PRDM13 (PR/SET domain 13)

Gene

• Entrez ID: 59336
• Gene name: PR/SET domain 13
• Gene symbol: PRDM13
• Synonyms (NCBI Gene): CDIDHH, MU-MB-20.220, PCH17, PFM10
• Chromosome: 6
• Chromosome location: 6q16.2

miRNA

miRTarBase ID	miRNA	Experiments	Reference
MIRT022704	hsa-miR-124-3p	Microarray	18668037
MIRT029490	hsa-miR-26b-5p	Microarray	19088304
MIRT2076577	hsa-miR-1246	CLIP-seq
MIRT2076578	hsa-miR-4764-5p	CLIP-seq
MIRT2303182	hsa-miR-4682	CLIP-seq
MIRT2457102	hsa-miR-146a	CLIP-seq
MIRT2457103	hsa-miR-146b-5p	CLIP-seq
MIRT2457104	hsa-miR-4773	CLIP-seq
MIRT2457105	hsa-miR-489	CLIP-seq
MIRT2457106	hsa-miR-514	CLIP-seq
MIRT2457107	hsa-miR-514b-3p	CLIP-seq
MIRT2457108	hsa-miR-589	CLIP-seq

Gene ontology (GO)

GO ID	Ontology	Definition	Evidence	Reference
GO:0000122	Process	Negative regulation of transcription by RNA polymerase II	IEA
GO:0003677	Function	DNA binding	IEA
GO:0003682	Function	Chromatin binding	IEA
GO:0005634	Component	Nucleus	IBA
GO:0005634	Component	Nucleus	IEA
GO:0005634	Component	Nucleus	ISS
GO:0006338	Process	Chromatin remodeling	IEA
GO:0008168	Function	Methyltransferase activity	IEA
GO:0008270	Function	Zinc ion binding	IEA
GO:0010468	Process	Regulation of gene expression	IBA
GO:0016740	Function	Transferase activity	IEA
GO:0021979	Process	Hypothalamus cell differentiation	IEA
GO:0022008	Process	Neurogenesis	IEA
GO:0032259	Process	Methylation	IEA
GO:0042054	Function	Histone methyltransferase activity	IEA
GO:0042054	Function	Histone methyltransferase activity	ISS
GO:0046872	Function	Metal ion binding	IEA
GO:0061629	Function	RNA polymerase II-specific DNA-binding transcription factor binding	IEA
GO:0097154	Process	GABAergic neuron differentiation	IEA

Other IDs

• MIM: 616741
• HGNC: 13998
• e!Ensembl: ENSG00000112238

Protein

• UniProt ID: Q9H4Q3
• Protein name: PR domain zinc finger protein 13 (EC 2.1.1.-) (PR domain-containing protein 13)
• Protein function: May be involved in transcriptional regulation. Is required for the differentiation of KISS1-expressing neurons in the arcuate (Arc) nucleus of the hypothalamus. Is a critical regulator of GABAergic cell fate in the cerebellum, required for norma
• Family and domains:

  Pfam

  Accession	ID	Position in sequence	Description	Type
  PF00096	zf-C2H2	137 → 159	Zinc finger, C2H2 type	Domain
  PF00096	zf-C2H2	573 → 595	Zinc finger, C2H2 type	Domain
  PF00096	zf-C2H2	601 → 623	Zinc finger, C2H2 type	Domain
  PF00096	zf-C2H2	630 → 653	Zinc finger, C2H2 type	Domain

• Tissue specificity: TISSUE SPECIFICITY: In the embryo, expressed in neural stem cells of the hindbrain. {ECO:0000269|PubMed:35390279}.
• Sequence:

  MHGAARAPATSVSADCCIPAGLRLGPVPGTFKLGKYLSDRREPGPKKKVRMVRGELVDES
  GGSPLEWIGLIRAARNSQEQTLEAIADLPGGQIFYRALRDVQPGEELTVWYSNSLAQWFD
  IPTTATPTHDEKGEERYICWYCWRTFRYPNSLKAHLRFHCVFSGGGGGAFLHHEHAARQG
  AVPAADGLGLSPKPPAPDFAAPSQAGTLRPHPLGPPPVQACGAREGIKREASSAPSATSP
  TPGKWGQPKKGKEQLDRALDMSGAARGQGHFLGIVGGSSAGVGSLAFYPGVRSAFKPAGL
  ARAAAAAHGDPYREESSSKQGAGLALGRLLGGGRACGRPGSGENSAAGGAGHHHHHHAHH
  HHHPKCLLAGDPPPPPPPGLPCSGALRGFPLLSVPPEEASAFKHVERAPPAAAALPGARY
  AQLPPAPGLPLERCALPPLDPGGLKAYPGGECSHLPAVMPAFTVYNGELLYGSPATTAYY
  PLKLHFGGLLKYPESISYFSGPAAAALSPAELGSLASIDREIAMHNQQLSEMAAGKGRGR
  LDSGTLPPAVAAAGGTGGGGSGGSGAGKPKTGHLCLYCGKLYSRKYGLKIHMRTHTGYKP
  LKCKVCLRPFGDPSNLNKHIRLHAEGNTPYRCEFCGKVLVRRRDLERHVKSRHPGQSLLA
  KAGDGPGAEPGYPPEPGDPKSDDSDVDVCFTDDQSDPEVGGGGERDL

• Sequence length: 707

Associated diseases

Evidence Score:

• ★☆☆☆☆  Gene-disease association found in Text Mining only
• ★★☆☆☆  Found in Text Mining and Unknown/Other Associations
• ★★★☆☆  Reported in Unknown/Other Associations across ≥2 Sources
• ★★★★☆  ClinVar: Pathogenic/Likely Pathogenic (<5 Variants)
• ★★★★★  ClinVar: Pathogenic/Likely Pathogenic (≥5 Variants)

Causal
Phenotype Name	Clinical Significance	dbSNP ID	RCV Accession	Evidence Score
Cerebellar dysfunction, impaired intellectual development, and hypogonadotropic hypogonadism	Pathogenic	rs2114499502	RCV001838839	★★★★☆ ClinVar: Pathogenic / Likely Pathogenic (<5 Variants)
Pontocerebellar hypoplasia, IIA 17	Pathogenic	rs2114500026, rs2114500035, rs2114499988	RCV002260932 RCV002260933 RCV002260934	★★★★☆ ClinVar: Pathogenic / Likely Pathogenic (<5 Variants)

Unknown / Other Associations
Phenotype Name	Clinical Significance	Source	Evidence Score
CONGENITAL PONTOCEREBELLAR HYPOPLASIA	—	Disgenet	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
North Carolina macular dystrophy	Uncertain significance; Likely benign	ClinVar	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
PONTOCEREBELLAR HYPOPLASIA, TYPE 17	—	Disgenet, HPO Disgenet, HPO	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
PRDM13-related disorder	Likely benign; Benign; Uncertain significance	ClinVar	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Retinal dystrophy	Benign; Uncertain significance	ClinVar	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
RETINITIS PIGMENTOSA 1	—	CTD	★★☆☆☆ Found in Text Mining + Unknown/Other Associations

Associations from Text Mining
Disease Name	Disease (Merged)	Source	PMID	Relationship Type	Evidence Score
Cancer of Nasopharynx	Nasopharyngeal Cancer	BEFREE	12800201		★☆☆☆☆ Found in Text Mining only
Developmental Disabilities	Development Disorder	BEFREE	28973654		★☆☆☆☆ Found in Text Mining only
Glioma	Glioma	BEFREE	29767251		★☆☆☆☆ Found in Text Mining only
Glioma	Glioma	Pubtator	29767251	Inhibit	★☆☆☆☆ Found in Text Mining only
Macular Degeneration	Macular degeneration	Pubtator	26507665	Associate	★☆☆☆☆ Found in Text Mining only
Macular dystrophy retinal 1 North Carolina type	Macular dystrophy	Pubtator	26507665, 27777503, 32476814, 34125159, 34526759, 36402981, 39959174	Associate	★☆☆☆☆ Found in Text Mining only
Malignant neoplasm of nasopharynx	Nasopharyngeal carcinoma	BEFREE	12800201		★☆☆☆☆ Found in Text Mining only
Nasopharyngeal carcinoma	Nasopharyngeal Carcinoma	BEFREE	12800201		★☆☆☆☆ Found in Text Mining only
Neoplasms	Neoplasms	BEFREE	12800201		★☆☆☆☆ Found in Text Mining only
North Carolina macular dystrophy	North Carolina Macular Dystrophy	BEFREE	28635424, 28973654, 30710461		★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Prostatic Neoplasms	Prostatic neoplasm	Pubtator	26902887	Associate	★☆☆☆☆ Found in Text Mining only
Triple Negative Breast Neoplasms	Triple Negative Breast Neoplasms	BEFREE	31069014		★☆☆☆☆ Found in Text Mining only