Mutagenetix > Incidental Mutation

Incidental Mutation 'R7007:Vrk3'

544772

Institutional Source

Beutler Lab

Gene Symbol

Vrk3

Ensembl Gene

ENSMUSG00000002205

Gene Name

vaccinia related kinase 3

Synonyms

MMRRC Submission

045109-MU

Accession Numbers

Essential gene?

Non essential (E-score: 0.000) question?

Stock #

R7007 (G1)

Quality Score

225.009

Status

Validated

Chromosome

Chromosomal Location

44398049-44426939 bp(+) (GRCm39)

Type of Mutation

missense

DNA Base Change (assembly)

A to G at 44407187 bp (GRCm39)

Zygosity

Heterozygous

Amino Acid Change

Asparagine to Aspartic acid at position 53 (N53D)

Ref Sequence

ENSEMBL: ENSMUSP00000119073 (fasta)

Gene Model

predicted gene model for transcript(s): [ENSMUST00000002275] [ENSMUST00000125705] [ENSMUST00000144515] [ENSMUST00000147952] [ENSMUST00000165957] [ENSMUST00000171821]

AlphaFold

Q8K3G5

Predicted Effect

probably benign
Transcript: ENSMUST00000002275
AA Change: N53D

PolyPhen 2 Score 0.009 (Sensitivity: 0.96; Specificity: 0.77)

SMART Domains

Protein: ENSMUSP00000002275
Gene: ENSMUSG00000002205
AA Change: N53D

Domain	Start	End	E-Value	Type
Pfam:Pkinase_Tyr	212	432	3.2e-8	PFAM
Pfam:Pkinase	218	432	4.2e-10	PFAM

Predicted Effect

probably benign
Transcript: ENSMUST00000125705

Predicted Effect

probably damaging
Transcript: ENSMUST00000144515
AA Change: N53D

PolyPhen 2 Score 0.967 (Sensitivity: 0.77; Specificity: 0.95)

SMART Domains

Protein: ENSMUSP00000119073
Gene: ENSMUSG00000002205
AA Change: N53D

Domain	Start	End	E-Value	Type
Pfam:zf-ribbon_3	1	26	1.2e-11	PFAM
Pfam:zinc_ribbon_2	4	26	3e-10	PFAM
PDB:2JII\|B	97	176	3e-36	PDB

Predicted Effect

probably benign
Transcript: ENSMUST00000147952
AA Change: N53D

PolyPhen 2 Score 0.027 (Sensitivity: 0.95; Specificity: 0.81)

SMART Domains

Protein: ENSMUSP00000130331
Gene: ENSMUSG00000002205
AA Change: N53D

Domain	Start	End	E-Value	Type
Pfam:zf-ribbon_3	1	26	1.1e-11	PFAM
Pfam:zinc_ribbon_2	4	26	2.9e-10	PFAM
PDB:2JII\|B	117	162	1e-8	PDB

Predicted Effect

probably benign
Transcript: ENSMUST00000165957
AA Change: N53D

PolyPhen 2 Score 0.009 (Sensitivity: 0.96; Specificity: 0.77)

SMART Domains

Protein: ENSMUSP00000131704
Gene: ENSMUSG00000002205
AA Change: N53D

Domain	Start	End	E-Value	Type
Pfam:zf-ribbon_3	1	26	6.7e-12	PFAM
Pfam:zinc_ribbon_2	4	26	4.4e-10	PFAM
PDB:2JII\|B	117	204	7e-30	PDB

Predicted Effect

probably benign
Transcript: ENSMUST00000171821
AA Change: N53D

PolyPhen 2 Score 0.009 (Sensitivity: 0.96; Specificity: 0.77)

SMART Domains

Protein: ENSMUSP00000132748
Gene: ENSMUSG00000002205
AA Change: N53D

Domain	Start	End	E-Value	Type
Pfam:zf-ribbon_3	1	26	2.9e-12	PFAM
Pfam:zinc_ribbon_2	4	26	2e-10	PFAM

Coding Region Coverage

1x: 100.0%
3x: 100.0%
10x: 99.7%
20x: 99.0%

Validation Efficiency

95% (63/66)

MGI Phenotype

FUNCTION: [Summary is not available for the mouse gene. This summary is for the human ortholog.] This gene encodes a member of the vaccinia-related kinase (VRK) family of serine/threonine protein kinases. In both human and mouse, this gene has substitutions at several residues within the ATP binding motifs that in other kinases have been shown to be required for catalysis. In vitro assays indicate the protein lacks phosphorylation activity. The protein, however, likely retains its substrate binding capability. This gene is widely expressed in human tissues and its protein localizes to the nucleus. Alternative splicing results in multiple transcripts encoding different isoforms. [provided by RefSeq, Jul 2008]
PHENOTYPE: Mice homozygous for a null allele display impaired social behavior, decreased fear and anxiety relate behavior, impaired spatial memory, and abnormal hippocampal dendritic spine and synapse morphologies. [provided by MGI curators]

Allele List at MGI

Other mutations in this stock

Total: 66 list
Gene	Ref	Var	Chr/Loc	Mutation	Predicted Effect	Zygosity
4930474N05Rik	C	T	14: 35,817,121 (GRCm39)	T57I	probably benign	Het
Adcy8	T	C	15: 64,576,565 (GRCm39)	N999S	possibly damaging	Het
Adgrv1	T	A	13: 81,684,483 (GRCm39)	I1073F	possibly damaging	Het
Akap3	A	G	6: 126,843,439 (GRCm39)	D686G	probably damaging	Het
Alg2	A	T	4: 47,471,881 (GRCm39)	I309N	probably benign	Het
Ankrd36	A	G	11: 5,639,168 (GRCm39)	E1360G	probably benign	Het
Aox1	C	A	1: 58,370,051 (GRCm39)	Q788K	probably damaging	Het
Apoc2	A	T	7: 19,407,282 (GRCm39)	D26E	possibly damaging	Het
Bbx	G	A	16: 50,022,851 (GRCm39)	T703I	possibly damaging	Het
C2cd4d	T	C	3: 94,271,378 (GRCm39)	Y215H	probably benign	Het
C3	C	T	17: 57,525,809 (GRCm39)	E858K	probably benign	Het
Ciita	T	C	16: 10,329,171 (GRCm39)	L482P	probably damaging	Het
Cldn9	T	C	17: 23,902,052 (GRCm39)	E191G	probably benign	Het
Cnst	T	A	1: 179,438,133 (GRCm39)	S566T	probably damaging	Het
Col5a2	A	G	1: 45,417,609 (GRCm39)	I1322T	possibly damaging	Het
Cp	G	A	3: 20,024,137 (GRCm39)	V326M	probably damaging	Het
Cyp7b1	G	A	3: 18,151,782 (GRCm39)	Q144*	probably null	Het
Dnah10	T	C	5: 124,864,490 (GRCm39)	S2232P	probably damaging	Het
Dnah17	T	C	11: 118,009,697 (GRCm39)	E625G	possibly damaging	Het
Dnah7c	T	A	1: 46,571,910 (GRCm39)	D794E	probably benign	Het
Dusp10	G	A	1: 183,769,414 (GRCm39)	V127M	probably benign	Het
Dysf	G	C	6: 84,090,962 (GRCm39)	W1015C	probably damaging	Het
Fbxw17	T	C	13: 50,577,808 (GRCm39)	Y104H	probably damaging	Het
Gm6408	G	A	5: 146,420,647 (GRCm39)	E176K	probably damaging	Het
Gp1bb	T	A	16: 18,439,689 (GRCm39)	D135V	possibly damaging	Het
Gprin1	C	T	13: 54,886,069 (GRCm39)	C735Y	probably damaging	Het
Heatr9	T	A	11: 83,411,446 (GRCm39)	M30L	possibly damaging	Het
Hhat	G	A	1: 192,376,134 (GRCm39)	T333I	possibly damaging	Het
Htr5b	A	G	1: 121,438,223 (GRCm39)	F336S	probably damaging	Het
Ippk	T	G	13: 49,590,181 (GRCm39)		probably null	Het
Jph1	T	A	1: 17,074,410 (GRCm39)	H11L	possibly damaging	Het
Kif12	T	A	4: 63,084,717 (GRCm39)	I534L	probably benign	Het
Lemd3	A	T	10: 120,788,137 (GRCm39)	F523I	probably benign	Het
Lgsn	C	A	1: 31,229,508 (GRCm39)	H76Q	probably benign	Het
Lipm	T	A	19: 34,089,497 (GRCm39)	W152R	probably damaging	Het
Mei1	A	T	15: 81,978,200 (GRCm39)	R216W	probably damaging	Het
Mybpc1	C	T	10: 88,389,274 (GRCm39)	G379S	probably damaging	Het
Myh8	A	G	11: 67,179,142 (GRCm39)	T512A	probably benign	Het
Nf1	A	G	11: 79,337,849 (GRCm39)		probably null	Het
Npc1	T	C	18: 12,343,605 (GRCm39)	T463A	probably benign	Het
Or12e10	A	G	2: 87,640,230 (GRCm39)	N22S	probably damaging	Het
Or2y13	G	A	11: 49,415,011 (GRCm39)	V154M	probably benign	Het
Or6c7	A	T	10: 129,323,277 (GRCm39)	I133F	probably damaging	Het
Osbpl11	T	G	16: 33,047,309 (GRCm39)	I424R	possibly damaging	Het
Pnma8b	A	T	7: 16,680,181 (GRCm39)	K388N	possibly damaging	Het
Ppp1r26	A	T	2: 28,341,171 (GRCm39)	K267I	probably damaging	Het
Psmb5	A	T	14: 54,854,166 (GRCm39)	M104K	probably damaging	Het
Ptges2	T	C	2: 32,292,318 (GRCm39)	V378A	probably benign	Het
Rcan2	C	T	17: 44,147,216 (GRCm39)	S18F	probably benign	Het
Saxo5	A	T	8: 3,526,309 (GRCm39)	D154V	probably damaging	Het
Sf3b2	C	T	19: 5,324,545 (GRCm39)	R859Q	probably benign	Het
Slc7a1	G	A	5: 148,289,256 (GRCm39)			Het
Spata31d1a	T	A	13: 59,851,448 (GRCm39)	T227S	probably benign	Het
Sptbn2	T	A	19: 4,794,173 (GRCm39)	V1459E	possibly damaging	Het
Srgap2	T	C	1: 131,247,275 (GRCm39)	I586V	probably benign	Het
St6galnac1	G	A	11: 116,657,833 (GRCm39)	R356*	probably null	Het
Taf5	T	A	19: 47,059,650 (GRCm39)	F265I	probably damaging	Het
Tkfc	T	A	19: 10,573,727 (GRCm39)	I229L	probably benign	Het
Tmem132c	T	A	5: 127,436,679 (GRCm39)	L56Q	probably damaging	Het
Togaram2	C	T	17: 72,016,638 (GRCm39)	A665V	probably damaging	Het
Ttn	G	A	2: 76,537,390 (GRCm39)	T34846I	probably benign	Het
Tyr	G	A	7: 87,142,548 (GRCm39)	A4V	probably benign	Het
Ubap2	A	C	4: 41,206,221 (GRCm39)	F549L	probably damaging	Het
Usp2	T	C	9: 44,001,339 (GRCm39)	S294P	probably damaging	Het
Zfp324	T	C	7: 12,705,142 (GRCm39)	S444P	probably damaging	Het
Zfp597	T	C	16: 3,683,791 (GRCm39)	I322V	probably benign	Het

Other mutations in Vrk3

Allele	Source	Chr	Coord	Type	Predicted Effect	PPH Score
IGL00495:Vrk3	APN	7	44,419,071 (GRCm39)	missense	probably damaging	1.00
IGL01540:Vrk3	APN	7	44,416,568 (GRCm39)	missense	probably damaging	1.00
IGL02682:Vrk3	APN	7	44,403,244 (GRCm39)	missense	probably benign	0.19
R0462:Vrk3	UTSW	7	44,413,624 (GRCm39)	missense	possibly damaging	0.77
R0831:Vrk3	UTSW	7	44,414,227 (GRCm39)	missense	probably damaging	1.00
R1760:Vrk3	UTSW	7	44,417,895 (GRCm39)	missense	probably damaging	0.98
R2212:Vrk3	UTSW	7	44,424,866 (GRCm39)	missense	probably benign	0.00
R2289:Vrk3	UTSW	7	44,424,866 (GRCm39)	missense	probably benign	0.00
R2915:Vrk3	UTSW	7	44,424,866 (GRCm39)	missense	probably benign	0.00
R3027:Vrk3	UTSW	7	44,424,866 (GRCm39)	missense	probably benign	0.00
R3028:Vrk3	UTSW	7	44,424,866 (GRCm39)	missense	probably benign	0.00
R3416:Vrk3	UTSW	7	44,424,866 (GRCm39)	missense	probably benign	0.00
R3417:Vrk3	UTSW	7	44,424,866 (GRCm39)	missense	probably benign	0.00
R3613:Vrk3	UTSW	7	44,424,866 (GRCm39)	missense	probably benign	0.00
R3877:Vrk3	UTSW	7	44,412,460 (GRCm39)	splice site	probably null
R4357:Vrk3	UTSW	7	44,424,866 (GRCm39)	missense	probably benign	0.00
R4359:Vrk3	UTSW	7	44,424,866 (GRCm39)	missense	probably benign	0.00
R4379:Vrk3	UTSW	7	44,424,866 (GRCm39)	missense	probably benign	0.00
R4381:Vrk3	UTSW	7	44,424,866 (GRCm39)	missense	probably benign	0.00
R4439:Vrk3	UTSW	7	44,424,866 (GRCm39)	missense	probably benign	0.00
R4441:Vrk3	UTSW	7	44,424,866 (GRCm39)	missense	probably benign	0.00
R4773:Vrk3	UTSW	7	44,424,900 (GRCm39)	missense	probably benign
R5222:Vrk3	UTSW	7	44,409,220 (GRCm39)	missense	possibly damaging	0.67
R5808:Vrk3	UTSW	7	44,409,298 (GRCm39)	missense	probably damaging	0.96
R6180:Vrk3	UTSW	7	44,419,035 (GRCm39)	missense	possibly damaging	0.50
R7058:Vrk3	UTSW	7	44,417,890 (GRCm39)	missense	probably damaging	0.98
R7425:Vrk3	UTSW	7	44,420,348 (GRCm39)	critical splice donor site	probably null
R7995:Vrk3	UTSW	7	44,413,585 (GRCm39)	missense	probably damaging	1.00
R8804:Vrk3	UTSW	7	44,407,270 (GRCm39)	nonsense	probably null
R9123:Vrk3	UTSW	7	44,407,254 (GRCm39)	missense	possibly damaging	0.94
R9330:Vrk3	UTSW	7	44,424,910 (GRCm39)	missense	probably damaging	0.98
R9681:Vrk3	UTSW	7	44,403,356 (GRCm39)	missense	possibly damaging	0.96

Predicted Primers

PCR Primer
(F):5'- TTGCTCAGAAGACATCAGAATGAC -3'
(R):5'- ACCAAATGATCCACCTTTGTCTCAC -3'

Sequencing Primer
(F):5'- CATCAGAATGACAGGTGATGGAC -3'
(R):5'- TCTCACCCAGACAAGGACCAG -3'

Posted On

2019-05-13