Gene Gene information from NCBI Gene database. Download as csv Download as pdf
Entrez ID	59336
Gene name	PR/SET domain 13
Gene symbol	PRDM13
Synonyms (NCBI Gene)	CDIDHHMU-MB-20.220PCH17PFM10
Chromosome	6
Chromosome location	6q16.2

12 Show/Hide all (12)

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

19 Show/Hide all (19)

GO ID	Ontology	Definition	Evidence
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

MIM	HGNC	e!Ensembl
616741	13998	ENSG00000112238

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	601 → 623	Zinc finger, C2H2 type	Domain
PF00096	zf-C2H2	573 → 595	Zinc finger, C2H2 type	Domain
PF00096	zf-C2H2	137 → 159	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

Interactions

View interactions

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)

Phenotype Name	Clinical Significance	dbSNP ID	RCV Accession	Evidence Score
Causal Diseases associated with Pathogenic or Likely Pathogenic variants in ClinVar
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)

Phenotype Name	Clinical Significance	Source	Reference	Evidence Score
Unknown / Other Associations ClinVar entries with uncertain/conflicting evidence, and associations from other databases (OMIM, Orphanet, GWAS, etc.) where the gene is not established as causal. Show/Hide Unknown Diseases (6)
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

Disease Name	Disease (Merged)	Source	PMID	Relationship Type	Evidence Score
Associations from Text Mining Disease associations identified through text mining Show/Hide Text Mining Associations (12)
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

Related Gene	Shared Diseases	Shared Disease Names	Shared Pathway Names	Shared Evidence Sources	Shared Evidence Names
PPIL1	2	["Congenital pontocerebellar hypoplasia","Pontocerebellar hypoplasia"]	[]	4	["Disgenet (Congenital pontocerebellar hypoplasia)","ClinVar (Pontocerebellar hypoplasia)","Disgenet (Pontocerebellar hypoplasia)","HPO (Pontocerebellar hypoplasia)"]
CDC40	2	["Congenital pontocerebellar hypoplasia","Pontocerebellar hypoplasia"]	[]	4	["Disgenet (Congenital pontocerebellar hypoplasia)","ClinVar (Pontocerebellar hypoplasia)","Disgenet (Pontocerebellar hypoplasia)","HPO (Pontocerebellar hypoplasia)"]
CLP1	2	["Congenital pontocerebellar hypoplasia","Pontocerebellar hypoplasia"]	[]	4	["Disgenet (Congenital pontocerebellar hypoplasia)","GenCC (Pontocerebellar hypoplasia)","ClinVar (Pontocerebellar hypoplasia)","HPO (Pontocerebellar hypoplasia)"]
EXOSC8	2	["Congenital pontocerebellar hypoplasia","Pontocerebellar hypoplasia"]	[]	4	["Disgenet (Congenital pontocerebellar hypoplasia)","ClinVar (Pontocerebellar hypoplasia)","Disgenet (Pontocerebellar hypoplasia)","HPO (Pontocerebellar hypoplasia)"]
EXOSC9	2	["Congenital pontocerebellar hypoplasia","Pontocerebellar hypoplasia"]	[]	4	["Disgenet (Congenital pontocerebellar hypoplasia)","ClinVar (Pontocerebellar hypoplasia)","Disgenet (Pontocerebellar hypoplasia)","HPO (Pontocerebellar hypoplasia)"]

PRDM13 (PR/SET domain 13)

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