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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.
PRDM5
PR/SET domain 5
Chromosome 4 Β· 4q27
NCBI Gene: 11107Ensembl: ENSG00000138738.12HGNC: HGNC:9349UniProt: Q9NQX1
42PubMed Papers
21Diseases
0Drugs
56Pathogenic Variants
FUNCTIONAL ROLE
Transcription Factor
RESEARCH IMPACT
Variant-Rich
CLINICAL
OMIM Disease Gene
DATA QUALITY
βœ“ Experimental GO Evidenceβœ“ Swiss-Prot Reviewed
negative regulation of transcription by RNA polymerase IIpositive regulation of transcription by RNA polymerase IItranscription cis-regulatory region bindingnucleoplasmbrittle cornea syndromeAbnormality of the cardiovascular systemConnective tissue disease with eye involvementEhlers-Danlos syndrome
✦AI Summary

PRDM5 (PR/SET domain 5) is a sequence-specific DNA-binding transcription factor that functions primarily as a transcriptional repressor 1. It recruits histone methyltransferase EHMT2/G9A and histone deacetylases such as HDAC1 to suppress gene transcription. PRDM5 regulates genes involved in hematopoiesis and extracellular matrix development, including fibrillar collagens (COL4A1, COL11A1), connective tissue components (HAPLN1), and molecules regulating cell migration and adhesion (EDIL3, TGFB2). In cancer cells, PRDM5 induces G2/M arrest and apoptosis, suggesting tumor-suppressive functions 1. PRDM5 is frequently silenced in multiple cancer types through promoter hypermethylation, including breast, ovarian, liver, colorectal, and esophageal cancers 23. Low PRDM5 expression correlates with poor prognosis in esophageal squamous cell carcinoma and associates with reduced overall survival 34. Beyond malignancy, PRDM5 loss-of-function mutations cause brittle cornea syndrome, characterized by corneal thinning, myopia, and blue sclerae, reflecting its role in extracellular matrix integrity 56. Recent evidence implicates PRDM5 variants in aortic and arterial aneurysm diseases 6. In liver tumorigenesis, PRDM5 acts as a microenvironment-dependent lineage commitment factor 7.

Sources cited
1
PRDM5 is a PR-domain-containing transcription factor with growth suppressive activity that causes G2/M arrest and apoptosis in tumor cells and is silenced in breast, ovarian, and liver cancers
PMID: 15077163
2
PRDM5 functions as a microenvironment-dependent, epigenetically regulated lineage-commitment factor in liver tumorigenesis
PMID: 30209397
3
PRDM5 mutations cause brittle cornea syndrome with corneal thinning, myopia, and blue sclerae
PMID: 37713669
4
Circular PRDM5 regulates epithelial-to-mesenchymal transition and collagen expression in lens epithelial cells through miR-92b-3p/COL1A2 pathway
PMID: 35083632
5
PRDM5 is frequently methylated and silenced in colorectal cancers, particularly BRAF mutant serrated pathway cancers, acting as a tumor suppressor
PMID: 25613750
6
Low PRDM5 expression predicts poor prognosis in esophageal squamous cell carcinoma and correlates with overall survival
PMID: 35799142
7
PRDM5 suppresses esophageal squamous cell carcinoma proliferation and migration by negatively regulating 14-3-3zeta/Akt signaling
PMID: 34757658
8
PRDM5 mutations affect extracellular matrix components and are associated with aortic/arterial aneurysms and dissection diseases
PMID: 38892036
Disease Associationsβ“˜21
brittle cornea syndromeOpen Targets
0.78Strong
Abnormality of the cardiovascular systemOpen Targets
0.51Moderate
Connective tissue disease with eye involvementOpen Targets
0.50Moderate
Ehlers-Danlos syndromeOpen Targets
0.41Moderate
osteoarthritis, kneeOpen Targets
0.38Weak
osteoarthritisOpen Targets
0.36Weak
smoking initiationOpen Targets
0.36Weak
type 2 diabetes mellitusOpen Targets
0.35Weak
alcohol drinkingOpen Targets
0.33Weak
aortic stenosisOpen Targets
0.31Weak
inflammatory spondylopathyOpen Targets
0.30Weak
spondyloarthropathyOpen Targets
0.30Weak
DNA methylationOpen Targets
0.29Weak
arthritisOpen Targets
0.29Weak
joint diseaseOpen Targets
0.29Weak
intracranial hemorrhageOpen Targets
0.29Weak
osteoarthritis, hipOpen Targets
0.28Weak
tooth diseaseOpen Targets
0.27Weak
neurodegenerative diseaseOpen Targets
0.27Weak
benign prostatic hyperplasiaOpen Targets
0.27Weak
Brittle cornea syndrome 2UniProt
Pathogenic Variants56
NM_018699.4(PRDM5):c.1513dup (p.Arg505fs)Pathogenic
not provided|Brittle cornea syndrome 2|Cardiovascular phenotype
β˜…β˜…β˜†β˜†2026β†’ Residue 505
NM_018699.4(PRDM5):c.1623+1G>ALikely pathogenic
Brittle cornea syndrome 2|not provided
β˜…β˜…β˜†β˜†2025
NM_018699.4(PRDM5):c.865+1G>ALikely pathogenic
not provided|Brittle cornea syndrome 2
β˜…β˜…β˜†β˜†2025
NM_018699.4(PRDM5):c.307G>T (p.Glu103Ter)Pathogenic
not provided|Brittle cornea syndrome 2
β˜…β˜…β˜†β˜†2025β†’ Residue 103
NM_018699.4(PRDM5):c.1258C>T (p.Gln420Ter)Pathogenic
Brittle cornea syndrome 2|not provided
β˜…β˜…β˜†β˜†2025β†’ Residue 420
NM_018699.4(PRDM5):c.1036C>T (p.Arg346Ter)Pathogenic
Brittle cornea syndrome 2|not provided
β˜…β˜…β˜†β˜†2024β†’ Residue 346
NM_018699.4(PRDM5):c.1030G>T (p.Glu344Ter)Pathogenic
not provided|Brittle cornea syndrome 2
β˜…β˜…β˜†β˜†2024β†’ Residue 344
NM_018699.4(PRDM5):c.694C>T (p.Arg232Ter)Pathogenic
not provided|Brittle cornea syndrome 2
β˜…β˜…β˜†β˜†2024β†’ Residue 232
NM_018699.4(PRDM5):c.974del (p.Cys325fs)Pathogenic
Brittle cornea syndrome 2|not provided|Ehlers-Danlos syndrome
β˜…β˜…β˜†β˜†2023β†’ Residue 325
NM_018699.4(PRDM5):c.1666C>T (p.Gln556Ter)Pathogenic
Cardiovascular phenotype|not provided
β˜…β˜…β˜†β˜†2023β†’ Residue 556
NM_018699.4(PRDM5):c.800_806dup (p.Cys269Ter)Pathogenic
not provided
β˜…β˜†β˜†β˜†2026β†’ Residue 269
NM_018699.4(PRDM5):c.1258_1259del (p.Gln420fs)Pathogenic
not provided
β˜…β˜†β˜†β˜†2026β†’ Residue 420
NM_018699.4(PRDM5):c.271C>T (p.Gln91Ter)Pathogenic
not provided
β˜…β˜†β˜†β˜†2025β†’ Residue 91
NM_018699.4(PRDM5):c.1138_1140delinsTA (p.Leu380fs)Pathogenic
Brittle cornea syndrome 2
β˜…β˜†β˜†β˜†2025β†’ Residue 380
NM_018699.4(PRDM5):c.15C>A (p.Tyr5Ter)Pathogenic
not provided
β˜…β˜†β˜†β˜†2025β†’ Residue 5
NM_018699.4(PRDM5):c.243G>A (p.Trp81Ter)Pathogenic
not provided
β˜…β˜†β˜†β˜†2025β†’ Residue 81
NM_018699.4(PRDM5):c.320A>G (p.Tyr107Cys)Likely pathogenic
Brittle cornea syndrome 2
β˜…β˜†β˜†β˜†2024β†’ Residue 107
NM_018699.4(PRDM5):c.472A>T (p.Lys158Ter)Pathogenic
not provided
β˜…β˜†β˜†β˜†2024β†’ Residue 158
NM_018699.4(PRDM5):c.338_341del (p.Ile113fs)Pathogenic
not provided
β˜…β˜†β˜†β˜†2024β†’ Residue 113
NM_018699.4(PRDM5):c.1461_1468del (p.Lys487fs)Likely pathogenic
Brittle cornea syndrome 2
β˜…β˜†β˜†β˜†2024β†’ Residue 487
View on ClinVar β†—
Related Genes
MYBL2Shared pathway50%ZNRD2Shared pathway50%ZNF469Shared pathway50%NEDD1Shared pathway33%NEK9Shared pathway33%PBKShared pathway33%
Tissue Expression6 tissues
Ovary
100%
Bone Marrow
79%
Heart
49%
Lung
31%
Brain
11%
Liver
3%
Gene Interaction Network
Click a node to explore
PRDM5MYBL2ZNRD2ZNF469NEDD1NEK9PBK
PROTEIN STRUCTURE
Preparing viewer…
PDB6XAZ Β· 1.70 Γ… Β· X-ray
View on RCSB β†—
Constraintβ“˜
LOEUFβ“˜
0.90LoF Tolerant
pLIβ“˜
0.00Tolerant
Observed/Expected LoF0.71 [0.56–0.90]
RankingsWhere PRDM5 stands among ~20K protein-coding genes
  • #9,930of 20,598
    Most Researched42
  • #1,233of 5,498
    Most Pathogenic Variants56 Β· top quartile
  • #8,109of 17,882
    Most Constrained (LOEUF)0.90
Genes detectedPRDM5
Sources retrieved10 papers
Response timeβ€”
πŸ“„ Sources
10β–Ό
1
Necroptosis microenvironment directs lineage commitment in liver cancer.
PMID: 30209397
Nature Β· 2018
1.00
2
Identification and Management of a Novel PRDM5 Gene Pathologic Variant in a Family With Brittle Cornea Syndrome.
PMID: 37713669
Cornea Β· 2023
0.90
3
TGF-Ξ²2-induced circ-PRDM5 regulates migration, invasion, and EMT through the miR-92b-3p/COL1A2 pathway in human lens epithelial cells.
PMID: 35083632
J Mol Histol Β· 2022
0.80
4
PRDM5 is silenced in human cancers and has growth suppressive activities.
PMID: 15077163
Oncogene Β· 2004
0.70
5
An Eye into the Aorta: The Role of Extracellular Matrix Regulatory Genes
PMID: 38892036
Int J Mol Sci Β· 2024
0.60