PRDM10

Summary

PRDM10 (PR/SET domain 10, HGNC:13995) is a protein-coding gene on chromosome 11q24.3, encoding PR domain zinc finger protein 10 (Q9NQV6). Transcriptional activator, essential for early embryonic development and survival of embryonic stem cells (ESCs). It is a selective cancer dependency (DepMap: 44.5% of cell lines).

The protein encoded by this gene is a transcription factor that contains C2H2-type zinc-fingers. It also contains a positive regulatory domain, which has been found in several other zinc-finger transcription factors including those involved in B cell differentiation and tumor suppression. Studies of the mouse counterpart suggest that this protein may be involved in the development of the central nerve system (CNS), as well as in the pathogenesis of neuronal storage disease. Multiple alternatively spliced transcript variants encoding distinct isoforms have been observed.

Source: NCBI Gene 56980 — RefSeq curated summary.

At a glance

• Gene–disease (curated): Birt-Hogg-Dube syndrome 2 (Limited, GenCC)
• GWAS associations: 3
• Clinical variants (ClinVar): 153 total — 1 pathogenic
• Phenotypes (HPO): 26
• Druggable target: yes
• Cancer dependency (DepMap): dependent in 44.5% of screened cell lines
• MANE Select transcript: NM_199437

Identifiers

Gene identifiers

Field	Value
HGNC ID	HGNC:13995
Approved symbol	PRDM10
Name	PR/SET domain 10
Location	11q24.3
Locus type	gene with protein product
Status	Approved
Aliases	KIAA1231, PFM7, MGC131802
Ensembl gene	ENSG00000170325
Ensembl biotype	protein_coding
OMIM	618319
Entrez	56980

Gene structure

Transcript identifiers

Ensembl transcripts: 11 — 11 protein_coding

ENST00000304538, ENST00000358825, ENST00000360871, ENST00000423662, ENST00000526082, ENST00000527581, ENST00000528746, ENST00000531431, ENST00000887352, ENST00000935517, ENST00000960421

RefSeq mRNA: 14 — MANE Select: NM_199437 NM_001367890, NM_001367891, NM_001367892, NM_001367893, NM_001367894, NM_001367895, NM_001367896, NM_001367897, NM_001367898, NM_001367899, NM_020228, NM_199437, NM_199438, NM_199439

CCDS: CCDS44771, CCDS44772, CCDS8484, CCDS8485, CCDS91624

Canonical transcript exons

ENST00000360871 — 21 exons

Exon	Start	End
ENSE00001128837	129905638	129905741
ENSE00001128841	129910476	129910656
ENSE00001128848	129912085	129912225
ENSE00001128860	129914704	129915018
ENSE00001128879	129917127	129917237
ENSE00001128884	129918539	129918718
ENSE00001128888	129923248	129923403
ENSE00001128902	129931016	129931258
ENSE00001128908	129932102	129932231
ENSE00001128914	129935101	129935218
ENSE00001128918	129937598	129937670
ENSE00001128924	129942426	129942629
ENSE00001281801	129944771	129945012
ENSE00001372867	129960896	129961082
ENSE00001376456	129924882	129925229
ENSE00001376596	130002722	130002835
ENSE00001388304	129955512	129955571
ENSE00001388441	129957746	129957910
ENSE00001390246	129915660	129915860
ENSE00001390700	129947145	129947370
ENSE00003905948	129899711	129902516

Expression profiles

Bgee: expression breadth ubiquitous, 270 present calls, max score 98.25.

FANTOM5 (CAGE): breadth ubiquitous, TPM avg 3.9234 / max 48.3036, expressed in 1625 samples.

FANTOM5 promoters (6 alternative TSS)

Promoter ID	TPM avg	Samples expressed
123150	2.9684	1510
123149	0.5313	278
123148	0.4056	222
123147	0.0126	3
123146	0.0048	3
123145	0.0007	1

Top tissues by expression

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

Tissue	Anatomy ID	Expression score	Quality
secondary oocyte	CL:0000655	98.25	gold quality
oocyte	CL:0000023	96.84	gold quality
sural nerve	UBERON:0015488	84.89	gold quality
tibia	UBERON:0000979	83.67	gold quality
cortical plate	UBERON:0005343	81.45	gold quality
esophagus squamous epithelium	UBERON:0006920	80.86	gold quality
male germ line stem cell (sensu Vertebrata) in testis	CL:0000089 ∩ UBERON:0000473	79.00	gold quality
gastrocnemius	UBERON:0001388	78.81	gold quality
ganglionic eminence	UBERON:0004023	78.32	gold quality
muscle of leg	UBERON:0001383	78.23	gold quality
ventricular zone	UBERON:0003053	78.05	gold quality
cerebellar vermis	UBERON:0004720	77.92	gold quality
jejunal mucosa	UBERON:0000399	77.78	gold quality
cerebellar cortex	UBERON:0002129	77.37	gold quality
cerebellum	UBERON:0002037	77.36	gold quality
upper leg skin	UBERON:0004262	77.31	gold quality
cerebellar hemisphere	UBERON:0002245	77.30	gold quality
germinal epithelium of ovary	UBERON:0001304	77.22	gold quality
deltoid	UBERON:0001476	76.98	gold quality
right hemisphere of cerebellum	UBERON:0014890	76.66	gold quality
stromal cell of endometrium	CL:0002255	76.61	gold quality
epithelium of esophagus	UBERON:0001976	76.55	gold quality
primordial germ cell in gonad	CL:0000670 ∩ UBERON:0000991	75.95	gold quality
parietal pleura	UBERON:0002400	75.73	gold quality
skeletal muscle organ	UBERON:0014892	75.51	gold quality
muscle organ	UBERON:0001630	75.50	gold quality
hindlimb stylopod muscle	UBERON:0004252	75.41	gold quality
pleura	UBERON:0000977	75.29	gold quality
skin of hip	UBERON:0001554	75.27	gold quality
visceral pleura	UBERON:0002401	75.22	gold quality

Single-cell (SCXA)

Detected in 1 experiment(s), a significant marker in 0.

Experiment	Marker?	Max mean expression
E-ANND-3	no	5.19

Regulation

Is transcription factor: yes

Downstream targets (CollecTRI)

4 targets.

Target	Regulation
BCL2	Activation
CDKN2A
IFNB1
PRDM10

Upstream regulators (CollecTRI, top): PRDM10

miRNA regulators (miRDB)

153 targeting PRDM10, 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-7110-3P	100.00	73.18	2486
HSA-MIR-6873-3P	100.00	71.42	2626
HSA-MIR-1277-5P	100.00	73.95	5056
HSA-MIR-5692A	100.00	74.40	6850
HSA-MIR-6833-3P	100.00	70.63	3197
HSA-MIR-4768-5P	100.00	69.49	2861
HSA-MIR-3163	100.00	77.23	8605
HSA-LET-7A-3P	100.00	74.03	3932
HSA-LET-7B-3P	100.00	74.08	3913
HSA-LET-7F-1-3P	100.00	74.02	3928
HSA-MIR-98-3P	100.00	74.08	3907
HSA-MIR-9-5P	100.00	72.28	2361
HSA-MIR-3185	99.99	68.12	1959
HSA-MIR-548C-3P	99.99	74.01	7587
HSA-MIR-3662	99.99	73.82	5684
HSA-MIR-186-5P	99.99	70.83	3707
HSA-MIR-4775	99.98	75.00	6394
HSA-MIR-3692-3P	99.98	70.27	2139
HSA-MIR-548N	99.98	71.94	4170
HSA-MIR-5696	99.98	72.36	4487
HSA-MIR-3617-3P	99.98	67.86	918
HSA-MIR-548AT-5P	99.96	70.83	2666
HSA-MIR-590-3P	99.96	74.34	6478
HSA-MIR-1250-3P	99.96	70.04	4038
HSA-MIR-570-3P	99.96	72.41	4910
HSA-MIR-23A-3P	99.95	74.24	3163
HSA-MIR-23B-3P	99.95	74.24	3163
HSA-MIR-23C	99.95	73.92	3192
HSA-LET-7C-3P	99.95	73.42	2862
HSA-MIR-545-3P	99.95	70.74	2783

Functional genomics

DepMap (CRISPR cell-line fitness): dependent in 44.5% of screened cell lines.

Literature-anchored findings (GeneRIF, showing 6)

• Our results suggest that PRDM10 fusions are present in around 5% of Undifferentiated pleomorphic sarcoma (PMID:25516889)
• PRDM10-fusions represent the critical driver mutations in undifferentiated pleomorphic sarcomas. (PMID:31313299)
• PRDM10 directs FLCN expression in a novel disorder overlapping with Birt-Hogg-Dube syndrome and familial lipomatosis. (PMID:36440963)
• Recurrent PRDM10 Fusions in Superficial CD34-Positive Fibroblastic Tumors : A Clinicopathologic and Molecular Study of 10 Additional Cases of an Emerging Novel Entity. (PMID:36812381)
• PRDM10 RCC: A Birt-Hogg-Dube-like Syndrome Associated With Lipoma and Highly Penetrant, Aggressive Renal Tumors Morphologically Resembling Type 2 Papillary Renal Cell Carcinoma. (PMID:37331486)
• Autophagy-related LncRNA PRDM10-DT responds to UVB radiation in keratinocytes. (PMID:37566921)

Cross-species orthologs

3 orthologs

Organism	Symbol	Gene ID
danio_rerio	prdm10	ENSDARG00000104251
mus_musculus	Prdm10	ENSMUSG00000042496
rattus_norvegicus	Prdm10	ENSRNOG00000007853

Paralogs (36): ZBTB32 (ENSG00000011590), SNAI2 (ENSG00000019549), PRDM1 (ENSG00000057657), PRDM6 (ENSG00000061455), ZNF76 (ENSG00000065029), PATZ1 (ENSG00000100105), MAZ (ENSG00000103495), ZBTB16 (ENSG00000109906), ZNF451 (ENSG00000112200), ZBTB45 (ENSG00000119574), ZNF410 (ENSG00000119725), SNAI1 (ENSG00000124216), ZNF384 (ENSG00000126746), ZBTB1 (ENSG00000126804), VEZF1 (ENSG00000136451), PRDM14 (ENSG00000147596), ZNF276 (ENSG00000158805), ZNF362 (ENSG00000160094), ZNF653 (ENSG00000161914), ZNF281 (ENSG00000162702), ZNF148 (ENSG00000163848), ZNF143 (ENSG00000166478), HIC2 (ENSG00000169635), ZNF296 (ENSG00000170684), ZNF692 (ENSG00000171163), ZNF575 (ENSG00000176472), HIC1 (ENSG00000177374), ZBTB18 (ENSG00000179456), ZBTB42 (ENSG00000179627), ZBTB20 (ENSG00000181722), ZBTB7C (ENSG00000184828), SNAI3 (ENSG00000185669), ZFP91 (ENSG00000186660), MTF1 (ENSG00000188786), SCRT2 (ENSG00000215397), SCRT1 (ENSG00000261678)

Protein

Protein identifiers

PR domain zinc finger protein 10 — Q9NQV6 (reviewed: Q9NQV6)

Alternative names: PR domain-containing protein 10, Tristanin

All UniProt accessions (4): Q9NQV6, E9PIB4, E9PLV1, E9PS52

UniProt curated annotations — full annotation on UniProt →

Function. Transcriptional activator, essential for early embryonic development and survival of embryonic stem cells (ESCs). Supports cell growth and survival during early development by transcriptionally activating the expression of the translation initiation factor EIF3B, to sustain global translation. Activates the transcription of FLNC.

Subcellular location. Nucleus.

Disease relevance. Birt-Hogg-Dube syndrome 2 (BHD2) [MIM:620459] A form of Birt-Hogg-Dube syndrome, a rare genodermatosis usually manifesting in adulthood and characterized by multiple fibrofolliculomas, trichodiscomas, and acrochordons. Patients with this syndrome have an increased susceptibility to develop renal cell carcinoma, lung cysts, and spontaneous pneumothorax. BHD2 inheritance is autosomal dominant. The disease may be caused by variants affecting the gene represented in this entry.

Domain organisation. The SET domain is degenerated, suggesting that it has lost methyltransferase activity.

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

Isoforms (7)

UniProt ID	Names	Canonical?
Q9NQV6-3	3	yes
Q9NQV6-2	2
Q9NQV6-1	1
Q9NQV6-4	4
Q9NQV6-5	5
Q9NQV6-6	6
Q9NQV6-7	7

RefSeq proteins (14): NP_001354819, NP_001354820, NP_001354821, NP_001354822, NP_001354823, NP_001354824, NP_001354825, NP_001354826, NP_001354827, NP_001354828, NP_064613, NP_955469, NP_955470, NP_955471 (=MANE)

Domains & families (InterPro)

ID	Name	Type
IPR001214	SET_dom	Domain
IPR013087	Znf_C2H2_type	Domain
IPR036236	Znf_C2H2_sf	Homologous_superfamily
IPR044403	PRDM10_PR/SET	Domain
IPR046341	SET_dom_sf	Homologous_superfamily
IPR050688	Zinc_finger/UBP_domain	Family

Pfam: PF00096, PF12874, PF21549

UniProt features (54 total): zinc finger region 10, region of interest 9, strand 6, compositionally biased region 5, splice variant 5, sequence conflict 5, sequence variant 3, helix 3, turn 3, modified residue 2, chain 1, domain 1, cross-link 1

Structure

Experimental structures (PDB)

1 structures.

PDB	Method	Resolution (Å)
3IHX	X-RAY DIFFRACTION	2.5

Predicted structure (AlphaFold)

Model	pLDDT	Fraction very-high
AF-Q9NQV6-F1	55.87	0.06

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 (3): 424, 428, 380

Function

Pathways and Gene Ontology

Reactome pathways

0 pathways

MSigDB gene sets: 211 (showing top): MYAATNNNNNNNGGC_UNKNOWN, LFA1_Q6, CMYB_01, SP3_Q3, IVANOVA_HEMATOPOIESIS_LATE_PROGENITOR, GGGTGGRR_PAX4_03, CAGCAGG_MIR370, YY1_02, ZIC1_01, ATTCTTT_MIR186, LASTOWSKA_NEUROBLASTOMA_COPY_NUMBER_DN, GFI1_01, CREB_Q3, POU3F2_02, WHN_B

GO Biological Process (3): positive regulation of DNA-templated transcription (GO:0045893), positive regulation of transcription by RNA polymerase II (GO:0045944), methylation (GO:0032259)

GO Molecular Function (7): DNA binding (GO:0003677), DNA-binding transcription factor activity (GO:0003700), zinc ion binding (GO:0008270), protein binding (GO:0005515), methyltransferase activity (GO:0008168), transferase activity (GO:0016740), metal ion binding (GO:0046872)

GO Cellular Component (3): chromatin (GO:0000785), nucleus (GO:0005634), transcription repressor complex (GO:0017053)

GO top-level categories

Rollup of top GO terms by namespace:

Category	Terms
regulation of DNA-templated transcription	2
DNA-templated transcription	1
positive regulation of RNA biosynthetic process	1
regulation of transcription by RNA polymerase II	1
transcription by RNA polymerase II	1
positive regulation of DNA-templated transcription	1
metabolic process	1
nucleic acid binding	1
transcription cis-regulatory region binding	1
transcription regulator activity	1
transition metal ion binding	1
binding	1
transferase activity, transferring one-carbon groups	1
catalytic activity	1
cation binding	1
chromosome	1
cellular anatomical structure	1
intracellular membrane-bounded organelle	1
transcription regulator complex	1

Protein interactions and networks

STRING

1280 interactions, top by confidence (×1000):

Protein A	Protein B	Partner UniProt	Score
PRDM10	TOP2A	P11388	592
PRDM10	PRDM8	Q9NQV8	540
PRDM10	SETD4	Q9NVD3	505
PRDM10	AVPR2	P30518	502
PRDM10	ENTHD1	Q8IYW4	496
PRDM10	CITED2	Q99967	493
PRDM10	SLITRK1	Q96PX8	489
PRDM10	ZNHIT2	Q9UHR6	463
PRDM10	KATNA1	O75449	458
PRDM10	SRC	P12931	445
PRDM10	TP53	P04637	443
PRDM10	ZNF221	Q9UK13	431
PRDM10	GAPDH	P00354	427
PRDM10	VASN	Q6EMK4	425
PRDM10	PLAC8L1	A1L4L8	417

IntAct

82 interactions, top by confidence:

A	B	Type	Score
LARP7	CCNT1	psi-mi:“MI:0914”(association)	0.850
SDC2	PDPK1	psi-mi:“MI:0914”(association)	0.640
RAP1GDS1	DIRAS1	psi-mi:“MI:0914”(association)	0.640
PRDM10	REL	psi-mi:“MI:0915”(physical association)	0.560
REL	PRDM10	psi-mi:“MI:0915”(physical association)	0.560
N	NOP56	psi-mi:“MI:0914”(association)	0.530
N	RBM47	psi-mi:“MI:0914”(association)	0.530
RPS3	ZNF316	psi-mi:“MI:0914”(association)	0.530
CASQ2	PES1	psi-mi:“MI:0914”(association)	0.530
GPC3	CLGN	psi-mi:“MI:0914”(association)	0.530
PPAN	PPM1G	psi-mi:“MI:0914”(association)	0.530
H2AC20	PPM1G	psi-mi:“MI:0914”(association)	0.530
PRICKLE3	SIAH2	psi-mi:“MI:0914”(association)	0.530
BHLHA15	RPLP0	psi-mi:“MI:0914”(association)	0.530
PRICKLE3	TUBG1	psi-mi:“MI:0914”(association)	0.530
ABT1	ZNF316	psi-mi:“MI:0914”(association)	0.530
DAXX	TNRC18	psi-mi:“MI:0914”(association)	0.530
PRICKLE3	METTL18	psi-mi:“MI:0914”(association)	0.530
GPC3	CANX	psi-mi:“MI:0914”(association)	0.530
PRDM10	CHMP6	psi-mi:“MI:0915”(physical association)	0.400
FOXK2	PHF20L1	psi-mi:“MI:0914”(association)	0.350
CUL1	LGALS8	psi-mi:“MI:0914”(association)	0.350
N	RBM47	psi-mi:“MI:0914”(association)	0.350
GRHL1	POLRMT	psi-mi:“MI:0914”(association)	0.350

BioGRID (85): PRDM10 (Two-hybrid), PRDM10 (Affinity Capture-MS), PRDM10 (Affinity Capture-MS), PRDM10 (Affinity Capture-MS), PRDM10 (Affinity Capture-MS), PRDM10 (Affinity Capture-MS), PRDM10 (Affinity Capture-MS), PRDM10 (Affinity Capture-MS), PRDM10 (Affinity Capture-MS), PRDM10 (Affinity Capture-MS), PRDM10 (Affinity Capture-MS), PRDM10 (Affinity Capture-MS), PRDM10 (Affinity Capture-MS), PRDM10 (Affinity Capture-MS), PRDM10 (Affinity Capture-MS)

ESM2 similar proteins: A1L2U9, A2BID7, B1WAZ8, B4F6U4, E9Q8T2, F1QLG5, H2L008, O08785, O15164, P57071, P70121, Q05516, Q08BR4, Q0IH98, Q0P5J0, Q0VCJ6, Q2M1K9, Q2TAL8, Q3U288, Q3UA37, Q3UTQ7, Q53TQ3, Q56R14, Q5NBY9, Q5RAX9, Q5RGA4, Q5XJV7, Q64127, Q6E2N3, Q6INA9, Q6YND2, Q7Z3K3, Q8BZH4, Q8K0L9, Q8N1W2, Q8QGQ6, Q8R515, Q91YB0, Q91YB2, Q96BR9

Diamond homologs: A2BID7, B4F6U4, E9Q3T6, E9Q8T2, O75626, P57071, Q3UTQ7, Q5R5M1, Q5RAX9, Q60636, Q80V63, Q9NQV6, Q9QZP2, Q9UKN5, Q93560, Q9H4Q3, A1L2U9, A2AGX3, B1WAZ8, B1WBU4, Q02026, Q0IH98, Q0VCJ6, Q65XX7, Q6P882, Q8K3J5, Q96BR9, Q96IT1, Q9BS34, Q9CWH1, Q9GZV8, Q9NQV5, Q9UFB7, Q9UL36, Q9UPG8, A0A163UT06, A2AJ77, A6QPM3, I7HJS4, P0C6Y7

SIGNOR signaling

0 interactions.

Enriched among interaction partners

Reactome pathways and GO biological processes over-represented among this gene’s 97 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
Transport of Mature Transcript to Cytoplasm	5	32.3×	5e-06
Nonsense-Mediated Decay (NMD)	8	31.6×	3e-09
Eukaryotic Translation Initiation	6	31.4×	5e-07
Cap-dependent Translation Initiation	6	31.4×	5e-07
SARS-CoV-1 modulates host translation machinery	6	31.4×	5e-07
Eukaryotic Translation Elongation	6	28.3×	9e-07
Activation of the mRNA upon binding of the cap-binding complex and eIFs, and subsequent binding to 43S	6	27.6×	1e-06
Peptide chain elongation	11	23.7×	7e-11

GO biological processes:

GO term	Partners	Fold	FDR
cytoplasmic translation	12	24.4×	4e-11
ribosomal small subunit biogenesis	9	22.5×	6e-08
regulation of alternative mRNA splicing, via spliceosome	5	13.4×	3e-03
translation	9	10.2×	5e-05
rRNA processing	6	9.3×	3e-03

Disease & clinical

Clinical variants and AI predictions

ClinVar

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

Classification	Count (floor)
Pathogenic	1
Likely pathogenic	0
Uncertain significance	116
Likely benign	4
Benign	6

Top pathogenic / likely-pathogenic (1)

Variant ID	HGVS	Classification
4820053	NC_000011.10:g.127919827_135076614del	Pathogenic

SpliceAI

3555 predictions. Top by Δscore:

Variant	Effect	Δscore
11:129902515:CC:C	acceptor_gain	1.0000
11:129902516:CC:C	acceptor_gain	1.0000
11:129905738:GATG:G	acceptor_gain	1.0000
11:129905740:TG:T	acceptor_gain	1.0000
11:129905742:C:CC	acceptor_gain	1.0000
11:129910470:A:AC	donor_gain	1.0000
11:129910471:C:CC	donor_gain	1.0000
11:129910471:CTTA:C	donor_gain	1.0000
11:129910472:TTA:T	donor_loss	1.0000
11:129910473:TA:T	donor_loss	1.0000
11:129910474:A:AC	donor_gain	1.0000
11:129910474:ACAAT:A	donor_loss	1.0000
11:129910475:C:CG	donor_gain	1.0000
11:129910475:CA:C	donor_gain	1.0000
11:129910475:CAAT:C	donor_gain	1.0000
11:129910475:CAATA:C	donor_gain	1.0000
11:129910653:ATAC:A	acceptor_gain	1.0000
11:129910654:TAC:T	acceptor_gain	1.0000
11:129910656:CCT:C	acceptor_loss	1.0000
11:129910657:C:CA	acceptor_loss	1.0000
11:129910657:C:CC	acceptor_gain	1.0000
11:129910658:T:A	acceptor_loss	1.0000
11:129914714:TGA:T	donor_gain	1.0000
11:129915014:TTGGT:T	acceptor_gain	1.0000
11:129915015:TGGT:T	acceptor_gain	1.0000
11:129915015:TGGTC:T	acceptor_gain	1.0000
11:129915016:GGT:G	acceptor_gain	1.0000
11:129915016:GGTCT:G	acceptor_gain	1.0000
11:129915017:GT:G	acceptor_gain	1.0000
11:129915017:GTC:G	acceptor_gain	1.0000

AlphaMissense

7637 scored. Top likely-pathogenic:

dbSNP variants (sampled 300 via entrez): RS1000002154 (11:129935173 C>T), RS1000002878 (11:129972182 C>G,T), RS1000039688 (11:129990723 C>T), RS1000102716 (11:129985879 T>C), RS1000113135 (11:129969802 G>A), RS1000148364 (11:129950081 C>A,G), RS1000197346 (11:129941815 G>A,C), RS1000259790 (11:129997162 G>C), RS1000308305 (11:129920043 T>C), RS1000320302 (11:129913859 C>G), RS1000324506 (11:130002005 GC>G), RS1000382499 (11:129965182 A>T), RS1000395038 (11:129947129 C>A), RS1000406217 (11:129904735 A>T), RS1000422976 (11:129988802 C>T)

Disease associations

OMIM: gene MIM:618319 | disease phenotypes: MIM:620459, MIM:147791

GenCC curated gene-disease

Disease	Classification	Inheritance
Birt-Hogg-Dube syndrome 2	Limited	Autosomal dominant

Mondo (2): Birt-Hogg-Dube syndrome 2 (MONDO:0800455), Jacobsen syndrome (MONDO:0007838)

Orphanet (1): Jacobsen syndrome (Orphanet:2308)

HPO phenotypes

26 total (26 of 26 shown, HPO-id order):

HPO	Term
HP:0000006	Autosomal dominant inheritance
HP:0000107	Renal cyst
HP:0001012	Multiple lipomas
HP:0002107	Pneumothorax
HP:0002108	Spontaneous pneumothorax
HP:0002664	Neoplasm
HP:0002865	Medullary thyroid carcinoma
HP:0002897	Parathyroid adenoma
HP:0005584	Renal cell carcinoma
HP:0005948	Multiple pulmonary cysts
HP:0006522	Repeated pneumothoraces
HP:0006770	Clear cell renal cell carcinoma
HP:0010609	Skin tags
HP:0010615	Angiofibromas
HP:0011462	Young adult onset
HP:0012056	Cutaneous melanoma
HP:0025388	Thyroid nodule
HP:0030436	Fibrofolliculoma
HP:0031523	Salivary gland oncocytoma
HP:0032225	Perifollicular fibroma
HP:0032228	Trichodiscoma
HP:0032445	Pulmonary cyst
HP:0200040	Epidermoid cyst
HP:6000022	Collagenoma
HP:6000853	Thyroid cyst
HP:6000957	Oral mucosal papule

GWAS associations

3 associations (top):

Study	Trait	p-value
GCST003542_66	Night sleep phenotypes	1.000000e-06
GCST007040_3	Carotid intima media thickness in rheumatoid arthritis	4.000000e-07
GCST008758_14	Pre-treatment viral load in HIV-1 infection	2.000000e-18

EFO canonical traits (2, from GWAS)

EFO ID	Trait name
EFO:0007827	nighttime rest measurement
EFO:0010125	viral load

Drugs & pharmacology

Drug and pharmacology data

Is drug target: yes

ChEMBL targets (1): CHEMBL5214863 (SINGLE PROTEIN)

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

CTD chemical–gene interactions

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

Chemical	Actions (top 5)	PubMed papers
Valproic Acid	affects expression, decreases expression, increases methylation	3
(+)-JQ1 compound	decreases expression	2
Acetaminophen	decreases expression	2
Aflatoxin B1	increases methylation	2
FR900359	increases phosphorylation	1
dicrotophos	increases expression	1
bisphenol A	increases methylation	1
trichostatin A	decreases expression	1
thallium sulfate	increases expression	1
beta-lapachone	increases expression	1
sodium arsenite	affects cotreatment, increases abundance, increases expression	1
butyraldehyde	decreases expression	1
manganese chloride	affects cotreatment, increases abundance, increases expression	1
methacrylaldehyde	affects cotreatment, increases expression	1
di-n-butylphosphoric acid	affects expression	1
CGP 52608	affects binding, increases reaction	1
abrine	decreases expression	1
bisphenol S	decreases methylation	1
PCI 5002	affects cotreatment, increases expression	1
Sunitinib	increases expression	1
Acrolein	affects cotreatment, increases expression	1
Arsenic	affects cotreatment, increases abundance, increases expression	1
Benzo(a)pyrene	affects methylation	1
Cadmium	decreases expression, increases abundance	1
Diazinon	increases methylation	1
Estradiol	decreases expression	1
Gallic Acid	increases expression	1
Manganese	affects cotreatment, increases abundance, increases expression	1
Ozone	affects cotreatment, increases expression	1
Quercetin	increases expression	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
CHEMBL5214668	Binding	Selectivity interaction (Methyltransferase panel (DSF assay)) EUB0000234b PRDM10	Selectivity Literature for EUbOPEN Chemogenomics Library wave 3

Cellosaurus cell lines

1 cell lines: 1 transformed cell line

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

Cellosaurus	Name	Category	Sex
CVCL_HC89	HEK293 eGFP-PRDM10	Transformed cell line	Female

Clinical trials (associated diseases)

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

Trial	Phase	Status	Title
NCT04463316	Not specified	RECRUITING	GROWing Up With Rare GENEtic Syndromes