Mutagenetix > Incidental Mutation

Incidental Mutation 'R0499:Cdkl3'

47035

Institutional Source

Beutler Lab

Gene Symbol

Cdkl3

Ensembl Gene

ENSMUSG00000020389

Gene Name

cyclin dependent kinase like 3

Synonyms

B230379H01Rik

MMRRC Submission

038695-MU

Accession Numbers

Essential gene?

Probably essential (E-score: 0.863) question?

Stock #

R0499 (G1)

Quality Score

225

Status

Validated

Chromosome

Chromosomal Location

51895048-51980611 bp(+) (GRCm39)

Type of Mutation

missense

DNA Base Change (assembly)

T to C at 51923243 bp (GRCm39)

Zygosity

Heterozygous

Amino Acid Change

Serine to Proline at position 507 (S507P)

Ref Sequence

ENSEMBL: ENSMUSP00000123279 (fasta)

Gene Model

predicted gene model for transcript(s): [ENSMUST00000063303] [ENSMUST00000063321] [ENSMUST00000109076] [ENSMUST00000109077] [ENSMUST00000109078] [ENSMUST00000109079] [ENSMUST00000109080] [ENSMUST00000120374] [ENSMUST00000143228] [ENSMUST00000121591] [ENSMUST00000109081] [ENSMUST00000128853] [ENSMUST00000150736]

AlphaFold

Q8BLF2

Predicted Effect

probably benign
Transcript: ENSMUST00000063303
AA Change: S507P

PolyPhen 2 Score 0.267 (Sensitivity: 0.91; Specificity: 0.88)

SMART Domains

Protein: ENSMUSP00000064315
Gene: ENSMUSG00000020389
AA Change: S507P

Domain	Start	End	E-Value	Type
S_TKc	4	286	2.27e-95	SMART
Blast:S_TKc	361	477	1e-18	BLAST

Predicted Effect

probably benign
Transcript: ENSMUST00000063321
AA Change: S507P

PolyPhen 2 Score 0.267 (Sensitivity: 0.91; Specificity: 0.88)

SMART Domains

Protein: ENSMUSP00000065128
Gene: ENSMUSG00000020389
AA Change: S507P

Domain	Start	End	E-Value	Type
S_TKc	4	286	2.27e-95	SMART
Blast:S_TKc	361	477	9e-19	BLAST

Predicted Effect

probably benign
Transcript: ENSMUST00000109076

SMART Domains

Protein: ENSMUSP00000104704
Gene: ENSMUSG00000020389

Domain	Start	End	E-Value	Type
S_TKc	4	286	2.27e-95	SMART

Predicted Effect

probably benign
Transcript: ENSMUST00000109077

SMART Domains

Protein: ENSMUSP00000104705
Gene: ENSMUSG00000020389

Domain	Start	End	E-Value	Type
S_TKc	4	286	2.27e-95	SMART

Predicted Effect

probably benign
Transcript: ENSMUST00000109078

SMART Domains

Protein: ENSMUSP00000104706
Gene: ENSMUSG00000020389

Domain	Start	End	E-Value	Type
S_TKc	4	286	2.27e-95	SMART
Blast:S_TKc	361	457	8e-14	BLAST

Predicted Effect

probably benign
Transcript: ENSMUST00000109079
AA Change: S507P

PolyPhen 2 Score 0.267 (Sensitivity: 0.91; Specificity: 0.88)

SMART Domains

Protein: ENSMUSP00000104707
Gene: ENSMUSG00000020389
AA Change: S507P

Domain	Start	End	E-Value	Type
S_TKc	4	286	2.27e-95	SMART
Blast:S_TKc	361	477	9e-19	BLAST

Predicted Effect

probably benign
Transcript: ENSMUST00000109080
AA Change: S507P

PolyPhen 2 Score 0.122 (Sensitivity: 0.93; Specificity: 0.86)

SMART Domains

Protein: ENSMUSP00000104708
Gene: ENSMUSG00000020389
AA Change: S507P

Domain	Start	End	E-Value	Type
S_TKc	4	286	2.27e-95	SMART
Blast:S_TKc	361	477	1e-18	BLAST

Predicted Effect

probably benign
Transcript: ENSMUST00000120374
AA Change: S507P

PolyPhen 2 Score 0.122 (Sensitivity: 0.93; Specificity: 0.86)

SMART Domains

Protein: ENSMUSP00000113303
Gene: ENSMUSG00000020389
AA Change: S507P

Domain	Start	End	E-Value	Type
S_TKc	4	286	2.27e-95	SMART
Blast:S_TKc	361	477	1e-18	BLAST

Predicted Effect

possibly damaging
Transcript: ENSMUST00000143228
AA Change: S507P

PolyPhen 2 Score 0.523 (Sensitivity: 0.88; Specificity: 0.90)

SMART Domains

Protein: ENSMUSP00000123279
Gene: ENSMUSG00000020389
AA Change: S507P

Domain	Start	End	E-Value	Type
S_TKc	4	286	2.27e-95	SMART
Blast:S_TKc	361	477	1e-18	BLAST

Predicted Effect

probably benign
Transcript: ENSMUST00000121591
AA Change: S507P

PolyPhen 2 Score 0.267 (Sensitivity: 0.91; Specificity: 0.88)

SMART Domains

Protein: ENSMUSP00000112477
Gene: ENSMUSG00000020389
AA Change: S507P

Domain	Start	End	E-Value	Type
S_TKc	4	286	2.27e-95	SMART
Blast:S_TKc	361	477	1e-18	BLAST

Predicted Effect

probably benign
Transcript: ENSMUST00000109081
AA Change: S507P

PolyPhen 2 Score 0.267 (Sensitivity: 0.91; Specificity: 0.88)

SMART Domains

Protein: ENSMUSP00000104709
Gene: ENSMUSG00000020389
AA Change: S507P

Domain	Start	End	E-Value	Type
S_TKc	4	286	2.27e-95	SMART
Blast:S_TKc	361	477	1e-18	BLAST

Predicted Effect

probably benign
Transcript: ENSMUST00000128853
AA Change: S140P

PolyPhen 2 Score 0.003 (Sensitivity: 0.98; Specificity: 0.44)

SMART Domains

Protein: ENSMUSP00000121945
Gene: ENSMUSG00000020389
AA Change: S140P

Domain	Start	End	E-Value	Type
Blast:S_TKc	1	110	2e-15	BLAST

Predicted Effect

probably benign
Transcript: ENSMUST00000150736
AA Change: S19P

PolyPhen 2 Score 0.003 (Sensitivity: 0.98; Specificity: 0.44)

Predicted Effect

unknown
Transcript: ENSMUST00000147874
AA Change: S65P

SMART Domains

Protein: ENSMUSP00000119505
Gene: ENSMUSG00000020389
AA Change: S65P

Domain	Start	End	E-Value	Type
Blast:S_TKc	2	36	5e-7	BLAST

Predicted Effect

probably benign
Transcript: ENSMUST00000207272

Predicted Effect

noncoding transcript
Transcript: ENSMUST00000181262

Predicted Effect

probably benign
Transcript: ENSMUST00000136021

Predicted Effect

probably benign
Transcript: ENSMUST00000154701

Meta Mutation Damage Score

0.1795

Coding Region Coverage

1x: 99.2%
3x: 98.5%
10x: 96.8%
20x: 94.2%

Validation Efficiency

99% (97/98)

MGI Phenotype

FUNCTION: [Summary is not available for the mouse gene. This summary is for the human ortholog.] The protein encoded by this gene is a member of cyclin-dependent protein kinase (CDK) family. CDK family members are highly similar to the gene products of Saccharomyces cerevisiae cdc28, and Schizosaccharomyces pombe cdc2, and are known to be important regulators of cell cycle progression. This gene was identified as a gene absent in leukemic patients with chromosome 5q deletion. This loss may be an important determinant of dysmyelopoiesis. Alternative splicing results in multiple transcript variants encoding different isoforms. [provided by RefSeq, Jul 2008]

Allele List at MGI

Other mutations in this stock

Total: 94 list
Gene	Ref	Var	Chr/Loc	Mutation	Predicted Effect	Zygosity
Acad9	T	C	3: 36,139,564 (GRCm39)	V388A	probably damaging	Het
Acp3	T	C	9: 104,197,201 (GRCm39)	E146G	probably damaging	Het
Adap2	A	T	11: 80,066,905 (GRCm39)	R276S	probably damaging	Het
Agbl3	A	T	6: 34,816,270 (GRCm39)	M727L	probably benign	Het
Ahnak	T	A	19: 8,977,628 (GRCm39)		probably benign	Het
Ankmy1	G	T	1: 92,813,948 (GRCm39)	D410E	probably damaging	Het
Ankra2	T	C	13: 98,402,962 (GRCm39)	S70P	probably damaging	Het
Aox4	T	C	1: 58,302,556 (GRCm39)		probably null	Het
Arl13b	G	A	16: 62,622,096 (GRCm39)	T399I	probably benign	Het
Atad2	A	T	15: 57,966,636 (GRCm39)	D652E	possibly damaging	Het
Atad2	T	G	15: 57,984,345 (GRCm39)	M328L	probably benign	Het
Ccnb1	T	C	13: 100,916,642 (GRCm39)		probably null	Het
Ccr2	G	C	9: 123,905,976 (GRCm39)	K85N	possibly damaging	Het
Ccr2	A	T	9: 123,906,163 (GRCm39)	T148S	possibly damaging	Het
Cdc20b	T	C	13: 113,192,484 (GRCm39)	V59A	probably benign	Het
Cdin1	C	T	2: 115,473,172 (GRCm39)	R101W	probably damaging	Het
Celf6	C	A	9: 59,510,161 (GRCm39)	T86K	probably benign	Het
Ces1g	A	G	8: 94,060,317 (GRCm39)	F101L	probably benign	Het
Cimap1d	T	C	10: 79,476,099 (GRCm39)	D155G	probably damaging	Het
Cntnap3	C	T	13: 65,006,492 (GRCm39)	D107N	probably benign	Het
Col15a1	A	T	4: 47,262,950 (GRCm39)	D534V	probably damaging	Het
Col27a1	A	G	4: 63,218,978 (GRCm39)		probably benign	Het
Csmd3	T	C	15: 47,710,527 (GRCm39)	T1687A	probably benign	Het
Cstf3	A	G	2: 104,479,950 (GRCm39)	I272M	possibly damaging	Het
Cyp2d40	T	C	15: 82,645,418 (GRCm39)	T150A	probably benign	Het
Dnah8	T	A	17: 30,934,483 (GRCm39)	F1489L	possibly damaging	Het
Dop1b	A	T	16: 93,567,325 (GRCm39)	T1251S	probably benign	Het
Dtx2	G	A	5: 136,057,957 (GRCm39)	G421R	probably damaging	Het
Epb41l3	T	A	17: 69,554,654 (GRCm39)	D251E	probably benign	Het
Erg	A	C	16: 95,161,842 (GRCm39)	Y305*	probably null	Het
Exosc4	G	A	15: 76,213,766 (GRCm39)	A197T	probably benign	Het
Fam227b	T	A	2: 125,942,829 (GRCm39)	I323L	probably benign	Het
Far1	G	T	7: 113,153,503 (GRCm39)		probably benign	Het
Fmod	A	G	1: 133,968,934 (GRCm39)	I325V	possibly damaging	Het
Fshr	C	G	17: 89,316,713 (GRCm39)	S169T	probably benign	Het
Gm4076	G	T	13: 85,275,345 (GRCm39)		noncoding transcript	Het
Gm5134	A	T	10: 75,828,359 (GRCm39)	Y313F	probably benign	Het
H2-Q6	T	A	17: 35,644,179 (GRCm39)	F54I	probably damaging	Het
Hcrtr2	C	A	9: 76,161,954 (GRCm39)	L145F	probably damaging	Het
Hepacam2	A	G	6: 3,476,121 (GRCm39)	L268P	probably damaging	Het
Herc2	C	A	7: 55,834,117 (GRCm39)	C3107*	probably null	Het
Herc4	T	C	10: 63,099,811 (GRCm39)	V78A	probably damaging	Het
Hyal5	T	C	6: 24,877,920 (GRCm39)	W339R	probably damaging	Het
Igfbp6	T	A	15: 102,056,419 (GRCm39)		probably null	Het
Il18rap	A	T	1: 40,564,218 (GRCm39)	H112L	probably benign	Het
Il1r2	T	A	1: 40,162,309 (GRCm39)	Y317*	probably null	Het
Ints8	C	A	4: 11,246,097 (GRCm39)	V190L	probably benign	Het
Ipo11	T	C	13: 107,061,595 (GRCm39)	T22A	probably benign	Het
Itgb4	C	A	11: 115,870,521 (GRCm39)	R117S	probably benign	Het
Lcorl	C	G	5: 45,891,711 (GRCm39)	G214A	probably benign	Het
Lgals3bp	T	A	11: 118,289,019 (GRCm39)		probably null	Het
Lyst	T	A	13: 13,791,298 (GRCm39)	L54I	probably damaging	Het
Mcm9	T	C	10: 53,414,250 (GRCm39)	T1015A	probably benign	Het
Mef2d	T	A	3: 88,063,825 (GRCm39)	I84N	probably damaging	Het
Mmrn2	A	G	14: 34,119,913 (GRCm39)	N261S	probably damaging	Het
Mpdz	T	C	4: 81,210,768 (GRCm39)	T1693A	probably benign	Het
Mss51	T	A	14: 20,534,756 (GRCm39)	Q338L	possibly damaging	Het
Mstn	T	A	1: 53,103,143 (GRCm39)	Y160N	probably damaging	Het
Muc6	T	C	7: 141,226,735 (GRCm39)	T1431A	probably benign	Het
Nek9	A	T	12: 85,348,657 (GRCm39)	M959K	probably benign	Het
Or2ak6	G	A	11: 58,593,069 (GRCm39)	V181I	probably benign	Het
Or4f58	A	T	2: 111,851,777 (GRCm39)	C141S	probably damaging	Het
Or8b47	A	T	9: 38,435,801 (GRCm39)	M258L	probably benign	Het
Otog	G	T	7: 45,923,256 (GRCm39)	G1044W	probably damaging	Het
Pcdh9	G	A	14: 94,123,671 (GRCm39)	T833M	probably damaging	Het
Pdcd10	T	C	3: 75,434,958 (GRCm39)	K111R	probably damaging	Het
Pde5a	A	G	3: 122,542,107 (GRCm39)	N199S	probably damaging	Het
Plekhg1	T	C	10: 3,887,971 (GRCm39)	V355A	probably damaging	Het
Podn	G	T	4: 107,878,791 (GRCm39)	L359I	probably damaging	Het
Psd	T	C	19: 46,310,600 (GRCm39)	E483G	probably damaging	Het
Ptch2	T	A	4: 116,968,340 (GRCm39)	L905*	probably null	Het
Rxfp2	T	A	5: 149,989,880 (GRCm39)	N420K	probably damaging	Het
Scpppq1	C	A	5: 104,222,747 (GRCm39)	G24*	probably null	Het
Sde2	T	A	1: 180,689,992 (GRCm39)	D237E	probably benign	Het
Serpina1d	A	T	12: 103,732,016 (GRCm39)	L281Q	probably damaging	Het
Serpina9	T	C	12: 103,967,729 (GRCm39)	N222S	probably benign	Het
Sh3bgrl2	A	G	9: 83,459,612 (GRCm39)	K57E	probably damaging	Het
Shc3	C	T	13: 51,634,264 (GRCm39)		probably benign	Het
Sik3	T	C	9: 46,120,038 (GRCm39)	M659T	possibly damaging	Het
Slc23a2	A	G	2: 131,913,937 (GRCm39)	L280P	probably damaging	Het
Smchd1	G	T	17: 71,694,083 (GRCm39)	Q1221K	probably benign	Het
Spmip2	T	A	3: 79,313,093 (GRCm39)	W56R	probably damaging	Het
Spocd1	A	G	4: 129,849,263 (GRCm39)	N694S	possibly damaging	Het
Styxl2	C	A	1: 165,926,670 (GRCm39)	V981L	probably benign	Het
Tecta	T	C	9: 42,263,359 (GRCm39)	D1409G	probably damaging	Het
Tmem131	A	T	1: 36,880,754 (GRCm39)	V172D	probably damaging	Het
Trpm3	T	C	19: 22,964,237 (GRCm39)	M1244T	possibly damaging	Het
Ugcg	G	C	4: 59,217,036 (GRCm39)	V187L	possibly damaging	Het
Usp17le	T	C	7: 104,417,708 (GRCm39)	N478S	probably benign	Het
Usp36	A	G	11: 118,164,397 (GRCm39)	V205A	probably damaging	Het
Vmn1r25	T	A	6: 57,955,494 (GRCm39)	Q265L	probably damaging	Het
Vwf	A	T	6: 125,615,077 (GRCm39)	H1176L	probably benign	Het
Zfyve28	C	T	5: 34,389,550 (GRCm39)	D217N	possibly damaging	Het
Zranb3	A	C	1: 127,882,817 (GRCm39)		probably null	Het

Other mutations in Cdkl3

Allele	Source	Chr	Coord	Type	Predicted Effect	PPH Score
IGL00425:Cdkl3	APN	11	51,920,683 (GRCm39)	missense	probably benign	0.28
IGL01632:Cdkl3	APN	11	51,895,899 (GRCm39)	missense	probably damaging	1.00
IGL01768:Cdkl3	APN	11	51,916,744 (GRCm39)	missense	probably damaging	1.00
IGL01974:Cdkl3	APN	11	51,902,064 (GRCm39)	missense	probably damaging	1.00
IGL01981:Cdkl3	APN	11	51,895,896 (GRCm39)	missense	probably benign	0.43
IGL02510:Cdkl3	APN	11	51,902,097 (GRCm39)	missense	probably damaging	1.00
R0027:Cdkl3	UTSW	11	51,923,176 (GRCm39)	unclassified	probably benign
R0027:Cdkl3	UTSW	11	51,923,176 (GRCm39)	unclassified	probably benign
R0480:Cdkl3	UTSW	11	51,895,882 (GRCm39)	missense	probably damaging	1.00
R0627:Cdkl3	UTSW	11	51,902,135 (GRCm39)	missense	probably damaging	1.00
R0848:Cdkl3	UTSW	11	51,902,094 (GRCm39)	missense	probably damaging	1.00
R1510:Cdkl3	UTSW	11	51,924,341 (GRCm39)	missense	possibly damaging	0.90
R1558:Cdkl3	UTSW	11	51,923,337 (GRCm39)	missense	possibly damaging	0.62
R2046:Cdkl3	UTSW	11	51,917,677 (GRCm39)	missense	probably benign
R2077:Cdkl3	UTSW	11	51,917,666 (GRCm39)	missense	probably damaging	0.98
R2207:Cdkl3	UTSW	11	51,918,020 (GRCm39)	makesense	probably null
R2271:Cdkl3	UTSW	11	51,923,322 (GRCm39)	missense	probably benign	0.07
R2272:Cdkl3	UTSW	11	51,923,322 (GRCm39)	missense	probably benign	0.07
R4032:Cdkl3	UTSW	11	51,902,118 (GRCm39)	missense	probably damaging	1.00
R4839:Cdkl3	UTSW	11	51,895,861 (GRCm39)	missense	probably damaging	1.00
R4971:Cdkl3	UTSW	11	51,901,995 (GRCm39)	missense	possibly damaging	0.48
R6541:Cdkl3	UTSW	11	51,913,571 (GRCm39)	missense	probably damaging	1.00
R6559:Cdkl3	UTSW	11	51,916,696 (GRCm39)	missense	probably benign	0.04
R7034:Cdkl3	UTSW	11	51,918,042 (GRCm39)	missense	probably benign	0.00
R7068:Cdkl3	UTSW	11	51,902,154 (GRCm39)	critical splice donor site	probably null
R7406:Cdkl3	UTSW	11	51,924,369 (GRCm39)	missense	probably benign	0.11
R7658:Cdkl3	UTSW	11	51,918,009 (GRCm39)	missense	not run
R7870:Cdkl3	UTSW	11	51,909,284 (GRCm39)	critical splice donor site	probably null
R8324:Cdkl3	UTSW	11	51,913,706 (GRCm39)	critical splice donor site	probably null
R8331:Cdkl3	UTSW	11	51,917,704 (GRCm39)	missense	probably benign	0.04
R8349:Cdkl3	UTSW	11	51,975,260 (GRCm39)	missense
R8449:Cdkl3	UTSW	11	51,975,260 (GRCm39)	missense
R8806:Cdkl3	UTSW	11	51,923,295 (GRCm39)	missense	possibly damaging	0.66
R9262:Cdkl3	UTSW	11	51,916,702 (GRCm39)	missense	probably benign	0.21
R9360:Cdkl3	UTSW	11	51,924,349 (GRCm39)	missense	probably null	0.00
R9385:Cdkl3	UTSW	11	51,926,779 (GRCm39)	missense	probably benign	0.01
R9623:Cdkl3	UTSW	11	51,895,816 (GRCm39)	missense	probably damaging	1.00
R9729:Cdkl3	UTSW	11	51,895,770 (GRCm39)	missense	probably benign	0.44

Predicted Primers

PCR Primer
(F):5'- CACTTGGAAAATGTCCCTGGGAGTC -3'
(R):5'- CGCTTTCCCCACATTATGTATGGAACG -3'

Sequencing Primer
(F):5'- AGTCTGGCTGCTTCAGTG -3'
(R):5'- gaaggaggaagcaggcag -3'

Posted On

2013-06-12