Incidental Mutation 'R5783:Chka'
| ID |
447890 |
| Institutional Source |
Beutler Lab
|
| Gene Symbol |
Chka
|
| Ensembl Gene |
ENSMUSG00000024843 |
| Gene Name |
choline kinase alpha |
| Synonyms |
Chk, ChoK, EtnK-alpha, choline/ethanolamine kinase alpha, CK/EK-alpha |
| MMRRC Submission |
043380-MU
|
| Accession Numbers |
|
| Essential gene? |
Essential
(E-score: 1.000)
|
| Stock # |
R5783 (G1)
|
| Quality Score |
225 |
|
Status
|
Not validated
|
| Chromosome |
19 |
| Chromosomal Location |
3901773-3944369 bp(+) (GRCm39) |
| Type of Mutation |
missense |
| DNA Base Change (assembly) |
A to G
at 3914661 bp (GRCm39)
|
| Zygosity |
Heterozygous |
| Amino Acid Change |
Asparagine to Aspartic acid
at position 118
(N118D)
|
| Ref Sequence |
ENSEMBL: ENSMUSP00000119919
(fasta)
|
| Gene Model |
predicted gene model for transcript(s):
[ENSMUST00000025760]
[ENSMUST00000072055]
[ENSMUST00000128694]
|
| AlphaFold |
O54804 |
| Predicted Effect |
probably damaging
Transcript: ENSMUST00000025760
AA Change: N118D
PolyPhen 2
Score 0.999 (Sensitivity: 0.14; Specificity: 0.99)
|
| SMART Domains |
Protein: ENSMUSP00000025760
Gene: ENSMUSG00000024843
AA Change: N118D
| Domain | Start | End | E-Value | Type |
|---|
|
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 |
probably damaging
Transcript: ENSMUST00000072055
AA Change: N118D
PolyPhen 2
Score 0.999 (Sensitivity: 0.14; Specificity: 0.99)
|
| SMART Domains |
Protein: ENSMUSP00000071933
Gene: ENSMUSG00000024843
AA Change: N118D
| Domain | Start | End | E-Value | Type |
|---|
|
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 |
noncoding transcript
Transcript: ENSMUST00000124219
|
| Predicted Effect |
noncoding transcript
Transcript: ENSMUST00000125411
|
| Predicted Effect |
unknown
Transcript: ENSMUST00000125640
AA Change: N22D
|
| SMART Domains |
Protein: ENSMUSP00000119493
Gene: ENSMUSG00000024843
AA Change: N22D
| Domain | Start | End | E-Value | Type |
|---|
|
Pfam:Choline_kinase
|
40 |
230 |
2.2e-49 |
PFAM |
|
| Predicted Effect |
noncoding transcript
Transcript: ENSMUST00000125859
|
| Predicted Effect |
probably damaging
Transcript: ENSMUST00000128694
AA Change: N118D
PolyPhen 2
Score 0.999 (Sensitivity: 0.14; Specificity: 0.99)
|
| SMART Domains |
Protein: ENSMUSP00000119919
Gene: ENSMUSG00000024843
AA Change: N118D
| Domain | Start | End | E-Value | Type |
|---|
|
PDB:4DA5|B
|
1 |
150 |
2e-60 |
PDB |
|
| Predicted Effect |
unknown
Transcript: ENSMUST00000139655
AA Change: N109D
|
| SMART Domains |
Protein: ENSMUSP00000116427
Gene: ENSMUSG00000024843
AA Change: N109D
| Domain | Start | End | E-Value | Type |
|---|
|
low complexity region
|
5 |
16 |
N/A |
INTRINSIC |
|
PDB:4DA5|B
|
17 |
160 |
3e-68 |
PDB |
|
| Predicted Effect |
noncoding transcript
Transcript: ENSMUST00000154467
|
| Coding Region Coverage |
- 1x: 99.4%
- 3x: 98.8%
- 10x: 97.6%
- 20x: 96.0%
|
| Validation Efficiency |
|
| 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: 52 list
| Gene | Ref | Var | Chr/Loc | Mutation | Predicted Effect | Zygosity |
|---|
| 1700093K21Rik |
T |
A |
11: 23,468,787 (GRCm39) |
Y48F |
probably damaging |
Het |
| Apob |
A |
G |
12: 8,051,022 (GRCm39) |
D1082G |
probably damaging |
Het |
| Cald1 |
G |
A |
6: 34,730,468 (GRCm39) |
A236T |
possibly damaging |
Het |
| Ccdc88b |
A |
C |
19: 6,831,284 (GRCm39) |
C553G |
probably benign |
Het |
| Cenpe |
A |
G |
3: 134,967,341 (GRCm39) |
D2161G |
probably benign |
Het |
| Cep78 |
G |
T |
19: 15,933,723 (GRCm39) |
N618K |
probably benign |
Het |
| Dennd5a |
A |
C |
7: 109,493,843 (GRCm39) |
I1263S |
probably damaging |
Het |
| Dnaaf9 |
A |
C |
2: 130,581,003 (GRCm39) |
F582L |
possibly damaging |
Het |
| Dnm3 |
T |
C |
1: 162,183,040 (GRCm39) |
T92A |
possibly damaging |
Het |
| Dpp9 |
T |
C |
17: 56,518,655 (GRCm39) |
K50E |
probably damaging |
Het |
| Fen1 |
G |
T |
19: 10,178,194 (GRCm39) |
Y83* |
probably null |
Het |
| Gm1110 |
A |
G |
9: 26,793,632 (GRCm39) |
I532T |
probably benign |
Het |
| H2bc21 |
T |
C |
3: 96,128,615 (GRCm39) |
V45A |
possibly damaging |
Het |
| Impdh1 |
A |
T |
6: 29,206,342 (GRCm39) |
F140Y |
possibly damaging |
Het |
| Kcnc4 |
T |
C |
3: 107,355,188 (GRCm39) |
D420G |
possibly damaging |
Het |
| Kctd19 |
A |
G |
8: 106,113,612 (GRCm39) |
V664A |
probably benign |
Het |
| Krt80 |
C |
T |
15: 101,257,360 (GRCm39) |
|
probably null |
Het |
| Lars2 |
T |
G |
9: 123,290,661 (GRCm39) |
M876R |
probably benign |
Het |
| Lrrc9 |
A |
G |
12: 72,502,827 (GRCm39) |
E266G |
possibly damaging |
Het |
| Mesd |
T |
A |
7: 83,544,883 (GRCm39) |
V120E |
probably damaging |
Het |
| Mogs |
C |
T |
6: 83,095,652 (GRCm39) |
T823I |
probably damaging |
Het |
| Mrgprh |
C |
A |
17: 13,096,333 (GRCm39) |
T191N |
probably benign |
Het |
| Mtss1 |
C |
T |
15: 58,815,373 (GRCm39) |
S729N |
probably benign |
Het |
| Muc5b |
G |
T |
7: 141,412,165 (GRCm39) |
E1704* |
probably null |
Het |
| Or2ag13 |
C |
A |
7: 106,472,541 (GRCm39) |
V304F |
probably damaging |
Het |
| Or51m1 |
A |
T |
7: 103,578,149 (GRCm39) |
I40F |
probably damaging |
Het |
| Or8k30 |
T |
C |
2: 86,338,982 (GRCm39) |
Y60H |
probably damaging |
Het |
| Osbpl8 |
T |
A |
10: 111,103,644 (GRCm39) |
L216* |
probably null |
Het |
| Pcdha5 |
T |
C |
18: 37,095,534 (GRCm39) |
V681A |
probably benign |
Het |
| Pgap3 |
A |
C |
11: 98,281,290 (GRCm39) |
V190G |
probably benign |
Het |
| Ppp2r5a |
A |
T |
1: 191,086,837 (GRCm39) |
Y373N |
probably damaging |
Het |
| Prkdc |
T |
C |
16: 15,535,665 (GRCm39) |
L1675P |
probably damaging |
Het |
| Rapgef2 |
T |
G |
3: 78,995,300 (GRCm39) |
I635L |
probably benign |
Het |
| Rusc1 |
T |
C |
3: 88,995,452 (GRCm39) |
D193G |
probably damaging |
Het |
| Ryr3 |
C |
T |
2: 112,483,343 (GRCm39) |
V4140I |
probably benign |
Het |
| Scamp5 |
A |
G |
9: 57,353,353 (GRCm39) |
|
probably null |
Het |
| Shoc1 |
A |
T |
4: 59,076,239 (GRCm39) |
L568* |
probably null |
Het |
| Slc41a3 |
T |
C |
6: 90,596,524 (GRCm39) |
I31T |
probably benign |
Het |
| Smad9 |
T |
C |
3: 54,701,863 (GRCm39) |
V368A |
probably benign |
Het |
| Smim8 |
TTTAATGAAGAGCT |
TT |
4: 34,771,261 (GRCm39) |
|
probably benign |
Het |
| St8sia1 |
T |
C |
6: 142,909,340 (GRCm39) |
N52S |
possibly damaging |
Het |
| Svop |
T |
G |
5: 114,202,996 (GRCm39) |
D72A |
possibly damaging |
Het |
| Sybu |
T |
C |
15: 44,609,810 (GRCm39) |
I153V |
probably damaging |
Het |
| Tmem266 |
G |
T |
9: 55,305,087 (GRCm39) |
S32I |
probably damaging |
Het |
| Trpm4 |
G |
T |
7: 44,959,813 (GRCm39) |
R694S |
probably benign |
Het |
| Uqcrfs1 |
A |
G |
13: 30,729,187 (GRCm39) |
L15P |
probably damaging |
Het |
| Vrtn |
T |
A |
12: 84,697,251 (GRCm39) |
L667Q |
probably benign |
Het |
| Zc3h14 |
T |
A |
12: 98,723,434 (GRCm39) |
S241R |
probably damaging |
Het |
| Zfp318 |
TGAAGAAGAAGAAGAAGAAGAAGAAGAAG |
TGAAGAAGAAGAAGAAGAAGAAG |
17: 46,723,440 (GRCm39) |
|
probably benign |
Het |
| Zfp617 |
C |
A |
8: 72,686,308 (GRCm39) |
H213N |
probably damaging |
Het |
| Zfp638 |
G |
A |
6: 83,921,829 (GRCm39) |
G652D |
possibly damaging |
Het |
| Zmiz2 |
T |
C |
11: 6,355,081 (GRCm39) |
L916P |
probably damaging |
Het |
|
| Other mutations in Chka |
| Allele | Source | Chr | Coord | Type | Predicted Effect | PPH Score |
|---|
|
IGL00937:Chka
|
APN |
19 |
3,942,189 (GRCm39) |
missense |
probably benign |
0.16 |
|
IGL02630:Chka
|
APN |
19 |
3,942,112 (GRCm39) |
missense |
possibly damaging |
0.94 |
|
R1432:Chka
|
UTSW |
19 |
3,924,809 (GRCm39) |
splice site |
probably benign |
|
|
R1840:Chka
|
UTSW |
19 |
3,936,460 (GRCm39) |
missense |
probably benign |
0.00 |
|
R1898:Chka
|
UTSW |
19 |
3,942,205 (GRCm39) |
missense |
probably damaging |
1.00 |
|
R3822:Chka
|
UTSW |
19 |
3,932,038 (GRCm39) |
intron |
probably benign |
|
|
R4272:Chka
|
UTSW |
19 |
3,925,737 (GRCm39) |
splice site |
probably benign |
|
|
R4329:Chka
|
UTSW |
19 |
3,925,803 (GRCm39) |
splice site |
probably benign |
|
|
R4573:Chka
|
UTSW |
19 |
3,935,960 (GRCm39) |
missense |
probably damaging |
1.00 |
|
R4720:Chka
|
UTSW |
19 |
3,936,375 (GRCm39) |
missense |
probably damaging |
0.99 |
|
R4923:Chka
|
UTSW |
19 |
3,942,105 (GRCm39) |
critical splice acceptor site |
probably null |
|
|
R5936:Chka
|
UTSW |
19 |
3,934,580 (GRCm39) |
missense |
probably benign |
0.25 |
|
R5979:Chka
|
UTSW |
19 |
3,934,513 (GRCm39) |
missense |
probably damaging |
1.00 |
|
R7429:Chka
|
UTSW |
19 |
3,942,787 (GRCm39) |
missense |
probably damaging |
1.00 |
|
R7430:Chka
|
UTSW |
19 |
3,942,787 (GRCm39) |
missense |
probably damaging |
1.00 |
|
R8189:Chka
|
UTSW |
19 |
3,925,759 (GRCm39) |
nonsense |
probably null |
|
|
R8213:Chka
|
UTSW |
19 |
3,935,882 (GRCm39) |
missense |
probably damaging |
1.00 |
|
R8397:Chka
|
UTSW |
19 |
3,902,414 (GRCm39) |
critical splice donor site |
probably null |
|
|
R8440:Chka
|
UTSW |
19 |
3,943,375 (GRCm39) |
missense |
probably damaging |
1.00 |
|
R9289:Chka
|
UTSW |
19 |
3,935,953 (GRCm39) |
missense |
possibly damaging |
0.75 |
|
| Predicted Primers |
PCR Primer
(F):5'- AAGGGGCTTCTTCCTTGGTC -3'
(R):5'- AGTACTTAGGATCTCTTTGCAGGTATC -3'
Sequencing Primer
(F):5'- GTGATTCAATGGGTCCAACTCTAG -3'
(R):5'- CTCTTTGCAGGTATCTTAGGAAAGAG -3'
|
| Posted On |
2016-12-15 |
Incidental Mutation