Mutagenetix > Incidental Mutation

Incidental Mutation 'R3859:Cps1'

276275

Institutional Source

Beutler Lab

Gene Symbol

Cps1

Ensembl Gene

ENSMUSG00000025991

Gene Name

carbamoyl-phosphate synthetase 1

Synonyms

CPS, 4732433M03Rik, D1Ucla3, CPSase I

MMRRC Submission

040787-MU

Accession Numbers

Essential gene?

Essential (E-score: 1.000) question?

Stock #

R3859 (G1)

Quality Score

225

Status

Validated

Chromosome

Chromosomal Location

67162185-67270418 bp(+) (GRCm39)

Type of Mutation

missense

DNA Base Change (assembly)

A to G at 67207437 bp (GRCm39)

Zygosity

Heterozygous

Amino Acid Change

Tyrosine to Cysteine at position 582 (Y582C)

Ref Sequence

ENSEMBL: ENSMUSP00000027144 (fasta)

Gene Model

predicted gene model for transcript(s): [ENSMUST00000027144]

AlphaFold

Q8C196

Predicted Effect

probably damaging
Transcript: ENSMUST00000027144
AA Change: Y582C

PolyPhen 2 Score 0.998 (Sensitivity: 0.27; Specificity: 0.99)

SMART Domains

Protein: ENSMUSP00000027144
Gene: ENSMUSG00000025991
AA Change: Y582C

Domain	Start	End	E-Value	Type
CPSase_sm_chain	44	184	2.5e-70	SMART
Pfam:GATase	221	397	1.5e-40	PFAM
low complexity region	426	436	N/A	INTRINSIC
Pfam:ATP-grasp_4	543	724	6.8e-12	PFAM
Pfam:CPSase_L_D2	546	750	1.7e-85	PFAM
Pfam:ATP-grasp	554	722	4.9e-8	PFAM
Pfam:Dala_Dala_lig_C	561	718	1.5e-7	PFAM
CPSase_L_D3	839	962	1.18e-57	SMART
Pfam:ATP-grasp_4	1085	1264	1e-19	PFAM
Pfam:CPSase_L_D2	1088	1291	7.4e-32	PFAM
Pfam:Dala_Dala_lig_C	1095	1279	1.6e-6	PFAM
Pfam:ATP-grasp	1096	1263	2.8e-12	PFAM
MGS	1373	1465	1.53e-15	SMART

Meta Mutation Damage Score

0.9725

Coding Region Coverage

1x: 99.2%
3x: 98.7%
10x: 97.5%
20x: 95.6%

Validation Efficiency

95% (36/38)

MGI Phenotype

FUNCTION: This gene encodes a protein localized to the inner mitochondrial matrix. The encoded protein plays a role in the detoxification of ammonia by catalyzing the first step in the urea cycle in which carbomyl-phosphate is synthesized from ammonia and bicarbonate. Carbamoyl-phosphate is subsequently converted to urea that is excreted by the kidneys. Deficiency of the encoded enzyme leads to an accumulation of ammonia in the blood. High levels of ammonia are toxic to the central nervous system and result in neurological disorders. [provided by RefSeq, Oct 2013]
PHENOTYPE: Homozygous mutation of this gene results in death by 36 hours after birth and hyperammonemia. [provided by MGI curators]

Allele List at MGI

Other mutations in this stock

Total: 37 list
Gene	Ref	Var	Chr/Loc	Mutation	Predicted Effect	Zygosity
Acot4	A	G	12: 84,090,218 (GRCm39)	N305S	probably benign	Het
Ahnak	A	G	19: 8,988,223 (GRCm39)	E3169G	possibly damaging	Het
Cav2	G	T	6: 17,281,462 (GRCm39)	D35Y	probably damaging	Het
Cemip2	A	G	19: 21,829,598 (GRCm39)	T1236A	probably benign	Het
Ctla2b	T	A	13: 61,043,857 (GRCm39)	Y128F	possibly damaging	Het
Dnajc5b	G	T	3: 19,628,966 (GRCm39)	G87*	probably null	Het
Erc2	A	G	14: 28,197,599 (GRCm39)		probably benign	Het
Ezhip	A	G	X: 5,994,710 (GRCm39)	S102P	possibly damaging	Het
Fat3	G	A	9: 15,908,524 (GRCm39)	Q2493*	probably null	Het
Fbl	G	A	7: 27,873,935 (GRCm39)		probably benign	Het
Fbp1	C	T	13: 63,012,930 (GRCm39)	G88S	probably damaging	Het
Fzd3	A	T	14: 65,477,288 (GRCm39)	C89S	possibly damaging	Het
Gnao1	C	T	8: 94,538,273 (GRCm39)		probably benign	Het
Hspa14	A	T	2: 3,495,616 (GRCm39)	C304*	probably null	Het
Itih4	T	C	14: 30,614,286 (GRCm39)	L412P	probably damaging	Het
Kdm2b	A	G	5: 123,018,290 (GRCm39)	L995P	probably damaging	Het
Krt12	G	A	11: 99,309,319 (GRCm39)	L314F	possibly damaging	Het
Nfatc1	T	C	18: 80,708,490 (GRCm39)		probably benign	Het
Or4c111	A	G	2: 88,844,405 (GRCm39)	M1T	probably null	Het
Or5b119	T	A	19: 13,457,494 (GRCm39)	I23F	possibly damaging	Het
Or8b55	G	A	9: 38,727,443 (GRCm39)	V215I	probably benign	Het
Papss1	T	A	3: 131,313,096 (GRCm39)	L349Q	probably benign	Het
Pcdha6	C	T	18: 37,102,984 (GRCm39)	P6S	possibly damaging	Het
Pik3r2	T	C	8: 71,222,630 (GRCm39)	E487G	probably damaging	Het
Pkd1	A	G	17: 24,797,066 (GRCm39)		probably benign	Het
Prl8a9	C	T	13: 27,742,147 (GRCm39)	G238E	probably damaging	Het
Pth2r	A	T	1: 65,361,206 (GRCm39)	I52F	probably damaging	Het
Purg	T	C	8: 33,876,587 (GRCm39)	F75S	possibly damaging	Het
Rpgrip1l	T	C	8: 91,990,286 (GRCm39)	T719A	probably benign	Het
Slc8a3	G	A	12: 81,361,646 (GRCm39)	P391L	probably damaging	Het
Syne2	T	C	12: 75,976,558 (GRCm39)	L1241P	possibly damaging	Het
Tdrd12	A	G	7: 35,193,245 (GRCm39)	F402L	possibly damaging	Het
Tle4	G	A	19: 14,445,577 (GRCm39)	T223I	probably benign	Het
Tram2	A	C	1: 21,074,204 (GRCm39)	F245V	probably damaging	Het
Trim30b	T	C	7: 104,006,487 (GRCm39)	E123G	probably benign	Het
Unc13c	G	T	9: 73,606,390 (GRCm39)	Y1323*	probably null	Het
Zfp2	T	C	11: 50,790,923 (GRCm39)	I373M	possibly damaging	Het

Other mutations in Cps1

Allele	Source	Chr	Coord	Type	Predicted Effect	PPH Score
IGL00757:Cps1	APN	1	67,191,539 (GRCm39)	splice site	probably benign
IGL00897:Cps1	APN	1	67,254,723 (GRCm39)	missense	probably benign	0.08
IGL00928:Cps1	APN	1	67,162,393 (GRCm39)	missense	probably benign
IGL01063:Cps1	APN	1	67,234,325 (GRCm39)	missense	possibly damaging	0.91
IGL01081:Cps1	APN	1	67,245,983 (GRCm39)	missense	probably damaging	1.00
IGL01361:Cps1	APN	1	67,234,304 (GRCm39)	missense	probably benign	0.03
IGL01396:Cps1	APN	1	67,196,945 (GRCm39)	missense	probably damaging	1.00
IGL01516:Cps1	APN	1	67,269,443 (GRCm39)	missense	probably damaging	0.99
IGL01695:Cps1	APN	1	67,236,194 (GRCm39)	missense	probably benign
IGL02022:Cps1	APN	1	67,212,031 (GRCm39)	splice site	probably benign
IGL02032:Cps1	APN	1	67,269,474 (GRCm39)	missense	probably benign	0.03
IGL02049:Cps1	APN	1	67,183,113 (GRCm39)	missense	possibly damaging	0.68
IGL02197:Cps1	APN	1	67,196,923 (GRCm39)	missense	probably benign
IGL02217:Cps1	APN	1	67,213,541 (GRCm39)	missense	probably benign	0.06
IGL02555:Cps1	APN	1	67,253,180 (GRCm39)	missense	probably benign	0.06
IGL02570:Cps1	APN	1	67,187,862 (GRCm39)	splice site	probably benign
IGL02633:Cps1	APN	1	67,162,396 (GRCm39)	missense	probably benign
IGL02711:Cps1	APN	1	67,251,676 (GRCm39)	splice site	probably benign
IGL02737:Cps1	APN	1	67,187,933 (GRCm39)	missense	probably benign	0.35
IGL03030:Cps1	APN	1	67,182,080 (GRCm39)	missense	probably damaging	1.00
IGL03255:Cps1	APN	1	67,184,960 (GRCm39)	nonsense	probably null
Madman	UTSW	1	67,200,030 (GRCm39)	missense	probably damaging	0.96
maniac	UTSW	1	67,197,037 (GRCm39)	critical splice donor site	probably null
R0109:Cps1	UTSW	1	67,268,577 (GRCm39)	missense	possibly damaging	0.82
R0109:Cps1	UTSW	1	67,268,577 (GRCm39)	missense	possibly damaging	0.82
R0140:Cps1	UTSW	1	67,219,275 (GRCm39)	missense	probably benign
R0318:Cps1	UTSW	1	67,216,173 (GRCm39)	missense	probably damaging	0.99
R0486:Cps1	UTSW	1	67,204,551 (GRCm39)	missense	probably damaging	1.00
R0488:Cps1	UTSW	1	67,187,967 (GRCm39)	splice site	probably benign
R0492:Cps1	UTSW	1	67,196,995 (GRCm39)	missense	probably damaging	1.00
R0521:Cps1	UTSW	1	67,254,723 (GRCm39)	missense	probably benign	0.02
R0534:Cps1	UTSW	1	67,183,059 (GRCm39)	missense	probably benign	0.06
R0565:Cps1	UTSW	1	67,205,608 (GRCm39)	missense	possibly damaging	0.57
R0609:Cps1	UTSW	1	67,211,961 (GRCm39)	missense	probably damaging	1.00
R0612:Cps1	UTSW	1	67,178,929 (GRCm39)	missense	probably benign	0.01
R1185:Cps1	UTSW	1	67,234,358 (GRCm39)	missense	probably benign	0.00
R1185:Cps1	UTSW	1	67,234,358 (GRCm39)	missense	probably benign	0.00
R1185:Cps1	UTSW	1	67,234,358 (GRCm39)	missense	probably benign	0.00
R1220:Cps1	UTSW	1	67,243,862 (GRCm39)	critical splice donor site	probably null
R1321:Cps1	UTSW	1	67,182,178 (GRCm39)	splice site	probably benign
R1343:Cps1	UTSW	1	67,248,768 (GRCm39)	missense	probably damaging	1.00
R1373:Cps1	UTSW	1	67,268,583 (GRCm39)	missense	possibly damaging	0.89
R1374:Cps1	UTSW	1	67,269,440 (GRCm39)	missense	probably damaging	0.97
R1481:Cps1	UTSW	1	67,183,041 (GRCm39)	missense	probably damaging	0.99
R1711:Cps1	UTSW	1	67,207,533 (GRCm39)	splice site	probably null
R1712:Cps1	UTSW	1	67,269,440 (GRCm39)	missense	probably damaging	0.97
R1774:Cps1	UTSW	1	67,210,041 (GRCm39)	missense	possibly damaging	0.94
R1799:Cps1	UTSW	1	67,248,801 (GRCm39)	missense	probably damaging	1.00
R1954:Cps1	UTSW	1	67,234,355 (GRCm39)	missense	possibly damaging	0.71
R2074:Cps1	UTSW	1	67,243,797 (GRCm39)	missense	probably benign	0.21
R2078:Cps1	UTSW	1	67,234,424 (GRCm39)	missense	possibly damaging	0.74
R2078:Cps1	UTSW	1	67,196,965 (GRCm39)	missense	probably damaging	1.00
R2111:Cps1	UTSW	1	67,216,139 (GRCm39)	missense	probably benign	0.01
R2112:Cps1	UTSW	1	67,216,139 (GRCm39)	missense	probably benign	0.01
R2146:Cps1	UTSW	1	67,191,538 (GRCm39)	splice site	probably benign
R2355:Cps1	UTSW	1	67,195,383 (GRCm39)	missense	probably damaging	1.00
R2375:Cps1	UTSW	1	67,257,019 (GRCm39)	missense	probably benign	0.00
R2860:Cps1	UTSW	1	67,205,534 (GRCm39)	missense	probably benign	0.44
R2861:Cps1	UTSW	1	67,205,534 (GRCm39)	missense	probably benign	0.44
R2979:Cps1	UTSW	1	67,243,863 (GRCm39)	critical splice donor site	probably null
R3427:Cps1	UTSW	1	67,213,653 (GRCm39)	missense	probably damaging	1.00
R3833:Cps1	UTSW	1	67,178,946 (GRCm39)	missense	probably damaging	1.00
R3857:Cps1	UTSW	1	67,207,437 (GRCm39)	missense	probably damaging	1.00
R3858:Cps1	UTSW	1	67,207,437 (GRCm39)	missense	probably damaging	1.00
R3886:Cps1	UTSW	1	67,204,659 (GRCm39)	missense	possibly damaging	0.83
R3887:Cps1	UTSW	1	67,204,659 (GRCm39)	missense	possibly damaging	0.83
R3888:Cps1	UTSW	1	67,204,659 (GRCm39)	missense	possibly damaging	0.83
R3889:Cps1	UTSW	1	67,204,659 (GRCm39)	missense	possibly damaging	0.83
R4386:Cps1	UTSW	1	67,210,154 (GRCm39)	critical splice donor site	probably null
R4497:Cps1	UTSW	1	67,244,358 (GRCm39)	missense	probably null	1.00
R4671:Cps1	UTSW	1	67,235,719 (GRCm39)	missense	probably damaging	1.00
R4774:Cps1	UTSW	1	67,259,671 (GRCm39)	missense	probably damaging	0.99
R4799:Cps1	UTSW	1	67,182,145 (GRCm39)	missense	probably damaging	0.96
R4853:Cps1	UTSW	1	67,195,361 (GRCm39)	missense	possibly damaging	0.51
R4884:Cps1	UTSW	1	67,216,183 (GRCm39)	missense	probably benign	0.11
R4900:Cps1	UTSW	1	67,200,063 (GRCm39)	missense	probably damaging	1.00
R4906:Cps1	UTSW	1	67,178,922 (GRCm39)	missense	probably benign	0.10
R5091:Cps1	UTSW	1	67,268,679 (GRCm39)	critical splice donor site	probably null
R5102:Cps1	UTSW	1	67,245,952 (GRCm39)	missense	probably benign	0.00
R5215:Cps1	UTSW	1	67,205,539 (GRCm39)	missense	possibly damaging	0.62
R5290:Cps1	UTSW	1	67,211,868 (GRCm39)	missense	probably benign	0.21
R5732:Cps1	UTSW	1	67,196,923 (GRCm39)	missense	probably benign	0.22
R5818:Cps1	UTSW	1	67,205,647 (GRCm39)	missense	possibly damaging	0.96
R5878:Cps1	UTSW	1	67,197,037 (GRCm39)	critical splice donor site	probably null
R6002:Cps1	UTSW	1	67,211,914 (GRCm39)	missense	possibly damaging	0.94
R6034:Cps1	UTSW	1	67,196,872 (GRCm39)	splice site	probably null
R6034:Cps1	UTSW	1	67,196,872 (GRCm39)	splice site	probably null
R6199:Cps1	UTSW	1	67,201,774 (GRCm39)	frame shift	probably null
R6310:Cps1	UTSW	1	67,182,140 (GRCm39)	missense	probably benign	0.00
R6554:Cps1	UTSW	1	67,213,628 (GRCm39)	nonsense	probably null
R6700:Cps1	UTSW	1	67,268,682 (GRCm39)	splice site	probably null
R6731:Cps1	UTSW	1	67,200,030 (GRCm39)	missense	probably damaging	0.96
R7052:Cps1	UTSW	1	67,237,569 (GRCm39)	missense	probably damaging	1.00
R7278:Cps1	UTSW	1	67,210,080 (GRCm39)	missense	probably damaging	1.00
R7313:Cps1	UTSW	1	67,237,517 (GRCm39)	missense	probably damaging	0.99
R7323:Cps1	UTSW	1	67,197,028 (GRCm39)	missense	probably benign	0.03
R7339:Cps1	UTSW	1	67,236,174 (GRCm39)	missense	possibly damaging	0.64
R7485:Cps1	UTSW	1	67,179,016 (GRCm39)	missense	probably damaging	1.00
R7505:Cps1	UTSW	1	67,219,240 (GRCm39)	missense	probably benign
R7748:Cps1	UTSW	1	67,178,965 (GRCm39)	missense	probably damaging	1.00
R7853:Cps1	UTSW	1	67,213,640 (GRCm39)	missense	possibly damaging	0.92
R8097:Cps1	UTSW	1	67,267,429 (GRCm39)	missense	probably benign	0.08
R8357:Cps1	UTSW	1	67,196,013 (GRCm39)	missense	probably damaging	1.00
R8435:Cps1	UTSW	1	67,251,589 (GRCm39)	missense	probably benign	0.07
R8457:Cps1	UTSW	1	67,196,013 (GRCm39)	missense	probably damaging	1.00
R8680:Cps1	UTSW	1	67,243,772 (GRCm39)	missense	probably damaging	1.00
R8805:Cps1	UTSW	1	67,216,110 (GRCm39)	missense	probably damaging	1.00
R8811:Cps1	UTSW	1	67,253,246 (GRCm39)	missense	probably benign	0.03
R8819:Cps1	UTSW	1	67,267,439 (GRCm39)	missense	possibly damaging	0.56
R8820:Cps1	UTSW	1	67,267,439 (GRCm39)	missense	possibly damaging	0.56
R8854:Cps1	UTSW	1	67,200,048 (GRCm39)	missense	probably damaging	1.00
R9138:Cps1	UTSW	1	67,254,569 (GRCm39)	missense	probably damaging	1.00
R9185:Cps1	UTSW	1	67,248,831 (GRCm39)	missense	probably benign	0.08
R9273:Cps1	UTSW	1	67,191,445 (GRCm39)	missense	possibly damaging	0.69
R9286:Cps1	UTSW	1	67,198,030 (GRCm39)	missense	probably damaging	0.99
R9308:Cps1	UTSW	1	67,200,118 (GRCm39)	critical splice donor site	probably null
R9326:Cps1	UTSW	1	67,248,795 (GRCm39)	missense	probably damaging	1.00
R9449:Cps1	UTSW	1	67,259,671 (GRCm39)	missense	probably damaging	0.99
R9454:Cps1	UTSW	1	67,219,311 (GRCm39)	missense	probably damaging	0.97
R9518:Cps1	UTSW	1	67,259,662 (GRCm39)	missense	probably damaging	1.00
R9564:Cps1	UTSW	1	67,198,048 (GRCm39)	missense	probably benign	0.26
R9585:Cps1	UTSW	1	67,195,341 (GRCm39)	missense	probably damaging	0.99
R9618:Cps1	UTSW	1	67,196,975 (GRCm39)	missense	possibly damaging	0.87
R9641:Cps1	UTSW	1	67,234,342 (GRCm39)	missense	probably benign	0.03
R9650:Cps1	UTSW	1	67,254,636 (GRCm39)	missense
R9668:Cps1	UTSW	1	67,213,649 (GRCm39)	missense	probably benign	0.24
R9726:Cps1	UTSW	1	67,195,395 (GRCm39)	missense	probably benign	0.39
X0024:Cps1	UTSW	1	67,162,406 (GRCm39)	missense	probably benign
Z1176:Cps1	UTSW	1	67,187,878 (GRCm39)	frame shift	probably null
Z1176:Cps1	UTSW	1	67,162,427 (GRCm39)	missense	possibly damaging	0.54

Predicted Primers

PCR Primer
(F):5'- CTCCCCTCTGTGCAAATCAG -3'
(R):5'- GGTAGAGTGACCACTAGTTTACC -3'

Sequencing Primer
(F):5'- CAGCCAATTAACCTGAGTTTCTGGG -3'
(R):5'- GAGTGACCACTAGTTTACCTAAAGTC -3'

Posted On

2015-04-06