PRDM13

Summary

PRDM13 (PR/SET domain 13, HGNC:13998) is a protein-coding gene on chromosome 6q16.2, encoding PR domain zinc finger protein 13 (Q9H4Q3). May be involved in transcriptional regulation.

Predicted to enable histone methyltransferase activity. Predicted to be involved in regulation of gene expression. Predicted to act upstream of or within negative regulation of transcription by RNA polymerase II and neurogenesis. Predicted to be active in nucleus. Implicated in pontocerebellar hypoplasia.

Source: NCBI Gene 59336 — RefSeq curated summary.

At a glance

• Gene–disease (curated): North Carolina macular dystrophy (Definitive, GenCC) — +3 more curated relationships
• GWAS associations: 5
• Clinical variants (ClinVar): 528 total — 5 pathogenic
• Phenotypes (HPO): 48
• Druggable target: yes
• MANE Select transcript: NM_021620

Identifiers

Gene identifiers

Field	Value
HGNC ID	HGNC:13998
Approved symbol	PRDM13
Name	PR/SET domain 13
Location	6q16.2
Locus type	gene with protein product
Status	Approved
Aliases	PFM10
Ensembl gene	ENSG00000112238
Ensembl biotype	protein_coding
OMIM	616741
Entrez	59336

Gene structure

Transcript identifiers

Ensembl transcripts: 2 — 1 nonsense_mediated_decay, 1 protein_coding

ENST00000369214, ENST00000369215

RefSeq mRNA: 1 — MANE Select: NM_021620 NM_021620

CCDS: CCDS43487

Canonical transcript exons

ENST00000369215 — 4 exons

Exon	Start	End
ENSE00000840235	99608741	99608872
ENSE00001449183	99606833	99607178
ENSE00001817192	99613033	99615562
ENSE00003702584	99609187	99609307

Expression profiles

Bgee: expression breadth tissue_specific, 7 present calls, max score 81.50.

FANTOM5 (CAGE): breadth tissue_specific, TPM avg 0.1053 / max 9.0051, expressed in 77 samples.

FANTOM5 promoters (1 alternative TSS)

Promoter ID	TPM avg	Samples expressed
68990	0.1053	77

Top tissues by expression

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

Tissue	Anatomy ID	Expression score	Quality
male germ line stem cell (sensu Vertebrata) in testis	CL:0000089 ∩ UBERON:0000473	81.50	silver quality
buccal mucosa cell	CL:0002336	71.76	gold quality
hair follicle	UBERON:0002073	62.68	gold quality
diaphragm	UBERON:0001103	62.02	gold quality
primordial germ cell in gonad	CL:0000670 ∩ UBERON:0000991	61.14	gold quality
periodontal ligament	UBERON:0008266	57.99	gold quality
decidua	UBERON:0002450	56.55	gold quality
pancreatic ductal cell	CL:0002079	51.47	silver quality
ileal mucosa	UBERON:0000331	50.05	silver quality
Brodmann (1909) area 46	UBERON:0006483	49.90	gold quality
epithelial cell of pancreas	CL:0000083	49.72	gold quality
blood vessel layer	UBERON:0004797	49.29	gold quality
cervix squamous epithelium	UBERON:0006922	49.20	gold quality
olfactory bulb	UBERON:0002264	48.92	gold quality
choroid plexus epithelium	UBERON:0003911	48.89	gold quality
quadriceps femoris	UBERON:0001377	48.88	gold quality
myocardium	UBERON:0002349	48.87	gold quality
type B pancreatic cell	CL:0000169	48.83	gold quality
cardiac muscle of right atrium	UBERON:0003379	48.55	gold quality
CA1 field of hippocampus	UBERON:0003881	48.50	gold quality
deltoid	UBERON:0001476	48.38	gold quality
vastus lateralis	UBERON:0001379	48.25	gold quality
left ventricle myocardium	UBERON:0006566	48.24	gold quality
orbitofrontal cortex	UBERON:0004167	48.20	gold quality
upper arm skin	UBERON:0004263	48.06	gold quality
cervix epithelium	UBERON:0004801	48.04	gold quality
oviduct epithelium	UBERON:0004804	48.00	gold quality
tongue squamous epithelium	UBERON:0006919	47.92	gold quality
mucosa of urinary bladder	UBERON:0001259	47.80	gold quality
lower lobe of lung	UBERON:0008949	47.79	silver quality

Single-cell (SCXA)

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

Experiment	Marker?	Max mean expression
E-ANND-3	yes	2.63

Regulation

Is transcription factor: yes

Downstream targets (CollecTRI)

3 targets.

Target	Regulation
PTF1A
TLX1	Repression
TLX3

JASPAR motifs

Motif	Name	Family
MA2536.1	PRDM13	Factors with multiple dispersed zinc fingers

JASPAR matrix evidence (PMIDs): PMID:28850031

Upstream regulators (CollecTRI, top): NKX2-1, PTF1A

miRNA regulators (miRDB)

51 targeting PRDM13, 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-30A-5P	100.00	76.31	3233
HSA-MIR-30B-5P	100.00	76.29	3248
HSA-MIR-30C-5P	100.00	76.29	3248
HSA-MIR-30D-5P	100.00	76.32	3233
HSA-MIR-30E-5P	100.00	76.32	3242
HSA-MIR-5692A	100.00	74.40	6850
HSA-MIR-190A-3P	100.00	80.35	5520
HSA-MIR-8485	100.00	77.57	4731
HSA-MIR-371B-5P	99.99	75.34	4759
HSA-MIR-373-5P	99.98	75.36	4753
HSA-MIR-616-5P	99.98	75.58	4775
HSA-MIR-25-3P	99.98	74.60	1817
HSA-MIR-32-5P	99.98	75.21	1964
HSA-MIR-363-3P	99.98	74.72	1821
HSA-MIR-367-3P	99.98	74.83	1819
HSA-MIR-92A-3P	99.98	75.21	1960
HSA-MIR-92B-3P	99.98	75.25	1955
HSA-MIR-548AN	99.97	70.91	2817
HSA-MIR-548AA	99.96	70.64	3753
HSA-MIR-548AP-3P	99.96	70.64	3753
HSA-MIR-548T-3P	99.96	70.64	3753
HSA-MIR-124-3P	99.89	73.74	3043
HSA-MIR-506-3P	99.89	73.55	3057
HSA-MIR-3065-3P	99.87	70.25	1407
HSA-LET-7A-2-3P	99.87	70.53	1921
HSA-MIR-3941	99.86	70.54	2735
HSA-MIR-383-3P	99.85	65.84	1359
HSA-LET-7G-3P	99.85	70.43	1929
HSA-MIR-4495	99.82	72.08	3080
HSA-MIR-548AU-3P	99.70	68.22	1373

Literature-anchored findings (GeneRIF, showing 9)

• Findings indicate that Prdm13/Nkx2-1-mediated signaling in the DMC declines with advanced age, leading to decreased sleep quality and increased adiposity. (PMID:25546159)
• The duplication found in the RFS355 family is distinct from the previously reported duplication and provides additional support that dysregulation of PRDM13, not CCNC, is the cause of NCMD mapped to the MCDR1 locus. (PMID:27777503)
• The over-expression of PRDM13 upregulated deleted in liver cancer 1 (DLC1) to inhibit the proliferation and invasion of U87 cells. (PMID:29767251)
• These results prompt us to propose RECQL5 as a gene that would be worth to analyze in larger studies to explore its possible implication in BC susceptibility. (PMID:30710461)
• A unique PRDM13-associated variant in a Georgian Jewish family with probable North Carolina macular dystrophy and the possible contribution of a unique CFH variant. (PMID:32476814)
• North Carolina Macular Dystrophy: Phenotypic Variability and Computational Analysis of Disease-Associated Noncoding Variants. (PMID:34125159)
• A novel duplication involving PRDM13 in a Turkish family supports its role in North Carolina macular dystrophy (NCMD/MCDR1). (PMID:34526759)
• A recessive PRDM13 mutation results in congenital hypogonadotropic hypogonadism and cerebellar hypoplasia. (PMID:34730112)
• Two novel non-coding single nucleotide variants in the DNase1 hypersensitivity site of PRDM13 causing North Carolina macular dystrophy in Korea. (PMID:38601016)

Cross-species orthologs

4 orthologs

Organism	Symbol	Gene ID
danio_rerio	prdm13	ENSDARG00000078701
mus_musculus	Prdm13	ENSMUSG00000040478
rattus_norvegicus	Prdm13	ENSRNOG00000083626
drosophila_melanogaster	Prdm13	FBGN0035687

Paralogs (28): ZNF280C (ENSG00000056277), ZBTB25 (ENSG00000089775), BCL6 (ENSG00000113916), FEZF1 (ENSG00000128610), ZBTB46 (ENSG00000130584), PRDM12 (ENSG00000130711), ZNF280D (ENSG00000137871), NACC2 (ENSG00000148411), FEZF2 (ENSG00000153266), ZBTB7B (ENSG00000160685), NACC1 (ENSG00000160877), BCL6B (ENSG00000161940), GFI1 (ENSG00000162676), GFI1B (ENSG00000165702), ZBTB49 (ENSG00000168826), ZNF280A (ENSG00000169548), ZNF581 (ENSG00000171425), ZNF524 (ENSG00000171443), ZBTB26 (ENSG00000171448), ZBTB21 (ENSG00000173276), ZNF683 (ENSG00000176083), ZBTB33 (ENSG00000177485), ZBTB3 (ENSG00000185670), ZBTB6 (ENSG00000186130), ZBTB14 (ENSG00000198081), ZBTB12 (ENSG00000204366), ZNF580 (ENSG00000213015), ZNF280B (ENSG00000275004)

Protein

Protein identifiers

PR domain zinc finger protein 13 — Q9H4Q3 (reviewed: Q9H4Q3)

Alternative names: PR domain-containing protein 13

All UniProt accessions (2): Q9H4Q3, A0A0A0MRL5

UniProt curated annotations — full annotation on UniProt →

Function. May be involved in transcriptional regulation. Is required for the differentiation of KISS1-expressing neurons in the arcuate (Arc) nucleus of the hypothalamus. Is a critical regulator of GABAergic cell fate in the cerebellum, required for normal postnatal cerebellar development.

Subcellular location. Nucleus.

Tissue specificity. In the embryo, expressed in neural stem cells of the hindbrain.

Disease relevance. Cerebellar dysfunction, impaired intellectual development, and hypogonadotropic hypogonadism (CDIDHH) [MIM:619761] An autosomal recessive disorder characterized by delayed motor development, ataxia with cerebellar hypoplasia, severe progressive scoliosis, moderate to severe intellectual disability, and delayed puberty with congenital hypogonadotropic hypogonadism. The disease is caused by variants affecting the gene represented in this entry. Pontocerebellar hypoplasia 17 (PCH17) [MIM:619909] A form of pontocerebellar hypoplasia, a disorder characterized by structural defects of the pons and cerebellum, evident upon brain imaging. PCH17 is an autosomal recessive, severe form clinically characterized by neonatal hypotonia, feeding and respiratory difficulties, central apnea, and bradycardia. Most affected individuals die in infancy. Brain imaging shows cerebellar and brainstem hypoplasia. The disease is caused by variants affecting the gene represented in this entry.

Similarity. Belongs to the class V-like SAM-binding methyltransferase superfamily.

RefSeq proteins (1): NP_067633* (*=MANE)

Domains & families (InterPro)

ID	Name	Type
IPR001214	SET_dom	Domain
IPR013087	Znf_C2H2_type	Domain
IPR036236	Znf_C2H2_sf	Homologous_superfamily
IPR044407	PRDM13_PR/SET	Domain
IPR046341	SET_dom_sf	Homologous_superfamily
IPR050331	Zinc_finger_PRDM4/PRDM1/PRDM14	Family

Pfam: PF00096, PF21549

UniProt features (15 total): region of interest 5, zinc finger region 4, compositionally biased region 3, chain 1, domain 1, sequence variant 1

Structure

Experimental structures (PDB)

0 structures.

Predicted structure (AlphaFold)

Model	pLDDT	Fraction very-high
AF-Q9H4Q3-F1	53.52	0.01

Function

Pathways and Gene Ontology

Reactome pathways

0 pathways

MSigDB gene sets: 217 (showing top): BENPORATH_ES_WITH_H3K27ME3, GCANCTGNY_MYOD_Q6, GOBP_NEUROGENESIS, GGGTGGRR_PAX4_03, CAGCTG_AP4_Q5, GOBP_FOREBRAIN_DEVELOPMENT, GOBP_GABAERGIC_NEURON_DIFFERENTIATION, PAX2_01, NKX61_01, GTGCCTT_MIR506, GOBP_HYPOTHALAMUS_DEVELOPMENT, TCF4_Q5, IRF7_01, TGANTCA_AP1_C, PPAR_DR1_Q2

GO Biological Process (7): negative regulation of transcription by RNA polymerase II (GO:0000122), regulation of gene expression (GO:0010468), hypothalamus cell differentiation (GO:0021979), methylation (GO:0032259), GABAergic neuron differentiation (GO:0097154), chromatin remodeling (GO:0006338), neurogenesis (GO:0022008)

GO Molecular Function (9): DNA binding (GO:0003677), chromatin binding (GO:0003682), zinc ion binding (GO:0008270), histone methyltransferase activity (GO:0042054), RNA polymerase II-specific DNA-binding transcription factor binding (GO:0061629), protein binding (GO:0005515), methyltransferase activity (GO:0008168), transferase activity (GO:0016740), metal ion binding (GO:0046872)

GO Cellular Component (1): nucleus (GO:0005634)

GO top-level categories

Rollup of top GO terms by namespace:

Category	Terms
cell differentiation	2
binding	2
regulation of transcription by RNA polymerase II	1
transcription by RNA polymerase II	1
negative regulation of DNA-templated transcription	1
gene expression	1
regulation of macromolecule biosynthetic process	1
hypothalamus development	1
metabolic process	1
neuron differentiation	1
chromatin organization	1
nervous system development	1
nucleic acid binding	1
transition metal ion binding	1
protein methyltransferase activity	1
histone modifying activity	1
DNA-binding transcription factor binding	1
transferase activity, transferring one-carbon groups	1
catalytic activity	1
cation binding	1
intracellular membrane-bounded organelle	1

Protein interactions and networks

STRING

1174 interactions, top by confidence (×1000):

Protein A	Protein B	Partner UniProt	Score
PRDM13	PTF1A	Q7RTS3	546
PRDM13	PRDM7	Q9NQW5	510
PRDM13	TLX3	O43711	500
PRDM13	BHLHE22	Q8NFJ8	499
PRDM13	PRDM2	Q13029	490
PRDM13	PRDM11	Q9NQV5	482
PRDM13	PCMTD2	Q9NV79	474
PRDM13	CCNC	P24863	474
PRDM13	DPY19L3	Q6ZPD9	473
PRDM13	PRPSAP1	Q14558	459
PRDM13	SMYD5	Q6GMV2	449
PRDM13	FAXC	Q5TGI0	448
PRDM13	PPP1R3G	B7ZBB8	443
PRDM13	NLRP13	Q86W25	433
PRDM13	CHST10	O43529	432

IntAct

3 interactions, top by confidence:

A	B	Type	Score
PRDM13	HNRNPDL	psi-mi:“MI:0915”(physical association)	0.400
PRDM13	H2BC12	psi-mi:“MI:0914”(association)	0.350

BioGRID (10): PRDM13 (Affinity Capture-MS), PRDM13 (Proximity Label-MS), PRDM13 (Affinity Capture-MS), EIF4B (Affinity Capture-MS), PRDM13 (Affinity Capture-MS), PRDM13 (Affinity Capture-MS), PRDM13 (Affinity Capture-MS), PRDM13 (Affinity Capture-MS), PRDM13 (Affinity Capture-MS), PRDM13 (Affinity Capture-MS)

ESM2 similar proteins: A0A8I6AGW3, A2A9A2, A6NMB9, A8MYZ6, E9PZZ1, J3QK54, O02755, O02756, O35392, O35767, O60548, O70220, P05554, P17676, P21272, P28033, P35713, P42582, P49715, P49716, P52952, P53566, P58012, Q12952, Q13461, Q14526, Q60843, Q61345, Q63244, Q63250, Q6BEB4, Q6VFT5, Q6VFT6, Q6ZQN5, Q70KY4, Q8IU81, Q8MIP2, Q8NDY6, Q8R2I0, Q98937

Diamond homologs: A1L2U9, A2A884, A2ANX9, A7Y7X5, B0X9H6, B0YDH7, B1WAZ8, B1WBU4, E9PW05, E9PZZ1, G5EBU4, O15391, O60315, O62836, O75362, O77459, O95863, P08048, P0CS62, P0CS63, P10925, P15822, P17010, P17012, P20662, P22227, P25490, P28166, P31509, P31629, P36197, P52739, P52746, P56270, P56670, P56671, P60319, P80944, Q00899, Q00900

SIGNOR signaling

0 interactions.

Disease & clinical

Clinical variants and AI predictions

ClinVar

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

Classification	Count (floor)
Pathogenic	5
Likely pathogenic	0
Uncertain significance	333
Likely benign	171
Benign	11

Top pathogenic / likely-pathogenic (5)

Variant ID	HGVS	Classification
1342163	NM_021620.4(PRDM13):c.398-2_408del	Pathogenic
1693529	NM_021620.4(PRDM13):c.839del (p.Ala280fs)	Pathogenic
1693530	NM_021620.4(PRDM13):c.844del (p.Val282fs)	Pathogenic
1693531	NM_021620.4(PRDM13):c.800del (p.Gly267fs)	Pathogenic
2426678	NC_000006.11:g.(?100040906)(100062635_?)dup	Pathogenic

SpliceAI

513 predictions. Top by Δscore:

Variant	Effect	Δscore
6:99609179:C:CA	acceptor_gain	1.0000
6:99607066:GC:G	donor_gain	0.9900
6:99609177:T:A	acceptor_gain	0.9900
6:99609181:TCCCA:T	acceptor_loss	0.9900
6:99609182:CCCA:C	acceptor_loss	0.9900
6:99609183:CCAG:C	acceptor_loss	0.9900
6:99609184:CAGA:C	acceptor_loss	0.9900
6:99609185:A:AG	acceptor_gain	0.9900
6:99609186:G:A	acceptor_loss	0.9900
6:99609186:G:GG	acceptor_gain	0.9900
6:99609303:GAAAG:G	donor_gain	0.9900
6:99609304:AAAG:A	donor_loss	0.9900
6:99609305:AAGG:A	donor_loss	0.9900
6:99609306:AGG:A	donor_loss	0.9900
6:99609307:GGTAC:G	donor_loss	0.9900
6:99609308:G:T	donor_loss	0.9900
6:99609309:T:A	donor_loss	0.9900
6:99607166:GCC:G	donor_gain	0.9800
6:99607165:GGCC:G	donor_gain	0.9700
6:99607175:AAAGG:A	donor_loss	0.9700
6:99607178:GGTAT:G	donor_loss	0.9700
6:99607179:GT:G	donor_loss	0.9700
6:99607180:T:A	donor_loss	0.9700
6:99609186:GAT:G	acceptor_gain	0.9700
6:99612723:C:G	acceptor_gain	0.9700
6:99609177:T:TA	acceptor_loss	0.9500
6:99613031:AG:A	acceptor_gain	0.9500
6:99613031:AGG:A	acceptor_gain	0.9500
6:99613032:GG:G	acceptor_gain	0.9500
6:99613032:GGG:G	acceptor_gain	0.9500

AlphaMissense

4514 scored. Top likely-pathogenic:

Variant	Protein change	am_pathogenicity
6:99613050:T:C	C139R	1.000
6:99614358:T:A	C575S	1.000
6:99614358:T:C	C575R	1.000
6:99614359:G:A	C575Y	1.000
6:99614359:G:C	C575S	1.000
6:99614360:C:G	C575W	1.000
6:99614367:T:C	C578R	1.000
6:99614368:G:A	C578Y	1.000
6:99614369:T:G	C578W	1.000
6:99614395:G:A	G587E	1.000
6:99614398:T:C	L588P	1.000
6:99614404:T:A	I590N	1.000
6:99614404:T:C	I590T	1.000
6:99614404:T:G	I590S	1.000
6:99614406:C:A	H591N	1.000
6:99614406:C:G	H591D	1.000
6:99614407:A:G	H591R	1.000
6:99614408:C:A	H591Q	1.000
6:99614408:C:G	H591Q	1.000
6:99614418:C:G	H595D	1.000
6:99614420:C:A	H595Q	1.000
6:99614420:C:G	H595Q	1.000
6:99614442:T:A	C603S	1.000
6:99614442:T:C	C603R	1.000
6:99614443:G:A	C603Y	1.000
6:99614443:G:C	C603S	1.000
6:99614444:C:G	C603W	1.000
6:99614451:T:A	C606S	1.000
6:99614451:T:C	C606R	1.000
6:99614452:G:A	C606Y	1.000

dbSNP variants (sampled 300 via entrez): RS1000154305 (6:99605038 G>A), RS1000441901 (6:99610511 A>G), RS1000644538 (6:99609748 C>A,G,T), RS1000722704 (6:99605838 T>A), RS1000776277 (6:99611842 C>T), RS1001075155 (6:99606062 C>T), RS1001497224 (6:99611527 G>A), RS1002157709 (6:99610198 C>G,T), RS1002343986 (6:99607354 G>A), RS1002601517 (6:99606816 C>A), RS1002667757 (6:99608574 C>T), RS1002720101 (6:99608291 T>A), RS1002758356 (6:99613502 C>A,T), RS1002772195 (6:99608020 G>A), RS1003028640 (6:99606521 G>T)

Disease associations

OMIM: gene MIM:616741 | disease phenotypes: MIM:136550, MIM:619761, MIM:619909

GenCC curated gene-disease

Disease	Classification	Inheritance
North Carolina macular dystrophy	Definitive	Autosomal dominant
cerebellar dysfunction, impaired intellectual development, and hypogonadotropic hypogonadism	Strong	Autosomal recessive
pontocerebellar hypoplasia, IIA 17	Strong	Autosomal recessive
progressive bifocal chorioretinal atrophy	Strong	Autosomal dominant

Mondo (5): North Carolina macular dystrophy (MONDO:0007630), cerebellar dysfunction, impaired intellectual development, and hypogonadotropic hypogonadism (MONDO:0859229), inherited retinal dystrophy (MONDO:0019118), pontocerebellar hypoplasia, IIA 17 (MONDO:0030890), progressive bifocal chorioretinal atrophy (MONDO:0010932)

Orphanet (2): North Carolina macular dystrophy (Orphanet:75327), OBSOLETE: Inherited retinal disorder (Orphanet:71862)

HPO phenotypes

48 total (30 of 48 shown, HPO-id order):

HPO	Term
HP:0000007	Autosomal recessive inheritance
HP:0000028	Cryptorchidism
HP:0000044	Hypogonadotropic hypogonadism
HP:0000054	Micropenis
HP:0000286	Epicanthus
HP:0000294	Low anterior hairline
HP:0000308	Microretrognathia
HP:0000316	Hypertelorism
HP:0000486	Strabismus
HP:0000582	Upslanted palpebral fissure
HP:0000639	Nystagmus
HP:0000823	Delayed puberty
HP:0001249	Intellectual disability
HP:0001250	Seizure
HP:0001252	Hypotonia
HP:0001263	Global developmental delay
HP:0001265	Hyporeflexia
HP:0001270	Motor delay
HP:0001276	Hypertonia
HP:0001290	Generalized hypotonia
HP:0001310	Dysmetria
HP:0001320	Cerebellar vermis hypoplasia
HP:0001321	Cerebellar hypoplasia
HP:0001347	Hyperreflexia
HP:0001511	Intrauterine growth retardation
HP:0001561	Polyhydramnios
HP:0001629	Ventricular septal defect
HP:0001643	Patent ductus arteriosus
HP:0001684	Secundum atrial septal defect
HP:0002015	Dysphagia

GWAS associations

5 associations (top):

Study	Trait	p-value
GCST000880_9	Menarche (age at onset)	2.000000e-08
GCST007118_1	Erectile dysfunction	2.000000e-37
GCST010002_330	Refractive error	2.000000e-15
GCST011494_33	Daytime nap	3.000000e-10
GCST012419_6	Longevity (100 years and older)	4.000000e-08

EFO canonical traits (2, from GWAS)

EFO ID	Trait name
EFO:0004703	age at menarche
EFO:0007828	daytime rest measurement

MeSH disease descriptors (3)

Descriptor	Name	Tree numbers
D058499	Retinal Dystrophies	C11.768.585.658
C535356	Chorioretinal atrophy, progressive bifocal (supp.)
C537835	Macular dystrophy, retinal, 1, North Carolina type (supp.)

Drugs & pharmacology

Drug and pharmacology data

Is drug target: yes

ChEMBL targets (1): CHEMBL5214859 (SINGLE PROTEIN)

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

CTD chemical–gene interactions

24 total (human), top 24 by PubMed support.

Chemical	Actions (top 5)	PubMed papers
Acetaminophen	decreases expression, increases expression	2
bisphenol F	increases methylation	1
propionaldehyde	increases expression	1
bisphenol A	affects cotreatment, decreases methylation	1
arsenite	increases methylation	1
butyraldehyde	increases expression	1
pentanal	increases expression	1
CGP 52608	affects binding, increases reaction	1
nutlin 3	affects cotreatment, increases expression	1
abrine	decreases expression	1
MRK 003	decreases expression	1
jinfukang	affects cotreatment, increases expression	1
Resveratrol	affects cotreatment, decreases expression	1
Fulvestrant	affects cotreatment, decreases methylation, increases methylation	1
Aldehydes	increases expression	1
Benzo(a)pyrene	decreases methylation, increases methylation	1
Camptothecin	increases expression	1
Cisplatin	affects cotreatment, increases expression	1
Dactinomycin	affects cotreatment, increases expression	1
Plant Extracts	affects cotreatment, decreases expression	1
Silicon Dioxide	increases expression	1
Valproic Acid	increases expression	1
Cyclosporine	decreases methylation	1
Aflatoxin B1	decreases methylation	1

ChEMBL screening assays

1 unique, capped per target: 1 binding

Representative assays (with source publication via chembl_document):

Assay ID	Type	Description	Source paper
CHEMBL5214662	Binding	Selectivity interaction (Methyltransferase panel (DSF assay)) EUB0000234b PRDM13	Selectivity Literature for EUbOPEN Chemogenomics Library wave 3

Cellosaurus cell lines

3 cell lines: 3 embryonic stem cell

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

Cellosaurus	Name	Category	Sex
CVCL_A5P9	SEES3-1V human PRDM13, clone1	Embryonic stem cell	Male
CVCL_A5Q0	SEES3-1V human PRDM13, clone2	Embryonic stem cell	Male
CVCL_A5Q1	SEES3-1V human PRDM13, clone3	Embryonic stem cell	Male

Clinical trials (associated diseases)

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

Trial	Phase	Status	Title
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
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]
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)
NCT04855045	PHASE2/PHASE3	UNKNOWN	An Open-label, Dose Escalation and Double-masked, Randomized, Controlled Trial Evaluating Safety and Tolerability of Sepofarsen in Children (<8 Years of Age) With LCA10 Caused by Mutations in the CEP290 Gene.
NCT03872479	PHASE1/PHASE2	UNKNOWN	Single Ascending Dose Study in Participants With LCA10
NCT04123626	PHASE1/PHASE2	ACTIVE_NOT_RECRUITING	A Study to Evaluate the Safety and Tolerability of QR-1123 in Subjects With Autosomal Dominant Retinitis Pigmentosa Due to the P23H Mutation in the RHO Gene
NCT04545736	PHASE1/PHASE2	RECRUITING	Oral Metformin for Treatment of ABCA4 Retinopathy
NCT06212297	PHASE1/PHASE2	ACTIVE_NOT_RECRUITING	Fellow-eye Study (FE) of LX101 in Subjects With Inherited Retinal Dystrophy
NCT06852963	PHASE1/PHASE2	ACTIVE_NOT_RECRUITING	A Repeat-Dose, Open-Label, Two Arm Safety and Efficacy Study of Two Doses of VP-001 Administered Intravitreally in Participants With Confirmed PRPF31 Mutation-Associated Retinal Dystrophy, Including Participants Previously Treated With VP001
NCT07177196	PHASE1/PHASE2	ACTIVE_NOT_RECRUITING	Personalized Antisense Oligonucleotide Therapy for a Single Participant With PRPH2 Mutation Associated With Retinal Dystrophy
NCT07063030	EARLY_PHASE1	RECRUITING	A Study of LX107 Gene Therapy in AIPL1-IRD Patients
NCT01546181	Not specified	COMPLETED	Retinal Imaging by Adaptive Optics in Healthy Eyes and During Retinal and General Diseases
NCT01876147	Not specified	COMPLETED	Visual and Functional Assessment in Low Vision Patients
NCT01920867	Not specified	UNKNOWN	Stem Cell Ophthalmology Treatment Study
NCT02014389	Not specified	RECRUITING	Evaluation of Objective Perimetry Using Chromatic Multifocal Pupillometer
NCT02983305	Not specified	COMPLETED	Optical Head-Mounted Display Technology for Low Vision Rehabilitation
NCT03592017	Not specified	COMPLETED	Performance of Long-wavelength Autofluorescence Imaging
NCT03662386	Not specified	TERMINATED	Prospective Analysis of Genotype-phenotype Correlations Observed in a Large Cohort of Patients With Hereditary Retinal Dystrophies - GEPHIRD
NCT03691168	Not specified	UNKNOWN	Multi-center Observation of the Natural Course of Inherited Retinal Dystrophies
NCT03843840	Not specified	COMPLETED	Dual Wavelength OCT
NCT03853252	Not specified	COMPLETED	iPS Cells of Patients for Models of Retinal Dystrophies
NCT05130385	Not specified	UNKNOWN	High Resolution Optical Coherence Tomography
NCT05294978	Not specified	RECRUITING	EyeConic: Qualification for Cone-Optogenetics
NCT05573984	Not specified	ACTIVE_NOT_RECRUITING	Natural History of PRPF31 Mutation-Associated Retinal Dystrophy
NCT05793515	Not specified	COMPLETED	Mechanisms of Inherited Retinal Dystrophies Using Whole Genome Sequencing and in Vitro and in Vivo Models
NCT05820100	Not specified	COMPLETED	Observational Study to Assess the Reliability and Validity of the MLYMT and MLSDT
NCT05976139	Not specified	RECRUITING	Micropulsed Laser in Patients With Macular Oedema in Retinal Dystrophies
NCT06162585	Not specified	ACTIVE_NOT_RECRUITING	Non-Interventional Long Term Follow-up Study of Participants Previously Enrolled in the RESTORE Study
NCT06177977	Not specified	RECRUITING	SS-HH-OCT as a Novel Diagnostic Modality for Early-Onset Retinal Dystrophies (EORDs)
NCT06375239	Not specified	RECRUITING	Observational Study to Assess Endpoint Operational Feasibility & Measurement Properties in Patients with Retinal Degeneration
NCT06908161	Not specified	NOT_YET_RECRUITING	Functional Assessments in Vision Impairment
NCT07085533	Not specified	RECRUITING	Natural History Study of Inherited Retinal Diseases
NCT07502664	Not specified	RECRUITING	Development and Evaluation of Functional Visual Field and Navigation Endpoints in Moderate to Profound Inherited Retinal Disease (DEFINE-IRD)
NCT07529041	Not specified	ENROLLING_BY_INVITATION	Real-time Acoustic Biofeedback for Enhancing Fixation Stability: A Proof-of-concept Study to Improve Ophthalmic Imaging Diagnostic Quality