Mutagenetix > Incidental Mutations

Incidental Mutation 'R1432:Chka'

162351

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

039487-MU

Accession Numbers

Is this an essential gene?

Essential (E-score: 1.000) question?

Stock #

R1432 (G1)

Quality Score

225

Status

Validated

Chromosome

Chromosomal Location

3851773-3894369 bp(+) (GRCm38)

Type of Mutation

splice site

DNA Base Change (assembly)

T to C at 3874809 bp (GRCm38)

Zygosity

Heterozygous

Amino Acid Change

Ref Sequence

ENSEMBL: ENSMUSP00000115861 (fasta)

Gene Model

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

AlphaFold

O54804

Predicted Effect

probably benign
Transcript: ENSMUST00000025760

SMART Domains

Protein: ENSMUSP00000025760
Gene: ENSMUSG00000024843

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

SMART Domains

Protein: ENSMUSP00000071933
Gene: ENSMUSG00000024843

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

probably benign
Transcript: ENSMUST00000125640

SMART Domains

Protein: ENSMUSP00000119493
Gene: ENSMUSG00000024843

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

noncoding transcript
Transcript: ENSMUST00000146463

Predicted Effect

noncoding transcript
Transcript: ENSMUST00000148325

Predicted Effect

probably benign
Transcript: ENSMUST00000153343

Coding Region Coverage

1x: 98.9%
3x: 97.8%
10x: 94.4%
20x: 86.1%

Validation Efficiency

98% (90/92)

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: 88 list
Gene	Ref	Var	Chr/Loc	Mutation	Predicted Effect	Zygosity
2700049A03Rik	A	G	12: 71,170,587		probably null	Het
9130401M01Rik	A	T	15: 58,028,860	L117Q	probably damaging	Het
Abcb1b	A	G	5: 8,837,771	K886E	possibly damaging	Het
Acaa2	A	T	18: 74,787,127	I9F	probably damaging	Het
Acap2	A	T	16: 31,111,083	S386T	probably damaging	Het
Acsm2	A	T	7: 119,573,575	I138F	possibly damaging	Het
Agl	T	C	3: 116,746,693	Y1424C	probably damaging	Het
Apc2	T	C	10: 80,312,349	V1079A	probably benign	Het
Arhgef6	T	C	X: 57,338,562	M5V	probably benign	Het
Armc8	C	T	9: 99,523,132		probably benign	Het
BC005561	T	C	5: 104,518,104	F164S	probably damaging	Het
Catsperb	A	G	12: 101,622,217	Y953C	probably damaging	Het
Cdk13	G	A	13: 17,718,416	A720V	probably damaging	Het
Clcc1	T	C	3: 108,668,102	I165T	probably benign	Het
Cndp1	G	A	18: 84,634,652		probably benign	Het
Dip2c	C	A	13: 9,553,304	P297Q	probably damaging	Het
Dnah17	A	T	11: 118,023,327	W4429R	probably damaging	Het
Doxl2	T	A	6: 48,975,654	F171Y	probably damaging	Het
Dram2	T	C	3: 106,570,766	V138A	possibly damaging	Het
Dus4l	T	C	12: 31,648,771	N78S	probably benign	Het
Dync1h1	G	A	12: 110,636,509	E2195K	probably benign	Het
Ebf1	T	C	11: 45,004,706		probably benign	Het
Epm2a	T	A	10: 11,390,843	Y111N	probably damaging	Het
Gm773	T	C	X: 56,202,017	T52A	probably benign	Het
Gpam	C	A	19: 55,079,261	M483I	probably damaging	Het
Gpr12	T	C	5: 146,583,425	H229R	probably damaging	Het
Gpr149	T	C	3: 62,531,018	T573A	probably damaging	Het
Gtf3c3	C	T	1: 54,417,778	A488T	probably damaging	Het
Hells	T	A	19: 38,957,184		probably null	Het
Herc1	T	A	9: 66,465,469	N3102K	probably benign	Het
Herc3	A	T	6: 58,916,842	T968S	possibly damaging	Het
Ift88	A	G	14: 57,437,279	Y69C	probably benign	Het
Incenp	G	A	19: 9,885,526	T388M	unknown	Het
Jrkl	A	G	9: 13,245,332	F108S	probably benign	Het
Khdc1a	A	G	1: 21,350,318	E54G	possibly damaging	Het
Kif6	T	A	17: 49,620,700	F58L	probably damaging	Het
Klk14	T	C	7: 43,694,918	S218P	probably damaging	Het
Kmt2e	T	C	5: 23,450,321	M19T	probably benign	Het
Llgl1	G	T	11: 60,708,554	G454C	probably damaging	Het
Lyrm4	A	G	13: 36,092,915	V33A	probably benign	Het
Mcam	C	T	9: 44,141,291	R606C	probably damaging	Het
Mgam	T	A	6: 40,756,367	M692K	probably damaging	Het
Mkl2	A	G	16: 13,401,002	N504S	probably benign	Het
Mmp28	C	T	11: 83,442,939	R392H	probably damaging	Het
Mpdz	G	A	4: 81,292,551	T1699M	probably damaging	Het
Mrps11	T	C	7: 78,783,562		probably benign	Het
Msmo1	A	G	8: 64,727,616		probably benign	Het
Mst1	A	G	9: 108,084,204	E571G	probably benign	Het
Myh14	T	C	7: 44,616,299	E1585G	probably damaging	Het
Myrfl	A	G	10: 116,777,427	C824R	probably damaging	Het
Ncapd3	C	T	9: 27,069,872		probably benign	Het
Nlrp4a	G	GGTTCTTC	7: 26,464,197		probably null	Het
Nos1	C	T	5: 117,949,619		probably benign	Het
Notch3	T	C	17: 32,164,224	S47G	probably benign	Het
Npsr1	A	G	9: 24,310,075	Y122C	probably damaging	Het
Olfr1335	T	C	4: 118,809,238	M209V	probably benign	Het
Olfr339	C	T	2: 36,421,643	L82F	probably damaging	Het
Olfr420	T	A	1: 174,158,917	V48E	possibly damaging	Het
Olfr76	G	T	19: 12,120,239	R158S	possibly damaging	Het
Olfr786	C	T	10: 129,436,938	T42I	probably damaging	Het
Olfr877	T	A	9: 37,855,252	L145M	possibly damaging	Het
Otog	G	T	7: 46,300,583	V2490F	probably damaging	Het
Pibf1	T	C	14: 99,112,989	V191A	probably benign	Het
Pip	A	G	6: 41,849,918	M66V	probably benign	Het
Plxna2	C	T	1: 194,767,463	R830C	probably benign	Het
Prkca	A	T	11: 107,939,520	V248E	probably benign	Het
Prmt7	T	A	8: 106,237,284	L253*	probably null	Het
Prrc2a	G	T	17: 35,153,912		probably benign	Het
Rasgrf1	A	G	9: 90,012,800	D1091G	probably benign	Het
Rbm7	C	A	9: 48,489,945	G161V	probably benign	Het
Scn1a	A	T	2: 66,322,429	I736N	probably damaging	Het
Skint6	A	G	4: 112,869,524		probably benign	Het
Slc22a2	C	T	17: 12,584,308	H10Y	possibly damaging	Het
Sned1	G	A	1: 93,281,654	V830M	possibly damaging	Het
Stam2	A	G	2: 52,714,809		probably benign	Het
Stk40	T	C	4: 126,136,833	L282P	probably damaging	Het
Tas2r110	A	G	6: 132,868,368	N121D	probably damaging	Het
Tbc1d32	A	G	10: 56,017,662	Y1272H	probably damaging	Het
Tmem131l	T	C	3: 83,928,714	D696G	probably damaging	Het
Trdmt1	T	C	2: 13,519,846	Y266C	probably damaging	Het
Trim5	G	T	7: 104,279,519	H72N	probably benign	Het
Trim5	A	C	7: 104,279,521	L71R	probably benign	Het
Twf2	T	A	9: 106,214,813		probably benign	Het
Ubap2l	T	C	3: 90,019,328	T580A	probably benign	Het
Ugt1a10	C	T	1: 88,216,260	R201C	probably damaging	Het
Unc5a	A	G	13: 55,004,472		probably benign	Het
Vmn2r85	T	C	10: 130,425,286	N394S	possibly damaging	Het
Wrn	A	T	8: 33,319,141		probably benign	Het

Other mutations in Chka

Allele	Source	Chr	Coord	Type	Predicted Effect	PPH Score
IGL00937:Chka	APN	19	3892189	missense	probably benign	0.16
IGL02630:Chka	APN	19	3892112	missense	possibly damaging	0.94
R1840:Chka	UTSW	19	3886460	missense	probably benign	0.00
R1898:Chka	UTSW	19	3892205	missense	probably damaging	1.00
R3822:Chka	UTSW	19	3882038	intron	probably benign
R4272:Chka	UTSW	19	3875737	splice site	probably benign
R4329:Chka	UTSW	19	3875803	splice site	probably benign
R4573:Chka	UTSW	19	3885960	missense	probably damaging	1.00
R4720:Chka	UTSW	19	3886375	missense	probably damaging	0.99
R4923:Chka	UTSW	19	3892105	critical splice acceptor site	probably null
R5783:Chka	UTSW	19	3864661	missense	probably damaging	1.00
R5936:Chka	UTSW	19	3884580	missense	probably benign	0.25
R5979:Chka	UTSW	19	3884513	missense	probably damaging	1.00
R7429:Chka	UTSW	19	3892787	missense	probably damaging	1.00
R7430:Chka	UTSW	19	3892787	missense	probably damaging	1.00
R8189:Chka	UTSW	19	3875759	nonsense	probably null
R8213:Chka	UTSW	19	3885882	missense	probably damaging	1.00
R8397:Chka	UTSW	19	3852414	critical splice donor site	probably null
R8440:Chka	UTSW	19	3893375	missense	probably damaging	1.00
R9289:Chka	UTSW	19	3885953	missense	possibly damaging	0.75

Predicted Primers

PCR Primer
(F):5'- GTACTCACCCGCATGGTATGTTCC -3'
(R):5'- GCAAATTACTGGCAACCAGGCTTC -3'

Sequencing Primer
(F):5'- TAGGAGCCTCTTGCAGATAGC -3'
(R):5'- ACAGACTGGATCATCGACTG -3'

Posted On

2014-03-14