Mutagenetix > Incidental Mutation

Incidental Mutation 'R5936:Chka'

462302

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

044130-MU

Accession Numbers

Essential gene?

Essential (E-score: 1.000) question?

Stock #

R5936 (G1)

Quality Score

225

Status

Validated

Chromosome

Chromosomal Location

3901773-3944369 bp(+) (GRCm39)

Type of Mutation

missense

DNA Base Change (assembly)

A to G at 3934580 bp (GRCm39)

Zygosity

Heterozygous

Amino Acid Change

Isoleucine to Valine at position 205 (I205V)

Ref Sequence

ENSEMBL: ENSMUSP00000025760 (fasta)

Gene Model

predicted gene model for transcript(s): [ENSMUST00000025760] [ENSMUST00000072055] [ENSMUST00000128694] [ENSMUST00000153343]

AlphaFold

O54804

Predicted Effect

probably benign
Transcript: ENSMUST00000025760
AA Change: I205V

PolyPhen 2 Score 0.247 (Sensitivity: 0.91; Specificity: 0.88)

SMART Domains

Protein: ENSMUSP00000025760
Gene: ENSMUSG00000024843
AA Change: I205V

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 benign
Transcript: ENSMUST00000072055
AA Change: I187V

PolyPhen 2 Score 0.040 (Sensitivity: 0.94; Specificity: 0.83)

SMART Domains

Protein: ENSMUSP00000071933
Gene: ENSMUSG00000024843
AA Change: I187V

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

unknown
Transcript: ENSMUST00000125640
AA Change: I128V

SMART Domains

Protein: ENSMUSP00000119493
Gene: ENSMUSG00000024843
AA Change: I128V

Domain	Start	End	E-Value	Type
Pfam:Choline_kinase	40	230	2.2e-49	PFAM

Predicted Effect

noncoding transcript
Transcript: ENSMUST00000125859

Predicted Effect

noncoding transcript
Transcript: ENSMUST00000127544

Predicted Effect

probably benign
Transcript: ENSMUST00000128694

SMART Domains

Protein: ENSMUSP00000119919
Gene: ENSMUSG00000024843

Domain	Start	End	E-Value	Type
PDB:4DA5\|B	1	150	2e-60	PDB

Predicted Effect

probably benign
Transcript: ENSMUST00000139655

SMART Domains

Protein: ENSMUSP00000116427
Gene: ENSMUSG00000024843

Domain	Start	End	E-Value	Type
low complexity region	5	16	N/A	INTRINSIC
PDB:4DA5\|B	17	160	3e-68	PDB

Predicted Effect

silent
Transcript: ENSMUST00000153343

Predicted Effect

noncoding transcript
Transcript: ENSMUST00000146463

Predicted Effect

noncoding transcript
Transcript: ENSMUST00000148325

Meta Mutation Damage Score

0.1498

Coding Region Coverage

1x: 99.9%
3x: 99.5%
10x: 97.7%
20x: 93.0%

Validation Efficiency

91% (77/85)

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: 75 list
Gene	Ref	Var	Chr/Loc	Mutation	Predicted Effect	Zygosity
4933409G03Rik	A	T	2: 68,445,848 (GRCm39)		probably benign	Het
Acnat2	T	C	4: 49,383,362 (GRCm39)	T64A	probably benign	Het
Afap1	A	G	5: 36,131,740 (GRCm39)	N356D	possibly damaging	Het
Ahi1	A	G	10: 20,841,832 (GRCm39)	D301G	probably damaging	Het
Alpk2	G	A	18: 65,483,591 (GRCm39)	T139M	probably damaging	Het
Ankrd46	T	C	15: 36,479,428 (GRCm39)	D221G	probably benign	Het
Ano6	T	A	15: 95,870,482 (GRCm39)	L900H	probably damaging	Het
Asphd2	G	A	5: 112,533,623 (GRCm39)	R343*	probably null	Het
Atosa	T	C	9: 74,916,586 (GRCm39)	L395P	probably benign	Het
Brdt	A	G	5: 107,507,261 (GRCm39)	T554A	probably damaging	Het
Cacna1d	A	G	14: 29,893,271 (GRCm39)	V401A	possibly damaging	Het
Cbs	T	C	17: 31,844,068 (GRCm39)	T188A	probably damaging	Het
Cfap54	T	A	10: 92,798,274 (GRCm39)	T1662S	probably benign	Het
Chsy1	T	A	7: 65,822,025 (GRCm39)	N753K	possibly damaging	Het
Cpz	A	G	5: 35,659,987 (GRCm39)	S553P	probably benign	Het
Crtac1	A	G	19: 42,312,276 (GRCm39)	Y146H	probably damaging	Het
Csf1r	A	T	18: 61,258,880 (GRCm39)	I700F	probably damaging	Het
Ddx20	C	A	3: 105,587,903 (GRCm39)	E392D	possibly damaging	Het
Dhrs11	G	T	11: 84,716,350 (GRCm39)	Y67*	probably null	Het
Diaph3	G	T	14: 87,009,552 (GRCm39)	Q1076K	possibly damaging	Het
Dop1a	T	A	9: 86,418,565 (GRCm39)	L2037*	probably null	Het
Dst	G	T	1: 34,346,539 (GRCm39)	V5336L	probably damaging	Het
Etv1	C	A	12: 38,885,209 (GRCm39)	H248Q	probably damaging	Het
Fcgbp	T	C	7: 27,786,117 (GRCm39)	V518A	probably damaging	Het
Fchsd2	T	C	7: 100,840,908 (GRCm39)	L139S	probably damaging	Het
Fer	A	T	17: 64,231,058 (GRCm39)	T270S	probably benign	Het
Fgd5	A	G	6: 91,964,892 (GRCm39)	E375G	probably damaging	Het
Firrm	T	G	1: 163,814,581 (GRCm39)	I121L	probably benign	Het
Gabarapl1	T	A	6: 129,515,566 (GRCm39)	I68N	probably benign	Het
Gopc	C	T	10: 52,222,295 (GRCm39)	V30M	probably damaging	Het
Hbp1	T	C	12: 31,987,095 (GRCm39)		probably null	Het
Helz2	A	G	2: 180,872,560 (GRCm39)	V2480A	probably damaging	Het
Igfbp3	T	A	11: 7,159,472 (GRCm39)	Y247F	probably damaging	Het
Kbtbd11	C	A	8: 15,077,534 (GRCm39)	S44R	probably benign	Het
Kcnk10	G	T	12: 98,456,191 (GRCm39)	S213R	probably benign	Het
Kcnq3	T	A	15: 65,871,959 (GRCm39)	D570V	probably damaging	Het
Kif21a	A	G	15: 90,819,850 (GRCm39)	F1594S	possibly damaging	Het
Klf3	A	G	5: 64,980,303 (GRCm39)	D31G	probably damaging	Het
Mapkapk3	T	C	9: 107,166,369 (GRCm39)	K59E	probably damaging	Het
Myo18a	A	G	11: 77,709,039 (GRCm39)	T484A	probably damaging	Het
Nlrp6	T	A	7: 140,502,725 (GRCm39)	L277*	probably null	Het
Nr5a1	G	T	2: 38,591,790 (GRCm39)		probably benign	Het
Nsmaf	C	T	4: 6,421,017 (GRCm39)		probably benign	Het
Or4f58	T	A	2: 111,851,932 (GRCm39)	H89L	probably benign	Het
Orc1	A	G	4: 108,459,180 (GRCm39)	T450A	probably benign	Het
Pacsin1	A	T	17: 27,923,971 (GRCm39)	I122F	probably benign	Het
Pced1b	T	A	15: 97,283,061 (GRCm39)	Y367N	possibly damaging	Het
Pced1b	T	A	15: 97,283,063 (GRCm39)	Y367*	probably null	Het
Pdpk1	A	G	17: 24,312,203 (GRCm39)	F281L	probably damaging	Het
Piwil1	T	C	5: 128,828,142 (GRCm39)	V714A	probably benign	Het
Plcd3	C	T	11: 102,969,173 (GRCm39)	V265M	probably damaging	Het
Ppp1r1c	A	T	2: 79,586,798 (GRCm39)	E48V	possibly damaging	Het
Prl2b1	T	G	13: 27,572,432 (GRCm39)	T53P	probably damaging	Het
Ptch2	T	G	4: 116,965,491 (GRCm39)	F359V	probably benign	Het
R3hdm2	G	A	10: 127,307,681 (GRCm39)	S314N	probably damaging	Het
Rictor	A	T	15: 6,813,642 (GRCm39)	S1043C	probably damaging	Het
Rtn4rl2	A	T	2: 84,710,775 (GRCm39)	L163Q	probably damaging	Het
Sarnp	T	A	10: 128,684,640 (GRCm39)	S129T	probably benign	Het
Scube3	A	T	17: 28,384,461 (GRCm39)	K585M	probably damaging	Het
Sgk3	C	T	1: 9,956,045 (GRCm39)		probably benign	Het
Skint6	C	T	4: 112,953,790 (GRCm39)	S458N	probably benign	Het
Slc25a54	A	G	3: 109,005,954 (GRCm39)	H154R	possibly damaging	Het
Sorbs1	A	C	19: 40,313,216 (GRCm39)	I690S	probably damaging	Het
Sqle	C	A	15: 59,202,678 (GRCm39)	A512D	probably damaging	Het
Tedc2	A	C	17: 24,435,315 (GRCm39)	L358R	probably damaging	Het
Tfr2	A	G	5: 137,585,268 (GRCm39)	S767G	probably benign	Het
Thoc5	A	G	11: 4,854,133 (GRCm39)	E27G	probably damaging	Het
Trappc8	A	T	18: 21,007,745 (GRCm39)	F123L	probably damaging	Het
Ube3d	C	T	9: 86,254,512 (GRCm39)	G323D	probably benign	Het
Unc13c	T	A	9: 73,485,774 (GRCm39)	H1642L	probably damaging	Het
Vmn1r10	A	T	6: 57,091,302 (GRCm39)	H298L	probably benign	Het
Xpo4	A	T	14: 57,880,956 (GRCm39)	Y26N	probably benign	Het
Zer1	A	G	2: 29,997,679 (GRCm39)	L409P	probably damaging	Het
Zfyve28	A	T	5: 34,382,332 (GRCm39)	L256Q	probably damaging	Het
Zgrf1	A	G	3: 127,355,902 (GRCm39)	E376G	possibly 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
R5783:Chka	UTSW	19	3,914,661 (GRCm39)	missense	probably damaging	1.00
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'- TCCTGAGCTAGCACTTCCTG -3'
(R):5'- ACTCACCAGATACTGTGCACTTC -3'

Sequencing Primer
(F):5'- GAGCTAGCACTTCCTGTCTAGG -3'
(R):5'- CAGATACTGTGCACTTCTGAGGAC -3'

Posted On

2017-02-28