PRDM6 PR/SET domain 6 [Homo sapiens (human)] - Gene

Summary

Official Symbol: PRDM6provided by HGNC
Official Full Name: PR/SET domain 6provided by HGNC
Primary source: HGNC:HGNC:9350
See related: Ensembl:ENSG00000061455 MIM:616982; AllianceGenome:HGNC:9350
Gene type: protein coding
RefSeq status: REVIEWED
Organism: Homo sapiens
Lineage: Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Primates; Haplorrhini; Catarrhini; Hominidae; Homo
Also known as: PDA3; KMT8C; PRISM
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]
Expression: Broad expression in gall bladder (RPKM 2.3), placenta (RPKM 2.0) and 16 other tissues See more
Orthologs: mouse all
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Genomic context

Location:: 5q23.2

Exon count:: 11

Annotation release	Status	Assembly	Chr	Location
RS_2024_08	current	GRCh38.p14 (GCF_000001405.40)	5	NC_000005.10 (123089241..123194266)
RS_2024_08	current	T2T-CHM13v2.0 (GCF_009914755.1)	5	NC_060929.1 (123605724..123710965)
RS_2024_09	previous assembly	GRCh37.p13 (GCF_000001405.25)	5	NC_000005.9 (122424936..122529960)

Chromosome 5 - NC_000005.10 Genomic Context describing neighboring genes

Genomic regions, transcripts, and products

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Genomic Sequence:

Go to nucleotide: Graphics FASTA GenBank

Expression

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See details

Project title: HPA RNA-seq normal tissues HPA RNA-seq normal tissues
Description: RNA-seq was performed of tissue samples from 95 human individuals representing 27 different tissues in order to determine tissue-specificity of all protein-coding genes
BioProject: PRJEB4337
Publication: PMID 24309898
Analysis date: Wed Apr 4 07:08:55 2018

Bibliography

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GeneRIFs: Gene References Into Functions

What's a GeneRIF?

PRDM6 promotes medulloblastoma by repressing chromatin accessibility and altering gene expression.
Title: PRDM6 promotes medulloblastoma by repressing chromatin accessibility and altering gene expression.
Patent ductus arteriosus and coarctation of the aorta in association with PRDM6 variants.
Title: Patent ductus arteriosus and coarctation of the aorta in association with PRDM6 variants.
we detected a novel obesity and BMI-associated locus at PKHD1 and novel variants driving associations at previously established signals (e.g. rs205262 at the SNRPC/C6orf106 locus and rs112446794 at the PRDM6-CEP120 locus).
Title: Genetic architecture of human thinness compared to severe obesity.
Mutations in the Histone Modifier PRDM6 Are Associated with Isolated Nonsyndromic Patent Ductus Arteriosus.
Title: Mutations in the Histone Modifier PRDM6 Are Associated with Isolated Nonsyndromic Patent Ductus Arteriosus.
Three novel loci were identified in East Asians with cardiac arrhythmias: rs2483280 (PRDM16 locus) and rs335206 (PRDM6 locus) were associated with QRS duration; and rs17026156 (SLC8A1 locus) correlated with PR interval.
Title: Identification of three novel genetic variations associated with electrocardiographic traits (QRS duration and PR interval) in East Asians.
Clinical trial of gene-disease association and gene-environment interaction. (HuGE Navigator)
Title: Personalized smoking cessation: interactions between nicotine dose, dependence and quit-success genotype score.

Submit: New GeneRIF Correction

Phenotypes

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Find tests for this gene in the NIH Genetic Testing Registry (GTR)

Review eQTL and phenotype association data in this region using PheGenI

Associated conditions

Description	Tests
Patent ductus arteriosus 3 MedGen: C4310753 OMIM: 617039 GeneReviews: Not available	Compare labs

Copy number response

Description
Copy number response Haploinsufficency No evidence available (Last evaluated 2017-12-14) ClinGen Genome Curation Page Triplosensitivity No evidence available (Last evaluated 2017-12-14) ClinGen Genome Curation Page

EBI GWAS Catalog

Description
Genome-wide association study identifies multiple loci associated with both mammographic density and breast cancer risk. EBI GWAS Catalog EBI GWAS CatalogPubMed
Identification of three novel genetic variations associated with electrocardiographic traits (QRS duration and PR interval) in East Asians. EBI GWAS Catalog EBI GWAS CatalogPubMed

Variation

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See variants in ClinVar

See studies and variants in dbVar

See Variation Viewer (GRCh37.p13)

See Variation Viewer (GRCh38)

Interactions

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Products	Interactant	Other Gene	Complex	Source	Pubs	Description

General gene information

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Markers

SHGC-149439 (e-PCR)
- UniSTS:184097

L28179 (e-PCR)
- UniSTS:14298

Gene Ontology Provided by GOA

Function	Evidence Code	Pubs
enables histone H4K20 monomethyltransferase activity	IEA Inferred from Electronic Annotation more info
enables identical protein binding	IPI Inferred from Physical Interaction more info	PubMed
enables metal ion binding	IEA Inferred from Electronic Annotation more info
enables protein binding	IPI Inferred from Physical Interaction more info	PubMed

Process	Evidence Code	Pubs
involved_in chromatin remodeling	IEA Inferred from Electronic Annotation more info
involved_in methylation	IEA Inferred from Electronic Annotation more info
involved_in negative regulation of smooth muscle cell differentiation	IEA Inferred from Electronic Annotation more info
involved_in negative regulation of transcription by RNA polymerase II	IDA Inferred from Direct Assay more info	PubMed
involved_in neurogenesis	IEA Inferred from Electronic Annotation more info
involved_in regulation of gene expression	IBA Inferred from Biological aspect of Ancestor more info

Component	Evidence Code	Pubs
is_active_in nucleus	IBA Inferred from Biological aspect of Ancestor more info

General protein information

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Preferred Names: putative histone-lysine N-methyltransferase PRDM6

Names: PR domain 6; PR domain containing 6; PR domain-containing protein 6; PR-domain zinc finger protein 6

NP_001129711.1

EC 2.1.1.361

XP_011542028.1

EC 2.1.1.361

XP_047273834.1

EC 2.1.1.361

XP_054209774.1

EC 2.1.1.361

XP_054209775.1

EC 2.1.1.361

NCBI Reference Sequences (RefSeq)

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RefSeqs maintained independently of Annotated Genomes

These reference sequences exist independently of genome builds. Explain

These reference sequences are curated independently of the genome annotation cycle, so their versions may not match the RefSeq versions in the current genome build. Identify version mismatches by comparing the version of the RefSeq in this section to the one reported in Genomic regions, transcripts, and products above.

Genomic

NG_053114.1 RefSeqGene

Range

5139..110164

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GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

NM_001136239.4 → NP_001129711.1 putative histone-lysine N-methyltransferase PRDM6

See identical proteins and their annotated locations for NP_001129711.1

Status: REVIEWED

Source sequence(s)

AC008548, AC106786

Consensus CDS

CCDS47259.1

UniProtKB/Swiss-Prot

B5MCJ4, Q9NQW9, Q9NQX0

Related

ENSP00000384725.3, ENST00000407847.5

Conserved Domains (5) summary

COG5048
Location:404 → 584

COG5048; FOG: Zn-finger [General function prediction only]

sd00017
Location:503 → 523

ZF_C2H2; C2H2 Zn finger [structural motif]

pfam00096
Location:501 → 523

zf-C2H2; Zinc finger, C2H2 type

pfam00856
Location:260 → 365

SET; SET domain

pfam13465
Location:544 → 568

zf-H2C2_2; Zinc-finger double domain

RefSeqs of Annotated Genomes: GCF_000001405.40-RS_2024_08

The following sections contain reference sequences that belong to a specific genome build. Explain

Reference GRCh38.p14 Primary Assembly

Genomic

NC_000005.10 Reference GRCh38.p14 Primary Assembly

Range

123089241..123194266

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GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

XM_047417878.1 → XP_047273834.1 putative histone-lysine N-methyltransferase PRDM6 isoform X2
XM_011543726.4 → XP_011542028.1 putative histone-lysine N-methyltransferase PRDM6 isoform X1

Conserved Domains (5) summary

COG5048
Location:306 → 378

COG5048; FOG: Zn-finger [General function prediction only]

sd00017
Location:303 → 323

ZF_C2H2; C2H2 Zn finger [structural motif]

pfam00096
Location:301 → 323

zf-C2H2; Zinc finger, C2H2 type

pfam00856
Location:60 → 165

SET; SET domain

pfam13465
Location:344 → 368

zf-H2C2_2; Zinc-finger double domain

RNA

XR_001742346.2 RNA Sequence

Alternate T2T-CHM13v2.0

Genomic

NC_060929.1 Alternate T2T-CHM13v2.0

Range

123605724..123710965

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GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

XM_054353800.1 → XP_054209775.1 putative histone-lysine N-methyltransferase PRDM6 isoform X2
XM_054353799.1 → XP_054209774.1 putative histone-lysine N-methyltransferase PRDM6 isoform X1