Mutagenetix > Incidental Mutation

Incidental Mutation 'R9566:Prkd3'

721638

Institutional Source

Beutler Lab

Gene Symbol

Prkd3

Ensembl Gene

ENSMUSG00000024070

Gene Name

protein kinase D3

Synonyms

4930557O20Rik, PKD3, 5730497N19Rik, Prkcn

MMRRC Submission

Accession Numbers

Essential gene?

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

Stock #

R9566 (G1)

Quality Score

225.009

Status

Not validated

Chromosome

Chromosomal Location

79256834-79328245 bp(-) (GRCm39)

Type of Mutation

missense

DNA Base Change (assembly)

A to T at 79292652 bp (GRCm39)

Zygosity

Heterozygous

Amino Acid Change

Valine to Aspartic acid at position 140 (V140D)

Ref Sequence

ENSEMBL: ENSMUSP00000113395 (fasta)

Gene Model

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

AlphaFold

Q8K1Y2

Predicted Effect

probably damaging
Transcript: ENSMUST00000003191
AA Change: V140D

PolyPhen 2 Score 0.999 (Sensitivity: 0.14; Specificity: 0.99)

SMART Domains

Protein: ENSMUSP00000003191
Gene: ENSMUSG00000024070
AA Change: V140D

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: V45D

PolyPhen 2 Score 0.999 (Sensitivity: 0.14; Specificity: 0.99)

SMART Domains

Protein: ENSMUSP00000113232
Gene: ENSMUSG00000024070
AA Change: V45D

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 damaging
Transcript: ENSMUST00000118991
AA Change: V36D

PolyPhen 2 Score 0.998 (Sensitivity: 0.27; Specificity: 0.99)

SMART Domains

Protein: ENSMUSP00000112775
Gene: ENSMUSG00000024070
AA Change: V36D

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: V140D

PolyPhen 2 Score 0.999 (Sensitivity: 0.14; Specificity: 0.99)

SMART Domains

Protein: ENSMUSP00000113395
Gene: ENSMUSG00000024070
AA Change: V140D

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

probably damaging
Transcript: ENSMUST00000168887
AA Change: V140D

PolyPhen 2 Score 0.999 (Sensitivity: 0.14; Specificity: 0.99)

SMART Domains

Protein: ENSMUSP00000132004
Gene: ENSMUSG00000024070
AA Change: V140D

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

Coding Region Coverage

1x: 100.0%
3x: 99.9%
10x: 99.7%
20x: 99.1%

Validation Efficiency

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
4921509C19Rik	G	A	2: 151,314,226 (GRCm39)	T484I	probably benign	Het
4930568D16Rik	C	A	2: 35,244,645 (GRCm39)	E236*	probably null	Het
Abca13	C	A	11: 9,414,927 (GRCm39)	T3998K	probably damaging	Het
Adam8	A	G	7: 139,565,285 (GRCm39)	V643A	probably benign	Het
Adamtsl2	T	C	2: 26,979,773 (GRCm39)		probably null	Het
Akr1c18	A	T	13: 4,195,203 (GRCm39)		probably null	Het
Atf7ip2	C	T	16: 10,044,893 (GRCm39)	S222L	probably benign	Het
Atp2c1	A	T	9: 105,343,828 (GRCm39)	I127N	probably damaging	Het
Bcl11b	A	G	12: 107,881,784 (GRCm39)	Y844H	possibly damaging	Het
Bean1	CT	C	8: 104,908,664 (GRCm39)		probably null	Het
Btnl4	A	G	17: 34,688,263 (GRCm39)	I505T	probably benign	Het
Cacna1b	G	A	2: 24,498,092 (GRCm39)	Q2024*	probably null	Het
Cars1	A	G	7: 143,113,384 (GRCm39)		probably null	Het
Ccne2	A	G	4: 11,193,026 (GRCm39)	K49E	probably benign	Het
Ccnk	A	G	12: 108,152,695 (GRCm39)	N4S	probably benign	Het
Cfap91	A	G	16: 38,155,996 (GRCm39)	F76L	probably damaging	Het
Clasp1	A	G	1: 118,479,801 (GRCm39)	D1027G	probably benign	Het
Copb1	A	T	7: 113,825,997 (GRCm39)	N662K	probably benign	Het
Cox8b	C	T	7: 140,478,926 (GRCm39)	S63N	probably benign	Het
Cpa4	C	A	6: 30,579,608 (GRCm39)	D138E	probably benign	Het
Dcc	A	G	18: 71,943,866 (GRCm39)	C262R	possibly damaging	Het
Dennd5a	C	T	7: 109,533,254 (GRCm39)	G172E	probably benign	Het
Dgke	C	T	11: 88,932,273 (GRCm39)		probably null	Het
Dnah11	A	G	12: 117,938,728 (GRCm39)	Y3247H	possibly damaging	Het
Dnajc21	T	G	15: 10,464,019 (GRCm39)	I49L	possibly damaging	Het
Dnm1	A	G	2: 32,228,011 (GRCm39)		probably null	Het
Ecd	A	T	14: 20,393,368 (GRCm39)	Y93*	probably null	Het
Epm2aip1	T	C	9: 111,101,807 (GRCm39)	L260P	probably damaging	Het
Eqtn	G	A	4: 94,813,185 (GRCm39)	P134S	probably damaging	Het
Ercc1	T	A	7: 19,088,377 (GRCm39)	C243*	probably null	Het
Fbln2	C	A	6: 91,231,513 (GRCm39)	H537N	probably benign	Het
Ffar2	A	G	7: 30,518,847 (GRCm39)	F231S	probably damaging	Het
Fhod1	G	A	8: 106,064,516 (GRCm39)	A172V	unknown	Het
Gbp8	C	T	5: 105,198,799 (GRCm39)	V39M	probably damaging	Het
Gm5773	T	C	3: 93,680,742 (GRCm39)	L138P	probably damaging	Het
Gtf2ird2	A	G	5: 134,246,256 (GRCm39)	E838G	probably damaging	Het
Gucy2e	C	A	11: 69,118,947 (GRCm39)	V682L	probably damaging	Het
Hmcn1	T	G	1: 150,498,660 (GRCm39)	N4073T	probably benign	Het
Il22b	A	T	10: 118,130,860 (GRCm39)	L12H	probably damaging	Het
Ist1	A	T	8: 110,408,816 (GRCm39)	S94T	probably benign	Het
Klhl24	A	T	16: 19,934,669 (GRCm39)	N381Y	probably damaging	Het
Krtap24-1	C	T	16: 88,408,886 (GRCm39)	C80Y		Het
Lcp2	T	A	11: 34,000,944 (GRCm39)	D42E		Het
Map1s	G	A	8: 71,365,580 (GRCm39)	A162T	probably benign	Het
Mbd5	T	G	2: 49,169,521 (GRCm39)	V1564G	probably damaging	Het
Mettl15	A	T	2: 108,923,592 (GRCm39)	S277T	possibly damaging	Het
Mfsd12	C	G	10: 81,196,962 (GRCm39)	T177S	probably benign	Het
Mlxipl	A	G	5: 135,152,616 (GRCm39)	D244G	possibly damaging	Het
Mutyh	G	A	4: 116,673,780 (GRCm39)	V164M	probably damaging	Het
Mypop	A	G	7: 18,726,534 (GRCm39)	D167G	probably benign	Het
Nbeal2	C	T	9: 110,457,989 (GRCm39)	V2169M	probably benign	Het
Nifk	G	T	1: 118,260,492 (GRCm39)	V259F	probably damaging	Het
Oasl1	A	G	5: 115,066,331 (GRCm39)	T150A	probably benign	Het
Obox6	G	A	7: 15,568,352 (GRCm39)	R175C		Het
Or2y11	T	C	11: 49,443,162 (GRCm39)	V196A	probably benign	Het
Or5p52	T	A	7: 107,502,409 (GRCm39)	C162S	possibly damaging	Het
Or5p69	A	T	7: 107,966,783 (GRCm39)	I29F	probably benign	Het
Per3	A	G	4: 151,113,335 (GRCm39)	F331S		Het
Pitrm1	A	G	13: 6,613,452 (GRCm39)	D508G	probably benign	Het
Plec	T	A	15: 76,062,790 (GRCm39)	I2427F	possibly damaging	Het
Prpf3	G	A	3: 95,760,800 (GRCm39)	A34V	probably damaging	Het
Ptar1	A	G	19: 23,686,206 (GRCm39)	T173A	probably benign	Het
Resf1	A	G	6: 149,227,352 (GRCm39)	N133D	possibly damaging	Het
Rest	G	T	5: 77,416,277 (GRCm39)	E164*	probably null	Het
Rnpepl1	A	C	1: 92,847,468 (GRCm39)	D685A		Het
Sc5d	T	C	9: 42,170,008 (GRCm39)	N71S	probably damaging	Het
Serpinb3c	A	T	1: 107,200,425 (GRCm39)	S239R	probably damaging	Het
Slc28a3	C	T	13: 58,758,653 (GRCm39)		probably benign	Het
Smagp	T	C	15: 100,519,844 (GRCm39)	Y60C	probably damaging	Het
Spink10	T	A	18: 62,790,939 (GRCm39)	M75K	probably benign	Het
Spryd7	T	C	14: 61,777,639 (GRCm39)	N147S	probably benign	Het
Steap4	A	G	5: 8,025,646 (GRCm39)	E69G	possibly damaging	Het
Svil	C	A	18: 5,099,661 (GRCm39)	H1732Q	probably damaging	Het
Tgoln1	T	C	6: 72,592,911 (GRCm39)	T190A	probably benign	Het
Tmem63c	C	T	12: 87,108,305 (GRCm39)	S106F	possibly damaging	Het
Trpv5	T	C	6: 41,637,456 (GRCm39)	D375G	probably null	Het
Tyw1	G	A	5: 130,298,065 (GRCm39)	R202Q	probably damaging	Het
Ugt2b38	A	G	5: 87,558,209 (GRCm39)	L484P	probably damaging	Het
Uox	A	T	3: 146,330,308 (GRCm39)	T179S	possibly damaging	Het
Usp34	A	G	11: 23,317,529 (GRCm39)	I882V		Het
Vmn2r124	A	G	17: 18,293,581 (GRCm39)	K556R	probably benign	Het
Vmn2r57	A	G	7: 41,077,089 (GRCm39)	F359S	probably benign	Het
Wasf2	T	C	4: 132,921,766 (GRCm39)	V295A	unknown	Het
Znhit1	G	A	5: 137,015,785 (GRCm39)		probably benign	Het
Zscan22	C	T	7: 12,640,866 (GRCm39)	T370M	probably damaging	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
R1459:Prkd3	UTSW	17	79,278,796 (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
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'- AACTGGCAATCCCTCAAGCTTC -3'
(R):5'- ACTAGCACTATGTCAAGACACTTC -3'

Sequencing Primer
(F):5'- TGGCAATCCCTCAAGCTTCAAAAC -3'
(R):5'- GTAGACTATTTGTAACAGCAGAAAGC -3'

Posted On

2022-08-09