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

Causal
Phenotype Name	Clinical Significance	dbSNP ID	RCV Accession
Early-onset Lafora body disease	Pathogenic	rs863225286	RCV000201931

Unknown
Phenotype Name	Clinical Significance	dbSNP ID	RCV Accession
Hepatocellular carcinoma	Benign; Likely benign	rs200010979	RCV005897164
PRDM8-related disorder	Likely benign; Benign	rs377684484, rs373726901, rs372621624, rs144810863, rs374280707, rs150632206, rs755316101, rs560049733	RCV003946064 RCV003946151 RCV003948433 RCV003962603 RCV003935539 RCV003980029 RCV003952876 RCV003905775

Associations from Text Mining
Disease Name	Relationship Type	References
Aging Premature	Associate	32819411
Anemia Aplastic	Associate	26909595, 32819411
Arthritis Rheumatoid	Associate	31037071
Bone Marrow Failure Disorders	Associate	26909595, 32819411
Cerebellar Ataxia	Associate	37584462
Cerebellar Ataxia Deafness and Narcolepsy	Associate	37584462
Dementia	Associate	37584462
Down Syndrome	Associate	28861129, 32819411
Dyskeratosis Congenita	Associate	26909595, 28861129, 32819411
Epilepsies Myoclonic	Associate	22961547
Lafora Disease	Associate	22961547
Multiple Sclerosis	Associate	34873174
Neuroblastoma	Associate	36572864
Progeria	Associate	32819411
Psychotic Disorders	Associate	37584462