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GeneE
10 sources retrieved Β· Most recent: April 2026 Β· Index updated 15 days ago
β“˜GeneE is for informational purposes only. It is not a substitute for professional medical advice, diagnosis, or treatment.
PRDM6
PR/SET domain 6
Chromosome 5 Β· 5q23.2
NCBI Gene: 93166Ensembl: ENSG00000061455.12HGNC: HGNC:9350UniProt: Q9NQX0
20PubMed Papers
21Diseases
0Drugs
3Pathogenic Variants
FUNCTIONAL ROLE
Transcription Factor
CLINICAL
OMIM Disease Gene
DATA QUALITY
βœ“ Experimental GO Evidenceβœ“ Swiss-Prot Reviewed
protein bindingidentical protein bindingnegative regulation of transcription by RNA polymerase IIregulation of gene expressionpersistent fetal circulation syndromehypertensionessential hypertensionneurodegenerative disease
✦AI Summary

PRDM6 is a transcriptional repressor that functions as a putative histone methyltransferase with significant roles in development and disease. The protein localizes predominantly to the nucleus where it causes widespread repression of chr5 accessibility and binds to chr5 regions marked by histone H3 lysine 27 trimethylation 1. In cardiovascular development, PRDM6 is essential for ductus arteriosus closure by promoting smooth muscle cell identity and contractility, with depletion resulting in patent ductus arteriosus 2. PRDM6 contains binding sites in approximately 50% of genes it regulates and drives expression of smooth muscle cell-selective contractile proteins 2. In cancer, PRDM6 demonstrates oncogenic potential, particularly in medulloblastoma where it promotes tumor formation through chr5 repression and altered gene expression patterns 1. Activating enhancer hijacking events targeting PRDM6 have been identified as driver alterations in Group 4 medulloblastoma 3. PRDM6 alterations also contribute to Group 4 medulloblastoma through mutations affecting the CBFA complex 4. Additionally, PRDM6 has been implicated in head and neck cancer progression by modulating immune gene expression 5. Given its minimal expression in normal tissues but oncogenic activity, PRDM6 represents a potential therapeutic target 1.

Sources cited
1
PRDM6 localizes to nucleus, represses chromatin accessibility, and binds H3K27me3-marked regions
PMID: 38992221
2
PRDM6 is essential for ductus arteriosus closure and smooth muscle cell function
PMID: 36749647
3
Enhancer hijacking events activate PRDM6 in medulloblastoma
PMID: 28726821
4
PRDM6 alterations contribute to Group 4 medulloblastoma through CBFA complex mutations
PMID: 36131014
5
PRDM6 promotes head and neck cancer by modulating immune gene expression
PMID: 40936897
Disease Associationsβ“˜21
persistent fetal circulation syndromeOpen Targets
0.66Moderate
hypertensionOpen Targets
0.54Moderate
essential hypertensionOpen Targets
0.50Moderate
neurodegenerative diseaseOpen Targets
0.50Moderate
androgenetic alopeciaOpen Targets
0.47Moderate
Increased blood pressureOpen Targets
0.44Moderate
aortic aneurysmOpen Targets
0.43Moderate
cardiovascular diseaseOpen Targets
0.43Moderate
familial patent arterial ductOpen Targets
0.40Weak
aneurysmOpen Targets
0.38Weak
coronary artery diseaseOpen Targets
0.33Weak
asthmaOpen Targets
0.33Weak
response to xenobiotic stimulusOpen Targets
0.33Weak
Abdominal Aortic AneurysmOpen Targets
0.33Weak
alopeciaOpen Targets
0.30Weak
atrial fibrillationOpen Targets
0.29Weak
thoracic aortic aneurysmOpen Targets
0.29Weak
Genu valgumOpen Targets
0.27Weak
Genu varumOpen Targets
0.27Weak
ovarian neoplasmOpen Targets
0.27Weak
Patent ductus arteriosus 3UniProt
Pathogenic Variants3
NM_001136239.4(PRDM6):c.1646G>A (p.Arg549Gln)Pathogenic
Patent ductus arteriosus 3
β˜†β˜†β˜†β˜†2016β†’ Residue 549
NM_001136239.4(PRDM6):c.788G>C (p.Cys263Ser)Pathogenic
Patent ductus arteriosus 3
β˜†β˜†β˜†β˜†2016β†’ Residue 263
NM_001136239.4(PRDM6):c.1385A>G (p.Gln462Arg)Pathogenic
Patent ductus arteriosus 3
β˜†β˜†β˜†β˜†2016β†’ Residue 462
View on ClinVar β†—
Related Genes
PRDM13Shared pathway100%KDM4FShared pathway100%KDM4EShared pathway100%CBFA2T2Protein interaction85%PRDM14Protein interaction85%KDM6AShared pathway67%
Tissue Expression6 tissues
Lung
100%
Ovary
92%
Heart
28%
Liver
10%
Brain
7%
Bone Marrow
0%
Gene Interaction Network
Click a node to explore
PRDM6PRDM13KDM4FKDM4ECBFA2T2PRDM14KDM6A
PROTEIN STRUCTURE
Preparing viewer…
AlphaFoldAI-predicted Β· UniProt Q9NQX0
View on AlphaFold β†—
Constraintβ“˜
LOEUFβ“˜
0.65LoF Tolerant
pLIβ“˜
0.01Tolerant
Observed/Expected LoF0.46 [0.34–0.65]
RankingsWhere PRDM6 stands among ~20K protein-coding genes
  • #14,232of 20,598
    Most Researched20
  • #4,151of 5,498
    Most Pathogenic Variants3
  • #4,708of 17,882
    Most Constrained (LOEUF)0.65
Genes detectedPRDM6
Sources retrieved10 papers
Response timeβ€”
πŸ“„ Sources
10β–Ό
1
The whole-genome landscape of medulloblastoma subtypes.
PMID: 28726821
Nature Β· 2017
1.00
2
PRDM6 promotes medulloblastoma by repressing chromatin accessibility and altering gene expression.
PMID: 38992221
Sci Rep Β· 2024
0.90
3
Failure of human rhombic lip differentiation underlies medulloblastoma formation.
PMID: 36131014
Nature Β· 2022
0.80
4
Oncogene aberrations drive medulloblastoma progression, not initiation.
PMID: 40335697
Nature Β· 2025
0.70
5
PRDM6 promotes medulloblastoma by repressing chromatin accessibility and altering gene expression.
PMID: 37693484
bioRxiv Β· 2023
0.60