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

Gene Gene SNPs miRNA Gene ontology Other IDs Protein Pathways Associated diseases
Entrez ID Entrez Gene ID - the GENE ID in NCBI Gene database.	93166
Gene name Gene Name - the full gene name approved by the HGNC.	PR/SET domain 6
Gene symbol Gene Symbol - the official gene symbol approved by the HGNC.	PRDM6
Synonyms (NCBI Gene) Gene synonyms aliases	KMT8C, PDA3, PRISM
Chromosome Chromosome number	5
Chromosome location Chromosomal Location - indicates the cytogenetic location of the gene or region on the chromosome.	5q23.2
Summary Summary of gene provided in NCBI Entrez Gene.	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

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 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

Show/Hide Causal Diseases (1)

Disease merge term	Disease name	dbSNP ID	References
Causal Diseases caused by PATHOGENIC or LIKELY PATHOGENIC variants from ClinVar only
Patent ductus arteriosus	patent ductus arteriosus 3	rs879255278, rs879255279, rs879253872	N/A

Show/Hide Unknown Diseases (6)

Disease merge term	Disease name	Evidence	References	Source
Unknown Includes: (1) ClinVar NON-pathogenic variants (Uncertain, Benign, Conflicting, VUS), (2) GenCC associations, (3) GWAS associations, (4) CBGDA evidence-based associations. NOTE: Diseases with pathogenic evidence are excluded to avoid conflicts.
Breast Cancer	Breast cancer	N/A	N/A	GWAS
Coronary artery disease	Coronary artery disease	N/A	N/A	GWAS
Diabetes	Type ii diabetes, Type 2 diabetes	N/A	N/A	GWAS
Hypertension	Hypertension (confirmatory factor analysis Factor 12), Hypertension (PheCode 401), Essential hypertension (PheCode 401.1), High blood pressure / hypertension	N/A	N/A	GWAS
Metabolic Syndrome	Metabolic syndrome	N/A	N/A	GWAS
Prostate cancer	Prostate cancer	N/A	N/A	GWAS

Show/Hide Text Mining Associations (8)

Disease Name	Relationship Type	References
Associations from Text Mining Disease associations identified through Pubtator
Breast Neoplasms	Associate	25342443, 36344993
Ductus Arteriosus Patent	Associate	27181681
Hypomagnesemia primary	Associate	40335697
Medulloblastoma	Associate	28726821, 36131014, 40335697
Nonsyndromic Deafness	Associate	27181681
Obesity	Associate	29145611
Osteoporosis	Associate	29145611
Thinness	Associate	30677029

PRDM6 (PR/SET domain 6)