PRDM11

Summary

PRDM11 (PR/SET domain 11, HGNC:13996) is a protein-coding gene on chromosome 11p11.2, encoding PR domain-containing protein 11 (Q9NQV5). May be involved in transcription regulation.

Predicted to enable DNA-binding transcription factor activity; RNA polymerase II cis-regulatory region sequence-specific DNA binding activity; and chromatin binding activity. Involved in several processes, including negative regulation of cell growth; positive regulation of fibroblast apoptotic process; and regulation of DNA-templated transcription. Located in cytosol and nucleus.

Source: NCBI Gene 56981 — RefSeq curated summary.

At a glance

• GWAS associations: 26
• Clinical variants (ClinVar): 11 total
• Druggable target: yes
• MANE Select transcript: NM_001384648

Identifiers

Gene identifiers

Field	Value
HGNC ID	HGNC:13996
Approved symbol	PRDM11
Name	PR/SET domain 11
Location	11p11.2
Locus type	gene with protein product
Status	Approved
Aliases	PFM8
Ensembl gene	ENSG00000019485
Ensembl biotype	protein_coding
OMIM	616347
Entrez	56981

Gene structure

Transcript identifiers

Ensembl transcripts: 7 — 6 protein_coding, 1 protein_coding_CDS_not_defined

ENST00000424263, ENST00000528980, ENST00000530656, ENST00000534751, ENST00000622142, ENST00000683152, ENST00000959457

RefSeq mRNA: 7 — MANE Select: NM_001384648 NM_001256695, NM_001256696, NM_001359633, NM_001384648, NM_001384649, NM_001384650, NM_001384651

CCDS: CCDS58130, CCDS73277, CCDS91463

Canonical transcript exons

ENST00000683152 — 8 exons

Exon	Start	End
ENSE00000711598	45182861	45183123
ENSE00001300816	45224217	45224843
ENSE00001324832	45182246	45182349
ENSE00002168602	45146639	45146877
ENSE00003474412	45204711	45204778
ENSE00003617000	45219570	45219757
ENSE00003659674	45181761	45181885
ENSE00003922067	45225995	45235109

Expression profiles

Bgee: expression breadth ubiquitous, 214 present calls, max score 87.62.

FANTOM5 (CAGE): breadth ubiquitous, TPM avg 3.5778 / max 45.8352, expressed in 1463 samples.

FANTOM5 promoters (3 alternative TSS)

Promoter ID	TPM avg	Samples expressed
114017	2.6313	1256
114018	0.6963	393
114019	0.2502	153

Top tissues by expression

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

Tissue	Anatomy ID	Expression score	Quality
epithelial cell of pancreas	CL:0000083	87.62	silver quality
descending thoracic aorta	UBERON:0002345	85.06	gold quality
thoracic aorta	UBERON:0001515	84.14	gold quality
ascending aorta	UBERON:0001496	84.03	gold quality
aorta	UBERON:0000947	83.35	gold quality
germinal epithelium of ovary	UBERON:0001304	83.08	gold quality
popliteal artery	UBERON:0002250	82.87	gold quality
right coronary artery	UBERON:0001625	82.84	gold quality
tibial artery	UBERON:0007610	82.83	gold quality
lower esophagus muscularis layer	UBERON:0035833	82.56	gold quality
lower esophagus	UBERON:0013473	82.50	gold quality
esophagogastric junction muscularis propria	UBERON:0035841	82.41	gold quality
body of uterus	UBERON:0009853	82.39	gold quality
endothelial cell	CL:0000115	82.00	silver quality
primary visual cortex	UBERON:0002436	81.93	gold quality
sural nerve	UBERON:0015488	81.87	gold quality
left coronary artery	UBERON:0001626	81.72	gold quality
mucosa of stomach	UBERON:0001199	81.52	gold quality
coronary artery	UBERON:0001621	81.29	gold quality
apex of heart	UBERON:0002098	81.23	gold quality
right atrium auricular region	UBERON:0006631	81.23	gold quality
cardiac atrium	UBERON:0002081	80.86	gold quality
muscle layer of sigmoid colon	UBERON:0035805	80.72	gold quality
smooth muscle tissue	UBERON:0001135	80.43	gold quality
left uterine tube	UBERON:0001303	80.28	gold quality
heart left ventricle	UBERON:0002084	80.26	gold quality
pigmented layer of retina	UBERON:0001782	80.18	gold quality
prefrontal cortex	UBERON:0000451	80.07	gold quality
ectocervix	UBERON:0012249	79.83	gold quality
right ovary	UBERON:0002118	79.82	gold quality

Single-cell (SCXA)

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

Experiment	Marker?	Max mean expression
E-ANND-3	no	3.60

Regulation

Is transcription factor: yes

Downstream targets (CollecTRI)

3 targets.

Target	Regulation
FOS	Repression
JUN	Repression
VAV3	Repression

Literature-anchored findings (GeneRIF, showing 1)

• We characterize PRDM11 as a putative novel tumor suppressor that controls the expression of key oncogenes, and we add new mechanistic insight into B-cell lymphomagenesis. (PMID:25499759)

Cross-species orthologs

3 orthologs

Organism	Symbol	Gene ID
danio_rerio	prdm11	ENSDARG00000074468
mus_musculus	Prdm11	ENSMUSG00000075028
rattus_norvegicus	Prdm11	ENSRNOG00000008674

Paralogs (1): PRDM7 (ENSG00000126856)

Protein

Protein identifiers

PR domain-containing protein 11 — Q9NQV5 (reviewed: Q9NQV5)

All UniProt accessions (3): A0A087WWZ6, Q9NQV5, H3BSZ2

UniProt curated annotations — full annotation on UniProt →

Function. May be involved in transcription regulation.

Subcellular location. Nucleus. Cytoplasm.

Tissue specificity. Highly expressed in lung, including bronchial epithelial cells and airway smooth muscle cells, as well as in peripheral blood mononuclear cells. In tonsils, expressed in B-cell types, including naive B-cells, centroblasts, centrocytes and memory B-cells (at protein level). In benign hyperplastic lymph nodes, expressed in germinal center cells in both the dark and light zones, as well as in scattered cells in the mantle zone and the interfollicular area (at protein level).

Polymorphism. A genome-wide association analysis shows PRDM11 association with forced vital capacity (FVC), a spirometric measure of pulmonary function, that reflects lung volume and is used to diagnose and monitor lung diseases.

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

Isoforms (2)

UniProt ID	Names	Canonical?
Q9NQV5-1	1	yes
Q9NQV5-2	2

RefSeq proteins (7): NP_001243624, NP_001243625, NP_001346562, NP_001371577, NP_001371578, NP_001371579, NP_001371580 (=MANE)

Domains & families (InterPro)

ID	Name	Type
IPR001214	SET_dom	Domain
IPR044405	PRDM11_PR/SET	Domain
IPR046341	SET_dom_sf	Homologous_superfamily
IPR050331	Zinc_finger_PRDM4/PRDM1/PRDM14	Family

Pfam: PF21549

UniProt features (34 total): strand 12, cross-link 5, turn 4, sequence conflict 3, helix 3, sequence variant 2, chain 1, domain 1, region of interest 1, modified residue 1, splice variant 1

Structure

Experimental structures (PDB)

1 structures.

PDB	Method	Resolution (Å)
3RAY	X-RAY DIFFRACTION	1.73

Predicted structure (AlphaFold)

Model	pLDDT	Fraction very-high
AF-Q9NQV5-F1	61.94	0.25

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 (6): 63, 88, 155, 172, 200, 214

Function

Pathways and Gene Ontology

Reactome pathways

0 pathways

MSigDB gene sets: 98 (showing top): GSE45365_NK_CELL_VS_CD8A_DC_MCMV_INFECTION_UP, GOBP_NEGATIVE_REGULATION_OF_CELL_GROWTH, GOZGIT_ESR1_TARGETS_DN, GOBP_GROWTH, GOBP_REGULATION_OF_CELL_CYCLE, JAATINEN_HEMATOPOIETIC_STEM_CELL_UP, GOBP_METHYLATION, GOBP_CELL_FATE_COMMITMENT, GOBP_CELL_GROWTH, GOBP_REGULATION_OF_GROWTH, GOMF_CHROMATIN_BINDING, GOMF_TRANSFERASE_ACTIVITY_TRANSFERRING_ONE_CARBON_GROUPS, GOMF_SEQUENCE_SPECIFIC_DNA_BINDING, RODRIGUES_THYROID_CARCINOMA_ANAPLASTIC_DN, GOBP_FIBROBLAST_APOPTOTIC_PROCESS

GO Biological Process (9): regulation of transcription by RNA polymerase II (GO:0006357), negative regulation of cell growth (GO:0030308), methylation (GO:0032259), regulation of MAPK cascade (GO:0043408), cell fate commitment (GO:0045165), negative regulation of DNA-templated transcription (GO:0045892), positive regulation of DNA-templated transcription (GO:0045893), regulation of cell cycle (GO:0051726), positive regulation of fibroblast apoptotic process (GO:2000271)

GO Molecular Function (6): RNA polymerase II cis-regulatory region sequence-specific DNA binding (GO:0000978), chromatin binding (GO:0003682), DNA-binding transcription factor activity (GO:0003700), methyltransferase activity (GO:0008168), protein binding (GO:0005515), transferase activity (GO:0016740)

GO Cellular Component (3): nucleus (GO:0005634), cytoplasm (GO:0005737), cytosol (GO:0005829)

GO top-level categories

Rollup of top GO terms by namespace:

Category	Terms
regulation of DNA-templated transcription	4
DNA-templated transcription	2
binding	2
cellular anatomical structure	2
transcription by RNA polymerase II	1
regulation of cell growth	1
cell growth	1
negative regulation of growth	1
negative regulation of cellular process	1
metabolic process	1
MAPK cascade	1
regulation of intracellular signal transduction	1
cell differentiation	1
cellular developmental process	1
negative regulation of RNA biosynthetic process	1
positive regulation of RNA biosynthetic process	1
cell cycle	1
regulation of cellular process	1
positive regulation of apoptotic process	1
fibroblast apoptotic process	1
regulation of fibroblast apoptotic process	1
RNA polymerase II transcription regulatory region sequence-specific DNA binding	1
cis-regulatory region sequence-specific DNA binding	1
transcription cis-regulatory region binding	1
transcription regulator activity	1
transferase activity, transferring one-carbon groups	1
catalytic activity	1
intracellular membrane-bounded organelle	1
intracellular anatomical structure	1
cytoplasm	1

Protein interactions and networks

STRING

524 interactions, top by confidence (×1000):

Protein A	Protein B	Partner UniProt	Score
PRDM11	PRDM16	Q9HAZ2	597
PRDM11	PRDM12	Q9H4Q4	542
PRDM11	PRDM5	Q9NQX1	538
PRDM11	MBIP	Q9NS73	514
PRDM11	CAPNS2	Q96L46	507
PRDM11	ITPK1	Q13572	505
PRDM11	PRDM8	Q9NQV8	495
PRDM11	ASH1L	Q9NR48	487
PRDM11	PRDM13	Q9H4Q3	482
PRDM11	PDE8B	O95263	479
PRDM11	MECOM	Q03112	465
PRDM11	SETD4	Q9NVD3	450
PRDM11	C11orf71	Q6IPW1	446
PRDM11	B4GALT6	Q9UBX8	442
PRDM11	PDE10A	Q9Y233	431

IntAct

8 interactions, top by confidence:

A	B	Type	Score
FHL2	PRDM11	psi-mi:“MI:0915”(physical association)	0.560
KXD1	HIP1	psi-mi:“MI:0914”(association)	0.530
KXD1	TRAK2	psi-mi:“MI:0914”(association)	0.530
PRDM11	ERCC3	psi-mi:“MI:0914”(association)	0.350
PRDM11	LONRF3	psi-mi:“MI:0914”(association)	0.350
FHL2	PRDM11	psi-mi:“MI:0915”(physical association)	0.000

BioGRID (21): PRDM11 (Affinity Capture-RNA), PRDM11 (Affinity Capture-MS), FHL2 (Two-hybrid), PRDM11 (Affinity Capture-MS), PRDM11 (Affinity Capture-MS), GTF2H2C (Affinity Capture-MS), PRDM11 (Affinity Capture-MS), GTF2F1 (Affinity Capture-MS), GTF2H1 (Affinity Capture-MS), GTF2H4 (Affinity Capture-MS), PRDM11 (Affinity Capture-MS), PRDM11 (Affinity Capture-MS), ACP1 (Affinity Capture-MS), RPS27 (Affinity Capture-MS), PRDM11 (Affinity Capture-MS)

ESM2 similar proteins: A0A5K7RLP0, A1YEX3, A2AGX3, A2AKB4, A7YWH3, A8MVX0, C9JSJ3, O08715, O88286, O88884, P24278, P97303, P97432, Q17RG1, Q1XFL1, Q3KNY0, Q3USH1, Q495C1, Q4V7B1, Q501R9, Q562E2, Q5SYB0, Q5VT97, Q5XIN1, Q6P2K3, Q6PCP7, Q6ZSG2, Q7TSX9, Q80SU3, Q80TL0, Q80W88, Q80XI1, Q8BLK9, Q8BSV3, Q8BW86, Q8K3E9, Q8K451, Q8N7W2, Q8NE31, Q8NFN8

Diamond homologs: A0A163UT06, A2A935, A2AGX3, A2AJ77, B8A5Y1, E9Q3T6, O75626, P0C6Y7, P14404, Q03112, Q13029, Q3UZD5, Q60636, Q63755, Q6P2A1, Q8BZ97, Q96EQ9, Q9GZV8, Q9H4Q4, Q9HAZ2, Q9NQV5, Q9NQV7, Q9NQV8, Q9NQW5, A6QPM3, E9Q8T2, P57071, Q5R5M1, Q80V63, Q9NQX0, Q9QZP2, Q9UKN5, E9PZZ1, Q9CXE0, Q9H4Q3, Q5HZG9, Q96MN9, A2BID7, Q6DCW1, Q9VH70

SIGNOR signaling

0 interactions.

Disease & clinical

Clinical variants and AI predictions

ClinVar

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

Classification	Count (floor)
Pathogenic	0
Likely pathogenic	0
Uncertain significance	0
Likely benign	0
Benign	0

Top pathogenic / likely-pathogenic (0)

SpliceAI

2101 predictions. Top by Δscore:

Variant	Effect	Δscore
11:45181721:T:A	acceptor_gain	1.0000
11:45181733:T:A	acceptor_gain	1.0000
11:45181735:T:TA	acceptor_gain	1.0000
11:45181738:T:TA	acceptor_gain	1.0000
11:45181745:A:AG	acceptor_gain	1.0000
11:45181753:C:CA	acceptor_gain	1.0000
11:45181760:GGACA:G	acceptor_gain	1.0000
11:45181868:GGA:G	donor_gain	1.0000
11:45181869:GAG:G	donor_gain	1.0000
11:45181871:G:GG	donor_gain	1.0000
11:45182224:T:TA	acceptor_gain	1.0000
11:45182226:C:CA	acceptor_gain	1.0000
11:45182227:G:A	acceptor_gain	1.0000
11:45182234:T:A	acceptor_gain	1.0000
11:45182239:T:TA	acceptor_gain	1.0000
11:45182345:CTGGT:C	donor_gain	1.0000
11:45182346:TGGT:T	donor_gain	1.0000
11:45182347:GGTG:G	donor_gain	1.0000
11:45182348:GT:G	donor_gain	1.0000
11:45182349:TG:T	donor_loss	1.0000
11:45182350:G:GG	donor_gain	1.0000
11:45182851:A:AG	acceptor_gain	1.0000
11:45182852:T:G	acceptor_gain	1.0000
11:45182857:CCA:C	acceptor_loss	1.0000
11:45182858:CAGT:C	acceptor_loss	1.0000
11:45182859:A:AG	acceptor_gain	1.0000
11:45182859:A:T	acceptor_loss	1.0000
11:45182859:AGTCT:A	acceptor_gain	1.0000
11:45182860:G:A	acceptor_loss	1.0000
11:45182860:G:GA	acceptor_gain	1.0000

AlphaMissense

0 scored. Top likely-pathogenic:

dbSNP variants (sampled 300 via entrez): RS1000004841 (11:45145279 G>A), RS1000044787 (11:45162821 T>A,C), RS1000045409 (11:45166677 G>A,T), RS1000075852 (11:45162618 G>C), RS1000123919 (11:45092817 A>G), RS1000140118 (11:45205591 C>A,T), RS1000145306 (11:45115066 C>T), RS1000161022 (11:45209527 C>G), RS1000175605 (11:45126446 A>G), RS1000225598 (11:45203902 A>G), RS1000250581 (11:45159433 GT>G), RS1000265121 (11:45199358 C>T), RS1000278298 (11:45209723 C>T), RS1000279041 (11:45168854 G>A,T), RS1000283783 (11:45165970 C>G)

Disease associations

OMIM: gene MIM:616347 | disease phenotypes:

GenCC curated gene-disease

Mondo (0):

Orphanet (0):

HPO phenotypes

0 total (0 of 0 shown, HPO-id order):

GWAS associations

26 associations (top):

Study	Trait	p-value
GCST001856_29	Thyroid hormone levels	3.000000e-07
GCST001856_9	Thyroid hormone levels	9.000000e-11
GCST002483_4	Lung function (forced vital capacity)	9.000000e-10
GCST004278_29	Pulse pressure	7.000000e-09
GCST006138_2	Resting-state electroencephalogram vigilance	8.000000e-06
GCST006193_3	Diastolic blood pressure x smoking status (current vs non-current) interaction (2df test)	1.000000e-09
GCST006194_6	Diastolic blood pressure x smoking status (current vs non-current) interaction (1df test)	1.000000e-08
GCST006268_464	Reaction time	9.000000e-10
GCST006268_521	Reaction time	2.000000e-09
GCST006268_522	Reaction time	1.000000e-09
GCST006268_523	Reaction time	1.000000e-09
GCST006268_524	Reaction time	1.000000e-09
GCST006897_4	Hyperthyroidism	3.000000e-11
GCST006956_5	Erectile dysfunction	9.000000e-06
GCST007096_190	Pulse pressure	5.000000e-12
GCST007097_13	Pulse pressure	2.000000e-06
GCST007429_144	Lung function (FVC)	7.000000e-09
GCST007432_141	FEV1	1.000000e-10
GCST010043_48	Asthma	1.000000e-11
GCST010653_46	Thyroid stimulating hormone levels	3.000000e-41
GCST012047_6	Fasting glucose	7.000000e-07
GCST012100_8	Hypertrophic cardiomyopathy (sarcomere positive)	2.000000e-06
GCST90020025_935	Waist-to-hip ratio adjusted for BMI	4.000000e-08
GCST90020026_790	Hip index	2.000000e-08
GCST90020026_791	Hip index	4.000000e-12
GCST90020027_1460	Waist-hip index	2.000000e-08

EFO canonical traits (10, from GWAS)

EFO ID	Trait name
EFO:0004730	hormone measurement
EFO:0004312	vital capacity
EFO:0005763	pulse pressure measurement
EFO:0004357	electroencephalogram measurement
EFO:0006336	diastolic blood pressure
EFO:0006527	smoking status measurement
EFO:0008393	reaction time measurement
EFO:0004314	forced expiratory volume
EFO:0007788	BMI-adjusted waist-hip ratio
EFO:0008039	BMI-adjusted hip circumference

Drugs & pharmacology

Drug and pharmacology data

Is drug target: yes

ChEMBL targets (1): CHEMBL5214857 (SINGLE PROTEIN)

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

CTD chemical–gene interactions

25 total (human), top 25 by PubMed support.

Chemical	Actions (top 5)	PubMed papers
Benzo(a)pyrene	affects methylation, increases expression, increases methylation	3
Valproic Acid	decreases expression, increases methylation	3
bisphenol A	decreases methylation, affects cotreatment, increases expression	2
bisphenol F	affects cotreatment, increases expression	1
TAK-243	decreases sumoylation	1
dicrotophos	increases expression	1
methylmercuric chloride	decreases expression	1
triphenyl phosphate	affects expression	1
benzo(e)pyrene	increases methylation	1
ferrous chloride	decreases expression	1
aflatoxin B2	increases methylation, decreases methylation	1
cylindrospermopsin	increases expression	1
CGP 52608	affects binding, increases reaction	1
abrine	increases expression	1
Cisplatin	decreases expression	1
Dexamethasone	affects cotreatment, increases expression	1
Doxorubicin	decreases expression	1
Indomethacin	affects cotreatment, increases expression	1
Lead	affects expression	1
Methapyrilene	increases methylation	1
Smoke	decreases expression	1
Tretinoin	decreases expression	1
Urethane	decreases expression	1
1-Methyl-3-isobutylxanthine	affects cotreatment, increases expression	1
Palmitic Acid	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
CHEMBL5214660	Binding	Selectivity interaction (Methyltransferase panel (DSF assay)) EUB0000234b PRDM11	Selectivity Literature for EUbOPEN Chemogenomics Library wave 3

Clinical trials (associated diseases)

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