Incidental Mutation 'R5215:Cdk5'
ID 470627
Institutional Source Beutler Lab
Gene Symbol Cdk5
Ensembl Gene ENSMUSG00000028969
Gene Name cyclin dependent kinase 5
Synonyms Crk6
MMRRC Submission 042788-MU
Accession Numbers
Essential gene? Probably essential (E-score: 0.776) question?
Stock # R5215 (G1)
Quality Score 225
Status Validated
Chromosome 5
Chromosomal Location 24623239-24628528 bp(-) (GRCm39)
Type of Mutation missense
DNA Base Change (assembly) T to A at 24624459 bp (GRCm39)
Zygosity Heterozygous
Amino Acid Change Asparagine to Isoleucine at position 265 (N265I)
Ref Sequence ENSEMBL: ENSMUSP00000030814 (fasta)
Gene Model predicted gene model for transcript(s): [ENSMUST00000030814] [ENSMUST00000049346] [ENSMUST00000141966] [ENSMUST00000153274] [ENSMUST00000196296] [ENSMUST00000198990]
AlphaFold P49615
Predicted Effect probably benign
Transcript: ENSMUST00000030814
AA Change: N265I

PolyPhen 2 Score 0.241 (Sensitivity: 0.91; Specificity: 0.88)
SMART Domains Protein: ENSMUSP00000030814
Gene: ENSMUSG00000028969
AA Change: N265I

DomainStartEndE-ValueType
S_TKc 4 286 6.11e-101 SMART
Predicted Effect probably benign
Transcript: ENSMUST00000049346
SMART Domains Protein: ENSMUSP00000039914
Gene: ENSMUSG00000038276

DomainStartEndE-ValueType
Pfam:ASC 21 458 2.5e-89 PFAM
Predicted Effect noncoding transcript
Transcript: ENSMUST00000127315
Predicted Effect probably benign
Transcript: ENSMUST00000141966
SMART Domains Protein: ENSMUSP00000117215
Gene: ENSMUSG00000028962

DomainStartEndE-ValueType
low complexity region 93 110 N/A INTRINSIC
low complexity region 113 129 N/A INTRINSIC
Predicted Effect probably benign
Transcript: ENSMUST00000153274
Predicted Effect probably benign
Transcript: ENSMUST00000196296
SMART Domains Protein: ENSMUSP00000143083
Gene: ENSMUSG00000038276

DomainStartEndE-ValueType
Pfam:ASC 21 459 4e-155 PFAM
Predicted Effect noncoding transcript
Transcript: ENSMUST00000197210
Predicted Effect probably benign
Transcript: ENSMUST00000198990
AA Change: N233I

PolyPhen 2 Score 0.152 (Sensitivity: 0.92; Specificity: 0.87)
SMART Domains Protein: ENSMUSP00000142413
Gene: ENSMUSG00000028969
AA Change: N233I

DomainStartEndE-ValueType
Pfam:Pkinase 4 101 9.7e-23 PFAM
Pfam:Pkinase_Tyr 4 102 2.7e-13 PFAM
Pfam:Pkinase 97 254 6.6e-30 PFAM
Pfam:Pkinase_Tyr 102 200 9.4e-6 PFAM
Predicted Effect noncoding transcript
Transcript: ENSMUST00000198241
Predicted Effect noncoding transcript
Transcript: ENSMUST00000197619
Predicted Effect probably benign
Transcript: ENSMUST00000198442
Meta Mutation Damage Score 0.4588 question?
Coding Region Coverage
  • 1x: 99.3%
  • 3x: 98.7%
  • 10x: 97.5%
  • 20x: 95.8%
Validation Efficiency 100% (79/79)
MGI Phenotype FUNCTION: [Summary is not available for the mouse gene. This summary is for the human ortholog.] This gene encodes a proline-directed serine/threonine kinase that is a member of the cyclin-dependent kinase family of proteins. Unlike other members of the family, the protein encoded by this gene does not directly control cell cycle regulation. Instead the protein, which is predominantly expressed at high levels in mammalian postmitotic central nervous system neurons, functions in diverse processes such as synaptic plasticity and neuronal migration through phosphorylation of proteins required for cytoskeletal organization, endocytosis and exocytosis, and apoptosis. In humans, an allelic variant of the gene that results in undetectable levels of the protein has been associated with lethal autosomal recessive lissencephaly-7. Alternative splicing results in multiple transcript variants. [provided by RefSeq, May 2015]
PHENOTYPE: Homozygous mutation of this gene results in perinatal lethality and abnormalities of the cerebellum and nervous system. Mutant mice are cyanotic, hypoactive, exhibit shallow breathing, and fail to suckle. [provided by MGI curators]
Allele List at MGI
Other mutations in this stock
Total: 68 list
GeneRefVarChr/LocMutationPredicted EffectZygosity
Alas1 C A 9: 106,120,574 (GRCm39) A73S probably benign Het
Aldoart2 G A 12: 55,612,204 (GRCm39) R43Q probably benign Het
Ano4 T C 10: 89,153,165 (GRCm39) H49R possibly damaging Het
Atic T C 1: 71,603,666 (GRCm39) S161P probably damaging Het
Atp6v1c2 T C 12: 17,341,659 (GRCm39) E244G probably benign Het
Cd164l2 C A 4: 132,948,789 (GRCm39) L42I unknown Het
Cdc42ep2 T C 19: 5,968,238 (GRCm39) R156G probably benign Het
Cdc45 C T 16: 18,614,647 (GRCm39) R205H probably damaging Het
Cfap69 G T 5: 5,639,133 (GRCm39) N262K possibly damaging Het
Chd6 C T 2: 160,791,873 (GRCm39) V2495M probably damaging Het
Cps1 T A 1: 67,205,539 (GRCm39) F521I possibly damaging Het
Crb2 A G 2: 37,683,765 (GRCm39) E1089G probably benign Het
Decr1 T C 4: 15,929,795 (GRCm39) D166G probably damaging Het
Dhodh G A 8: 110,332,975 (GRCm39) probably benign Het
Dnaaf5 G A 5: 139,147,632 (GRCm39) V399I probably benign Het
Dnah11 T C 12: 118,121,096 (GRCm39) T526A probably benign Het
Drosha T C 15: 12,885,219 (GRCm39) probably benign Het
Elfn2 T A 15: 78,558,401 (GRCm39) I49F probably damaging Het
Gabra1 T C 11: 42,045,655 (GRCm39) T152A probably damaging Het
Gigyf2 C A 1: 87,292,988 (GRCm39) T85K probably damaging Het
Gimap8 A T 6: 48,628,017 (GRCm39) Y258F possibly damaging Het
Glmn A G 5: 107,709,752 (GRCm39) C351R probably benign Het
Gm10032 T C 14: 67,029,998 (GRCm39) noncoding transcript Het
Gorasp2 G A 2: 70,519,598 (GRCm39) A328T probably benign Het
Grin1 A T 2: 25,193,919 (GRCm39) H392Q probably benign Het
Gzmn A G 14: 56,405,319 (GRCm39) V55A probably damaging Het
Herc4 T A 10: 63,124,876 (GRCm39) S497T probably benign Het
Hrc A T 7: 44,985,515 (GRCm39) D222V probably damaging Het
Iars2 T C 1: 185,026,966 (GRCm39) H761R probably damaging Het
Jmjd1c T A 10: 67,076,480 (GRCm39) D2101E possibly damaging Het
Kcng1 C T 2: 168,105,053 (GRCm39) M264I probably benign Het
Klra14-ps C A 6: 130,134,646 (GRCm39) noncoding transcript Het
Krtap5-3 T A 7: 141,755,974 (GRCm39) C270* probably null Het
Lama3 A G 18: 12,710,957 (GRCm39) H3164R probably damaging Het
Lcor T C 19: 41,574,371 (GRCm39) I1042T probably damaging Het
Mdn1 T C 4: 32,741,418 (GRCm39) M3840T possibly damaging Het
Mtor A T 4: 148,538,440 (GRCm39) H166L probably benign Het
Mx1 T C 16: 97,249,560 (GRCm39) N556D possibly damaging Het
Oca2 A T 7: 55,945,246 (GRCm39) R285* probably null Het
Or12d13 T A 17: 37,647,704 (GRCm39) I140F probably benign Het
Or2at1 A G 7: 99,416,717 (GRCm39) E116G probably damaging Het
Or4k39 T C 2: 111,239,631 (GRCm39) noncoding transcript Het
Or56a3b G A 7: 104,775,771 (GRCm39) H246Y probably damaging Het
Or8g33 A T 9: 39,337,919 (GRCm39) Y149* probably null Het
Pan3 A G 5: 147,391,915 (GRCm39) probably null Het
Pard3 G A 8: 128,104,745 (GRCm39) V496M probably damaging Het
Pdcd2l A T 7: 33,892,314 (GRCm39) V185D possibly damaging Het
Pgghg T C 7: 140,526,477 (GRCm39) V623A possibly damaging Het
Pigu C A 2: 155,177,249 (GRCm39) probably benign Het
Pkmyt1 G A 17: 23,951,566 (GRCm39) R40Q probably benign Het
Prag1 G A 8: 36,567,043 (GRCm39) A65T probably benign Het
Prkdc C A 16: 15,589,985 (GRCm39) T2616N possibly damaging Het
Prpf8 G A 11: 75,391,030 (GRCm39) E1360K probably benign Het
Ptprt C T 2: 162,120,084 (GRCm39) V128M probably damaging Het
Rp1l1 C T 14: 64,267,462 (GRCm39) S1016L probably benign Het
Rprd1a G T 18: 24,621,257 (GRCm39) D307E probably damaging Het
Slc11a1 A T 1: 74,422,936 (GRCm39) probably benign Het
Slc22a16 T A 10: 40,457,386 (GRCm39) M209K probably damaging Het
Slf2 T G 19: 44,936,476 (GRCm39) L707R probably damaging Het
Son T A 16: 91,453,563 (GRCm39) M770K probably damaging Het
Taf6l T C 19: 8,755,417 (GRCm39) probably benign Het
Tbc1d2 C A 4: 46,614,006 (GRCm39) V692L probably benign Het
Tnpo3 C T 6: 29,582,152 (GRCm39) probably benign Het
Txndc16 A T 14: 45,448,597 (GRCm39) probably benign Het
Ubr1 T C 2: 120,734,525 (GRCm39) K1125R probably benign Het
Vmn2r9 A G 5: 108,994,351 (GRCm39) S433P probably benign Het
Zc3h12a A G 4: 125,020,706 (GRCm39) S46P probably benign Het
Zwilch T G 9: 64,054,156 (GRCm39) I490L probably benign Het
Other mutations in Cdk5
AlleleSourceChrCoordTypePredicted EffectPPH Score
IGL01311:Cdk5 APN 5 24,624,593 (GRCm39) splice site probably null
IGL02147:Cdk5 APN 5 24,625,318 (GRCm39) missense probably benign 0.01
IGL02395:Cdk5 APN 5 24,624,635 (GRCm39) missense possibly damaging 0.79
IGL02557:Cdk5 APN 5 24,624,651 (GRCm39) missense probably benign 0.00
R4503:Cdk5 UTSW 5 24,624,617 (GRCm39) missense possibly damaging 0.75
R5103:Cdk5 UTSW 5 24,627,833 (GRCm39) missense probably damaging 1.00
R7972:Cdk5 UTSW 5 24,624,656 (GRCm39) missense probably benign
R8057:Cdk5 UTSW 5 24,625,782 (GRCm39) missense probably damaging 1.00
R8923:Cdk5 UTSW 5 24,625,284 (GRCm39) missense possibly damaging 0.86
R8968:Cdk5 UTSW 5 24,627,379 (GRCm39) missense probably damaging 1.00
Predicted Primers PCR Primer
(F):5'- ACCACCATATCATCAGACTGTGG -3'
(R):5'- ATCCTTGGTGAACGTCGTGC -3'

Sequencing Primer
(F):5'- CACCATATCATCAGACTGTGGGAAAG -3'
(R):5'- TCGTGCCCAAGCTCAATG -3'
Posted On 2017-03-31