Gene Details | GeDiPNet - Complete Gene Info, Disease Associations & Pathways

Gene Gene information from NCBI Gene database. Gene SNPs miRNA Gene ontology Other IDs Protein Pathways Associated diseases
Entrez ID	93166
Gene name	PR/SET domain 6
Gene symbol	PRDM6
Synonyms (NCBI Gene)	KMT8CPDA3PRISM
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) cont

Show/Hide all (3)

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

Show/Hide all (63)

miRTarBase ID	miRNA	Experiments	Reference
MIRT311378	hsa-miR-3617-5p	PAR-CLIP	20371350
MIRT311377	hsa-miR-641	PAR-CLIP	20371350
MIRT311381	hsa-miR-4802-3p	PAR-CLIP	20371350
MIRT311379	hsa-miR-3688-3p	PAR-CLIP	20371350
MIRT311382	hsa-miR-5093	PAR-CLIP	20371350
MIRT311376	hsa-miR-7-5p	PAR-CLIP	20371350
MIRT560126	hsa-miR-6077	PAR-CLIP	20371350
MIRT560125	hsa-miR-5187-5p	PAR-CLIP	20371350
MIRT311383	hsa-miR-6728-5p	PAR-CLIP	20371350
MIRT496220	hsa-miR-4311	PAR-CLIP	22291592
MIRT496219	hsa-miR-6792-5p	PAR-CLIP	22291592
MIRT496218	hsa-miR-4503	PAR-CLIP	22291592
MIRT311378	hsa-miR-3617-5p	PAR-CLIP	20371350
MIRT311377	hsa-miR-641	PAR-CLIP	20371350
MIRT311381	hsa-miR-4802-3p	PAR-CLIP	20371350
MIRT311379	hsa-miR-3688-3p	PAR-CLIP	20371350
MIRT311382	hsa-miR-5093	PAR-CLIP	20371350
MIRT311376	hsa-miR-7-5p	PAR-CLIP	20371350
MIRT560126	hsa-miR-6077	PAR-CLIP	20371350
MIRT560125	hsa-miR-5187-5p	PAR-CLIP	20371350
MIRT311383	hsa-miR-6728-5p	PAR-CLIP	20371350
MIRT496220	hsa-miR-4311	PAR-CLIP	22291592
MIRT496219	hsa-miR-6792-5p	PAR-CLIP	22291592
MIRT496218	hsa-miR-4503	PAR-CLIP	22291592
MIRT1260324	hsa-miR-1178	CLIP-seq
MIRT1260325	hsa-miR-1273d	CLIP-seq
MIRT1260326	hsa-miR-132	CLIP-seq
MIRT1260327	hsa-miR-204	CLIP-seq
MIRT1260328	hsa-miR-211	CLIP-seq
MIRT1260329	hsa-miR-212	CLIP-seq
MIRT1260330	hsa-miR-3125	CLIP-seq
MIRT1260331	hsa-miR-3140-3p	CLIP-seq
MIRT1260332	hsa-miR-3192	CLIP-seq
MIRT1260333	hsa-miR-3199	CLIP-seq
MIRT1260334	hsa-miR-3916	CLIP-seq
MIRT1260335	hsa-miR-4257	CLIP-seq
MIRT1260336	hsa-miR-4287	CLIP-seq
MIRT1260337	hsa-miR-4314	CLIP-seq
MIRT1260338	hsa-miR-4328	CLIP-seq
MIRT1260339	hsa-miR-4646-5p	CLIP-seq
MIRT1260340	hsa-miR-4669	CLIP-seq
MIRT1260341	hsa-miR-4685-3p	CLIP-seq
MIRT1260342	hsa-miR-4691-5p	CLIP-seq
MIRT1260343	hsa-miR-4720-3p	CLIP-seq
MIRT1260344	hsa-miR-4740-5p	CLIP-seq
MIRT1260345	hsa-miR-4804-3p	CLIP-seq
MIRT1260346	hsa-miR-488	CLIP-seq
MIRT1260347	hsa-miR-595	CLIP-seq
MIRT1260348	hsa-miR-659	CLIP-seq
MIRT1260349	hsa-miR-9	CLIP-seq
MIRT2076654	hsa-miR-3179	CLIP-seq
MIRT2076655	hsa-miR-4446-3p	CLIP-seq
MIRT2076656	hsa-miR-4675	CLIP-seq
MIRT2076657	hsa-miR-4718	CLIP-seq
MIRT2076658	hsa-miR-4741	CLIP-seq
MIRT2076659	hsa-miR-642b	CLIP-seq
MIRT2076660	hsa-miR-922	CLIP-seq
MIRT2303368	hsa-miR-199a-5p	CLIP-seq
MIRT2303369	hsa-miR-199b-5p	CLIP-seq
MIRT2303370	hsa-miR-4676-5p	CLIP-seq
MIRT2303371	hsa-miR-4731-5p	CLIP-seq
MIRT2303372	hsa-miR-486-3p	CLIP-seq
MIRT2303373	hsa-miR-575	CLIP-seq

Show/Hide all (20)

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
GO:0005634	Component	Nucleus	IEA
GO:0006325	Process	Chromatin organization	IEA
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:0022008	Process	Neurogenesis	IEA
GO:0032259	Process	Methylation	IEA
GO:0042054	Function	Histone methyltransferase activity	IEA
GO:0042802	Function	Identical protein binding	IEA
GO:0042802	Function	Identical protein binding	IPI	32296183
GO:0045892	Process	Negative regulation of DNA-templated transcription	IEA
GO:0045892	Process	Negative regulation of DNA-templated transcription	IEA
GO:0046872	Function	Metal ion binding	IEA
GO:0051151	Process	Negative regulation of smooth muscle cell differentiation	IEA
GO:0140944	Function	Histone H4K20 monomethyltransferase activity	IEA

MIM	HGNC	e!Ensembl
616982	9350	ENSG00000061455

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 prolifera

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

Interactions

View interactions

	KEGG
	Lysine degradation Metabolic pathways

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)

Show/Hide Causal Diseases (1)

Phenotype Name	Clinical Significance	dbSNP ID	RCV Accession	Evidence Score
Causal Diseases associated with Pathogenic or Likely Pathogenic variants in ClinVar
Patent ductus arteriosus 3	Pathogenic	rs879255278, rs879255279, rs879253872	RCV000235045 RCV000235065 RCV000235086	★★★★★ ★★★★☆ ClinVar: Pathogenic / Likely Pathogenic (<5 Variants)

Show/Hide Unknown Diseases (17)

Phenotype Name	Clinical Significance	Source	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.
ANDROGENETIC ALOPECIA	—	GWAS catalog	★★★★★ ★★☆☆☆ Found in Text Mining + Unknown/Other Associations
ATRIAL FIBRILLATION	—	GWAS catalog	★★★★★ ★★☆☆☆ Found in Text Mining + Unknown/Other Associations
BREAST CANCER	—	GWAS catalog	★★★★★ ★★☆☆☆ Found in Text Mining + Unknown/Other Associations
BREAST CARCINOMA	—	GWAS catalog	★★★★★ ★★☆☆☆ Found in Text Mining + Unknown/Other Associations
CARDIOVASCULAR DISEASE	—	GWAS catalog	★★★★★ ★★☆☆☆ Found in Text Mining + Unknown/Other Associations
CORONARY ARTERY DISEASE	—	GWAS catalog	★★★★★ ★★☆☆☆ Found in Text Mining + Unknown/Other Associations
DUCTUS ARTERIOSUS, PATENT	—	CTD	★★★★★ ★★☆☆☆ Found in Text Mining + Unknown/Other Associations
ESSENTIAL HYPERTENSION	—	GWAS catalog	★★★★★ ★★☆☆☆ Found in Text Mining + Unknown/Other Associations
HYPERTENSION	—	GWAS catalog	★★★★★ ★★☆☆☆ Found in Text Mining + Unknown/Other Associations
LUNG ADENOCARCINOMA	—	GWAS catalog	★★★★★ ★★☆☆☆ Found in Text Mining + Unknown/Other Associations
METABOLIC SYNDROME	—	GWAS catalog	★★★★★ ★★☆☆☆ Found in Text Mining + Unknown/Other Associations
OBESITY	—	GWAS catalog	★★★★★ ★★☆☆☆ Found in Text Mining + Unknown/Other Associations
PATENT DUCTUS ARTERIOSUS	—	Disgenet	★★★★★ ★★☆☆☆ Found in Text Mining + Unknown/Other Associations
PRDM6-related disorder	Uncertain significance; Benign; Likely benign	ClinVar	★★★★★ ★★☆☆☆ Found in Text Mining + Unknown/Other Associations
PROSTATE CANCER	—	GWAS catalog	★★★★★ ★★☆☆☆ Found in Text Mining + Unknown/Other Associations
PROSTATE CARCINOMA	—	GWAS catalog	★★★★★ ★★☆☆☆ Found in Text Mining + Unknown/Other Associations
TYPE 2 DIABETES MELLITUS	—	GWAS catalog	★★★★★ ★★☆☆☆ Found in Text Mining + Unknown/Other Associations

Show/Hide Text Mining Associations (41)

Disease Name	Disease (Merged)	Source	PMID	Relationship Type	Evidence Score
Associations from Text Mining Disease associations identified through text mining
Alopecia	Alopecia	GWASCAT_DG	28196072		★★★★★ ★☆☆☆☆ Found in Text Mining only
Anxiety	Anxiety Disorder	BEFREE	28744463		★★★★★ ★☆☆☆☆ Found in Text Mining only
Anxiety Disorders	Anxiety Disorder	BEFREE	28744463		★★★★★ ★☆☆☆☆ Found in Text Mining only
Breast Carcinoma	Breast Carcinoma	GWASCAT_DG	29059683		★★★★★ ★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Breast Neoplasms	Breast neoplasm	Pubtator	25342443, 36344993	Associate	★★★★★ ★☆☆☆☆ Found in Text Mining only
Cardiovascular Diseases	Cardiovascular Diseases	GWASCAT_DG	30595370		★★★★★ ★☆☆☆☆ Found in Text Mining only
Classical phenylketonuria	Phenylketonuria	BEFREE	30022433		★★★★★ ★☆☆☆☆ Found in Text Mining only
Congenital Heart Defects	Congenital heart defects	BEFREE	30819207		★★★★★ ★☆☆☆☆ Found in Text Mining only
Coronary Artery Disease	Coronary artery disease	GWASCAT_DG	29212778		★★★★★ ★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Delirium	Delirium	BEFREE	29543606		★★★★★ ★☆☆☆☆ Found in Text Mining only
Diabetes Mellitus, Insulin-Dependent	Diabetes Mellitus	BEFREE	19530270		★★★★★ ★☆☆☆☆ Found in Text Mining only
Diabetes Mellitus, Non-Insulin-Dependent	Diabetes Mellitus	BEFREE	21741858		★★★★★ ★☆☆☆☆ Found in Text Mining only
Ductus Arteriosus Patent	Patent ductus arteriosus	Pubtator	27181681	Associate	★★★★★ ★☆☆☆☆ Found in Text Mining only
Gastroesophageal reflux disease	Gastroesophageal Reflux Disease	BEFREE	28116591		★★★★★ ★☆☆☆☆ Found in Text Mining only
Hypertrophic Cardiomyopathy	Hypertrophic cardiomyopathy	BEFREE	10220146		★★★★★ ★☆☆☆☆ Found in Text Mining only
Intracranial Aneurysm	Intracranial Aneurysm	BEFREE	22438818		★★★★★ ★☆☆☆☆ Found in Text Mining only
Irritable Bowel Syndrome	Irritable Bowel Syndrome	BEFREE	28744463		★★★★★ ★☆☆☆☆ Found in Text Mining only
Kidney Failure, Acute	Kidney Failure	BEFREE	31165253		★★★★★ ★☆☆☆☆ Found in Text Mining only
Leukemia, Myelocytic, Acute	Leukemia	BEFREE	31510697		★★★★★ ★☆☆☆☆ Found in Text Mining only
Long QT Syndrome	Long QT Syndrome	BEFREE	10220146		★★★★★ ★☆☆☆☆ Found in Text Mining only
Malignant neoplasm of prostate	Prostate cancer	BEFREE	28810879		★★★★★ ★☆☆☆☆ Found in Text Mining only
Malignant neoplasm of thyroid	Thyroid cancer	BEFREE	29644472		★★★★★ ★☆☆☆☆ Found in Text Mining only
Malignant Neoplasms	Malignant Neoplasm	BEFREE	26928769		★★★★★ ★☆☆☆☆ Found in Text Mining only
Medulloblastoma	Medulloblastoma	Pubtator	28726821, 36131014, 40335697	Associate	★★★★★ ★☆☆☆☆ Found in Text Mining only
Neoplasms	Neoplasms	BEFREE	12495474, 26928769, 31510697		★★★★★ ★☆☆☆☆ Found in Text Mining only
Obesity	Obesity	BEFREE	29145611		★★★★★ ★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Obesity	Obesity	Pubtator	29145611	Associate	★★★★★ ★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Osteoporosis	Osteoporosis	BEFREE	29145611		★★★★★ ★☆☆☆☆ Found in Text Mining only
Osteoporosis	Osteoporosis	Pubtator	29145611	Associate	★★★★★ ★☆☆☆☆ Found in Text Mining only
Parkinson Disease	Parkinson disease	BEFREE	28024573		★★★★★ ★☆☆☆☆ Found in Text Mining only
Patent ductus arteriosus	Patent ductus arteriosus	BEFREE	27181681		★★★★★ ★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Patent ductus arteriosus	Patent ductus arteriosus	CTD_human_DG			★★★★★ ★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Patent ductus arteriosus	Patent ductus arteriosus	HPO_DG			★★★★★ ★★☆☆☆ Found in Text Mining + Unknown/Other Associations
PATENT DUCTUS ARTERIOSUS 3	Patent ductus arteriosus	UNIPROT_DG	27181681		★★★★★ ★★★★☆ ClinVar: Pathogenic / Likely Pathogenic (<5 Variants)
PATENT DUCTUS ARTERIOSUS 3	Patent ductus arteriosus	CLINVAR_DG			★★★★★ ★★★★☆ ClinVar: Pathogenic / Likely Pathogenic (<5 Variants)
PATENT DUCTUS ARTERIOSUS 3	Patent ductus arteriosus	GENOMICS_ENGLAND_DG			★★★★★ ★★★★☆ ClinVar: Pathogenic / Likely Pathogenic (<5 Variants)
Patent Ductus Arteriosus Familial	Patent ductus arteriosus	CTD_human_DG			★★★★★ ★☆☆☆☆ Found in Text Mining only
Phenylketonurias	Phenylketonuria	BEFREE	29628378, 30022433		★★★★★ ★☆☆☆☆ Found in Text Mining only
Prostate carcinoma	Prostate cancer	BEFREE	28810879		★★★★★ ★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Thyroid carcinoma	Thyroid Carcinoma	BEFREE	29644472		★★★★★ ★☆☆☆☆ Found in Text Mining only
Thyroid Neoplasm	Thyroid Neoplasm	BEFREE	29644472		★★★★★ ★☆☆☆☆ Found in Text Mining only

PRDM6 (PR/SET domain 6)