Incidental Mutation 'R4737:Cilk1'
ID 359350
Institutional Source Beutler Lab
Gene Symbol Cilk1
Ensembl Gene ENSMUSG00000009828
Gene Name ciliogenesis associated kinase 1
Synonyms 2210420N10Rik, Ick
MMRRC Submission 042024-MU
Accession Numbers
Essential gene? Probably essential (E-score: 0.803) question?
Stock # R4737 (G1)
Quality Score 225
Status Validated
Chromosome 9
Chromosomal Location 78016474-78079389 bp(+) (GRCm39)
Type of Mutation missense
DNA Base Change (assembly) A to G at 78057936 bp (GRCm39)
Zygosity Heterozygous
Amino Acid Change Threonine to Alanine at position 162 (T162A)
Ref Sequence ENSEMBL: ENSMUSP00000113655 (fasta)
Gene Model predicted gene model for transcript(s): [ENSMUST00000044551] [ENSMUST00000117330] [ENSMUST00000118869]
AlphaFold Q9JKV2
Predicted Effect probably damaging
Transcript: ENSMUST00000044551
AA Change: T162A

PolyPhen 2 Score 0.999 (Sensitivity: 0.14; Specificity: 0.99)
SMART Domains Protein: ENSMUSP00000048234
Gene: ENSMUSG00000009828
AA Change: T162A

DomainStartEndE-ValueType
S_TKc 4 284 2.7e-102 SMART
low complexity region 310 327 N/A INTRINSIC
low complexity region 331 344 N/A INTRINSIC
low complexity region 413 422 N/A INTRINSIC
low complexity region 457 471 N/A INTRINSIC
low complexity region 513 551 N/A INTRINSIC
Predicted Effect probably damaging
Transcript: ENSMUST00000117330
AA Change: T162A

PolyPhen 2 Score 1.000 (Sensitivity: 0.00; Specificity: 1.00)
SMART Domains Protein: ENSMUSP00000113655
Gene: ENSMUSG00000009828
AA Change: T162A

DomainStartEndE-ValueType
S_TKc 4 284 2.7e-102 SMART
low complexity region 310 327 N/A INTRINSIC
low complexity region 331 344 N/A INTRINSIC
low complexity region 413 422 N/A INTRINSIC
low complexity region 457 471 N/A INTRINSIC
low complexity region 513 539 N/A INTRINSIC
Predicted Effect probably damaging
Transcript: ENSMUST00000118869
AA Change: T162A

PolyPhen 2 Score 0.999 (Sensitivity: 0.14; Specificity: 0.99)
SMART Domains Protein: ENSMUSP00000112961
Gene: ENSMUSG00000009828
AA Change: T162A

DomainStartEndE-ValueType
S_TKc 4 284 2.7e-102 SMART
low complexity region 310 327 N/A INTRINSIC
low complexity region 331 344 N/A INTRINSIC
low complexity region 413 422 N/A INTRINSIC
low complexity region 457 471 N/A INTRINSIC
low complexity region 513 551 N/A INTRINSIC
Predicted Effect noncoding transcript
Transcript: ENSMUST00000142402
Meta Mutation Damage Score 0.7871 question?
Coding Region Coverage
  • 1x: 99.2%
  • 3x: 98.6%
  • 10x: 97.2%
  • 20x: 95.3%
Validation Efficiency 100% (94/94)
MGI Phenotype FUNCTION: [Summary is not available for the mouse gene. This summary is for the human ortholog.] Eukaryotic protein kinases are enzymes that belong to a very extensive family of proteins which share a conserved catalytic core common with both serine/threonine and tyrosine protein kinases. This gene encodes an intestinal serine/threonine kinase harboring a dual phosphorylation site found in mitogen-activating protein (MAP) kinases. The protein localizes to the intestinal crypt region and is thought to be important in intestinal epithelial cell proliferation and differentiation. Alternative splicing has been observed at this locus and two variants, encoding the same isoform, have been identified. [provided by RefSeq, Jul 2008]
PHENOTYPE: Mice homozygous for a null allele exhibit abnormal primary cilium morphology and Shh signaling during limb digit patterning, peripheral edema, cleft palate, hydrocephalus, polydactyly, delayed skeletal development, and embryonic lethality at late stages of gestation. [provided by MGI curators]
Allele List at MGI

All alleles(29) : Targeted, other(1) Gene trapped(28)

Other mutations in this stock
Total: 88 list
GeneRefVarChr/LocMutationPredicted EffectZygosity
A430110L20Rik A G 1: 181,055,384 (GRCm39) noncoding transcript Het
Acp2 A T 2: 91,041,068 (GRCm39) R419W probably benign Het
Actr5 A G 2: 158,469,991 (GRCm39) N207S probably damaging Het
Afap1 G A 5: 36,119,126 (GRCm39) V254M probably benign Het
Arfgef1 A T 1: 10,259,836 (GRCm39) M544K possibly damaging Het
Arhgap5 A T 12: 52,565,860 (GRCm39) M944L probably benign Het
Bnip3l-ps G A 12: 18,266,773 (GRCm39) noncoding transcript Het
Carf A G 1: 60,148,477 (GRCm39) T58A probably benign Het
Carns1 A G 19: 4,220,927 (GRCm39) probably benign Het
Ccp110 T A 7: 118,323,771 (GRCm39) I670K possibly damaging Het
Cftr T A 6: 18,299,882 (GRCm39) D1218E probably benign Het
Chrna9 A T 5: 66,125,214 (GRCm39) T52S probably damaging Het
Chst9 T C 18: 15,585,834 (GRCm39) Y243C probably damaging Het
Ciao3 A T 17: 26,000,283 (GRCm39) H322L probably damaging Het
Clk2 A T 3: 89,076,016 (GRCm39) H62L probably benign Het
Cntnap2 A T 6: 45,037,251 (GRCm39) R10W possibly damaging Het
Cpt1b C T 15: 89,305,609 (GRCm39) D369N probably benign Het
Crhr2 G T 6: 55,068,290 (GRCm39) H423Q probably damaging Het
D8Ertd738e T A 8: 84,976,150 (GRCm39) I33F probably damaging Het
Dbt T C 3: 116,332,781 (GRCm39) I200T probably damaging Het
Ddhd1 A T 14: 45,866,278 (GRCm39) probably benign Het
Ddx27 A G 2: 166,871,219 (GRCm39) I480V probably benign Het
Dpp9 A C 17: 56,505,970 (GRCm39) probably null Het
Dpy19l3 A T 7: 35,402,926 (GRCm39) M562K probably damaging Het
Dus3l T C 17: 57,074,868 (GRCm39) L330P probably damaging Het
Efcab7 C T 4: 99,719,805 (GRCm39) Q96* probably null Het
Egfr T C 11: 16,819,231 (GRCm39) F254L probably damaging Het
Eml5 C T 12: 98,765,111 (GRCm39) V1566M probably damaging Het
Entpd7 T A 19: 43,679,634 (GRCm39) Y62* probably null Het
Erbb4 T C 1: 68,383,059 (GRCm39) M313V probably damaging Het
Gm5528 A G 1: 72,043,711 (GRCm39) noncoding transcript Het
H2-M9 G T 17: 36,951,631 (GRCm39) Y281* probably null Het
Hmcn1 T G 1: 150,565,346 (GRCm39) K2260N possibly damaging Het
Hnf4a A G 2: 163,406,139 (GRCm39) I259V probably benign Het
Insm1 A T 2: 146,064,822 (GRCm39) T213S probably benign Het
Iqca1 T C 1: 90,005,544 (GRCm39) D488G probably damaging Het
Kdm5a T A 6: 120,382,976 (GRCm39) probably benign Het
Kdm7a G C 6: 39,129,773 (GRCm39) L468V possibly damaging Het
Lck G A 4: 129,449,777 (GRCm39) T229I possibly damaging Het
Lig3 T C 11: 82,678,553 (GRCm39) L265P probably damaging Het
Lipa T A 19: 34,479,034 (GRCm39) K229* probably null Het
Lrrk1 C T 7: 65,956,621 (GRCm39) S418N probably benign Het
Mark2 A G 19: 7,258,597 (GRCm39) V126A probably damaging Het
Met T C 6: 17,491,540 (GRCm39) C101R probably damaging Het
Mkln1 A T 6: 31,403,734 (GRCm39) K85M probably damaging Het
Mst1 A G 9: 107,957,720 (GRCm39) R15G probably benign Het
Muc6 T G 7: 141,226,426 (GRCm39) probably benign Het
Muc6 G T 7: 141,218,685 (GRCm39) T1996N possibly damaging Het
Myo7b T C 18: 32,131,655 (GRCm39) S514G probably damaging Het
Nars1 T C 18: 64,649,498 (GRCm39) E11G probably benign Het
Ogdh T A 11: 6,247,044 (GRCm39) F23I probably benign Het
Or10g9 A T 9: 39,911,718 (GRCm39) D268E probably damaging Het
Or12e9 T C 2: 87,202,665 (GRCm39) I263T probably damaging Het
Or4a39 C T 2: 89,236,830 (GRCm39) V198I probably benign Het
Or4b1b A G 2: 90,112,725 (GRCm39) S65P probably damaging Het
Or4c100 C T 2: 88,356,569 (GRCm39) S214F probably damaging Het
Or52r1c C T 7: 102,735,121 (GRCm39) A127V probably damaging Het
Or9k2 T A 10: 129,998,707 (GRCm39) T163S probably benign Het
Otub2 T A 12: 103,359,103 (GRCm39) L64Q probably benign Het
Pappa2 T C 1: 158,784,582 (GRCm39) R143G probably benign Het
Patl2 T A 2: 121,955,787 (GRCm39) T250S probably damaging Het
Pcdhac2 C T 18: 37,278,952 (GRCm39) T644I possibly damaging Het
Pi4kb C T 3: 94,911,649 (GRCm39) T690I probably damaging Het
Pla2g4d T C 2: 120,097,271 (GRCm39) Y776C probably benign Het
Plekhh2 C T 17: 84,871,387 (GRCm39) S215L probably benign Het
Psmd2 T G 16: 20,478,565 (GRCm39) probably benign Het
Ptpn21 T C 12: 98,675,103 (GRCm39) E183G probably benign Het
Ptprg T A 14: 12,226,314 (GRCm38) D527E probably damaging Het
Rhobtb1 T A 10: 69,115,327 (GRCm39) probably null Het
Scel T A 14: 103,809,473 (GRCm39) M271K possibly damaging Het
Senp3 A T 11: 69,569,655 (GRCm39) C310* probably null Het
Slc25a3 T C 10: 90,958,050 (GRCm39) T97A possibly damaging Het
Srsf11 A T 3: 157,732,369 (GRCm39) Y82* probably null Het
Tbc1d8 G A 1: 39,441,959 (GRCm39) T211I possibly damaging Het
Tbkbp1 T C 11: 97,039,474 (GRCm39) E145G probably damaging Het
Tln1 T C 4: 43,540,588 (GRCm39) N1471S probably benign Het
Tnn T G 1: 159,973,659 (GRCm39) D236A probably damaging Het
Trmt2a C T 16: 18,069,150 (GRCm39) probably benign Het
Ttn A T 2: 76,641,587 (GRCm39) L5176Q possibly damaging Het
Ubxn10 G A 4: 138,463,259 (GRCm39) probably benign Het
Ulk4 G A 9: 120,902,938 (GRCm39) Q1180* probably null Het
Usp43 T A 11: 67,746,331 (GRCm39) K1120N probably damaging Het
Uspl1 T A 5: 149,131,149 (GRCm39) L244Q possibly damaging Het
Vmn1r32 T C 6: 66,530,629 (GRCm39) H49R probably damaging Het
Vmn2r4 T C 3: 64,317,384 (GRCm39) D118G probably damaging Het
Vwce A G 19: 10,627,943 (GRCm39) I468V probably benign Het
Zbtb7c G T 18: 76,279,225 (GRCm39) R561L probably benign Het
Zfp956 T C 6: 47,939,476 (GRCm39) S175P probably damaging Het
Other mutations in Cilk1
AlleleSourceChrCoordTypePredicted EffectPPH Score
IGL00965:Cilk1 APN 9 78,071,821 (GRCm39) missense probably benign 0.00
IGL01679:Cilk1 APN 9 78,047,307 (GRCm39) missense possibly damaging 0.94
IGL02525:Cilk1 APN 9 78,067,675 (GRCm39) missense probably benign 0.37
IGL02719:Cilk1 APN 9 78,047,301 (GRCm39) missense probably damaging 0.99
BB001:Cilk1 UTSW 9 78,062,746 (GRCm39) missense probably damaging 1.00
BB011:Cilk1 UTSW 9 78,062,746 (GRCm39) missense probably damaging 1.00
H8930:Cilk1 UTSW 9 78,057,901 (GRCm39) missense possibly damaging 0.92
R0471:Cilk1 UTSW 9 78,062,799 (GRCm39) critical splice donor site probably null
R1626:Cilk1 UTSW 9 78,057,919 (GRCm39) missense probably damaging 1.00
R1824:Cilk1 UTSW 9 78,065,144 (GRCm39) missense probably benign
R2186:Cilk1 UTSW 9 78,038,769 (GRCm39) missense probably benign 0.07
R2872:Cilk1 UTSW 9 78,047,382 (GRCm39) splice site probably null
R2872:Cilk1 UTSW 9 78,047,382 (GRCm39) splice site probably null
R4609:Cilk1 UTSW 9 78,075,071 (GRCm39) utr 3 prime probably benign
R4792:Cilk1 UTSW 9 78,060,975 (GRCm39) missense probably damaging 1.00
R5001:Cilk1 UTSW 9 78,038,801 (GRCm39) missense probably damaging 1.00
R5060:Cilk1 UTSW 9 78,060,978 (GRCm39) missense probably benign 0.01
R5093:Cilk1 UTSW 9 78,047,303 (GRCm39) missense probably benign 0.24
R5393:Cilk1 UTSW 9 78,067,997 (GRCm39) missense probably benign
R6199:Cilk1 UTSW 9 78,071,921 (GRCm39) missense probably benign 0.04
R6412:Cilk1 UTSW 9 78,047,258 (GRCm39) missense probably damaging 1.00
R7038:Cilk1 UTSW 9 78,016,484 (GRCm39) unclassified probably benign
R7468:Cilk1 UTSW 9 78,065,221 (GRCm39) missense probably benign 0.00
R7660:Cilk1 UTSW 9 78,074,902 (GRCm39) missense probably benign
R7661:Cilk1 UTSW 9 78,074,902 (GRCm39) missense probably benign
R7662:Cilk1 UTSW 9 78,074,902 (GRCm39) missense probably benign
R7666:Cilk1 UTSW 9 78,074,902 (GRCm39) missense probably benign
R7693:Cilk1 UTSW 9 78,065,008 (GRCm39) missense probably benign
R7783:Cilk1 UTSW 9 78,042,927 (GRCm39) missense probably damaging 0.97
R7787:Cilk1 UTSW 9 78,074,902 (GRCm39) missense probably benign
R7788:Cilk1 UTSW 9 78,074,902 (GRCm39) missense probably benign
R7924:Cilk1 UTSW 9 78,062,746 (GRCm39) missense probably damaging 1.00
R8317:Cilk1 UTSW 9 78,060,933 (GRCm39) missense probably damaging 0.98
R8861:Cilk1 UTSW 9 78,071,844 (GRCm39) missense probably benign 0.01
R9131:Cilk1 UTSW 9 78,074,230 (GRCm39) missense possibly damaging 0.89
R9749:Cilk1 UTSW 9 78,060,999 (GRCm39) missense probably damaging 0.99
R9782:Cilk1 UTSW 9 78,048,520 (GRCm39) missense probably damaging 0.99
X0067:Cilk1 UTSW 9 78,062,685 (GRCm39) nonsense probably null
Predicted Primers PCR Primer
(F):5'- AGTGTTTGAGCTGCAGAGAGC -3'
(R):5'- ATCTGCAGGGTTTGAACTACTTG -3'

Sequencing Primer
(F):5'- CAGTGCAGAGGGAGTGTGTG -3'
(R):5'- TGGAACTCACTATATAGACCAGGCTG -3'
Posted On 2015-11-11