Mutagenetix > Incidental Mutation

Incidental Mutation 'R5979:Chka'

481353

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

044161-MU

Accession Numbers

Essential gene?

Essential (E-score: 1.000) question?

Stock #

R5979 (G1)

Quality Score

219.009

Status

Validated

Chromosome

Chromosomal Location

3851773-3894369 bp(+) (GRCm38)

Type of Mutation

missense

DNA Base Change (assembly)

T to G at 3884513 bp (GRCm38)

Zygosity

Heterozygous

Amino Acid Change

Isoleucine to Methionine at position 182 (I182M)

Ref Sequence

ENSEMBL: ENSMUSP00000025760 (fasta)

Gene Model

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

AlphaFold

O54804

Predicted Effect

probably damaging
Transcript: ENSMUST00000025760
AA Change: I182M

PolyPhen 2 Score 0.999 (Sensitivity: 0.14; Specificity: 0.99)

SMART Domains

Protein: ENSMUSP00000025760
Gene: ENSMUSG00000024843
AA Change: I182M

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: I164M

PolyPhen 2 Score 0.996 (Sensitivity: 0.55; Specificity: 0.98)

SMART Domains

Protein: ENSMUSP00000071933
Gene: ENSMUSG00000024843
AA Change: I164M

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: I105M

SMART Domains

Protein: ENSMUSP00000119493
Gene: ENSMUSG00000024843
AA Change: I105M

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

unknown
Transcript: ENSMUST00000153343
AA Change: F35C

Meta Mutation Damage Score

0.4720

Coding Region Coverage

1x: 99.9%
3x: 99.6%
10x: 98.4%
20x: 95.4%

Validation Efficiency

100% (87/87)

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: 85 list
Gene	Ref	Var	Chr/Loc	Mutation	Predicted Effect	Zygosity
Acss2	A	G	2: 155,522,109	I103V	possibly damaging	Het
Adam3	T	C	8: 24,677,367	N36S	probably benign	Het
Adamts3	A	G	5: 89,861,669	V45A	probably damaging	Het
Afg3l2	G	T	18: 67,421,259	L458M	probably damaging	Het
Agtpbp1	A	T	13: 59,534,046	L69*	probably null	Het
Alkbh5	T	A	11: 60,538,691	I90N	probably damaging	Het
Alx1	T	C	10: 103,022,259	Y193C	probably damaging	Het
Ankrd11	T	G	8: 122,892,400	D1571A	probably damaging	Het
Brd4	T	C	17: 32,198,726	D124G	probably benign	Het
C2cd2	G	A	16: 97,875,218	T443I	probably benign	Het
Casp8	A	T	1: 58,828,912	M171L	probably benign	Het
Cd200r4	G	A	16: 44,832,932	V22I	probably benign	Het
Cdcp2	A	G	4: 107,105,281	Y217C	probably damaging	Het
Cfh	C	A	1: 140,118,671	V556F	possibly damaging	Het
Cope	T	C	8: 70,302,543		probably null	Het
Coq10b	T	C	1: 55,052,918	V15A	probably benign	Het
Cpne9	T	A	6: 113,293,749	S309T	probably benign	Het
Daam2	T	A	17: 49,459,204	H992L	possibly damaging	Het
Dctn3	T	C	4: 41,715,393		probably null	Het
Dhx35	G	T	2: 158,842,869	R536L	probably benign	Het
Dnah8	G	T	17: 30,815,664	E4186*	probably null	Het
Dnah9	A	G	11: 65,834,481	L4282P	probably damaging	Het
Dpp10	A	G	1: 123,384,283		probably null	Het
Dst	T	A	1: 34,160,372		probably benign	Het
Ehbp1	C	A	11: 22,151,887	V214L	probably benign	Het
Fam131b	T	C	6: 42,321,971	D25G	probably damaging	Het
Fbxl13	T	A	5: 21,582,091	I283F	probably damaging	Het
Gabrr3	T	G	16: 59,434,568	N205K	possibly damaging	Het
Got1l1	C	T	8: 27,197,923		probably null	Het
Gprin1	G	A	13: 54,739,978	A161V	probably benign	Het
Hepacam2	A	T	6: 3,476,149	F183I	probably damaging	Het
Hmx2	A	G	7: 131,554,550	T82A	probably benign	Het
Igsf10	C	T	3: 59,336,473	E147K	probably damaging	Het
Kndc1	G	A	7: 139,939,827	A1700T	probably benign	Het
Knl1	T	C	2: 119,069,360	V514A	possibly damaging	Het
Lama2	T	C	10: 27,235,732	D764G	probably damaging	Het
Lgi3	G	A	14: 70,536,460	R358H	probably damaging	Het
Limd1	G	T	9: 123,479,414	Q59H	possibly damaging	Het
Lrrk2	A	G	15: 91,772,945	Y1814C	possibly damaging	Het
Lysmd3	G	A	13: 81,665,274		probably null	Het
Mroh7	T	C	4: 106,720,926	N185S	probably benign	Het
Muc2	A	G	7: 141,697,250		probably null	Het
Muc2	G	A	7: 141,751,406	G149D	probably damaging	Het
Nlrp3	T	C	11: 59,548,971	F458S	probably benign	Het
Nop58	A	T	1: 59,702,831	D173V	probably damaging	Het
Nrxn1	C	T	17: 91,088,203	R175H	possibly damaging	Het
Nxpe4	A	G	9: 48,396,562	N322S	probably benign	Het
Ocstamp	A	G	2: 165,397,547	S240P	probably damaging	Het
Olfr137	T	C	17: 38,305,192	K90E	probably benign	Het
Olfr311	A	G	11: 58,841,840	H242R	probably damaging	Het
Olfr713	G	A	7: 107,036,336	M60I	probably damaging	Het
Olfr883	ATTGCTGTTT	ATTGCTGTTTGCTGTTT	9: 38,026,540		probably null	Het
Ovch2	G	A	7: 107,794,388	T177I	possibly damaging	Het
Parn	A	C	16: 13,606,171	L454R	probably damaging	Het
Pcdhb12	T	A	18: 37,437,991	L730Q	possibly damaging	Het
Phf3	G	T	1: 30,805,746	F1377L	probably damaging	Het
Pign	G	T	1: 105,589,274	S542R	probably benign	Het
Prex2	G	T	1: 11,132,372	V502F	probably damaging	Het
Psmd1	A	T	1: 86,090,053	I529F	possibly damaging	Het
Ptafr	A	G	4: 132,579,305	E2G	probably benign	Het
R3hdm1	A	G	1: 128,211,223	N380S	probably benign	Het
Rbm12	A	C	2: 156,097,759		probably benign	Het
Rgl1	A	G	1: 152,557,493	Y174H	probably damaging	Het
Rps6kc1	A	G	1: 190,800,435	S457P	probably damaging	Het
Sall4	A	T	2: 168,750,343	S964T	probably benign	Het
Sart1	T	A	19: 5,381,223	I681F	probably damaging	Het
Serinc5	T	C	13: 92,661,136	L49P	probably benign	Het
Serpinb9e	T	C	13: 33,255,053	V154A	probably benign	Het
Skiv2l	A	T	17: 34,841,463	N851K	probably benign	Het
Smox	G	A	2: 131,516,414	V136I	probably damaging	Het
Sspo	C	T	6: 48,463,693	T1747I	probably benign	Het
Swt1	A	T	1: 151,407,588	D339E	possibly damaging	Het
Synpo2	A	G	3: 123,117,411	L195P	probably damaging	Het
Syt7	G	T	19: 10,443,479	G414W	probably damaging	Het
Tmem186	G	A	16: 8,636,160	T79I	probably damaging	Het
Tmem39a	A	T	16: 38,575,744	N113I	probably damaging	Het
Trim14	C	T	4: 46,507,239	V326M	probably damaging	Het
Trim58	A	G	11: 58,646,083	E234G	probably damaging	Het
Ttr	T	C	18: 20,670,002	L75P	probably damaging	Het
Ubr1	C	T	2: 120,946,382	V293I	probably benign	Het
Vmn1r91	T	A	7: 20,102,065	V303E	probably benign	Het
Vmn2r30	A	C	7: 7,312,335	I833S	probably damaging	Het
Zfp131	G	T	13: 119,776,446	N125K	probably benign	Het
Zfp169	A	T	13: 48,491,040		probably benign	Het
Zfp213	C	A	17: 23,557,911	E386*	probably null	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
R1432:Chka	UTSW	19	3874809	splice site	probably benign
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
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'- GAGCTAGATCCTGTATAAGCCC -3'
(R):5'- GTGTCCTGAGCAAAGCTAGG -3'

Sequencing Primer
(F):5'- CTAGATCCTGTATAAGCCCTGTGTG -3'
(R):5'- GCTAGGCAGTTTATAAATCCCAC -3'

Posted On

2017-06-26