PRDM6 (PR/SET domain 6)

Gene

• Entrez ID: 93166
• Gene name: PR/SET domain 6
• Gene symbol: PRDM6
• Synonyms: KMT8C, PDA3, PRISM
• Chromosome: 5
• Chromosome location: 5q23.2
• Summary: The protein encoded by this gene is a transcriptional repressor and a member of the PRDM family. Family members contain a PR domain and multiple zinc-finger domains. The encoded protein is involved in regulation of vascular smooth muscle cells (VSMC) contractile proteins. Mutations in this gene result in patent ductus arteriosus 3 (PDA3). [provided by RefSeq, Apr 2017]

SNPs

SNP ID	Visualize variation	Clinical significance	Consequence
rs879253872	A>G	Pathogenic	Coding sequence variant, non coding transcript variant, missense variant
rs879255278	G>A	Pathogenic	Non coding transcript variant, genic downstream transcript variant, missense variant, downstream transcript variant, coding sequence variant
rs879255279	G>C	Pathogenic	Coding sequence variant, non coding transcript variant, missense variant

miRNA

miRTarBase ID	miRNA	Experiments	Reference
MIRT311376	hsa-miR-7-5p	PAR-CLIP	20371350
MIRT311377	hsa-miR-641	PAR-CLIP	20371350
MIRT311378	hsa-miR-3617-5p	PAR-CLIP	20371350
MIRT311379	hsa-miR-3688-3p	PAR-CLIP	20371350
MIRT311381	hsa-miR-4802-3p	PAR-CLIP	20371350
MIRT311382	hsa-miR-5093	PAR-CLIP	20371350
MIRT311383	hsa-miR-6728-5p	PAR-CLIP	20371350
MIRT496218	hsa-miR-4503	PAR-CLIP	22291592
MIRT496219	hsa-miR-6792-5p	PAR-CLIP	22291592
MIRT496220	hsa-miR-4311	PAR-CLIP	22291592
MIRT560125	hsa-miR-5187-5p	PAR-CLIP	20371350
MIRT560126	hsa-miR-6077	PAR-CLIP	20371350

Gene ontology (GO)

GO ID	Ontology	Definition	Evidence	Reference
GO:0000122	Process	Negative regulation of transcription by RNA polymerase II	IDA	16537907
GO:0005515	Function	Protein binding	IPI	32296183
GO:0005634	Component	Nucleus	IBA	21873635
GO:0006325	Process	Chromatin organization	IEA
GO:0008168	Function	Methyltransferase activity	IEA
GO:0010468	Process	Regulation of gene expression	IBA	21873635
GO:0022008	Process	Neurogenesis	IEA
GO:0032259	Process	Methylation	IEA
GO:0042802	Function	Identical protein binding	IPI	32296183
GO:0046872	Function	Metal ion binding	IEA
GO:0051151	Process	Negative regulation of smooth muscle cell differentiation	IEA

Other IDs

• MIM: 616982
• HGNC: 9350
• e!Ensembl: ENSG00000061455

Protein

• UniProt ID: Q9NQX0
• Protein name: Putative histone-lysine N-methyltransferase PRDM6 (EC 2.1.1.361) (PR domain zinc finger protein 6) (PR domain-containing protein 6)
• Protein function: Putative histone methyltransferase that acts as a transcriptional repressor of smooth muscle gene expression. Promotes the transition from differentiated to proliferative smooth muscle by suppressing differentiation and maintaining the proliferative potential of vascular smooth muscle cells. Also plays a role in endothelial cells by inhibiting endothelial cell proliferation, survival and differentiation. It is unclear whether it has histone methyltransferase activity in vivo. According to some authors, it does not act as a histone methyltransferase by itself and represses transcription by recruiting EHMT2/G9a. According to others, it possesses histone methyltransferase activity when associated with other proteins and specifically methylates 'Lys-20' of histone H4 in vitro. 'Lys-20' methylation represents a specific tag for epigenetic transcriptional repression.
• Family and domains:

  Pfam

  Accession	ID	Position in sequence	Description	Type
  PF00856	SET	259 → 365	SET domain	Family
  PF00096	zf-C2H2	501 → 523	Zinc finger, C2H2 type	Domain
  PF00096	zf-C2H2	529 → 551	Zinc finger, C2H2 type	Domain
  PF00096	zf-C2H2	557 → 578	Zinc finger, C2H2 type	Domain

• Sequence:

  MLKPGDPGGSAFLKVDPAYLQHWQQLFPHGGAGPLKGSGAAGLLSAPQPLQPPPPPPPPE
  RAEPPPDSLRPRPASLSSASSTPASSSTSASSASSCAAAAAAAALAGLSALPVSQLPVFA
  PLAAAAVAAEPLPPKELCLGATSGPGPVKCGGGGGGGGEGRGAPRFRCSAEELDYYLYGQ
  QRMEIIPLNQHTSDPNNRCDMCADNRNGECPMHGPLHSLRRLVGTSSAAAAAPPPELPEW
  LRDLPREVCLCTSTVPGLAYGICAAQRIQQGTWIGPFQGVLLPPEKVQAGAVRNTQHLWE
  IYDQDGTLQHFIDGGEPSKSSWMRYIRCARHCGEQNLTVVQYRSNIFYRACIDIPRGTEL
  LVWYNDSYTSFFGIPLQCIAQDENLNVPSTVMEAMCRQDALQPFNKSSKLAPTTQQRSVV
  FPQTPCSRNFSLLDKSGPIESGFNQINVKNQRVLASPTSTSQLHSEFSDWHLWKCGQCFK
  TFTQRILLQMHVCTQNPDRPYQCGHCSQSFSQPSELRNHVVTHSSDRPFKCGYCGRAFAG
  ATTLNNHIRTHTGEKPFKCERCERSFTQATQLSRHQRMPNECKPITESPESIEVD

• Sequence length: 595

Pathways

KEGG:

Lysine degradation
Metabolic pathways

Associated diseases

Causal
Disease name	Disease term	dbSNP ID	References
Breast carcinoma	Breast Carcinoma	rs80359671, rs11540652, rs28934575, rs28897672, rs137886232, rs193922376, rs80357783, rs80359306, rs80359405, rs80359507, rs80359598, rs80358429, rs397507683, rs397515636, rs80359451, rs397507859, rs80359709, rs80359742, rs80359205, rs80357627, rs80357004, rs80357571, rs80357767, rs80357653, rs80358086, rs80357608, rs28897696, rs41293465, rs146650273, rs63751017, rs63750617, rs63750726, rs63750199, rs63749848, rs398122618, rs398122653, rs397509211, rs80357791, rs121912666, rs587778541, rs121908698, rs536907995, rs587781302, rs140342925, rs587781506, rs587782652, rs587782849, rs587783057, rs139770721, rs374950566, rs786202800, rs863224451, rs377153250, rs747727055, rs876658804, rs780001540, rs760815829, rs878854926, rs775248597, rs886040658, rs886040192, rs786203523, rs886040319, rs397508006, rs587782011, rs1060502772, rs1555461727, rs1553333072, rs1114167702, rs1257401983, rs886040950, rs1060502759, rs774684620, rs142947311, rs1555580883, rs748513310, rs376170600, rs863224499, rs1593909229, rs748453607, rs1294578913, rs1574737047, rs1593909960, rs2081922847, rs2082559544, rs2053694038	29059683
Coronary artery disease	Coronary Artery Disease	rs137852988, rs121918313, rs-1, rs121918529, rs121918531, rs137852340, rs405509, rs1555800701, rs1215189537	29212778
Patent ductus arteriosus	Patent ductus arteriosus, Patent Ductus Arteriosus Familial, PATENT DUCTUS ARTERIOSUS 3	rs80338911, rs879253870, rs879253871, rs879255278, rs879255279, rs879253872	27181681

Unknown
Disease name	Disease term	dbSNP ID	References
Alopecia	Alopecia		28196072
Cardiovascular diseases	Cardiovascular Diseases		30595370