Prkd1 MGI Mouse Gene Detail - MGI:99879 - protein kinase D1

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Prkd1 Gene Detail

Symbol

Prkd1
Name

protein kinase D1
Synonyms

Pkcm, PKD1, Prkcm

Feature Type

protein coding gene
IDs

MGI:99879
NCBI Gene: 18760
Alliance

gene page
Transcription Start Sites

3 TSS
Candidate for QTL

1 QTL

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Sequence Map

Chr12:50388014-50695881 bp, - strand
From Ensembl annotation of GRCm39
View this region in JBrowse
Genome Browsers

Ensembl | UCSC | NCBI

Genetic Map

Chromosome 12, 21.78 cM, cytoband C1
Mapping Data

2 experiments

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SNPs within 2kb

2927 from dbSNP Build 142
Strain Annotations

18

For selected strains:

Strain	Gene Model ID	Feature Type	Coordinates	Select Strains
C57BL/6J	MGI_C57BL6J_99879	protein coding gene	Chr12:50388009-50696075 (-)
129S1/SvImJ	MGP_129S1SvImJ_G0019720	protein coding gene	Chr12:49107793-49424952 (-)
A/J	MGP_AJ_G0019683	protein coding gene	Chr12:47368817-47669299 (-)
AKR/J	MGP_AKRJ_G0019654	protein coding gene	Chr12:48774860-49080870 (-)
BALB/cJ	MGP_BALBcJ_G0019661	protein coding gene	Chr12:47633622-47935734 (-)
C3H/HeJ	MGP_C3HHeJ_G0019464	protein coding gene	Chr12:48876920-49184818 (-)
C57BL/6NJ	MGP_C57BL6NJ_G0020107	protein coding gene	Chr12:50612311-50948145 (-)
CAROLI/EiJ	MGP_CAROLIEiJ_G0017732	protein coding gene	Chr12:45862416-46146808 (-)
CAST/EiJ	MGP_CASTEiJ_G0019017	protein coding gene	Chr12:43937093-44254769 (-)
CBA/J	MGP_CBAJ_G0019436	protein coding gene	Chr12:52358887-52675578 (-)
DBA/2J	MGP_DBA2J_G0019550	protein coding gene	Chr12:47226279-47537125 (-)
FVB/NJ	MGP_FVBNJ_G0019539	protein coding gene	Chr12:46683519-46996653 (-)
LP/J	MGP_LPJ_G0019620	protein coding gene	Chr12:49112223-49432817 (-)
NOD/ShiLtJ	MGP_NODShiLtJ_G0019575	protein coding gene	Chr12:53972616-54323191 (-)
NZO/HlLtJ	MGP_NZOHlLtJ_G0020147	protein coding gene	Chr12:48301761-48619672 (-)
PWK/PhJ	MGP_PWKPhJ_G0018784	protein coding gene	Chr12:41791675-42094266 (-)
SPRET/EiJ	MGP_SPRETEiJ_G0018576	protein coding gene	Chr12:42895755-43202046 (-)
WSB/EiJ	MGP_WSBEiJ_G0019067	protein coding gene	Chr12:48747221-49063306 (-)

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Human Ortholog

PRKD1, protein kinase D1

Vertebrate Orthologs

3

Vertebrate Orthology Source

Alliance of Genome Resources

Human Ortholog

PRKD1, protein kinase D1
Synonyms

CHDED, PKCM, PKC-MU, PKD, PRKCM
Links

HGNC:9407

NCBI Gene ID: 5587

neXtProt AC: NX_Q15139

UniProt: Q15139
Chr Location

14q12; chr14:29576479-30191898 (-) GRCh38

MGI Vertebrate Homology

Prkd1 stringent orthology
1 human;1 mouse;1 rat;1 zebrafish
HCOP

vertebrate homology predictions: PRKD1
Protein SuperFamily

PKC_mu_nu_D2
Gene Tree

Prkd1

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Diseases

1 with human PRKD1 associations

				Human Disease	Mouse Models
				congenital heart disease IDs congenital heart disease DOID:1682 ICD10CM:Q24.9 ICD9CM:746.9 MESH:D006330 NCI:C34666 UMLS_CUI:C0018798

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

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Phenotype Summary

13 phenotypes from 4 alleles in 4 genetic backgrounds
34 phenotype references

Phenotype Overview

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

17
Endonuclease-mediated

5
Gene trapped

1
Targeted

11
Incidental Mutations

Mutagenetix , APF , CvDC
Find Mice (IMSR)

55 strains or lines available
Comparison Matrix

Gene Expression + Phenotype

Mice homozygous for a knock-out allele exhibit partial embryonic lethality. Mice homozygous for a knock-in allele display partial embryonic and perinatal lethality.

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All GO Annotations

106
GO References

17

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	non-membrane-bounded organelle	nucleus	organelle envelope	organelle lumen	plasma membrane	protein-containing complex	synapse	vacuole

Click cells to view annotations.

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Expression Overview

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

851
Tissues

108
cDNA Data

42
Literature Summary

9

Tissue x Stage Matrix

Comparison Matrix

Gene Expression + Phenotype

Other Mouse Links

Allen Institute

GEO

Expression Atlas
Other Vertebrate Links

Xenbase prkd1

ZFIN prkd1

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All Sequences

57
RefSeq

31
UniProt

2
CCDS

CCDS49059.1

Ensembl

ENSMUSG00000002688 (Evidence)
NCBI Gene

18760

Representative Sequences				Length	Strain/Species	Flank
	genomic	ENSMUSG00000002688	Ensembl Gene Model \| MGI Sequence Detail	307868	C57BL/6J	± kb
	transcript	ENSMUST00000002765	Ensembl \| MGI Sequence Detail	3653	Not Applicable
	polypeptide	ENSMUSP00000002765	Ensembl \| MGI Sequence Detail	918	Not Applicable

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UniProt

2 Sequences
Protein Ontology

PR:000013236 serine/threonine-protein kinase D1

(term hierarchy)
EC

2.7.11.13
InterPro Domains

IPR046349 C1-like domain superfamily

IPR020454 Diacylglycerol/phorbol-ester binding

IPR011993 PH-like domain superfamily

IPR001849 Pleckstrin homology domain

IPR017441 Protein kinase, ATP binding site

IPR002219 Protein kinase C-like, phorbol ester/diacylglycerol-binding domain

IPR015727 Protein kinase C mu-related

IPR000719 Protein kinase domain

IPR011009 Protein kinase-like domain superfamily

IPR008271 Serine/threonine-protein kinase, active site

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All nucleic 47

cDNA 42

Primer pair 5

Microarray probesets 3

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MGD-MRK-16670

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Summaries

All 114

Developmental Gene Expression 9

Gene Ontology 17

Phenotypes 34
Earliest

J:14175 Osada S, et al., A phorbol ester receptor/protein kinase, nPKC eta, a new member of the protein kinase C family predominantly expressed in lung and skin. J Biol Chem. 1990 Dec 25;265(36):22434-40
Latest

J:346070 Godoy-Corchuelo JM, et al., TDP-43-M323K causes abnormal brain development and progressive cognitive and motor deficits associated with mislocalised and increased levels of TDP-43. Neurobiol Dis. 2024 Feb 15;193:106437

TSS for Prkd1:

(View these features in JBrowse)

Transcription Start Site	Location	Distance from Gene 5'-end
Tssr116236	Chr12:50695973-50696064 (-)	-138 bp
Tssr116235	Chr12:50458207-50458212 (-)	237,671 bp
Tssr116234	Chr12:50402814-50402817 (-)	293,065 bp

Prkd1 is Candidate Gene for:

QTL	Genetic Location*	Genome Location (GRCm39)	Reference	QTL Note
Fl1sa	Chr12, 13.69 cM		J:240255	The SMXA-5 mouse is an animal model of high-fat diet-induced fatty liver. The major QTL for fatty liver, Fl1sa on chromosome 12, was previously identified in a SM/J SMXA-5 intercross. The SMXA-5 genome consists of the SM/J and A/J genomes, and the A/J allele of Fl1sa is the fatty liver-susceptibility allele. The existence of the responsible genes for fatty liver within Fl1sa was confirmed in A/J-Chr 12 consomic mice. [J:124974]. The aim of the current study was to identify candidate genes for Fl1sa, and to investigate whether the identified genes affect the lipid metabolism. To identify candidate genes for Fl1sa, DNA microarray analysis was performed using the livers of A/J-Chr 12 and A/J mice that were fed a high-fat diet. The mRNA levels of three genes (Iah1, Rrm2, Prkd1) in the chromosomal region of Fl1sa were significantly different between the strains. Iah1 mRNA levels in the liver, kidney, and lung were significantly higher in A/J-Chr 12 mice than in A/J mice. The hepatic Iah1 mRNA level in A/J-Chr 12 mice was 3.2-fold higher than that in A/J mice. A stable cell line expressing the mouse Iah1 protein in mouse hepatoma Hepa1-6 cells was constructed. Overexpression of Iah1 in Hepa1-6 cells suppressed the mRNA levels of Cd36 and Dgat2, genes which play important roles in triglyceride synthesis and lipid metabolism.

*cM position of peak correlated region/marker

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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