PRDM8 (PR/SET domain 8)

Gene

• Entrez ID: 56978
• Gene name: PR/SET domain 8
• Gene symbol: PRDM8
• Synonyms (NCBI Gene): EPM10, KMT8D, PFM5
• Chromosome: 4
• Chromosome location: 4q21.21
• Summary: This gene encodes a protein that belongs to a conserved family of histone methyltransferases that predominantly act as negative regulators of transcription. The encoded protein contains an N-terminal Su(var)3-9, Enhancer-of-zeste, and Trithorax (SET) doma

SNPs

SNP ID	Visualize variation	Clinical significance	Consequence
rs863225286	T>C	Pathogenic	Coding sequence variant, missense variant

miRNA

miRTarBase ID	miRNA	Experiments	Reference
MIRT025734	hsa-miR-7-5p	Microarray	17612493
MIRT737368	hsa-miR-20a-5p	Immunoprecipitaion (IP), qRT-PCR	32344701
MIRT1260363	hsa-miR-1275	CLIP-seq
MIRT1260364	hsa-miR-1323	CLIP-seq
MIRT1260365	hsa-miR-1908	CLIP-seq
MIRT1260366	hsa-miR-3180	CLIP-seq
MIRT1260367	hsa-miR-3180-3p	CLIP-seq
MIRT1260368	hsa-miR-3196	CLIP-seq
MIRT1260369	hsa-miR-4488	CLIP-seq
MIRT1260370	hsa-miR-4665-5p	CLIP-seq
MIRT1260371	hsa-miR-4697-5p	CLIP-seq
MIRT1260372	hsa-miR-4793-5p	CLIP-seq
MIRT1260373	hsa-miR-548o	CLIP-seq
MIRT1260374	hsa-miR-663	CLIP-seq
MIRT1260375	hsa-miR-1343	CLIP-seq
MIRT2076681	hsa-miR-1909	CLIP-seq
MIRT2076682	hsa-miR-2113	CLIP-seq
MIRT2076683	hsa-miR-342-5p	CLIP-seq
MIRT2076684	hsa-miR-3944-5p	CLIP-seq
MIRT2076685	hsa-miR-4664-5p	CLIP-seq
MIRT2076686	hsa-miR-4708-3p	CLIP-seq
MIRT2303374	hsa-miR-425	CLIP-seq
MIRT2303375	hsa-miR-4684-3p	CLIP-seq
MIRT2688547	hsa-miR-320a	CLIP-seq
MIRT2688548	hsa-miR-320b	CLIP-seq
MIRT2688549	hsa-miR-320c	CLIP-seq
MIRT2688550	hsa-miR-320d	CLIP-seq
MIRT2688551	hsa-miR-320e	CLIP-seq
MIRT2688552	hsa-miR-3978	CLIP-seq
MIRT2688553	hsa-miR-4429	CLIP-seq
MIRT2688554	hsa-miR-4731-5p	CLIP-seq
MIRT2688555	hsa-miR-615-5p	CLIP-seq

Gene ontology (GO)

GO ID	Ontology	Definition	Evidence	Reference
GO:0003677	Function	DNA binding	IEA
GO:0003682	Function	Chromatin binding	IEA
GO:0003714	Function	Transcription corepressor activity	IEA
GO:0005515	Function	Protein binding	IPI	22961547
GO:0005634	Component	Nucleus	IBA
GO:0005634	Component	Nucleus	IDA	22961547
GO:0005634	Component	Nucleus	IEA
GO:0005654	Component	Nucleoplasm	IDA
GO:0005654	Component	Nucleoplasm	IEA
GO:0006338	Process	Chromatin remodeling	IEA
GO:0006355	Process	Regulation of DNA-templated transcription	IBA
GO:0007399	Process	Nervous system development	IEA
GO:0008168	Function	Methyltransferase activity	IEA
GO:0008270	Function	Zinc ion binding	IEA
GO:0014003	Process	Oligodendrocyte development	IBA
GO:0016604	Component	Nuclear body	IDA
GO:0016740	Function	Transferase activity	IEA
GO:0021540	Process	Corpus callosum morphogenesis	IEA
GO:0021952	Process	Central nervous system projection neuron axonogenesis	IEA
GO:0021957	Process	Corticospinal tract morphogenesis	IEA
GO:0022008	Process	Neurogenesis	IEA
GO:0032259	Process	Methylation	IEA
GO:0042054	Function	Histone methyltransferase activity	IEA
GO:0045892	Process	Negative regulation of DNA-templated transcription	IEA
GO:0046872	Function	Metal ion binding	IEA
GO:0046974	Function	Histone H3K9 methyltransferase activity	IEA

Other IDs

• MIM: 616639
• HGNC: 13993
• e!Ensembl: ENSG00000152784

Protein

• UniProt ID: Q9NQV8
• Protein name: PR domain zinc finger protein 8 (EC 2.1.1.-) (PR domain-containing protein 8)
• Protein function: Probable histone methyltransferase, preferentially acting on 'Lys-9' of histone H3 (By similarity). Involved in the control of steroidogenesis through transcriptional repression of steroidogenesis marker genes such as CYP17A1 and LHCGR (By simil
• Family and domains:

  Pfam

  Accession	ID	Position in sequence	Description	Type
  PF00096	zf-C2H2	666 → 688	Zinc finger, C2H2 type	Domain

• Tissue specificity: TISSUE SPECIFICITY: Expressed in brain, heart, skeletal muscle, testes, prostate. {ECO:0000269|PubMed:22961547}.
• Sequence:

  MEDTGIQRGIWDGDAKAVQQCLTDIFTSVYTTCDIPENAIFGPCVLSHTSLYDSIAFIAL
  KSTDKRTVPYIFRVDTSAANGSSEGLMWLRLVQSARDKEEQNLEAYIKNGQLFYRSLRRI
  AKDEELLVWYGKELTELLLLCPSRSHNKMNGSSPYTCLECSQRFQFEFPYVAHLRFRCPK
  RLHSADISPQDEQGGGVGTKDHGGGGGGGKDQQQQQQEAPLGPGPKFCKAGPLHHYPSPS
  PESSNPSAAAGGSSAKPSTDFHNLARELENSRGGSSCSPAQSLSSGSGSGGGGGHQEAEL
  SPDGIATGGGKGKRKFPEEAAEGGGGAGLVGGRGRFVERPLPASKEDLVCTPQQYRASGS
  YFGLEENGRLFAPPSPETGEAKRSAFVEVKKAARAASLQEEGTADGAGVASEDQDAGGGG
  GSSTPAAASPVGAEKLLAPRPGGPLPSRLEGGSPARGSAFTSVPQLGSAGSTSGGGGTGA
  GAAGGAGGGQGAASDERKSAFSQPARSFSQLSPLVLGQKLGALEPCHPADGVGPTRLYPA
  AADPLAVKLQGAADLNGGCGSLPSGGGGLPKQSPFLYATAFWPKSSAAAAAAAAAAAAGP
  LQLQLPSALTLLPPSFTSLCLPAQNWCAKCNASFRMTSDLVYHMRSHHKKEYAMEPLVKR
  RREEKLKCPICNESFRERHHLSRHMTSHN

• Sequence length: 689

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
Early-onset Lafora body disease	Pathogenic	rs863225286	RCV000201931	★★★★☆ ClinVar: Pathogenic / Likely Pathogenic (<5 Variants)

Unknown / Other Associations
Phenotype Name	Clinical Significance	Source	Evidence Score
ANDROGENETIC ALOPECIA	—	GWAS catalog	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
ATRIAL FIBRILLATION	—	GWAS catalog	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
ATRIAL FLUTTER	—	GWAS catalog	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
CARDIAC ARRHYTHMIA	—	GWAS catalog	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
CARDIOEMBOLIC STROKE	—	GWAS catalog	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
CARDIOVASCULAR DISEASE	—	GWAS catalog	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
CHRONIC KIDNEY DISEASE	—	GWAS catalog	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
CORONARY ARTERY DISEASE	—	GWAS catalog	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
EPILEPSY, PROGRESSIVE MYOCLONIC, 10	—	Disgenet, HPO Disgenet, HPO	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
ESSENTIAL HYPERTENSION	—	GWAS catalog	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
GOUT	—	GWAS catalog	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
HEART FAILURE	—	GWAS catalog	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Hepatocellular carcinoma	Benign; Likely benign	ClinVar	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
HYPERTENSION	—	GWAS catalog	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
HYPERTENSION, PREGNANCY-INDUCED	—	GWAS catalog	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
HYPERTENSIVE HEART DISEASE	—	GWAS catalog	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
KIDNEY DISEASE	—	GWAS catalog	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
KIDNEY FAILURE	—	GWAS catalog	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
MAJOR DEPRESSIVE DISORDER	—	GWAS catalog	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
MYOCARDIAL INFARCTION	—	GWAS catalog	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
POTASSIUM DEFICIENCY DISEASE	—	GWAS catalog	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
PRDM8-related disorder	Likely benign; Benign	ClinVar	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
PREECLAMPSIA	—	GWAS catalog	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
STROKE	—	GWAS catalog	★★☆☆☆ Found in Text Mining + Unknown/Other Associations

Associations from Text Mining
Disease Name	Disease (Merged)	Source	PMID	Relationship Type	Evidence Score
Action Myoclonus-Renal Failure Syndrome	Action Myoclonus-Renal Failure Syndrome	CTD_human_DG			★☆☆☆☆ Found in Text Mining only
Anemia Aplastic	Aplastic anemia	Pubtator	26909595, 32819411	Associate	★☆☆☆☆ Found in Text Mining only
Arthritis Rheumatoid	Rheumatoid arthritis	Pubtator	31037071	Associate	★☆☆☆☆ Found in Text Mining only
Atypical Inclusion-Body Disease	Inclusion-Body Disease	CTD_human_DG			★☆☆☆☆ Found in Text Mining only
Bone Marrow Failure Disorders	Bone marrow failure syndromes	Pubtator	26909595, 32819411	Associate	★☆☆☆☆ Found in Text Mining only
Bone Marrow failure syndromes	Bone marrow failure syndrome	BEFREE	26909595		★☆☆☆☆ Found in Text Mining only
Cerebellar Ataxia	Cerebellar ataxia	Pubtator	37584462	Associate	★☆☆☆☆ Found in Text Mining only
Cerebellar Ataxia Deafness and Narcolepsy	Cerebellar ataxia, deafness, and narcolepsy	Pubtator	37584462	Associate	★☆☆☆☆ Found in Text Mining only
Dementia	Dementia	Pubtator	37584462	Associate	★☆☆☆☆ Found in Text Mining only
Dementia	Dementia	HPO_DG			★☆☆☆☆ Found in Text Mining only
Dentatorubral-Pallidoluysian Atrophy	Dentatorubral Pallidoluysian Atrophy	CTD_human_DG			★☆☆☆☆ Found in Text Mining only
Down Syndrome	Down syndrome	Pubtator	28861129, 32819411	Associate	★☆☆☆☆ Found in Text Mining only
Dysarthria	Dysarthria	HPO_DG			★☆☆☆☆ Found in Text Mining only
Dyskeratosis Congenita	Dyskeratosis Congenita	BEFREE	26909595		★☆☆☆☆ Found in Text Mining only
Dyskeratosis Congenita	Dyskeratosis congenita	Pubtator	26909595, 28861129, 32819411	Associate	★☆☆☆☆ Found in Text Mining only
Early-onset Lafora body disease	Lafora Disease	BEFREE	22961547		★★★★☆ ClinVar: Pathogenic / Likely Pathogenic (<5 Variants)
Early-onset Lafora body disease	Lafora Disease	Orphanet			★★★★☆ ClinVar: Pathogenic / Likely Pathogenic (<5 Variants)
Epilepsies Myoclonic	Myoclonic epilepsy	Pubtator	22961547	Associate	★☆☆☆☆ Found in Text Mining only
EPILEPSY, PROGRESSIVE MYOCLONIC, 10	Myoclonic Epilepsy	GENOMICS_ENGLAND_DG	22961547		★★☆☆☆ Found in Text Mining + Unknown/Other Associations
EPILEPSY, PROGRESSIVE MYOCLONIC, 10	Myoclonic Epilepsy	UNIPROT_DG	22961547		★★☆☆☆ Found in Text Mining + Unknown/Other Associations
EPILEPSY, PROGRESSIVE MYOCLONIC, 10	Myoclonic Epilepsy	ORPHANET_DG	22961547		★★☆☆☆ Found in Text Mining + Unknown/Other Associations
EPILEPSY, PROGRESSIVE MYOCLONIC, 10	Myoclonic Epilepsy	CLINVAR_DG			★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Familial Progressive Myoclonic Epilepsy	Myoclonic Epilepsy	CTD_human_DG			★☆☆☆☆ Found in Text Mining only
Generalized myoclonic seizures	Myoclonic Seizures	HPO_DG			★☆☆☆☆ Found in Text Mining only
Hallucinations	Hallucinations	HPO_DG			★☆☆☆☆ Found in Text Mining only
Ki-1+ Anaplastic Large Cell Lymphoma	Anaplastic Lymphoma	BEFREE	30393995		★☆☆☆☆ Found in Text Mining only
Lafora Disease	Lafora disease	Pubtator	22961547	Associate	★☆☆☆☆ Found in Text Mining only
Liver carcinoma	Liver carcinoma	BEFREE	29572888		★☆☆☆☆ Found in Text Mining only
Lymphomatoid Papulosis	Lymphomatoid Papulosis	BEFREE	30393995		★☆☆☆☆ Found in Text Mining only
Malignant Neoplasms	Malignant Neoplasm	BEFREE	28556291		★☆☆☆☆ Found in Text Mining only
May-White Syndrome	May-White Syndrome	CTD_human_DG			★☆☆☆☆ Found in Text Mining only
Multiple Sclerosis	Multiple sclerosis	Pubtator	34873174	Associate	★☆☆☆☆ Found in Text Mining only
Myoclonic Epilepsies, Progressive	Myoclonic epilepsy	CTD_human_DG			★☆☆☆☆ Found in Text Mining only
Neoplasms	Neoplasms	BEFREE	29572888, 30393995		★☆☆☆☆ Found in Text Mining only
Neuroblastoma	Neuroblastoma	Pubtator	36572864	Associate	★☆☆☆☆ Found in Text Mining only
Paranoia	Paranoia	HPO_DG			★☆☆☆☆ Found in Text Mining only
Progressive cerebellar ataxia	Cerebellar Ataxia	HPO_DG			★☆☆☆☆ Found in Text Mining only
Psychotic Disorders	Psychotic disorders	Pubtator	37584462	Associate	★☆☆☆☆ Found in Text Mining only
Psychotic Disorders	Psychosis	HPO_DG			★☆☆☆☆ Found in Text Mining only
Rheumatoid Arthritis	Rheumatoid arthritis	BEFREE	31037071		★☆☆☆☆ Found in Text Mining only
Spastic Ataxia	Spastic Ataxia	HPO_DG			★☆☆☆☆ Found in Text Mining only
Spastic Quadriplegia	Spastic Quadriplegia	HPO_DG			★☆☆☆☆ Found in Text Mining only
Spastic tetraparesis	Spastic tetraparesis	HPO_DG			★☆☆☆☆ Found in Text Mining only