Mutagenetix > Incidental Mutation

Incidental Mutation 'R4849:Gpcpd1'

373368

Institutional Source

Beutler Lab

Gene Symbol

Gpcpd1

Ensembl Gene

ENSMUSG00000027346

Gene Name

glycerophosphocholine phosphodiesterase 1

Synonyms

Prei4, 2310004G06Rik, 2310032D16Rik

MMRRC Submission

042461-MU

Accession Numbers

Essential gene?

Probably essential (E-score: 0.936) question?

Stock #

R4849 (G1)

Quality Score

225

Status

Validated

Chromosome

Chromosomal Location

132371002-132420173 bp(-) (GRCm39)

Type of Mutation

missense

DNA Base Change (assembly)

C to T at 132376019 bp (GRCm39)

Zygosity

Heterozygous

Amino Acid Change

Glycine to Arginine at position 605 (G605R)

Ref Sequence

ENSEMBL: ENSMUSP00000105769 (fasta)

Gene Model

predicted gene model for transcript(s): [ENSMUST00000028822] [ENSMUST00000060955] [ENSMUST00000110136] [ENSMUST00000110142] [ENSMUST00000145694] [ENSMUST00000148833] [ENSMUST00000149854]

AlphaFold

Q8C0L9

Predicted Effect

probably damaging
Transcript: ENSMUST00000028822
AA Change: G421R

PolyPhen 2 Score 1.000 (Sensitivity: 0.00; Specificity: 1.00)

SMART Domains

Protein: ENSMUSP00000028822
Gene: ENSMUSG00000027346
AA Change: G421R

Domain	Start	End	E-Value	Type
Pfam:GDPD	142	432	1.3e-61	PFAM

Predicted Effect

probably damaging
Transcript: ENSMUST00000060955
AA Change: G605R

PolyPhen 2 Score 1.000 (Sensitivity: 0.00; Specificity: 1.00)

SMART Domains

Protein: ENSMUSP00000062221
Gene: ENSMUSG00000027346
AA Change: G605R

Domain	Start	End	E-Value	Type
CBM_2	3	110	3.78e-29	SMART
low complexity region	142	160	N/A	INTRINSIC
low complexity region	167	175	N/A	INTRINSIC
Pfam:GDPD	326	615	5.3e-61	PFAM

Predicted Effect

probably damaging
Transcript: ENSMUST00000110136
AA Change: G421R

PolyPhen 2 Score 1.000 (Sensitivity: 0.00; Specificity: 1.00)

SMART Domains

Protein: ENSMUSP00000105763
Gene: ENSMUSG00000027346
AA Change: G421R

Domain	Start	End	E-Value	Type
Pfam:GDPD	142	431	4.1e-59	PFAM

Predicted Effect

probably damaging
Transcript: ENSMUST00000110142
AA Change: G605R

PolyPhen 2 Score 1.000 (Sensitivity: 0.00; Specificity: 1.00)

SMART Domains

Protein: ENSMUSP00000105769
Gene: ENSMUSG00000027346
AA Change: G605R

Domain	Start	End	E-Value	Type
CBM_2	3	110	3.78e-29	SMART
low complexity region	142	160	N/A	INTRINSIC
low complexity region	167	175	N/A	INTRINSIC
Pfam:GDPD	326	615	6.1e-63	PFAM

Predicted Effect

probably benign
Transcript: ENSMUST00000124632

Predicted Effect

noncoding transcript
Transcript: ENSMUST00000127712

Predicted Effect

probably benign
Transcript: ENSMUST00000145694

SMART Domains

Protein: ENSMUSP00000116457
Gene: ENSMUSG00000027346

Domain	Start	End	E-Value	Type
CBM_2	3	110	3.78e-29	SMART

Predicted Effect

probably benign
Transcript: ENSMUST00000148833

SMART Domains

Protein: ENSMUSP00000116156
Gene: ENSMUSG00000027346

Domain	Start	End	E-Value	Type
CBM_2	3	99	1.02e-11	SMART

Predicted Effect

probably benign
Transcript: ENSMUST00000149854

SMART Domains

Protein: ENSMUSP00000116949
Gene: ENSMUSG00000027346

Domain	Start	End	E-Value	Type
CBM_2	3	94	5.54e-13	SMART

Meta Mutation Damage Score

0.8370

Coding Region Coverage

1x: 99.2%
3x: 98.5%
10x: 96.9%
20x: 94.2%

Validation Efficiency

98% (90/92)

Allele List at MGI

Other mutations in this stock

Total: 82 list
Gene	Ref	Var	Chr/Loc	Mutation	Predicted Effect	Zygosity
Acp7	G	T	7: 28,314,877 (GRCm39)	R239S	possibly damaging	Het
Angptl1	C	A	1: 156,684,735 (GRCm39)	N301K	probably benign	Het
Ankrd26	T	A	6: 118,509,257 (GRCm39)	T603S	probably benign	Het
App	T	C	16: 84,853,322 (GRCm39)	D252G	unknown	Het
Atxn3	A	G	12: 101,900,627 (GRCm39)	S219P	probably benign	Het
Birc6	T	C	17: 74,954,383 (GRCm39)	S3397P	probably damaging	Het
Bivm	A	G	1: 44,182,033 (GRCm39)	I414V	possibly damaging	Het
Cemip	A	G	7: 83,584,945 (GRCm39)	F1324L	possibly damaging	Het
Ckap5	T	A	2: 91,445,616 (GRCm39)	N1724K	probably damaging	Het
Corin	T	A	5: 72,460,178 (GRCm39)	M1035L	probably damaging	Het
Ctnna3	T	C	10: 64,709,094 (GRCm39)	I711T	probably damaging	Het
Cts6	A	T	13: 61,349,415 (GRCm39)	W98R	probably null	Het
Dip2a	A	G	10: 76,130,367 (GRCm39)	S580P	probably damaging	Het
Dock6	A	G	9: 21,723,068 (GRCm39)		probably null	Het
Dusp15	T	A	2: 152,791,002 (GRCm39)	T32S	probably damaging	Het
Eogt	T	A	6: 97,093,016 (GRCm39)	N387I	probably damaging	Het
Evx2	T	C	2: 74,489,675 (GRCm39)	D29G	probably benign	Het
Fat1	A	G	8: 45,466,007 (GRCm39)	N1422S	probably benign	Het
Fat2	T	C	11: 55,201,463 (GRCm39)	D537G	probably damaging	Het
Fat3	A	C	9: 16,289,244 (GRCm39)	I93S	probably benign	Het
Fem1b	T	C	9: 62,704,576 (GRCm39)	E228G	probably damaging	Het
Fh1	A	G	1: 175,448,072 (GRCm39)	T25A	probably benign	Het
Fndc3b	A	G	3: 27,514,097 (GRCm39)	W695R	probably damaging	Het
Gaa	G	A	11: 119,163,813 (GRCm39)	V222I	possibly damaging	Het
Ggnbp1	T	C	17: 27,251,947 (GRCm39)		probably null	Het
Gipc1	A	G	8: 84,388,756 (GRCm39)	Y154C	probably benign	Het
Gm5356	G	T	8: 89,913,670 (GRCm39)		noncoding transcript	Het
Gnl1	T	A	17: 36,298,603 (GRCm39)		probably null	Het
Guca1a	T	C	17: 47,705,662 (GRCm39)	T177A	possibly damaging	Het
Ifit1bl1	T	C	19: 34,572,076 (GRCm39)	E127G	probably damaging	Het
Ift81	A	T	5: 122,729,282 (GRCm39)	I350N	probably damaging	Het
Ikbke	GCC	G	1: 131,203,004 (GRCm39)		probably null	Het
Ing4	A	G	6: 125,020,946 (GRCm39)	R23G	probably damaging	Het
Ins1	A	G	19: 52,253,384 (GRCm39)	N108S	probably damaging	Het
Iqce	A	T	5: 140,679,214 (GRCm39)	M72K	possibly damaging	Het
Itga3	C	A	11: 94,967,097 (GRCm39)	M22I	probably benign	Het
Kctd18	T	C	1: 58,001,152 (GRCm39)	E201G	probably damaging	Het
Klc1	A	G	12: 111,748,129 (GRCm39)	N344S	probably damaging	Het
Klrb1f	A	T	6: 129,033,347 (GRCm39)	I192F	probably damaging	Het
Klrg2	A	T	6: 38,607,214 (GRCm39)		probably null	Het
Kntc1	A	C	5: 123,897,128 (GRCm39)	I164L	probably benign	Het
Ltf	T	A	9: 110,855,058 (GRCm39)	I357K	probably benign	Het
Mr1	T	C	1: 155,006,436 (GRCm39)	T304A	probably benign	Het
Msh6	C	T	17: 88,290,947 (GRCm39)	R178C	possibly damaging	Het
Mtch1	T	C	17: 29,566,565 (GRCm39)	D66G	probably benign	Het
Mtmr7	A	G	8: 41,062,040 (GRCm39)	V15A	probably benign	Het
Mtss2	A	T	8: 111,452,875 (GRCm39)	H40L	possibly damaging	Het
Mxra8	A	G	4: 155,925,331 (GRCm39)		probably benign	Het
Myo3b	T	C	2: 70,075,253 (GRCm39)	L535P	probably damaging	Het
Neurl2	T	A	2: 164,674,739 (GRCm39)		probably null	Het
Nfia	A	C	4: 97,970,048 (GRCm39)	T503P	probably damaging	Het
Noa1	T	C	5: 77,454,179 (GRCm39)	E487G	possibly damaging	Het
Nuak1	A	T	10: 84,211,143 (GRCm39)	V315D	probably damaging	Het
Nup205	A	G	6: 35,207,505 (GRCm39)	N1519S	possibly damaging	Het
Or10x1	T	A	1: 174,196,966 (GRCm39)	I161K	probably damaging	Het
Or1l4b	T	C	2: 37,036,266 (GRCm39)	L14P	probably damaging	Het
Or1o1	T	C	17: 37,716,589 (GRCm39)	V50A	probably benign	Het
Or51f1e	A	G	7: 102,747,526 (GRCm39)	I193V	possibly damaging	Het
Or6b13	G	T	7: 139,782,340 (GRCm39)	C114*	probably null	Het
Or9s18	G	A	13: 65,300,493 (GRCm39)	V152M	possibly damaging	Het
Peli1	T	A	11: 21,098,528 (GRCm39)		probably benign	Het
Ppp6r1	A	G	7: 4,646,206 (GRCm39)	L175P	probably damaging	Het
Prkcd	A	G	14: 30,321,700 (GRCm39)	L498P	probably damaging	Het
Prss30	T	A	17: 24,191,769 (GRCm39)	I251F	probably benign	Het
Psme3	A	T	11: 101,207,907 (GRCm39)	N21Y	probably benign	Het
Ptpra	T	C	2: 130,374,081 (GRCm39)	Y271H	probably damaging	Het
Ralgapa1	T	A	12: 55,745,588 (GRCm39)	N1303Y	probably damaging	Het
Rims4	T	C	2: 163,707,463 (GRCm39)	I121V	probably benign	Het
Rnf123	A	T	9: 107,933,290 (GRCm39)	L1149Q	probably damaging	Het
Ryr3	T	A	2: 112,738,807 (GRCm39)	L593F	probably damaging	Het
Sec23b	T	C	2: 144,427,519 (GRCm39)	F582S	probably damaging	Het
Sgpl1	T	C	10: 60,940,297 (GRCm39)	K335R	probably benign	Het
Sirpa	C	T	2: 129,451,163 (GRCm39)	T141I	probably damaging	Het
Slit1	G	T	19: 41,637,983 (GRCm39)	A270E	probably benign	Het
Snap91	T	C	9: 86,674,613 (GRCm39)	T533A	possibly damaging	Het
Sphkap	T	G	1: 83,255,105 (GRCm39)	E881D	probably benign	Het
Sptan1	C	A	2: 29,901,054 (GRCm39)	R1407S	probably damaging	Het
Tfdp1	A	G	8: 13,423,895 (GRCm39)	T353A	probably benign	Het
Ttyh1	A	G	7: 4,125,533 (GRCm39)	I62V	possibly damaging	Het
Vwde	A	T	6: 13,196,047 (GRCm39)	V326D	possibly damaging	Het
Zfp398	T	C	6: 47,836,446 (GRCm39)	I82T	possibly damaging	Het
Zp1	A	G	19: 10,896,198 (GRCm39)	Y176H	possibly damaging	Het

Other mutations in Gpcpd1

Allele	Source	Chr	Coord	Type	Predicted Effect	PPH Score
IGL00542:Gpcpd1	APN	2	132,398,903 (GRCm39)	splice site	probably null
IGL00672:Gpcpd1	APN	2	132,372,468 (GRCm39)	utr 3 prime	probably benign
IGL00676:Gpcpd1	APN	2	132,395,931 (GRCm39)	missense	probably damaging	1.00
IGL00832:Gpcpd1	APN	2	132,388,770 (GRCm39)	missense	probably damaging	1.00
IGL00931:Gpcpd1	APN	2	132,380,038 (GRCm39)	missense	probably benign	0.00
IGL01309:Gpcpd1	APN	2	132,392,244 (GRCm39)	missense	probably damaging	0.97
IGL01960:Gpcpd1	APN	2	132,381,818 (GRCm39)	critical splice donor site	probably null
IGL02110:Gpcpd1	APN	2	132,372,530 (GRCm39)	nonsense	probably null
IGL02267:Gpcpd1	APN	2	132,410,630 (GRCm39)	missense	probably damaging	1.00
IGL02570:Gpcpd1	APN	2	132,389,605 (GRCm39)	missense	probably benign	0.01
IGL02588:Gpcpd1	APN	2	132,376,673 (GRCm39)	missense	probably damaging	1.00
IGL03306:Gpcpd1	APN	2	132,375,993 (GRCm39)	critical splice donor site	probably null
Baependi	UTSW	2	132,386,355 (GRCm39)	missense	probably damaging	1.00
R0413:Gpcpd1	UTSW	2	132,406,543 (GRCm39)	splice site	probably benign
R1876:Gpcpd1	UTSW	2	132,376,673 (GRCm39)	missense	probably damaging	1.00
R4276:Gpcpd1	UTSW	2	132,382,207 (GRCm39)	missense	probably damaging	0.99
R4571:Gpcpd1	UTSW	2	132,392,270 (GRCm39)	missense	probably benign	0.05
R4930:Gpcpd1	UTSW	2	132,388,794 (GRCm39)	missense	probably damaging	1.00
R5060:Gpcpd1	UTSW	2	132,386,355 (GRCm39)	missense	probably damaging	1.00
R5081:Gpcpd1	UTSW	2	132,389,622 (GRCm39)	missense	probably benign	0.17
R5148:Gpcpd1	UTSW	2	132,376,110 (GRCm39)	nonsense	probably null
R5189:Gpcpd1	UTSW	2	132,395,892 (GRCm39)	missense	probably damaging	1.00
R5344:Gpcpd1	UTSW	2	132,400,597 (GRCm39)	intron	probably benign
R5623:Gpcpd1	UTSW	2	132,376,637 (GRCm39)	missense	probably damaging	1.00
R6086:Gpcpd1	UTSW	2	132,380,034 (GRCm39)	missense	probably damaging	1.00
R6787:Gpcpd1	UTSW	2	132,379,758 (GRCm39)	intron	probably benign
R6885:Gpcpd1	UTSW	2	132,395,994 (GRCm39)	missense	possibly damaging	0.56
R7223:Gpcpd1	UTSW	2	132,375,976 (GRCm39)	missense	probably benign	0.00
R7261:Gpcpd1	UTSW	2	132,410,619 (GRCm39)	missense	probably damaging	0.97
R7900:Gpcpd1	UTSW	2	132,376,659 (GRCm39)	missense	probably damaging	0.99
R8120:Gpcpd1	UTSW	2	132,395,943 (GRCm39)	missense	probably damaging	1.00
R8494:Gpcpd1	UTSW	2	132,386,355 (GRCm39)	missense	probably damaging	0.97
R9594:Gpcpd1	UTSW	2	132,388,848 (GRCm39)	missense	possibly damaging	0.80
X0018:Gpcpd1	UTSW	2	132,376,689 (GRCm39)	missense	probably damaging	1.00
X0060:Gpcpd1	UTSW	2	132,376,701 (GRCm39)	missense	probably damaging	1.00
X0066:Gpcpd1	UTSW	2	132,386,315 (GRCm39)	missense	probably benign	0.33

Predicted Primers

PCR Primer
(F):5'- AGGGCTTCTTAAGTGACTTTTGAC -3'
(R):5'- TCCTTTAGAGAGCACTAACCTGATC -3'

Sequencing Primer
(F):5'- TGACATATCTCAACATCTGGGAC -3'
(R):5'- AGAGAGCACTAACCTGATCATTTAG -3'

Posted On

2016-03-01