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10 sources retrieved Β· Most recent: April 2026 Β· Index updated 15 days ago
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PRDM13
PR/SET domain 13
Chromosome 6 Β· 6q16.2
NCBI Gene: 59336Ensembl: ENSG00000112238.12HGNC: HGNC:13998UniProt: Q9H4Q3
19PubMed Papers
22Diseases
0Drugs
4Pathogenic Variants
FUNCTIONAL ROLE
Transcription Factor
CLINICAL
OMIM Disease Gene
DATA QUALITY
βœ“ Experimental GO Evidenceβœ“ Swiss-Prot Reviewed
histone methyltransferase activityregulation of gene expressionnucleushypothalamus cell differentiationcerebellar dysfunction, impaired intellectual development, and hypogonadotropic hypogonadismpontocerebellar hypoplasia, IIA 17North Carolina macular dystrophyAbnormality of the skeletal system
✦AI Summary

PRDM13 (PR/SET domain 13) is a transcriptional regulator that functions as a critical determinant of neuronal cell fate specification, particularly in GABAergic inhibitory neuron development. The protein acts downstream of the transcription factor PTF1A to suppress alternative glutamatergic excitatory neuronal fates while promoting GABAergic lineages 1. In the cerebellum, PRDM13 is essential for specification of PAX2+ interneuron and Purkinje cell inhibitory neuronal lineages, with deficiency leading to increased TLX3+ excitatory neuronal lineages and cerebellar hypoplasia 12. PRDM13 also plays a crucial role in hypothalamic development, specifically in the differentiation of Kiss1-expressing neurons in the arcuate nucleus that regulate reproductive function 2. The protein is highly expressed in the dorsomedial hypothalamus where it contributes to sleep quality regulation and metabolic homeostasis 3. Clinically, recessive PRDM13 mutations cause a syndrome characterized by intellectual disability, cerebellar hypoplasia, congenital hypogonadotropic hypogonadism, and ataxia 24. Additionally, duplications affecting PRDM13 regulatory regions cause North Carolina macular dystrophy, a congenital retinal malformation 56. The gene may also function as a tumor suppressor, as overexpression inhibits glioma cell proliferation and invasion through DLC1 upregulation 7.

Sources cited
1
PRDM13 functions downstream of PTF1A to specify GABAergic inhibitory neurons and suppress glutamatergic fates in cerebellum
PMID: 40721003
2
Recessive PRDM13 mutations cause syndrome with cerebellar hypoplasia, intellectual disability, and congenital hypogonadotropic hypogonadism
PMID: 34730112
3
PRDM13 is highly expressed in dorsomedial hypothalamus and regulates sleep quality and metabolic homeostasis
PMID: 25546159
4
PRDM13 duplications cause North Carolina macular dystrophy with congenital macular malformation
PMID: 39959174
5
PRDM13 regulatory mechanisms involve retinal enhancer activity during retinogenesis
PMID: 36243009
6
PRDM13 variants identified in intellectual disability cohort
PMID: 36344539
7
PRDM13 overexpression inhibits glioma cell proliferation and invasion through DLC1 upregulation
PMID: 29767251
Disease Associationsβ“˜22
cerebellar dysfunction, impaired intellectual development, and hypogonadotropic hypogonadismOpen Targets
0.65Moderate
pontocerebellar hypoplasia, IIA 17Open Targets
0.64Moderate
North Carolina macular dystrophyOpen Targets
0.48Moderate
Abnormality of the skeletal systemOpen Targets
0.46Moderate
congenital hypogonadotropic hypogonadismOpen Targets
0.42Moderate
genetic disorderOpen Targets
0.42Moderate
neurodegenerative diseaseOpen Targets
0.37Weak
ovarian dysfunctionOpen Targets
0.32Weak
enuresisOpen Targets
0.23Weak
skin diseaseOpen Targets
0.23Weak
bronchiectasisOpen Targets
0.21Weak
Retinal dystrophyOpen Targets
0.18Weak
coronary atherosclerosisOpen Targets
0.13Weak
coronary artery diseaseOpen Targets
0.13Weak
obesityOpen Targets
0.12Weak
preeclampsiaOpen Targets
0.10Suggestive
retinitis pigmentosaOpen Targets
0.08Suggestive
Cone rod dystrophyOpen Targets
0.08Suggestive
gliomaOpen Targets
0.07Suggestive
age-related macular degenerationOpen Targets
0.07Suggestive
Cerebellar dysfunction, impaired intellectual development, and hypogonadotropic hypogonadismUniProt
Pontocerebellar hypoplasia 17UniProt
Pathogenic Variants4
NM_021620.4(PRDM13):c.839del (p.Ala280fs)Pathogenic
Pontocerebellar hypoplasia, IIA 17
β˜†β˜†β˜†β˜†2022β†’ Residue 280
NM_021620.4(PRDM13):c.844del (p.Val282fs)Pathogenic
Pontocerebellar hypoplasia, IIA 17
β˜†β˜†β˜†β˜†2022β†’ Residue 282
NM_021620.4(PRDM13):c.800del (p.Gly267fs)Pathogenic
Pontocerebellar hypoplasia, IIA 17
β˜†β˜†β˜†β˜†2022β†’ Residue 267
NM_021620.4(PRDM13):c.398-2_408delPathogenic
Cerebellar dysfunction, impaired intellectual development, and hypogonadotropic hypogonadism
β˜†β˜†β˜†β˜†2022
View on ClinVar β†—
Related Genes
KDM4FShared pathway100%KDM4EShared pathway100%PRDM6Shared pathway100%KDM6AShared pathway67%UTYShared pathway67%SRCAPShared pathway67%
Tissue Expression6 tissues
Brain
100%
Heart
0%
Lung
0%
Bone Marrow
0%
Ovary
0%
Liver
0%
Gene Interaction Network
Click a node to explore
PRDM13KDM4FKDM4EPRDM6KDM6AUTYSRCAP
PROTEIN STRUCTURE
Preparing viewer…
AlphaFoldAI-predicted Β· UniProt Q9H4Q3
View on AlphaFold β†—
Constraintβ“˜
LOEUFβ“˜
0.69LoF Tolerant
pLIβ“˜
0.08Tolerant
Observed/Expected LoF0.45 [0.30–0.69]
RankingsWhere PRDM13 stands among ~20K protein-coding genes
  • #14,504of 20,598
    Most Researched19
  • #3,861of 5,498
    Most Pathogenic Variants4
  • #5,257of 17,882
    Most Constrained (LOEUF)0.69
Genes detectedPRDM13
Sources retrieved10 papers
Response timeβ€”
πŸ“„ Sources
10β–Ό
1
Human genome meeting 2016 : Houston, TX, USA. 28 February - 2 March 2016.
PMID: 27294413
Hum Genomics Β· 2016
1.00
2
The diagnostic yield, candidate genes, and pitfalls for a genetic study of intellectual disability in 118 middle eastern families.
PMID: 36344539
Sci Rep Β· 2022
0.90
3
Deficiency of Prdm13, a dorsomedial hypothalamus-enriched gene, mimics age-associated changes in sleep quality and adiposity.
PMID: 25546159
Aging Cell Β· 2015
0.80
4
A novel
PMID: 39959174
Mol Vis Β· 2024
0.70
5
A recessive PRDM13 mutation results in congenital hypogonadotropic hypogonadism and cerebellar hypoplasia.
PMID: 34730112
J Clin Invest Β· 2021
0.60