Incidental Mutation 'R9289:Chka'
ID 704175
Institutional Source Beutler Lab
Gene Symbol Chka
Ensembl Gene ENSMUSG00000024843
Gene Name choline kinase alpha
Synonyms choline/ethanolamine kinase alpha, EtnK-alpha, CK/EK-alpha, Chk, ChoK
MMRRC Submission
Accession Numbers
Essential gene? Essential (E-score: 1.000) question?
Stock # R9289 (G1)
Quality Score 225.009
Status Validated
Chromosome 19
Chromosomal Location 3851773-3894369 bp(+) (GRCm38)
Type of Mutation missense
DNA Base Change (assembly) T to G at 3885953 bp (GRCm38)
Zygosity Heterozygous
Amino Acid Change Phenylalanine to Valine at position 220 (F220V)
Ref Sequence ENSEMBL: ENSMUSP00000071933 (fasta)
Gene Model predicted gene model for transcript(s): [ENSMUST00000025760] [ENSMUST00000072055] [ENSMUST00000128694] [ENSMUST00000153343]
AlphaFold O54804
Predicted Effect probably benign
Transcript: ENSMUST00000025760
AA Change: F238V

PolyPhen 2 Score 0.196 (Sensitivity: 0.92; Specificity: 0.87)
SMART Domains Protein: ENSMUSP00000025760
Gene: ENSMUSG00000024843
AA Change: F238V

low complexity region 13 24 N/A INTRINSIC
low complexity region 53 74 N/A INTRINSIC
Pfam:APH 108 373 2.4e-11 PFAM
Pfam:Choline_kinase 135 370 8.2e-82 PFAM
Pfam:EcKinase 211 345 2.5e-7 PFAM
Predicted Effect possibly damaging
Transcript: ENSMUST00000072055
AA Change: F220V

PolyPhen 2 Score 0.754 (Sensitivity: 0.85; Specificity: 0.92)
SMART Domains Protein: ENSMUSP00000071933
Gene: ENSMUSG00000024843
AA Change: F220V

low complexity region 13 24 N/A INTRINSIC
low complexity region 53 74 N/A INTRINSIC
Pfam:APH 108 358 6.4e-12 PFAM
Pfam:Choline_kinase 135 352 1.6e-84 PFAM
Pfam:EcKinase 190 329 2e-7 PFAM
Predicted Effect
SMART Domains Protein: ENSMUSP00000119493
Gene: ENSMUSG00000024843
AA Change: F161V

Pfam:Choline_kinase 40 230 2.2e-49 PFAM
Predicted Effect probably benign
Transcript: ENSMUST00000128694
SMART Domains Protein: ENSMUSP00000119919
Gene: ENSMUSG00000024843

PDB:4DA5|B 1 150 2e-60 PDB
Predicted Effect probably benign
Transcript: ENSMUST00000139655
SMART Domains Protein: ENSMUSP00000116427
Gene: ENSMUSG00000024843

low complexity region 5 16 N/A INTRINSIC
PDB:4DA5|B 17 160 3e-68 PDB
Predicted Effect probably benign
Transcript: ENSMUST00000153343
Coding Region Coverage
  • 1x: 100.0%
  • 3x: 99.9%
  • 10x: 99.6%
  • 20x: 98.7%
Validation Efficiency 100% (53/53)
MGI Phenotype FUNCTION: [Summary is not available for the mouse gene. This summary is for the human ortholog.] The major pathway for the biosynthesis of phosphatidylcholine occurs via the CDP-choline pathway. The protein encoded by this gene is the initial enzyme in the sequence and may play a regulatory role. The encoded protein also catalyzes the phosphorylation of ethanolamine. Two transcript variants encoding different isoforms have been found for this gene. [provided by RefSeq, Jul 2008]
PHENOTYPE: Mice homozygous for a null allele exhibit embryonic lethality between E3.5 and E7.5. [provided by MGI curators]
Allele List at MGI
Other mutations in this stock
Total: 54 list
GeneRefVarChr/LocMutationPredicted EffectZygosity
1700018F24Rik C T 5: 145,045,523 (GRCm38) T306I probably benign Het
Aurkb T C 11: 69,050,349 (GRCm38) I250T probably damaging Het
C1qtnf1 A G 11: 118,443,846 (GRCm38) T51A probably benign Het
C1rb G T 6: 124,575,313 (GRCm38) R330L possibly damaging Het
Cd8b1 G A 6: 71,329,793 (GRCm38) probably null Het
Cep57l1 A T 10: 41,731,086 (GRCm38) D160E probably damaging Het
Ces1f C T 8: 93,265,863 (GRCm38) S320N probably benign Het
Cfap54 A G 10: 92,821,074 (GRCm38) S3039P possibly damaging Het
Chia1 A T 3: 106,115,186 (GRCm38) probably benign Het
Cmtm2b A G 8: 104,322,348 (GRCm38) probably benign Het
Dgcr8 C T 16: 18,280,215 (GRCm38) probably benign Het
Dhx30 A T 9: 110,093,121 (GRCm38) D164E probably benign Het
Dhx30 T C 9: 110,091,535 (GRCm38) T304A possibly damaging Het
Dip2b A T 15: 100,173,271 (GRCm38) K661I probably damaging Het
Dlgap4 G T 2: 156,704,594 (GRCm38) R394L possibly damaging Het
Dop1b T A 16: 93,771,793 (GRCm38) L1581H probably damaging Het
Fam219a C A 4: 41,521,942 (GRCm38) G46V probably damaging Het
Fer1l6 G A 15: 58,618,917 (GRCm38) V1028M probably damaging Het
Glb1 C A 9: 114,420,490 (GRCm38) A129E probably damaging Het
Gm11492 T A 11: 87,568,966 (GRCm38) C513* probably null Het
Heatr1 T C 13: 12,432,727 (GRCm38) V1767A probably benign Het
Ift88 T A 14: 57,480,742 (GRCm38) S591T probably benign Het
Itgb4 A G 11: 115,994,361 (GRCm38) K1023R probably benign Het
Mfng C A 15: 78,759,257 (GRCm38) S250I probably damaging Het
Mmp9 A G 2: 164,954,880 (GRCm38) T723A probably benign Het
Mzf1 T A 7: 13,051,607 (GRCm38) H299L probably benign Het
Naa40 T C 19: 7,234,120 (GRCm38) K47E possibly damaging Het
Ncdn A C 4: 126,750,110 (GRCm38) F306L possibly damaging Het
Notch3 A G 17: 32,158,280 (GRCm38) C246R probably damaging Het
Npc1l1 A T 11: 6,218,355 (GRCm38) Y945* probably null Het
Or2av9 T A 11: 58,489,919 (GRCm38) I279L probably benign Het
Or2n1d A T 17: 38,335,429 (GRCm38) T91S possibly damaging Het
Or2y14 C T 11: 49,513,808 (GRCm38) P57S probably damaging Het
Or52n5 T C 7: 104,938,609 (GRCm38) W28R probably damaging Het
Pcnx1 C A 12: 81,982,079 (GRCm38) D1044E Het
Pgm2l1 T A 7: 100,270,422 (GRCm38) I575K probably damaging Het
Plat T C 8: 22,782,084 (GRCm38) I553T probably damaging Het
Prrc2c A G 1: 162,679,561 (GRCm38) V2513A probably benign Het
Qser1 A T 2: 104,787,248 (GRCm38) V983E possibly damaging Het
Ring1 A G 17: 34,022,573 (GRCm38) S190P possibly damaging Het
Rnf150 A G 8: 82,990,353 (GRCm38) E163G probably benign Het
Scgb2b12 T C 7: 32,326,635 (GRCm38) H44R probably benign Het
Shtn1 T C 19: 59,009,825 (GRCm38) K379E probably damaging Het
Slc52a2 G T 15: 76,540,275 (GRCm38) V238L probably benign Het
Smg1 T C 7: 118,145,416 (GRCm38) H3171R possibly damaging Het
Tada3 A G 6: 113,370,303 (GRCm38) V342A possibly damaging Het
Tbc1d20 T C 2: 152,311,342 (GRCm38) V264A probably damaging Het
Tmco5 G A 2: 116,880,264 (GRCm38) A22T probably benign Het
Tmem63b A G 17: 45,664,771 (GRCm38) F549S probably benign Het
Trav16d-dv11 T C 14: 53,047,629 (GRCm38) F54S probably benign Het
Trim7 A T 11: 48,845,454 (GRCm38) K5* probably null Het
Usp48 G A 4: 137,613,685 (GRCm38) G332E probably benign Het
Zfp78 T C 7: 6,378,368 (GRCm38) I139T probably benign Het
Zfp839 T A 12: 110,868,444 (GRCm38) V711D probably benign Het
Other mutations in Chka
AlleleSourceChrCoordTypePredicted EffectPPH Score
IGL00937:Chka APN 19 3,892,189 (GRCm38) missense probably benign 0.16
IGL02630:Chka APN 19 3,892,112 (GRCm38) missense possibly damaging 0.94
R1432:Chka UTSW 19 3,874,809 (GRCm38) splice site probably benign
R1840:Chka UTSW 19 3,886,460 (GRCm38) missense probably benign 0.00
R1898:Chka UTSW 19 3,892,205 (GRCm38) missense probably damaging 1.00
R3822:Chka UTSW 19 3,882,038 (GRCm38) intron probably benign
R4272:Chka UTSW 19 3,875,737 (GRCm38) splice site probably benign
R4329:Chka UTSW 19 3,875,803 (GRCm38) splice site probably benign
R4573:Chka UTSW 19 3,885,960 (GRCm38) missense probably damaging 1.00
R4720:Chka UTSW 19 3,886,375 (GRCm38) missense probably damaging 0.99
R4923:Chka UTSW 19 3,892,105 (GRCm38) critical splice acceptor site probably null
R5783:Chka UTSW 19 3,864,661 (GRCm38) missense probably damaging 1.00
R5936:Chka UTSW 19 3,884,580 (GRCm38) missense probably benign 0.25
R5979:Chka UTSW 19 3,884,513 (GRCm38) missense probably damaging 1.00
R7429:Chka UTSW 19 3,892,787 (GRCm38) missense probably damaging 1.00
R7430:Chka UTSW 19 3,892,787 (GRCm38) missense probably damaging 1.00
R8189:Chka UTSW 19 3,875,759 (GRCm38) nonsense probably null
R8213:Chka UTSW 19 3,885,882 (GRCm38) missense probably damaging 1.00
R8397:Chka UTSW 19 3,852,414 (GRCm38) critical splice donor site probably null
R8440:Chka UTSW 19 3,893,375 (GRCm38) missense probably damaging 1.00
Predicted Primers PCR Primer

Sequencing Primer
Posted On 2022-03-25