Mutagenetix > Incidental Mutation

Incidental Mutation 'R1459:Prkd3'

162008

Institutional Source

Beutler Lab

Gene Symbol

Prkd3

Ensembl Gene

ENSMUSG00000024070

Gene Name

protein kinase D3

Synonyms

4930557O20Rik, PKD3, 5730497N19Rik, Prkcn

MMRRC Submission

039514-MU

Accession Numbers

Essential gene?

Probably non essential (E-score: 0.135) question?

Stock #

R1459 (G1)

Quality Score

194

Status

Validated

Chromosome

Chromosomal Location

79256834-79328245 bp(-) (GRCm39)

Type of Mutation

missense

DNA Base Change (assembly)

T to C at 79278796 bp (GRCm39)

Zygosity

Heterozygous

Amino Acid Change

Aspartic acid to Glycine at position 430 (D430G)

Ref Sequence

ENSEMBL: ENSMUSP00000132004 (fasta)

Gene Model

predicted gene model for transcript(s): [ENSMUST00000003191] [ENSMUST00000118768] [ENSMUST00000118991] [ENSMUST00000119284] [ENSMUST00000168887]

AlphaFold

Q8K1Y2

Predicted Effect

probably damaging
Transcript: ENSMUST00000003191
AA Change: D430G

PolyPhen 2 Score 0.995 (Sensitivity: 0.68; Specificity: 0.97)

SMART Domains

Protein: ENSMUSP00000003191
Gene: ENSMUSG00000024070
AA Change: D430G

Domain	Start	End	E-Value	Type
C1	155	204	1.95e-13	SMART
C1	272	321	1.26e-16	SMART
PH	417	534	1.18e-10	SMART
S_TKc	575	831	4.5e-90	SMART

Predicted Effect

probably damaging
Transcript: ENSMUST00000118768
AA Change: D335G

PolyPhen 2 Score 0.995 (Sensitivity: 0.68; Specificity: 0.97)

SMART Domains

Protein: ENSMUSP00000113232
Gene: ENSMUSG00000024070
AA Change: D335G

Domain	Start	End	E-Value	Type
C1	60	109	1.95e-13	SMART
C1	177	226	1.26e-16	SMART
PH	322	439	1.18e-10	SMART
S_TKc	481	737	4.5e-90	SMART

Predicted Effect

probably benign
Transcript: ENSMUST00000118991

SMART Domains

Protein: ENSMUSP00000112775
Gene: ENSMUSG00000024070

Domain	Start	End	E-Value	Type
C1	51	100	1.95e-13	SMART
C1	168	217	1.26e-16	SMART

Predicted Effect

probably damaging
Transcript: ENSMUST00000119284
AA Change: D430G

PolyPhen 2 Score 0.995 (Sensitivity: 0.68; Specificity: 0.97)

SMART Domains

Protein: ENSMUSP00000113395
Gene: ENSMUSG00000024070
AA Change: D430G

Domain	Start	End	E-Value	Type
C1	155	204	1.95e-13	SMART
C1	272	321	1.26e-16	SMART
PH	417	534	1.18e-10	SMART
S_TKc	576	832	4.5e-90	SMART

Predicted Effect

noncoding transcript
Transcript: ENSMUST00000124229

Predicted Effect

noncoding transcript
Transcript: ENSMUST00000146917

Predicted Effect

probably damaging
Transcript: ENSMUST00000168887
AA Change: D430G

PolyPhen 2 Score 0.995 (Sensitivity: 0.68; Specificity: 0.97)

SMART Domains

Protein: ENSMUSP00000132004
Gene: ENSMUSG00000024070
AA Change: D430G

Domain	Start	End	E-Value	Type
C1	155	204	1.95e-13	SMART
C1	272	321	1.26e-16	SMART
PH	417	534	1.18e-10	SMART
S_TKc	575	831	4.5e-90	SMART

Meta Mutation Damage Score

0.4702

Coding Region Coverage

1x: 98.9%
3x: 98.0%
10x: 95.3%
20x: 89.5%

Validation Efficiency

96% (87/91)

MGI Phenotype

FUNCTION: [Summary is not available for the mouse gene. This summary is for the human ortholog.] This gene belongs to the multigene protein kinase D family of serine/threonine kinases, which bind diacylglycerol and phorbol esters. Members of this family are characterized by an N-terminal regulatory domain comprised of a tandem repeat of cysteine-rich zinc-finger motifs and a pleckstrin domain. The C-terminal region contains the catalytic domain and is distantly related to calcium-regulated kinases. Catalytic activity of this enzyme promotes its nuclear localization. This protein has been implicated in a variety of functions including negative regulation of human airway epithelial barrier formation, growth regulation of breast and prostate cancer cells, and vesicle trafficking. [provided by RefSeq, Jan 2015]
PHENOTYPE: Homozygous mutation of this gene results in abnormal vertebral trabecular bone morphology and abnormal femur morphology. [provided by MGI curators]

Allele List at MGI

Other mutations in this stock

Total: 85 list
Gene	Ref	Var	Chr/Loc	Mutation	Predicted Effect	Zygosity
4933430I17Rik	C	T	4: 62,450,578 (GRCm39)	R51W	probably damaging	Het
Abcb1a	T	A	5: 8,752,920 (GRCm39)	L557Q	probably damaging	Het
Abcb4	T	C	5: 8,968,662 (GRCm39)	F334L	possibly damaging	Het
Adamts14	T	A	10: 61,034,583 (GRCm39)	T1102S	probably benign	Het
Adamtsl1	T	C	4: 86,344,102 (GRCm39)	Y1719H	probably damaging	Het
Adcyap1	T	C	17: 93,507,550 (GRCm39)		probably null	Het
Ankrd13c	T	A	3: 157,677,947 (GRCm39)	L219Q	probably damaging	Het
Ano3	C	A	2: 110,711,174 (GRCm39)	A97S	probably benign	Het
Apaf1	T	C	10: 90,898,022 (GRCm39)	N245S	probably benign	Het
Apob	A	G	12: 8,056,047 (GRCm39)	T1510A	probably benign	Het
Apob	A	G	12: 8,061,937 (GRCm39)	D3473G	possibly damaging	Het
Arfgap3	G	A	15: 83,191,138 (GRCm39)	T12I	probably benign	Het
Bend4	A	G	5: 67,557,418 (GRCm39)	V466A	probably damaging	Het
Bend7	G	A	2: 4,749,239 (GRCm39)	E119K	probably damaging	Het
Capn5	G	T	7: 97,781,049 (GRCm39)	R243S	possibly damaging	Het
Cd84	A	G	1: 171,679,510 (GRCm39)	I63V	probably benign	Het
Cd86	T	A	16: 36,449,350 (GRCm39)	T16S	probably benign	Het
Cdc42bpb	A	G	12: 111,262,734 (GRCm39)		probably benign	Het
Cep20	G	A	16: 14,122,380 (GRCm39)	T128I	possibly damaging	Het
Cep95	C	T	11: 106,708,781 (GRCm39)	S26L	probably damaging	Het
Cldn19	C	T	4: 119,112,810 (GRCm39)	A14V	probably damaging	Het
Cluap1	T	A	16: 3,755,453 (GRCm39)	M356K	probably damaging	Het
Coq7	C	T	7: 118,109,260 (GRCm39)	G263S	unknown	Het
Ctnnd2	A	C	15: 30,847,445 (GRCm39)	T679P	probably damaging	Het
Dnah10	A	G	5: 124,820,750 (GRCm39)	D528G	possibly damaging	Het
Dvl1	T	A	4: 155,938,476 (GRCm39)	N133K	probably damaging	Het
Efcab7	T	G	4: 99,769,744 (GRCm39)	H550Q	probably null	Het
Fastkd5	C	T	2: 130,456,717 (GRCm39)	M624I	probably damaging	Het
Fbxo42	T	C	4: 140,895,073 (GRCm39)	V12A	probably benign	Het
Gabarapl1	T	A	6: 129,515,635 (GRCm39)	M91K	possibly damaging	Het
Gas7	A	G	11: 67,552,902 (GRCm39)	N154S	probably damaging	Het
Gm21814	T	A	6: 149,483,650 (GRCm39)		noncoding transcript	Het
Gnl3	G	A	14: 30,739,803 (GRCm39)	R12C	probably damaging	Het
Golga2	T	G	2: 32,187,807 (GRCm39)		probably null	Het
Grk3	T	A	5: 113,062,878 (GRCm39)	R656S	probably benign	Het
Gsap	T	A	5: 21,412,236 (GRCm39)		probably benign	Het
H60c	T	C	10: 3,210,240 (GRCm39)	Q103R	probably benign	Het
Hnrnpr	T	A	4: 136,056,755 (GRCm39)	S252T	probably damaging	Het
Itgb4	A	T	11: 115,869,937 (GRCm39)	T40S	probably benign	Het
Krtap27-1	T	C	16: 88,468,302 (GRCm39)	N81D	probably benign	Het
Lilrb4a	T	A	10: 51,367,683 (GRCm39)	L75Q	probably benign	Het
Lrp2	T	A	2: 69,290,821 (GRCm39)	E3546D	probably damaging	Het
Lrp2	T	A	2: 69,313,738 (GRCm39)	D2331V	probably damaging	Het
Lzts2	T	A	19: 45,009,893 (GRCm39)	V9E	probably damaging	Het
Matr3	T	A	18: 35,717,709 (GRCm39)	D302E	probably benign	Het
Mcoln2	A	G	3: 145,897,979 (GRCm39)		probably null	Het
Metap2	T	C	10: 93,704,811 (GRCm39)	D272G	probably damaging	Het
Mitf	A	G	6: 97,987,428 (GRCm39)	D337G	probably damaging	Het
Mrtfb	T	C	16: 13,219,433 (GRCm39)	V693A	possibly damaging	Het
Msh2	A	G	17: 87,985,771 (GRCm39)	E116G	probably benign	Het
Nlrp10	T	A	7: 108,523,555 (GRCm39)	M642L	probably benign	Het
Noxa1	G	T	2: 24,982,558 (GRCm39)	Q86K	probably benign	Het
Nrap	T	C	19: 56,372,562 (GRCm39)	T48A	probably benign	Het
Nup160	T	A	2: 90,520,494 (GRCm39)	H308Q	probably damaging	Het
Osbpl11	T	C	16: 33,056,699 (GRCm39)	L711P	probably damaging	Het
Osbpl6	A	G	2: 76,385,409 (GRCm39)	N281S	probably benign	Het
Pcnp	C	T	16: 55,844,703 (GRCm39)	E66K	possibly damaging	Het
Phf11	T	A	14: 59,482,227 (GRCm39)	E175D	probably damaging	Het
Pik3cg	A	G	12: 32,254,983 (GRCm39)	Y335H	probably damaging	Het
Plekhg4	T	C	8: 106,108,431 (GRCm39)	L1053S	probably damaging	Het
Plekhh2	G	T	17: 84,918,203 (GRCm39)	E1271*	probably null	Het
Ppp2r2b	T	A	18: 42,871,055 (GRCm39)	Y82F	probably damaging	Het
Prl7d1	C	T	13: 27,893,240 (GRCm39)	D224N	possibly damaging	Het
Ptpdc1	A	T	13: 48,740,173 (GRCm39)	N419K	possibly damaging	Het
Serinc5	T	A	13: 92,797,695 (GRCm39)		probably null	Het
Sipa1	A	G	19: 5,701,692 (GRCm39)	L981P	probably damaging	Het
Slc16a7	A	T	10: 125,066,489 (GRCm39)	C383*	probably null	Het
Slc19a1	C	G	10: 76,878,369 (GRCm39)	Y301*	probably null	Het
Slc22a14	A	T	9: 119,052,827 (GRCm39)	V14E	possibly damaging	Het
Slpi	C	A	2: 164,196,837 (GRCm39)	C95F	probably damaging	Het
Smurf2	G	A	11: 106,743,333 (GRCm39)	H225Y	possibly damaging	Het
Son	T	C	16: 91,452,230 (GRCm39)	S326P	possibly damaging	Het
Sptb	T	A	12: 76,658,657 (GRCm39)	K1262M	probably benign	Het
Sugp2	T	A	8: 70,696,714 (GRCm39)		probably benign	Het
Tatdn2	T	A	6: 113,687,031 (GRCm39)	H747Q	probably damaging	Het
Tcn2	C	A	11: 3,877,516 (GRCm39)	R44L	probably benign	Het
Tenm3	G	A	8: 48,689,006 (GRCm39)	R2194C	probably damaging	Het
Tnks2	T	A	19: 36,822,931 (GRCm39)		probably benign	Het
Top3a	A	T	11: 60,650,188 (GRCm39)	I120N	probably damaging	Het
Umodl1	T	A	17: 31,201,232 (GRCm39)		probably benign	Het
Umodl1	T	C	17: 31,205,478 (GRCm39)	V662A	probably benign	Het
Ush2a	T	C	1: 188,595,048 (GRCm39)	S3827P	probably benign	Het
Vasn	T	A	16: 4,466,473 (GRCm39)		probably null	Het
Vmn2r69	A	T	7: 85,055,908 (GRCm39)	C743*	probably null	Het
Vmn2r79	C	A	7: 86,687,002 (GRCm39)	H794Q	probably benign	Het

Other mutations in Prkd3

Allele	Source	Chr	Coord	Type	Predicted Effect	PPH Score
IGL00990:Prkd3	APN	17	79,261,952 (GRCm39)	missense	probably benign	0.00
IGL01775:Prkd3	APN	17	79,320,189 (GRCm39)	missense	probably damaging	1.00
IGL01875:Prkd3	APN	17	79,264,635 (GRCm39)	missense	possibly damaging	0.95
IGL01892:Prkd3	APN	17	79,279,930 (GRCm39)	missense	probably benign	0.13
FR4304:Prkd3	UTSW	17	79,283,249 (GRCm39)	splice site	probably null
R0070:Prkd3	UTSW	17	79,261,939 (GRCm39)	missense	probably damaging	1.00
R0070:Prkd3	UTSW	17	79,261,939 (GRCm39)	missense	probably damaging	1.00
R0374:Prkd3	UTSW	17	79,264,644 (GRCm39)	missense	probably null	1.00
R0688:Prkd3	UTSW	17	79,264,662 (GRCm39)	missense	probably damaging	0.99
R1112:Prkd3	UTSW	17	79,273,837 (GRCm39)	missense	probably damaging	1.00
R1364:Prkd3	UTSW	17	79,264,687 (GRCm39)	missense	probably damaging	1.00
R1382:Prkd3	UTSW	17	79,264,674 (GRCm39)	missense	probably damaging	1.00
R1522:Prkd3	UTSW	17	79,260,125 (GRCm39)	missense	probably damaging	1.00
R1645:Prkd3	UTSW	17	79,263,949 (GRCm39)	critical splice donor site	probably null
R2035:Prkd3	UTSW	17	79,282,802 (GRCm39)	critical splice donor site	probably null
R2187:Prkd3	UTSW	17	79,282,983 (GRCm39)	missense	probably benign
R2250:Prkd3	UTSW	17	79,275,507 (GRCm39)	missense	probably benign	0.15
R2850:Prkd3	UTSW	17	79,262,025 (GRCm39)	missense	possibly damaging	0.89
R3625:Prkd3	UTSW	17	79,292,733 (GRCm39)	missense	probably damaging	1.00
R3773:Prkd3	UTSW	17	79,266,535 (GRCm39)	missense	possibly damaging	0.52
R3973:Prkd3	UTSW	17	79,266,570 (GRCm39)	splice site	probably benign
R4089:Prkd3	UTSW	17	79,278,817 (GRCm39)	missense	possibly damaging	0.64
R4407:Prkd3	UTSW	17	79,290,987 (GRCm39)	missense	probably damaging	1.00
R4453:Prkd3	UTSW	17	79,290,975 (GRCm39)	missense	probably damaging	1.00
R4697:Prkd3	UTSW	17	79,268,600 (GRCm39)	missense	probably benign	0.02
R4715:Prkd3	UTSW	17	79,259,366 (GRCm39)	missense	possibly damaging	0.73
R4754:Prkd3	UTSW	17	79,264,043 (GRCm39)	missense	probably damaging	1.00
R4955:Prkd3	UTSW	17	79,260,156 (GRCm39)	missense	probably null	0.95
R5412:Prkd3	UTSW	17	79,262,140 (GRCm39)	missense	possibly damaging	0.85
R6163:Prkd3	UTSW	17	79,273,784 (GRCm39)	missense	possibly damaging	0.94
R6280:Prkd3	UTSW	17	79,289,360 (GRCm39)	missense	probably damaging	0.97
R7074:Prkd3	UTSW	17	79,282,236 (GRCm39)	nonsense	probably null
R7153:Prkd3	UTSW	17	79,273,784 (GRCm39)	missense	probably benign	0.04
R7335:Prkd3	UTSW	17	79,261,995 (GRCm39)	missense	probably damaging	0.99
R7492:Prkd3	UTSW	17	79,269,974 (GRCm39)	nonsense	probably null
R7819:Prkd3	UTSW	17	79,279,930 (GRCm39)	missense	probably benign	0.13
R7962:Prkd3	UTSW	17	79,315,691 (GRCm39)	start codon destroyed	not run
R8884:Prkd3	UTSW	17	79,282,193 (GRCm39)	missense	probably damaging	0.99
R8956:Prkd3	UTSW	17	79,278,883 (GRCm39)	missense	probably damaging	0.98
R9039:Prkd3	UTSW	17	79,280,003 (GRCm39)	missense	probably benign	0.01
R9110:Prkd3	UTSW	17	79,292,751 (GRCm39)	missense	probably damaging	1.00
R9139:Prkd3	UTSW	17	79,269,969 (GRCm39)	missense	possibly damaging	0.55
R9219:Prkd3	UTSW	17	79,273,628 (GRCm39)	missense	probably benign	0.13
R9399:Prkd3	UTSW	17	79,264,719 (GRCm39)	missense	probably damaging	1.00
R9466:Prkd3	UTSW	17	79,264,049 (GRCm39)	missense	probably damaging	0.97
R9566:Prkd3	UTSW	17	79,292,652 (GRCm39)	missense	probably damaging	1.00
X0063:Prkd3	UTSW	17	79,264,042 (GRCm39)	missense	probably damaging	1.00
X0066:Prkd3	UTSW	17	79,268,611 (GRCm39)	missense	probably damaging	1.00

Predicted Primers

PCR Primer
(F):5'- GCACTTACGCTGTCTATACACACCAAG -3'
(R):5'- TGGCTGGAAGATTCTTTCTGTTCCATC -3'

Sequencing Primer
(F):5'- CCAAAGATGACTATTCCTGTGC -3'
(R):5'- ctccccatcccctcccc -3'

Posted On

2014-03-14