PRDM7

Summary

PRDM7 (PR/SET domain 7, HGNC:9351) is a protein-coding gene on chromosome 16q24.3, encoding Histone-lysine N-methyltransferase PRDM7 (Q9NQW5). Histone methyltransferase that selectively methylates ‘Lys-4’ of dimethylated histone H3 (H3K4me2) to produce trimethylated ‘Lys-4’ histone H3 (H3K4me3).

This gene encodes a member of a family of proteins that may have roles in transcription and other nuclear processes. The encoded protein contains a KRAB (Kruppel-associated box) domain -A box and a SET (Su(var)3-9, Enhancer-of-zeste, Trithorax) domain and may function as a histone methyltransferase.

Source: NCBI Gene 11105 — RefSeq curated summary.

At a glance

• GWAS associations: 3
• Clinical variants (ClinVar): 70 total
• GTEx eGene: eQTL in 1 tissue, sQTL in 1 (q < 0.05)
• Constraint (gnomAD): pLI 0.00 (LoF-tolerant), LOEUF 1.00 (unconstrained)
• MANE Select transcript: NM_001098173
• Notable: 70 clinical variants but no curated precision-oncology (CIViC) evidence yet

Identifiers

Gene identifiers

Field	Value
HGNC ID	HGNC:9351
Approved symbol	PRDM7
Name	PR/SET domain 7
Location	16q24.3
Locus type	gene with protein product
Status	Approved
Aliases	ZNF910
Ensembl gene	ENSG00000126856
Ensembl biotype	protein_coding
OMIM	609759
Entrez	11105

Gene structure

Transcript identifiers

Ensembl transcripts: 6 — 2 protein_coding, 2 nonsense_mediated_decay, 1 retained_intron, 1 protein_coding_CDS_not_defined

MANE Select: ENST00000449207

Transcript support level (Ensembl TSL; 1 = fully mRNA-supported): TSL 1: 2, TSL 5: 3

ENST00000449207, ENST00000325921, ENST00000564210, ENST00000568473, ENST00000569206, ENST00001093116

RefSeq mRNA: 1 — MANE Select: NM_001098173 NM_001098173

CCDS: CCDS45557

Canonical transcript exons

ENST00000449207 — 11 exons

Exon	Start	End
ENSE00002500383	90060341	90060623
ENSE00002525756	90056566	90058534
ENSE00003486013	90075351	90075474
ENSE00003488323	90066861	90066910
ENSE00003567620	90061921	90062192
ENSE00003621307	90074916	90075023
ENSE00003636806	90062401	90062502
ENSE00003653773	90063612	90063768
ENSE00003679586	90061452	90061519
ENSE00003821970	90077226	90077331
ENSE00003824701	90075842	90075995

Expression profiles

Bgee: expression breadth broad, 77 present calls, max score 79.52.

Highest expression (Bgee): male germ line stem cell (sensu Vertebrata) in testis, tendon of biceps brachii, testis, buccal mucosa cell, primordial germ cell in gonad.

Genetic regulation across tissues (GTEx eQTL / sQTL)

PRDM7 is an eGene in GTEx v10 — its expression is genetically regulated (eQTL) in 1 tissue and its splicing (sQTL) in 1 (q < 0.05). Strongest associations first; slope = normalized effect of the lead variant’s alternative allele.

2 significant tissue × QTL associations:

Tissue	QTL	q-value	Slope	Lead variant
Testis	eqtl	1.1e-07	-0.29	16:90075679:G:A
Testis	sqtl	3.0e-04	-0.81	16:90059323:C:T

Top tissues by expression

showing 100 of 201 tissues 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	79.52	gold quality
tendon of biceps brachii	UBERON:0008188	73.71	silver quality
right testis	UBERON:0004534	67.74	gold quality
left testis	UBERON:0004533	65.86	gold quality
testis	UBERON:0000473	64.89	gold quality
buccal mucosa cell	CL:0002336	54.88	silver quality
primordial germ cell in gonad	CL:0000670 ∩ UBERON:0000991	54.75	gold quality
right uterine tube	UBERON:0001302	52.54	gold quality
monocyte	CL:0000576	50.81	gold quality
lower esophagus mucosa	UBERON:0035834	50.71	gold quality
leukocyte	CL:0000738	50.44	gold quality
body of pancreas	UBERON:0001150	45.12	gold quality
right ovary	UBERON:0002118	44.14	gold quality
skeletal muscle tissue of rectus abdominis	UBERON:0004511	43.37	gold quality
ovary	UBERON:0000992	43.25	gold quality
bone marrow	UBERON:0002371	43.23	gold quality
secondary oocyte	CL:0000655	42.57	gold quality
skeletal muscle tissue of biceps brachii	UBERON:0004502	42.45	gold quality
left ovary	UBERON:0002119	42.35	silver quality
pharyngeal mucosa	UBERON:0000355	42.29	gold quality
adult mammalian kidney	UBERON:0000082	42.20	gold quality
kidney	UBERON:0002113	42.20	silver quality
pancreas	UBERON:0001264	42.16	gold quality
Brodmann (1909) area 23	UBERON:0013554	41.60	gold quality
vastus lateralis	UBERON:0001379	41.41	gold quality
quadriceps femoris	UBERON:0001377	41.37	gold quality
superficial temporal artery	UBERON:0001614	41.33	gold quality
biceps brachii	UBERON:0001507	41.30	gold quality
oviduct epithelium	UBERON:0004804	41.27	gold quality
palpebral conjunctiva	UBERON:0001812	41.10	gold quality
bone marrow cell	CL:0002092	40.99	gold quality
mucosa of paranasal sinus	UBERON:0005030	40.98	gold quality
jejunal mucosa	UBERON:0000399	40.59	gold quality
epithelium of nasopharynx	UBERON:0001951	40.45	gold quality
myocardium	UBERON:0002349	40.45	gold quality
gingival epithelium	UBERON:0001949	40.43	gold quality
germinal epithelium of ovary	UBERON:0001304	40.33	gold quality
esophagus squamous epithelium	UBERON:0006920	40.29	gold quality
right lobe of thyroid gland	UBERON:0001119	40.26	silver quality
endocervix	UBERON:0000458	40.24	gold quality
jejunum	UBERON:0002115	40.18	gold quality
cartilage tissue	UBERON:0002418	40.06	gold quality
mammary duct	UBERON:0001765	39.98	gold quality
colonic mucosa	UBERON:0000317	39.96	gold quality
mucosa of sigmoid colon	UBERON:0004993	39.95	gold quality
ventricular zone	UBERON:0003053	39.94	gold quality
stromal cell of endometrium	CL:0002255	39.90	gold quality
deltoid	UBERON:0001476	39.83	gold quality
saphenous vein	UBERON:0007318	39.83	gold quality
parotid gland	UBERON:0001831	39.81	gold quality
oocyte	CL:0000023	39.80	gold quality
urethra	UBERON:0000057	39.80	gold quality
heart right ventricle	UBERON:0002080	39.79	gold quality
pericardium	UBERON:0002407	39.77	gold quality
layer of synovial tissue	UBERON:0007616	39.77	gold quality
endothelial cell	CL:0000115	39.75	gold quality
synovial joint	UBERON:0002217	39.70	gold quality
dorsal root ganglion	UBERON:0000044	39.68	gold quality
nipple	UBERON:0002030	39.68	gold quality
trabecular bone tissue	UBERON:0002483	39.68	gold quality
bronchial epithelial cell	CL:0002328	39.65	gold quality
decidua	UBERON:0002450	39.65	gold quality
penis	UBERON:0000989	39.64	gold quality
gingiva	UBERON:0001828	39.64	gold quality
bronchus	UBERON:0002185	39.64	gold quality
skeletal muscle tissue	UBERON:0001134	39.63	gold quality
trigeminal ganglion	UBERON:0001675	39.63	gold quality
inferior vagus X ganglion	UBERON:0005363	39.57	gold quality
mammalian vulva	UBERON:0000997	39.56	gold quality
superior surface of tongue	UBERON:0007371	39.56	gold quality
pylorus	UBERON:0001166	39.55	gold quality
renal medulla	UBERON:0000362	39.53	gold quality
pons	UBERON:0000988	39.51	gold quality
thymus	UBERON:0002370	39.50	gold quality
medulla oblongata	UBERON:0001896	39.48	gold quality
superior vestibular nucleus	UBERON:0007227	39.47	gold quality
cardia of stomach	UBERON:0001162	39.46	gold quality
parietal pleura	UBERON:0002400	39.45	gold quality
dorsal plus ventral thalamus	UBERON:0001897	39.38	gold quality
tongue	UBERON:0001723	39.37	gold quality
cerebellar vermis	UBERON:0004720	39.37	gold quality
oral cavity	UBERON:0000167	39.35	gold quality
subthalamic nucleus	UBERON:0001906	39.35	gold quality
ventral tegmental area	UBERON:0002691	39.35	gold quality
trachea	UBERON:0003126	39.33	gold quality
parietal lobe	UBERON:0001872	39.32	gold quality
vena cava	UBERON:0004087	39.31	gold quality
substantia nigra pars compacta	UBERON:0001965	39.23	gold quality
visceral pleura	UBERON:0002401	39.23	gold quality
postcentral gyrus	UBERON:0002581	39.23	gold quality
body of tongue	UBERON:0011876	39.22	gold quality
uterine cervix	UBERON:0000002	39.14	silver quality
substantia nigra pars reticulata	UBERON:0001966	39.11	gold quality
entorhinal cortex	UBERON:0002728	39.05	gold quality
nasal cavity epithelium	UBERON:0005384	39.04	gold quality
lateral nuclear group of thalamus	UBERON:0002736	39.00	gold quality
corpus epididymis	UBERON:0004359	38.98	gold quality
placenta	UBERON:0001987	38.97	silver quality
tibia	UBERON:0000979	38.93	gold quality
superior frontal gyrus	UBERON:0002661	38.93	gold quality

Single-cell (SCXA)

Detected in 3 experiment(s), a significant marker in 2.

Experiment	Marker?	Max mean expression
E-MTAB-9388	yes	11.42
E-ANND-3	yes	4.24
E-GEOD-111727	no	222.80

HPA expression

RNA tissue specificity: Not detected

35 HPA tissues / cells by nTPM:

Tissue / cell	Axis	nTPM	Protein (IHC)
Periaqueductal gray	tissue	1.4
Olfactory bulb	tissue	1.2
Testis	tissue	0.9	medium
Basal ganglia	tissue	0.9	not detected
Septum	tissue	0.8
Cerebellum	tissue	0.7	not detected
Cerebral cortex	tissue	0.6	not detected
Frontal cortex	tissue	0.6
Medulla oblongata	tissue	0.6
Hypothalamus	tissue	0.6
Corpus callosum	tissue	0.6
Hippocampal formation	tissue	0.6
Temporal cortex	tissue	0.6
Occipital cortex	tissue	0.6
Insular cortex	tissue	0.6
Pons	tissue	0.5
Motor cortex	tissue	0.5
Superior colliculi	tissue	0.5
Spinal cord	tissue	0.5
Ventral forebrain	tissue	0.5
Retrosplenial and cingulate cortex	tissue	0.5
Retrosplenial cortex	tissue	0.5
Prefrontal cortex	tissue	0.4
Amygdala	tissue	0.4
Midbrain	tissue	0.4
Substantia nigra	tissue	0.4
Entorhinal cortex	tissue	0.4
Somatosensory cortex	tissue	0.4
Putamen	tissue	0.3
Thalamus	tissue	0.3
Locus coeruleus	tissue	0.3
Caudate putamen	tissue	0.3
Nucleus accumbens	tissue	0.1
Hippocampus	tissue	0.1	not detected
Postcentral gyrus	tissue	0.1

Brain sub-regions (HPA Brain Atlas): detected in 172; highest nTPM — Dorsal hippocampus (0.6), Subiculum (0.6), Ventral hippocampus (0.6), White matter (0.6), Ventral spinal cord (0.5).

Regulation

Is transcription factor: no

miRNA regulators (miRDB)

Targeting PRDM7 by miRDB confidence (max_score; target_count = how many genes the miRNA targets in total — lower means more specific).

showing 30 of 73 miRNAs:

miRNA	Max score	Avg score	miRNA target_count
HSA-MIR-6867-5P	100.00	82.21	3464
HSA-MIR-8485	100.00	77.57	4731
HSA-MIR-6798-5P	100.00	65.77	699
HSA-MIR-4455	100.00	65.48	1587
HSA-MIR-3667-3P	99.99	67.17	1636
HSA-MIR-6870-5P	99.99	68.55	2115
HSA-MIR-4723-5P	99.97	68.70	2034
HSA-MIR-5698	99.97	68.49	2029
HSA-MIR-7111-5P	99.97	68.48	2062
HSA-MIR-1236-3P	99.94	68.04	1695
HSA-MIR-515-5P	99.92	69.82	2343
HSA-MIR-519E-5P	99.92	69.62	2358
HSA-MIR-7978	99.86	66.90	856
HSA-MIR-3941	99.86	70.54	2735
HSA-MIR-629-3P	99.85	67.99	1875
HSA-MIR-6756-5P	99.82	67.97	2466
HSA-MIR-6875-3P	99.82	70.26	2983
HSA-MIR-6817-3P	99.79	68.35	2126
HSA-MIR-4713-5P	99.78	67.80	1794
HSA-MIR-10393-3P	99.72	66.56	961
HSA-MIR-6801-5P	99.72	66.50	981
HSA-MIR-6766-5P	99.68	67.70	2325
HSA-MIR-3158-5P	99.65	67.51	1763
HSA-MIR-4276	99.56	67.66	2514
HSA-MIR-6832-3P	99.52	70.44	1726
HSA-MIR-766-5P	99.47	67.91	2225
HSA-MIR-422A	99.18	65.83	550
HSA-MIR-1911-3P	99.15	66.17	528
HSA-MIR-4784	99.15	67.41	1733
HSA-MIR-3150B-3P	98.81	67.21	1728

Functional genomics

gnomAD constraint: pLI 1.35e-14, LOEUF 1, missense Z 0.543 — population loss-of-function intolerance (pLI ≥ 0.9 = LoF-intolerant; lower LOEUF = more constrained). gnomAD

Regional missense constraint (gnomAD RMC): no regional variation along ENST00000449207 — one region, missense o/e 0.96.

Literature-anchored findings (GeneRIF, showing 2)

• Evolutionary analysis suggests that human PRDM7 and PRDM9 genes, a pair of close paralogs corresponding to a single mouse gene Prdm9, were generated by a recent gene duplication event after the divergence of the ancestors of human and mouse. (PMID:18231586)
• These studies indicate that after a single serine to tyrosine mutation at residue 357 (S357Y), PRDM7 regains the substrate specificities and catalytic activities similar to its evolutionary predecessor, including the ability to efficiently methylate H3K36. (PMID:27129774)

Cross-species orthologs

3 orthologs

Organism	Symbol	Gene ID
mus_musculus	Prdm9	ENSMUSG00000051977
rattus_norvegicus	Prdm9	ENSRNOG00000021493
caenorhabditis_elegans		WBGENE00011887

Paralogs (1): PRDM11 (ENSG00000019485)

Mouse-model phenotypes

Observed phenotypes of the mouse ortholog (MGI:2384854) from MGI (Alliance of Genome Resources) — knockout/mutant phenotypes, ranked by annotation count. 25 distinct phenotype terms.

Mouse phenotype (MP)	Records
male infertility	4
decreased testis weight	4
female infertility	3
azoospermia	3
arrest of male meiosis	3
abnormal chromosomal synapsis	3
small ovary	2
abnormal female meiosis	2
decreased oocyte number	2
abnormal ovarian folliculogenesis	1
small testis	1
reduced female fertility	1
abnormal gametogenesis	1
abnormal meiosis	1
abnormal spermiogenesis	1
abnormal germ cell morphology	1
abnormal seminiferous tubule morphology	1
absent ovarian follicles	1
decreased male germ cell number	1
abnormal DNA methylation during gametogenesis	1
abnormal chiasmata formation	1
abnormal female meiosis I arrest	1
abnormal double-strand DNA break repair	1
decreased elongated spermatid number	1
impaired double-strand DNA break repair	1

Additional cross-species homologs

Sequence homologs in species beyond Ensembl Compara’s model organisms, by Diamond local protein alignment (% sequence identity; best hit per species). Lower-identity rows are more distant homologs. The matched accessions’ gene symbols aren’t in biobtree yet, so each row shows the UniProt accession.

Organism	UniProt	Identity	Method
Pongo abelii	Q5R5M1	99.5%	Diamond
Danio rerio	Q6P2A1	49.7%	Diamond

Genomic neighbors (locus context)

Genes flanking this one on the chromosome (NCBI/Entrez gene neighborhood). Positional context only — some neighbors share regulatory elements (bidirectional promoters, antisense/overlapping transcripts), but chromosomal adjacency is not itself a functional relationship (see Interactions for that).

Symbol	Type	Entrez
DRC4	protein-coding	2622
GAS8-AS1	ncRNA	750
DBNDD1	protein-coding	79007
FAM157C	ncRNA	100996541

Protein

Protein identifiers

Histone-lysine N-methyltransferase PRDM7 — Q9NQW5 (reviewed: Q9NQW5)

Alternative names: PR domain zinc finger protein 7, PR domain-containing protein 7, [histone H3]-lysine4 N-methyltransferase PRDM7

All UniProt accessions (3): A4Q9G9, Q9NQW5, H3BUJ3

UniProt curated annotations — full annotation on UniProt →

Function. Histone methyltransferase that selectively methylates ‘Lys-4’ of dimethylated histone H3 (H3K4me2) to produce trimethylated ‘Lys-4’ histone H3 (H3K4me3). May play a role in epigenetic regulation of gene expression by defining an active chromatin state.

Subcellular location. Nucleus. Chromosome.

Miscellaneous. May be produced at very low levels due to a premature stop codon in the mRNA, leading to nonsense-mediated mRNA decay.

Isoforms (3)

UniProt ID	Names	Canonical?
Q9NQW5-3	1	yes
Q9NQW5-2	2, B
Q9NQW5-1	3, A

RefSeq proteins (1): NP_001091643* (*=MANE)

Domains & families (InterPro)

ID	Name	Type
IPR001214	SET_dom	Domain
IPR001909	KRAB	Domain
IPR003655	aKRAB	Domain
IPR019041	SSXRD_motif	Conserved_site
IPR036051	KRAB_dom_sf	Homologous_superfamily
IPR044417	PRDM7_9_PR-SET	Domain
IPR046341	SET_dom_sf	Homologous_superfamily

Pfam: PF01352, PF09514, PF21549

Enzyme classification (BRENDA)

• EC 2.1.1.354 — [histone H3]-lysine4 N-trimethyltransferase (BRENDA: 18 organisms, 22 substrates, 3 inhibitors, 20 Km, 20 kcat entries)

Substrate kinetics (BRENDA)

4 substrates with measured Km, best-characterized 4. Km ranges are aggregated across organisms/conditions.

Substrate	Km (mM)	Measurements
ART(KME1)QTARKSTGGKAPRKQLATKAA-GK-BIOTIN	0.0002–0.002	5
ART(KME2)QTARKSTGGKAPRKQLATKAA-GK-BIOTIN	0.0003–0.004	5
ARTKQTARKSTGGKAPRKQLATKAA-GK-BIOTIN	0.0002–0.0017	5
S-ADENOSYL-L-METHIONINE	0.014–0.9	5

Catalyzed reactions (Rhea)

• N(6),N(6)-dimethyl-L-lysyl(4)-[histone H3] + S-adenosyl-L-methionine = N(6),N(6),N(6)-trimethyl-L-lysyl(4)-[histone H3] + S-adenosyl-L-homocysteine + H(+) (RHEA:60272)

UniProt features (18 total): splice variant 4, sequence variant 3, mutagenesis site 3, domain 2, region of interest 2, compositionally biased region 2, chain 1, sequence conflict 1

Structure

Predicted structure (AlphaFold)

Model	pLDDT	Fraction very-high
AF-Q9NQW5-F1	60.59	0.27

Human Protein Atlas

Protein class: Predicted intracellular proteins

Protein evidence: Evidence at protein level

Subcellular location (HPA, imaging): nuclear speckles

Antibody reliability (HPA): IH approved · IF uncertain

Functional residue map

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

Mutagenesis-validated functional residues (3)

Position	Phenotype
289	gains the ability to sequentially mono-, di-, and tri-methylate both ’lys-4’ and ’lys-36’ of histone h3, albeit with lower efficiency when …
312	gains the ability to sequentially mono-, di-, and tri-methylate both ’lys-4’ and ’lys-36’ of histone h3, albeit with lower efficiency when …
357	substantially increases histone-lysine n-methyltransferase activity. gains the catalytic competency of prdm9. sequentially mono-, di-, and …

Function

Pathways and Gene Ontology

Reactome pathways

1 curated (TAS) of 3; 0 disease pathways. Curated-first; evidence = TAS (manually curated) vs IEA (electronic inference).

3 pathways:

ID	Pathway	Evidence
R-HSA-212436	Generic Transcription Pathway	curated
R-HSA-74160	Gene expression (Transcription)	—
R-HSA-73857	RNA Polymerase II Transcription	—

MSigDB gene sets: 28 (showing top): NIKOLSKY_BREAST_CANCER_16Q24_AMPLICON, GOBP_CHROMATIN_REMODELING, GOBP_METHYLATION, GOMF_N_METHYLTRANSFERASE_ACTIVITY, YKACATTT_UNKNOWN, GOMF_PROTEIN_METHYLTRANSFERASE_ACTIVITY, ROYLANCE_BREAST_CANCER_16Q_COPY_NUMBER_UP, GOMF_S_ADENOSYLMETHIONINE_DEPENDENT_METHYLTRANSFERASE_ACTIVITY, GOMF_TRANSFERASE_ACTIVITY_TRANSFERRING_ONE_CARBON_GROUPS, GOMF_LYSINE_N_METHYLTRANSFERASE_ACTIVITY, GOMF_HISTONE_H3K4_METHYLTRANSFERASE_ACTIVITY, GOMF_HISTONE_METHYLTRANSFERASE_ACTIVITY, MIR6867_5P, MIR6830_3P, MIR6852_3P

GO Biological Process (4): regulation of DNA-templated transcription (GO:0006355), methylation (GO:0032259), chromatin organization (GO:0006325), chromatin remodeling (GO:0006338)

GO Molecular Function (5): histone H3K4 methyltransferase activity (GO:0042800), protein binding (GO:0005515), methyltransferase activity (GO:0008168), transferase activity (GO:0016740), histone methyltransferase activity (GO:0042054)

GO Cellular Component (2): nucleus (GO:0005634), chromosome (GO:0005694)

Reactome top-level categories

2 top-level categories:

Category	Pathways
RNA Polymerase II Transcription	1
Gene expression (Transcription)	1

GO top-level categories

15 GO namespaces:

Category	Terms
DNA-templated transcription	1
regulation of gene expression	1
regulation of RNA biosynthetic process	1
metabolic process	1
cellular component organization	1
chromatin organization	1
protein-lysine N-methyltransferase activity	1
histone H3 methyltransferase activity	1
binding	1
transferase activity, transferring one-carbon groups	1
catalytic activity	1
protein methyltransferase activity	1
histone modifying activity	1
intracellular membrane-bounded organelle	1
intracellular membraneless organelle	1

Experimentally-supported GO annotations

GO terms backed by direct experimental evidence (ECO experimental codes) — 1 of 11 annotations. The rest are phylogenetic / computational / electronic (IEA).

1 experimentally-supported GO terms:

GO term	NS	Evidence
histone H3K4 methyltransferase activity	MF	direct assay

Protein interactions and networks

STRING

showing 15 of 484 interactions by confidence (×1000):

Protein A	Protein B	Partner UniProt	Score
PRDM7	PRDM13	Q9H4Q3	520
PRDM7	RNF212	Q495C1	460
PRDM7	PRDM5	Q9NQX1	427
PRDM7	SETD3	Q86TU7	425
PRDM7	ZNF862	O60290	410
PRDM7	CXXC1	Q9P0U4	401
PRDM7	SETD4	Q9NVD3	393
PRDM7	SMYD3	Q9H7B4	389
PRDM7	ZNF624	Q9P2J8	387
PRDM7	SMYD2	Q9NRG4	381
PRDM7	RAI1	Q7Z5J4	370
PRDM7	SPO11	Q9Y5K1	370
PRDM7	AMACR	Q9UHK6	370
PRDM7	SMYD1	Q8NB12	368
PRDM7	SETMAR	Q53H47	362

IntAct

Human interaction partners of PRDM7 in IntAct, one row per partner (best MIscore; records = supporting IntAct interaction records).

3 partners by confidence:

Partner	Interaction type	MIscore	Records
TRAF1	physical association	0.560	3
TUBB2B	physical association	0.400	1
SNRPD2	association	0.350	1

BioGRID (15 interactions; top human partners by supporting records): BIRC3 (Affinity Capture-MS), CEBPB (Affinity Capture-MS), CFL2 (Affinity Capture-MS), FHL3 (Affinity Capture-MS), GRHPR (Affinity Capture-MS), NUDT21 (Affinity Capture-RNA), NUP54 (Cross-Linking-MS (XL-MS)), RPS27A (Affinity Capture-MS), SNRPD2 (Affinity Capture-MS), SPIN2A (Affinity Capture-MS), SPIN3 (Affinity Capture-MS), TRAF1 (Two-hybrid), TUBB2B (Affinity Capture-MS), ZDHHC15 (Affinity Capture-MS)

Disease & clinical

Genetic variants

Variant evidence for PRDM7: 70 ClinVar records (0 pathogenic / likely pathogenic); 3 GWAS associations.

ClinVar

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

Classification	Count (floor)
Pathogenic	0
Likely pathogenic	0
Uncertain significance	63
Likely benign	3
Benign	1

SpliceAI

Top 10 splice-impact sites by Δscore (adjacent positions with the same effect merged into one range; 24 predictions of 828):

Position(s)	Effect	Δscore	Sites
16:90061450–90061451	donor_loss	1.0000	5
16:90074914–90074915	donor_loss	1.0000	4
16:90075024–90075025	acceptor_loss	1.0000	6
16:90075387	donor_gain	1.0000
16:90061520–90061521	acceptor_loss	0.9900	3
16:90061525	acceptor_gain	0.9900
16:90061529	acceptor_gain	0.9900
16:90074915	donor_loss	0.9900
16:90077255	donor_gain	0.9900
16:90060498	donor_gain	0.9800

AlphaMissense

262 missense substitutions predicted likely pathogenic (of 3,256 scored), across 94 residues. Top 20 hotspot residues, ranked by the number of likely-pathogenic substitutions (of those reachable by a single-nucleotide change), then by mean score:

Residue	Likely-pathogenic substitutions	Mean am_pathogenicity	Max am_pathogenicity
W40	7	0.811	0.927
F35	7	0.806	0.955
W315	7	0.790	0.900
W261	7	0.750	0.799
W293	7	0.702	0.812
C205	6	0.720	0.754
C208	6	0.701	0.772
N329	6	0.694	0.829
F73	5	0.911	0.961
F273	5	0.839	0.917
F224	5	0.830	0.939
F28	5	0.799	0.913
S241	5	0.788	0.912
D227	5	0.739	0.814
C216	5	0.666	0.719
M316	4	0.862	0.867
F212	4	0.839	0.904
F340	4	0.823	0.889
F333	4	0.803	0.857
K48	4	0.778	0.827

HPA cancer prognostics

RNA cancer specificity: Not detected

Disease associations

OMIM: gene MIM:609759 | disease phenotypes:

GWAS associations

3 associations:

Study	Trait	p-value
GCST005897_35	Low tan response	4e-139
GCST010703_232	Brain morphology (MOSTest)	2e-15
GCST005790_16	Rosacea symptom severity	1e-6

EFO canonical traits (from GWAS)

3 canonical traits:

EFO ID	Trait name
EFO:0009180	rosacea severity measurement
EFO:0004279	suntan
EFO:0004346	neuroimaging measurement

Drugs & pharmacology

Drug and pharmacology data

Is drug target: yes

ChEMBL targets (1): CHEMBL5214861 (SINGLE PROTEIN)

PharmGKB: 1 entry (CPIC guideline: no)

CTD chemical–gene interactions

12 total (human), top 12 by PubMed support.

Chemical	Actions (top 5)	PubMed papers
S-(1,2-dichlorovinyl)cysteine	increases expression, affects cotreatment	1
Acetaminophen	decreases expression	1
Air Pollutants	increases abundance, increases expression	1
Benzo(a)pyrene	affects methylation	1
Cisplatin	increases response to substance	1
Lipopolysaccharides	affects cotreatment, increases expression	1
S-Adenosylmethionine	affects binding	1
Tobacco Smoke Pollution	increases expression	1
Cadmium Chloride	increases expression	1
Okadaic Acid	increases expression	1
Copper Sulfate	increases expression	1
Particulate Matter	increases abundance, increases expression	1

ChEMBL screening assays

5 unique, capped per target: 5 binding

Representative assays (with source publication via chembl_document):

Assay ID	Type	Description	Source paper
CHEMBL5214664	Binding	Selectivity interaction (Methyltransferase panel (DSF assay)) EUB0000234b PRDM7	Selectivity Literature for EUbOPEN Chemogenomics Library wave 3

Clinical trials (associated diseases)

Via MONDO — disease-level, not drug-specific.

Predicted chemistry — Sugi Predict

The predicted patent-compound landscape for PRDM7 across ~30M SureChEMBL compounds — explore on Sugi Predict.