Prdm6 MGI Mouse Gene Detail - MGI:2684938

Symbol

Prdm6
Name

PR domain containing 6
Synonyms

LOC225518, PRISM

Feature Type

protein coding gene
IDs

MGI:2684938
NCBI Gene: 225518
Alliance

gene page
Transcription Start Sites

5 TSS

Sequence Map

Chr18:53597027-53708976 bp, + strand
From NCBI annotation of GRCm39
View this region in JBrowse
Genome Browsers

Ensembl | UCSC | NCBI

Genetic Map

Chromosome 18, 29.04 cM
Mapping Data

1 experiment

SNPs within 2kb

2800 from dbSNP Build 142
Strain Annotations

18

For selected strains:

Strain	Gene Model ID	Feature Type	Coordinates
C57BL/6J	MGI_C57BL6J_2684938	protein coding gene	Chr18:53596655-53708979 (+)
129S1/SvImJ	MGP_129S1SvImJ_G0024436	protein coding gene	Chr18:52646742-52759994 (+)
A/J	MGP_AJ_G0024402	protein coding gene	Chr18:50608666-50712247 (+)
AKR/J	MGP_AKRJ_G0024372	protein coding gene	Chr18:52019520-52127911 (+)
BALB/cJ	MGP_BALBcJ_G0024402	protein coding gene	Chr18:50794924-50898469 (+)
C3H/HeJ	MGP_C3HHeJ_G0024169	protein coding gene	Chr18:52161925-52268112 (+)
C57BL/6NJ	MGP_C57BL6NJ_G0024848	protein coding gene	Chr18:54402526-54515447 (+)
CAROLI/EiJ	MGP_CAROLIEiJ_G0022280	protein coding gene	Chr18:50378069-50480434 (+)
CAST/EiJ	MGP_CASTEiJ_G0023643	protein coding gene	Chr18:52138426-52255256 (+)
CBA/J	MGP_CBAJ_G0024139	protein coding gene	Chr18:56014396-56130277 (+)
DBA/2J	MGP_DBA2J_G0024269	protein coding gene	Chr18:50310434-50423615 (+)
FVB/NJ	MGP_FVBNJ_G0024236	protein coding gene	Chr18:49737608-49840936 (+)
LP/J	MGP_LPJ_G0024354	protein coding gene	Chr18:52666144-52773065 (+)
NOD/ShiLtJ	MGP_NODShiLtJ_G0024266	protein coding gene	Chr18:57749776-57895599 (+)
NZO/HlLtJ	MGP_NZOHlLtJ_G0024895	protein coding gene	Chr18:52053047-52163135 (+)
PWK/PhJ	MGP_PWKPhJ_G0023387	protein coding gene	Chr18:50326347-50433285 (+)
SPRET/EiJ	MGP_SPRETEiJ_G0023193	protein coding gene	Chr18:52224027-52331737 (+)
WSB/EiJ	MGP_WSBEiJ_G0023706	protein coding gene	Chr18:51974674-52092730 (+)

Human Ortholog

PRDM6, PR/SET domain 6

Vertebrate Orthologs

3

Vertebrate Orthology Source

Alliance of Genome Resources

Human Ortholog

PRDM6, PR/SET domain 6
Synonyms

KMT8C, PDA3, PRISM
Links

HGNC:9350

NCBI Gene ID: 93166

neXtProt AC: NX_Q9NQX0

UniProt: Q9NQX0
Chr Location

5q23.2

MGI Vertebrate Homology

Prdm6 stringent orthology
1 human;1 mouse;1 rat;1 zebrafish
HCOP

vertebrate homology predictions: PRDM6
Gene Tree

Prdm6

Diseases

1 with human PRDM6 associations

				Human Disease	Mouse Models
				patent ductus arteriosus IDs patent ductus arteriosus DOID:13832 ICD10CM:Q25.0 ICD9CM:747.0 MESH:D004374 NCI:C84492 OMIM:607411 UMLS_CUI:C0013274

Click on a disease name to see all genes associated with that disease.

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Phenotype Summary

11 phenotypes from 2 alleles in 2 genetic backgrounds
3 images
5 phenotype references

Phenotype Overview

Blue squares indicate phenotypes directly attributed to mutations/alleles of this gene.

adipose tissue	behavior/neurological	cardiovascular system	cellular	craniofacial	digestive/alimentary system	embryo	endocrine/exocrine glands	growth/size/body	hearing/vestibular/ear	hematopoietic system	homeostasis/metabolism	integument	immune system	limbs/digits/tail	liver/biliary system	mortality/aging	muscle	nervous system	pigmentation	renal/urinary system	reproductive system	respiratory system	skeleton	taste/olfaction	neoplasm	vision/eye

Click cells to view annotations.

All Mutations and Alleles

5
Spontaneous

1
Targeted

4
Genomic Mutations

1 involving Prdm6
Incidental Mutations

APF , CvDC
Find Mice (IMSR)

28 strains or lines available
Comparison Matrix

Gene Expression + Phenotype

Mice homozygous for a knock-out allele exhibit cardiovascular development defects.

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All GO Annotations

16
GO References

9

Molecular Function

carbohydrate derivative binding	cytoskeletal protein binding	DNA binding	enzyme regulator	hydrolase	ligase	lipid binding	oxidoreductase	RNA binding	signaling receptor activity	signaling receptor binding	transcription	transferase	transporter

Biological Process

carbohydrate derivative metabolism	cell differentiation	cell population proliferation	cellular component organization	DNA-templated transcription	establishment of localization	homeostatic process	immune system process	lipid metabolic process	programmed cell death	protein metabolic process	response to stimulus	signaling	system development

Cellular Component

cell projection	cytoplasmic vesicle	cytoskeleton	cytosol	endoplasmic reticulum	endosome	extracellular region	Golgi apparatus	mitochondrion	membraneless organelle	nucleus	organelle envelope	organelle lumen	plasma membrane	protein-containing complex	synapse	vacuole

Click cells to view annotations.

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Expression Overview

GXD's primary emphasis is on endogenous gene expression during development. Click on grid cells to view annotations.

Blue cells = expressed in wild-type.
Gray triangles = other expression annotations only
(e.g. absence of expression or data from mutants).

early conceptus	embryo ectoderm	embryo endoderm	embryo mesoderm	embryo mesenchyme	extraembryonic component	alimentary system	auditory system	branchial arches	cardiovascular system	connective tissue	endocrine system	exocrine system	hemolymphoid system	integumental system	limbs	liver and biliary system	musculoskeletal system	nervous system	olfactory system	reproductive system	respiratory system	urinary system	visual system

Click cells to view annotations.

Assay Results

810
Tissues

67
cDNA Data

13
Literature Summary

8

Images

Tissue x Stage Matrix

Comparison Matrix

Gene Expression + Phenotype

Other Mouse Links

Allen Institute

GEO

Expression Atlas
Other Vertebrate Links

GEISHA PRDM6

Xenbase prdm6

ZFIN prdm6

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All Sequences

44
RefSeq

8
UniProt

2
CCDS

CCDS29253.1

Ensembl

ENSMUSG00000069378 (Evidence)
NCBI Gene

225518

			Length	Strain/Species	Flank
genomic	225518	NCBI Gene Model \| MGI Sequence Detail	111950	C57BL/6J	± kb
transcript	NM_001033281	RefSeq \| MGI Sequence Detail	2601	C57BL/6
polypeptide	Q3UZD5	UniProt \| EBI \| MGI Sequence Detail	596	Not Applicable

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UniProt

2 Sequences
Protein Ontology

PR:000031139 putative histone-lysine N-methyltransferase PRDM6

(term hierarchy)
EC

2.1.1.361
InterPro Domains

IPR044416 PRDM6, PR/SET domain

IPR001214 SET domain

IPR046341 SET domain superfamily

IPR050331 Zinc finger

IPR036236 Zinc finger C2H2 superfamily

IPR013087 Zinc finger C2H2-type

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All nucleic 17

cDNA 13

Primer pair 2

Other 2

Microarray probesets 2

Summaries

All 34

Developmental Gene Expression 8

Gene Ontology 9

Phenotypes 5
Earliest

J:99680 The FANTOM Consortium and RIKEN Genome Exploration Research Group and Genome Science Group (Genome Network Project Core Group), The Transcriptional Landscape of the Mammalian Genome. Science. 2005;309(5740):1559-1563
Latest

J:334529 Zou M, et al., Prdm6 drives ductus arteriosus closure by promoting ductus arteriosus smooth muscle cell identity and contractility. JCI Insight. 2023 Mar 8;8(5)

TSS for Prdm6:

(View these features in JBrowse)

Transcription Start Site	Location	Distance from Gene 5'-end
Tssr151098	Chr18:53596482-53596495 (+)	-538 bp
Tssr151099	Chr18:53596570-53596591 (+)	-446 bp
Tssr151100	Chr18:53596816-53596857 (+)	-190 bp
Tssr151101	Chr18:53597254-53597257 (+)	229 bp
Tssr5318	Chr18:53604206-53604209 (+)	7,181 bp

Contributing Projects: Mouse Genome Database (MGD), Gene Expression Database (GXD), Mouse Models of Human Cancer database (MMHCdb) (formerly Mouse Tumor Biology (MTB)), Gene Ontology (GO)
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