000115	96.16	gold quality
parietal pleura	UBERON:0002400	95.97	gold quality
medial globus pallidus	UBERON:0002477	95.76	gold quality
pleura	UBERON:0000977	95.62	gold quality
visceral pleura	UBERON:0002401	95.52	gold quality
corpus callosum	UBERON:0002336	95.30	gold quality
palpebral conjunctiva	UBERON:0001812	95.28	gold quality
male germ line stem cell (sensu Vertebrata) in testis	CL:0000089 ∩ UBERON:0000473	95.00	gold quality
caput epididymis	UBERON:0004358	94.86	gold quality
cartilage tissue	UBERON:0002418	94.79	gold quality
amniotic fluid	UBERON:0000173	94.74	gold quality
colonic epithelium	UBERON:0000397	94.67	gold quality
eye	UBERON:0000970	94.67	gold quality
globus pallidus	UBERON:0001875	94.66	gold quality
ventricular zone	UBERON:0003053	94.31	gold quality
corpus epididymis	UBERON:0004359	94.25	gold quality
parotid gland	UBERON:0001831	94.17	gold quality
urethra	UBERON:0000057	94.15	gold quality
Brodmann (1909) area 23	UBERON:0013554	94.02	gold quality
pericardium	UBERON:0002407	93.47	gold quality
skeletal muscle tissue of rectus abdominis	UBERON:0004511	93.39	gold quality
skin of hip	UBERON:0001554	93.34	gold quality
tonsil	UBERON:0002372	93.09	gold quality
cauda epididymis	UBERON:0004360	93.04	gold quality

Single-cell (SCXA)

Detected in 2 experiment(s), a significant marker in 1.

Experiment	Marker?	Max mean expression
E-ANND-3	yes	8.97
E-MTAB-7606	no	1212.60

Regulation

Is transcription factor: no

miRNA regulators (miRDB)

176 targeting PHF3, top 30 by miRDB confidence (max_score; target_count = how many genes the miRNA targets in total — lower means more specific):

miRNA	Max score	Avg score	miRNA target_count
HSA-MIR-8485	100.00	77.57	4731
HSA-MIR-513A-5P	100.00	69.77	2465
HSA-MIR-3646	100.00	73.56	5283
HSA-MIR-4262	100.00	73.26	3931
HSA-MIR-5692A	100.00	74.40	6850
HSA-MIR-340-5P	100.00	72.50	4437
HSA-MIR-6740-5P	100.00	65.64	932
HSA-MIR-1277-5P	100.00	73.95	5056
HSA-MIR-4282	99.99	75.36	6408
HSA-MIR-520G-5P	99.99	66.76	658
HSA-MIR-3662	99.99	73.82	5684
HSA-MIR-181A-5P	99.99	72.96	2995
HSA-MIR-181B-5P	99.99	72.97	2996
HSA-MIR-181C-5P	99.99	72.95	2996
HSA-MIR-181D-5P	99.99	73.04	2997
HSA-MIR-548C-3P	99.99	74.01	7587
HSA-MIR-3185	99.99	68.12	1959
HSA-MIR-150-5P	99.99	66.69	1976
HSA-MIR-4775	99.98	75.00	6394
HSA-MIR-548P	99.98	72.25	3784
HSA-LET-7F-2-3P	99.98	70.98	2588
HSA-MIR-1185-1-3P	99.98	71.04	2593
HSA-MIR-1185-2-3P	99.98	71.04	2593
HSA-MIR-32-5P	99.98	75.21	1964
HSA-MIR-92A-3P	99.98	75.21	1960
HSA-MIR-92B-3P	99.98	75.25	1955
HSA-MIR-25-3P	99.98	74.60	1817
HSA-MIR-363-3P	99.98	74.72	1821
HSA-MIR-367-3P	99.98	74.83	1819
HSA-MIR-4789-5P	99.98	70.76	2721

Functional genomics

ClinGen dosage: haploinsufficiency 1 (little evidence), triplosensitivity 0 (no evidence). ClinGen Gene Dosage Map

Literature-anchored findings (GeneRIF, showing 6)

• novel member of a large class of regulatory proteins containing a LAP motif, and loss of its expression in glioblastoma may contribute to glioma development (PMID:11856869)
• Survival of patients with GLEA2 antibodies was increased to 17.4 months and for patients with PHF3 antibodies to 14.7 months, as compared to 7.2 months for patients without GLEA2 or PHF3 antibodies in glioblastoma. (PMID:15906353)
• Data conclude that the PHF3-PTP4A1 region appears to harbor a causal locus for alcohol dependence, and proteins encoded by PHF3 and/or PTP4A1 might play a functional role in the disorder. (PMID:22096494)
• PTP4A1-PHF3-EYS variants were associated with alcohol dependence. (PMID:23324950)
• We confirmed with our previous findings that PTP4A1-PHF3-EYS variants were significantly associated with alcohol dependence. (PMID:24961364)
• PHF3 regulates neuronal gene expression through the Pol II CTD reader domain SPOC. (PMID:34667177)

Cross-species orthologs

3 orthologs

Organism	Symbol	Gene ID
danio_rerio	phf3	ENSDARG00000034768
mus_musculus	Phf3	ENSMUSG00000048874
rattus_norvegicus	Phf3	ENSRNOG00000011756

Paralogs (2): DIDO1 (ENSG00000101191), SPOCD1 (ENSG00000134668)

Protein

Protein identifiers

PHD finger protein 3 — Q92576 (reviewed: Q92576)

All UniProt accessions (9): A0A1B0GX99, Q92576, D6R9X2, D6RBF0, D6REP0, E7ER40, E7EVH3, E9PE34, H0Y8L0

UniProt curated annotations — full annotation on UniProt →

Tissue specificity. Ubiquitous. Expression is significantly reduced or lost in glioblastomas, glioblastoma cell lines, anaplastic astrocytomas, and astrocytomas.

Isoforms (2)

UniProt ID	Names	Canonical?
Q92576-1	1	yes
Q92576-2	2

RefSeq proteins (6): NP_001277188, NP_001277189, NP_001357277, NP_001357278, NP_001357279, NP_055968 (=MANE)

Domains & families (InterPro)

ID	Name	Type
IPR001965	Znf_PHD	Domain
IPR003618	TFIIS_cen_dom	Domain
IPR011011	Znf_FYVE_PHD	Homologous_superfamily
IPR012921	SPOC_C	Domain
IPR013083	Znf_RING/FYVE/PHD	Homologous_superfamily
IPR019786	Zinc_finger_PHD-type_CS	Conserved_site
IPR019787	Znf_PHD-finger	Domain
IPR036575	TFIIS_cen_dom_sf	Homologous_superfamily

Pfam: PF00628, PF07500, PF07744

UniProt features (76 total): modified residue 15, compositionally biased region 14, region of interest 12, strand 11, helix 10, turn 4, cross-link 3, sequence variant 2, chain 1, domain 1, zinc finger region 1, splice variant 1, sequence conflict 1

Structure

Experimental structures (PDB)

5 structures.

PDB	Method	Resolution (Å)
6IC9	X-RAY DIFFRACTION	1.75
6IC8	X-RAY DIFFRACTION	1.93
6Q2V	X-RAY DIFFRACTION	2.59
6Q5Y	X-RAY DIFFRACTION	2.85
2DME	SOLUTION NMR

Predicted structure (AlphaFold)

Model	pLDDT	Fraction very-high
AF-Q92576-F1	43.24	0.08

Functional residue map

Curated UniProt residues grouped by drug-discovery relevance — catalytic, ligand-binding, modification, and mutation-validated positions. Source: UniProtKB sequence features.

Post-translational modifications (18): 97, 125, 283, 299, 680, 1014, 1133, 1148, 1178, 1614, 1642, 1867, 1877, 1898, 1925, 644, 964, 1931

Function

Pathways and Gene Ontology

Reactome pathways

0 pathways

MSigDB gene sets: 211 (showing top): MORF_MTA1, BROWNE_HCMV_INFECTION_6HR_DN, chr6q12, GRAESSMANN_APOPTOSIS_BY_DOXORUBICIN_DN, GENTILE_UV_RESPONSE_CLUSTER_D2, BRN2_01, MORF_RAB6A, TGTGTGA_MIR377, DACOSTA_UV_RESPONSE_VIA_ERCC3_COMMON_DN, HP1SITEFACTOR_Q6, GENTILE_UV_HIGH_DOSE_DN, TGANTCA_AP1_C, SCHLOSSER_SERUM_RESPONSE_DN, NAKAMURA_TUMOR_ZONE_PERIPHERAL_VS_CENTRAL_DN, MORF_SP3

GO Biological Process (2): DNA-templated transcription (GO:0006351), regulation of transcription by RNA polymerase II (GO:0006357)

GO Molecular Function (2): zinc ion binding (GO:0008270), metal ion binding (GO:0046872)

GO Cellular Component (2): nucleus (GO:0005634), Set1C/COMPASS complex (GO:0048188)

GO top-level categories

Rollup of top GO terms by namespace:

Category	Terms
gene expression	1
RNA biosynthetic process	1
regulation of DNA-templated transcription	1
transcription by RNA polymerase II	1
transition metal ion binding	1
cation binding	1
intracellular membrane-bounded organelle	1
histone methyltransferase complex	1

Protein interactions and networks

STRING

1750 interactions, top by confidence (×1000):

Protein A	Protein B	Partner UniProt	Score
PHF3	PTP4A1	Q93096	757
PHF3	TCEA3	O75764	535
PHF3	TCEA2	Q15560	527
PHF3	TCEA1	P23193	485
PHF3	UBN2	Q6ZU65	479
PHF3	SCAF8	Q9UPN6	454
PHF3	LGSN	Q5TDP6	448
PHF3	FAM47A	Q5JRC9	447
PHF3	RPRD1A	Q96P16	430
PHF3	ARHGAP12	Q8IWW6	423
PHF3	SERINC2	Q96SA4	420
PHF3	KIAA0040	Q15053	418
PHF3	ZNF835	Q9Y2P0	417
PHF3	MED13	Q9UHV7	415
PHF3	MED13L	Q71F56	408

IntAct

87 interactions, top by confidence:

A	B	Type	Score
MED21	MED19	psi-mi:“MI:0914”(association)	0.880
MAPK3	MAPK1	psi-mi:“MI:0914”(association)	0.770
MAPK1	DHPS	psi-mi:“MI:0914”(association)	0.640
YWHAG	BLTP3B	psi-mi:“MI:2364”(proximity)	0.640
YWHAH	PLEKHG3	psi-mi:“MI:0914”(association)	0.610
YWHAH	BLTP3B	psi-mi:“MI:0914”(association)	0.570
YWHAH	BLTP3B	psi-mi:“MI:2364”(proximity)	0.570
SUPT5H	POLR2D	psi-mi:“MI:0914”(association)	0.530
TMA16	TNPO2	psi-mi:“MI:0914”(association)	0.530
CPSF6	DDX39A	psi-mi:“MI:0914”(association)	0.480
H3C1	SMCHD1	psi-mi:“MI:2364”(proximity)	0.410
PHF3	H1-2	psi-mi:“MI:0915”(physical association)	0.400
PHF3	H1-5	psi-mi:“MI:0915”(physical association)	0.400
PHF3	HMGA1	psi-mi:“MI:0915”(physical association)	0.400
PHF3	UBA52	psi-mi:“MI:0915”(physical association)	0.400
PHF3	H3-4	psi-mi:“MI:0915”(physical association)	0.400
PHF3	MYH9	psi-mi:“MI:0915”(physical association)	0.400
PHF3	RSL1D1	psi-mi:“MI:0915”(physical association)	0.400
PHF3	NIFK	psi-mi:“MI:0915”(physical association)	0.400
ESR1	ESYT2	psi-mi:“MI:0914”(association)	0.350
YWHAB	PLEKHG3	psi-mi:“MI:0914”(association)	0.350
YWHAG	C1orf226	psi-mi:“MI:0914”(association)	0.350
MAPK3	HMMR	psi-mi:“MI:0914”(association)	0.350
FUS	SUPT5H	psi-mi:“MI:0914”(association)	0.350
H2BC21	SMCHD1	psi-mi:“MI:0914”(association)	0.350
SNRPA	DDX39A	psi-mi:“MI:0914”(association)	0.350
SNRPB	DDX39A	psi-mi:“MI:0914”(association)	0.350
SNRPC	DDX39A	psi-mi:“MI:0914”(association)	0.350
SNRPF	SUPT5H	psi-mi:“MI:0914”(association)	0.350

BioGRID (139): PHF3 (Affinity Capture-MS), PHF3 (Biochemical Activity), PHF3 (Affinity Capture-MS), PHF3 (Affinity Capture-MS), PHF3 (Affinity Capture-MS), PHF3 (Affinity Capture-MS), PHF3 (Affinity Capture-MS), PHF3 (Proximity Label-MS), PHF3 (Affinity Capture-MS), PHF3 (Affinity Capture-MS), PHF3 (Affinity Capture-RNA), PHF3 (Affinity Capture-MS), PHF3 (Affinity Capture-MS), PHF3 (Affinity Capture-MS), PHF3 (Affinity Capture-MS)

ESM2 similar proteins: A0JM80, A6H8Y1, A7MBJ2, D3ZF42, E9Q6J5, F4I700, F4J3S1, F4KCE9, F6QRE9, O04251, O82345, P23497, P46100, P48785, P48786, Q04996, Q05B65, Q0WTB8, Q13342, Q15361, Q32MZ4, Q3UZ39, Q3ZBR9, Q4QSC8, Q571C7, Q5H9K5, Q5RHP9, Q61687, Q66HF9, Q7YQM3, Q7YQM4, Q7Z5L2, Q8BJM3, Q8C4A5, Q8C9B9, Q8GZ87, Q8H991, Q8IW19, Q92576, Q940Y3

Diamond homologs: B1ASB6, P10711, P23193, Q148K0, Q15560, Q29RL9, Q4KLL0, Q6ZMY3, Q92576, A2WXR5, A2XTW9, A2Y0Q2, A2Y4R8, B8ADZ3, B8AMA8, B8B8C5, B8B8I3, B8BJV8, F4JL28, O81488, P0CF52, P0CH95, Q12830, Q2R837, Q3UWM4, Q40359, Q5EA28, Q5RHD1, Q5XEM9, Q60DW3, Q6BER5, Q6BXJ4, Q6YTY3, Q6Z7F4, Q6ZMT4, Q75IR6, Q7F2Z1, Q7XUW3, Q80TJ7, Q84TV4

SIGNOR signaling

2 interactions.

A	Effect	B	Mechanism
PHF3	“down-regulates activity”	“RNA Polymerase II”	binding
PHF3	“down-regulates activity”	POLR2A	binding

Enriched among interaction partners

Reactome pathways and GO biological processes over-represented among this gene’s 105 IntAct physical interaction partners (hypergeometric vs the genome-wide background, BH-FDR, gene-set size 15–500, ranked by fold). A functional readout of the neighbourhood — distinct from this gene’s own memberships above, and biased toward well-studied / hub proteins, so read it as themes rather than proof.

Reactome pathways:

Pathway	Partners	Fold	FDR
RHO GTPases activate PKNs	7	27.4×	7e-07
Intrinsic Pathway for Apoptosis	6	21.7×	2e-05
mRNA Polyadenylation	14	15.2×	2e-10
mRNA Splicing - Minor Pathway	5	13.8×	7e-04
SARS-CoV-1-host interactions	6	13.0×	2e-04
Apoptosis	6	12.4×	3e-04
mRNA Splicing	9	12.2×	6e-06
mRNA 3’-end processing	5	12.2×	1e-03

GO biological processes:

GO term	Partners	Fold	FDR
mRNA splicing, via spliceosome	11	10.4×	6e-06
nucleosome assembly	7	10.1×	2e-03

Disease & clinical

Clinical variants and AI predictions

ClinVar

339 variants total. Per-class counts are floors (≥ shown; pagination cap):

Classification	Count (floor)
Pathogenic	2
Likely pathogenic	5
Uncertain significance	251
Likely benign	38
Benign	13

Top pathogenic / likely-pathogenic (7)

Variant ID	HGVS	Classification
143115	NM_001142800.2(EYS):c.8805C>A (p.Tyr2935Ter)	Pathogenic
812311	NM_001142800.2(EYS):c.9223_9232del (p.Asn3075fs)	Pathogenic
143114	NM_001142800.2(EYS):c.8376_8379dup (p.Glu2794fs)	Likely pathogenic
1683284	NM_001142800.2(EYS):c.8628dup (p.Thr2877fs)	Likely pathogenic
1704515	NM_001142800.2(EYS):c.8541T>A (p.Cys2847Ter)	Likely pathogenic
517188	NM_001142800.2(EYS):c.8678del (p.Asn2893fs)	Likely pathogenic
812310	NM_001142800.2(EYS):c.9329G>C (p.Gly3110Ala)	Likely pathogenic

SpliceAI

3490 predictions. Top by Δscore:

Variant	Effect	Δscore
6:63646523:ATAG:A	acceptor_gain	1.0000
6:63646525:A:AG	acceptor_gain	1.0000
6:63646525:A:T	acceptor_loss	1.0000
6:63646525:AG:A	acceptor_gain	1.0000
6:63646526:G:GC	acceptor_gain	1.0000
6:63646526:GG:G	acceptor_gain	1.0000
6:63646526:GGGCT:G	acceptor_gain	1.0000
6:63646791:AACAG:A	donor_loss	1.0000
6:63646796:G:A	donor_loss	1.0000
6:63646797:T:G	donor_loss	1.0000
6:63679996:CTAG:C	acceptor_loss	1.0000
6:63679997:TAGTT:T	acceptor_loss	1.0000
6:63679998:A:AG	acceptor_gain	1.0000
6:63679998:AGT:A	acceptor_loss	1.0000
6:63679998:AGTT:A	acceptor_gain	1.0000
6:63679999:G:GG	acceptor_gain	1.0000
6:63679999:GT:G	acceptor_gain	1.0000
6:63679999:GTT:G	acceptor_gain	1.0000
6:63679999:GTTG:G	acceptor_gain	1.0000
6:63679999:GTTGT:G	acceptor_gain	1.0000
6:63680091:GAACT:G	donor_gain	1.0000
6:63680157:ACAAG:A	donor_loss	1.0000
6:63680158:CAAGG:C	donor_loss	1.0000
6:63680159:AAGG:A	donor_loss	1.0000
6:63680160:AGGTA:A	donor_loss	1.0000
6:63680161:GGTA:G	donor_loss	1.0000
6:63680162:G:GC	donor_loss	1.0000
6:63680163:T:G	donor_loss	1.0000
6:63692042:GG:G	donor_gain	1.0000
6:63692043:GG:G	donor_gain	1.0000

AlphaMissense

13617 scored. Top likely-pathogenic:

Variant	Protein change	am_pathogenicity
6:63685880:T:C	C720R	1.000
6:63685889:T:C	C723R	1.000
6:63691745:T:A	V733D	1.000
6:63691750:T:A	C735S	1.000
6:63691750:T:C	C735R	1.000
6:63691751:G:A	C735Y	1.000
6:63691751:G:C	C735S	1.000
6:63691752:T:G	C735W	1.000
6:63691759:T:A	C738S	1.000
6:63691759:T:C	C738R	1.000
6:63691760:G:A	C738Y	1.000
6:63691760:G:C	C738S	1.000
6:63691761:T:G	C738W	1.000
6:63691768:T:A	W741R	1.000
6:63691768:T:C	W741R	1.000
6:63691783:T:C	C746R	1.000
6:63691843:T:C	C766R	1.000
6:63691852:T:C	C769R	1.000
6:63698334:T:A	V931D	1.000
6:63698346:T:C	L935P	1.000
6:63698358:T:C	L939P	1.000
6:63698499:C:A	A959D	1.000
6:63698520:T:C	L966P	1.000
6:63698552:T:C	Y977H	1.000
6:63698557:G:C	K978N	1.000
6:63698557:G:T	K978N	1.000
6:63698564:T:G	Y981D	1.000
6:63698568:G:C	R982T	1.000
6:63698569:A:C	R982S	1.000
6:63698569:A:T	R982S	1.000

dbSNP variants (sampled 300 via entrez): RS1000033724 (6:63682839 G>A,T), RS1000039362 (6:63659977 A>T), RS1000045758 (6:63642892 C>T), RS1000117434 (6:63641581 A>G), RS1000142424 (6:63716452 T>A), RS1000160330 (6:63719599 G>A,T), RS1000184409 (6:63688612 G>A), RS1000187964 (6:63681561 A>G), RS1000239438 (6:63716092 C>G,T), RS1000258555 (6:63637345 T>A), RS1000275407 (6:63719362 A>T), RS1000298955 (6:63688886 A>G), RS1000326426 (6:63672080 G>A), RS1000386099 (6:63670955 T>A,C), RS1000436499 (6:63709532 C>T)

Disease associations

OMIM: gene MIM:607789 | disease phenotypes: MIM:602772, MIM:268000

GenCC curated gene-disease

Mondo (6): retinitis pigmentosa 25 (MONDO:0011272), inherited retinal dystrophy (MONDO:0019118), retinitis pigmentosa (MONDO:0019200), neurodevelopmental disorder (MONDO:0700092), autism spectrum disorder (MONDO:0005258), intellectual disability (MONDO:0001071)

Orphanet (4): OBSOLETE: Inherited retinal disorder (Orphanet:71862), Retinitis pigmentosa (Orphanet:791), NON RARE IN EUROPE: Autism (Orphanet:106), NON RARE IN EUROPE: Unexplained intellectual disability (Orphanet:319658)

HPO phenotypes

1 total (1 of 1 shown, HPO-id order):

HPO	Term
HP:0000556	Retinal dystrophy

GWAS associations

3 associations (top):

Study	Trait	p-value
GCST004946_57	Schizophrenia	3.000000e-08
GCST008508_3	Stress sensitivity (neuroticism score x major depressive disorder status interaction)	5.000000e-06
GCST009391_1291	Metabolite levels	9.000000e-06

EFO canonical traits (2, from GWAS)

EFO ID	Trait name
EFO:0007660	neuroticism measurement
EFO:0010548	xanthine measurement

MeSH disease descriptors (5)

Descriptor	Name	Tree numbers
D008607	Intellectual Disability	C10.597.606.360; C23.888.592.604.646; F01.700.687; F03.625.539
D065886	Neurodevelopmental Disorders	F03.625
D058499	Retinal Dystrophies	C11.768.585.658
D012174	Retinitis Pigmentosa	C11.270.684; C11.768.585.658.500; C16.320.290.684
C566425	Retinitis Pigmentosa 25 (supp.)

Drugs & pharmacology

Drug and pharmacology data

Is drug target: no

PharmGKB: 1 entry (VIP=true, CPIC=false)

CTD chemical–gene interactions

38 total (human), top 30 by PubMed support.

Chemical	Actions (top 5)	PubMed papers
trichostatin A	affects cotreatment, decreases expression, increases expression	3
Valproic Acid	decreases expression	3
bisphenol A	increases methylation, increases expression, affects cotreatment	2
7,8-Dihydro-7,8-dihydroxybenzo(a)pyrene 9,10-oxide	decreases expression	2
aristolochic acid I	decreases expression	1
GSK-J4	increases expression	1
FR900359	affects phosphorylation	1
TAK-243	decreases sumoylation	1
testosterone enanthate	affects expression	1
sodium arsenate	decreases expression	1
beta-lapachone	increases expression	1
arsenite	affects binding, decreases reaction	1
tris(1,3-dichloro-2-propyl)phosphate	increases expression	1
zinc chromate	increases abundance, increases expression	1
di-n-butylphosphoric acid	affects expression	1
chromium hexavalent ion	increases abundance, increases expression	1
perfluorooctane sulfonic acid	decreases expression	1
K 7174	increases expression	1
4-(5-benzo(1,3)dioxol-5-yl-4-pyridin-2-yl-1H-imidazol-2-yl)benzamide	affects cotreatment, decreases expression	1
dorsomorphin	affects cotreatment, decreases expression	1
Resveratrol	affects cotreatment, increases expression	1
Fulvestrant	affects cotreatment, increases methylation	1
Leflunomide	increases expression	1
Benzo(a)pyrene	decreases methylation	1
Caffeine	affects phosphorylation	1
Clorgyline	increases expression	1
Diuron	decreases expression	1
Doxorubicin	decreases expression	1
Enzyme Inhibitors	decreases activity, increases O-linked glycosylation	1
Melphalan	decreases expression	1

Cellosaurus cell lines

4 cell lines: 4 cancer cell line

First 10 cell lines (id-ordered, not curated):

Cellosaurus	Name	Category	Sex
CVCL_TD13	HAP1 PHF3 (-) 1	Cancer cell line	Male
CVCL_TD14	HAP1 PHF3 (-) 2	Cancer cell line	Male
CVCL_TD15	HAP1 PHF3 (-) 3	Cancer cell line	Male
CVCL_TD16	HAP1 PHF3 (-) 4	Cancer cell line	Male

Clinical trials (associated diseases)

259 trials via MONDO — disease-level, not drug-specific.

Trial	Phase	Status	Title
NCT00717080	PHASE4	COMPLETED	The Role of Capsular Tension Ring (CTR) in Anterior Capsular Contraction
NCT04224207	PHASE3	COMPLETED	Management of Retinitis Pigmentosa by Mesenchymal Stem Cells by Wharton’s Jelly Derived Mesenchymal Stem Cells
NCT07082855	PHASE3	NOT_YET_RECRUITING	A Multicenter, Randomized, Double-Blind, Controlled Clinical Study of Minocycline for the Treatment of Retinitis Pigmentosa
NCT00000114	PHASE3	COMPLETED	Randomized Trial of Vitamin A and Vitamin E Supplementation for Retinitis Pigmentosa
NCT00000116	PHASE3	COMPLETED	Randomized Trial of DHA for Retinitis Pigmentosa Patients Receiving Vitamin A
NCT00346333	PHASE3	COMPLETED	Clinical Trial of Lutein for Patients With Retinitis Pigmentosa Receiving Vitamin A
NCT01786395	PHASE3	TERMINATED	Phase III Efficacy and Safety Clinical Study of UF-021 for Treatment of Retinitis Pigmentosa
NCT04636853	PHASE3	COMPLETED	CB-PRP in Retinitis Pigmentosa and Dry Age-related Macular Degeneration
NCT05537220	PHASE3	ACTIVE_NOT_RECRUITING	Oral N-acetylcysteine for Retinitis Pigmentosa
NCT05800301	PHASE3	COMPLETED	Management of Retinitis Pigmentosa Via Combination of Wharton’s Jelly-derived Mesenchymal Stem Cells and Magnovision
NCT05926583	PHASE3	ACTIVE_NOT_RECRUITING	A Study of AAV5-hRKp.RPGR for the Treatment of Japanese Participants With X-linked Retinitis Pigmentosa
NCT06388200	PHASE3	ACTIVE_NOT_RECRUITING	A Phase 3 Study Of OCU400 Gene Therapy for the Treatment Of Retinitis Pigmentosa
NCT07290530	PHASE3	NOT_YET_RECRUITING	24-Month Trial of NPI-001 for the Preservation of Photoreceptors in Retinitis Pigmentosa Associated With Usher Syndrome
NCT03763227	PHASE2	COMPLETED	Intravitreal Ranibizumab (Lucentis®) in the Treatment of Non-leaking Macular Cysts in Retinal Dystrophy
NCT04068207	PHASE2	COMPLETED	Minocycline Treatment in Retinitis Pigmentosa
NCT04945772	PHASE2	COMPLETED	Efficacy and Safety of MCO-010 Optogenetic Therapy in Adults With Retinitis Pigmentosa [RESTORE]
NCT00100230	PHASE2	COMPLETED	DHA and X-Linked Retinitis Pigmentosa
NCT00447980	PHASE2	COMPLETED	A Study of Encapsulated Cell Technology (ECT) Implant for Participants With Early Stage Retinitis Pigmentosa
NCT00447993	PHASE2	COMPLETED	A Study of Encapsulated Cell Technology (ECT) Implant for Patients With Late Stage Retinitis Pigmentosa
NCT01233609	PHASE2	COMPLETED	Trial of Oral Valproic Acid for Retinitis Pigmentosa
NCT01399515	PHASE2	COMPLETED	Efficacy and Safety of Oral Valproic Acid for Retinitis Pigmentosa
NCT01530659	PHASE2	COMPLETED	Retinal Imaging in CNTF -Releasing Encapsulated Cell Implant Treated Patients for Early-stage Retinitis Pigmentosa
NCT01560715	PHASE2	COMPLETED	Autologous Bone Marrow-Derived Stem Cells Transplantation For Retinitis Pigmentosa
NCT02609165	PHASE2	COMPLETED	Nerve Growth Factor Eye Drops Treatment in Patients With Retinitis Pigmentosa and Cystoid Macular Edema
NCT02661711	PHASE2	COMPLETED	Aflibercept for Macular Oedema With Underlying Retinitis Pigmentosa (AMOUR) Study
NCT02804360	PHASE2	UNKNOWN	Intravitreal Dexamethasone Implant in Retinitis Pigmentosa-related Macular Edema- a Retrospective Study
NCT02837640	PHASE2	UNKNOWN	Studying a Potential Protective Effect of L-Dopa on Retinitis Pigmentosa
NCT03073733	PHASE2	COMPLETED	Safety and Efficacy of Intravitreal Injection of Human Retinal Progenitor Cells in Adults With Retinitis Pigmentosa
NCT04356716	PHASE2	COMPLETED	Sildenafil for Treatment of Choroidal Ischemia
NCT04604899	PHASE2	COMPLETED	Safety of Repeat Intravitreal Injection of Human Retinal Progenitor Cells (jCell) in Adult Subjects With Retinitis Pigmentosa
NCT04763369	PHASE2	UNKNOWN	Investigation of Therapeutic Efficacy and Safety of UMSCs for the Management of Retinitis Pigmentosa (RP)
NCT04864496	PHASE2	UNKNOWN	Effects of Treatment With N- Acetylcysteine on Visual Outcomes in Patients With Retinitis Pigmentosa
NCT05085964	PHASE2	TERMINATED	An Open-Label Extension Study to Evaluate Safety & Tolerability of QR-421a in Subjects With Retinitis Pigmentosa
NCT05392179	PHASE2	COMPLETED	A Study in Subjects With Retinitis Pigmentosa
NCT06627179	PHASE2	RECRUITING	Study to Evaluate Ultevursen in Subjects With Retinitis Pigmentosa (RP) Due to Mutations in Exon 13 of the USH2A Gene
NCT06628947	PHASE2	RECRUITING	A Phase II Study of Intravitreal KIO-301 in Patients With Late-stage Retinitis Pigmentosa
NCT06912633	PHASE2	RECRUITING	Safety of a Single, Intravitreal Injection of 6.0M jCell (Famzeretcel) in Retinitis Pigmentosa (RP)
NCT05902962	PHASE1	COMPLETED	SAD of IVT VP-001 in PRPF31 Mutation-Associated Retinal Dystrophy Subjects
NCT06319872	PHASE1	RECRUITING	The Effects of Disulfiram (Antabuse®) on Visual Acuity in Patients With Retinal Degeneration
NCT06455826	PHASE1	COMPLETED	MAD of IVT VP-001 in PRPF31 Mutation-Associated Retinal Dystrophy Subjects (Wallaby)