Mutagenetix > Incidental Mutations

Incidental Mutation 'R5081:Gpcpd1'

387111

Institutional Source

Beutler Lab

Gene Symbol

Gpcpd1

Ensembl Gene

ENSMUSG00000027346

Gene Name

glycerophosphocholine phosphodiesterase 1

Synonyms

2310004G06Rik, 2310032D16Rik, Prei4

MMRRC Submission

042670-MU

Accession Numbers

Is this an essential gene?

Probably essential (E-score: 0.945) question?

Stock #

R5081 (G1)

Quality Score

225

Status

Validated

Chromosome

Chromosomal Location

132529082-132587729 bp(-) (GRCm38)

Type of Mutation

missense

DNA Base Change (assembly)

A to T at 132547702 bp

Zygosity

Heterozygous

Amino Acid Change

Histidine to Glutamine at position 244 (H244Q)

Ref Sequence

ENSEMBL: ENSMUSP00000105769 (fasta)

Gene Model

predicted gene model for transcript(s): [ENSMUST00000028822] [ENSMUST00000060955] [ENSMUST00000110136] [ENSMUST00000110142] [ENSMUST00000124107] [ENSMUST00000145694] [ENSMUST00000148833] [ENSMUST00000149854]

Predicted Effect

probably benign
Transcript: ENSMUST00000028822
AA Change: H60Q

PolyPhen 2 Score 0.170 (Sensitivity: 0.92; Specificity: 0.87)

SMART Domains

Protein: ENSMUSP00000028822
Gene: ENSMUSG00000027346
AA Change: H60Q

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

Predicted Effect

probably benign
Transcript: ENSMUST00000060955
AA Change: H244Q

PolyPhen 2 Score 0.170 (Sensitivity: 0.92; Specificity: 0.87)

SMART Domains

Protein: ENSMUSP00000062221
Gene: ENSMUSG00000027346
AA Change: H244Q

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 benign
Transcript: ENSMUST00000110136
AA Change: H60Q

PolyPhen 2 Score 0.170 (Sensitivity: 0.92; Specificity: 0.87)

SMART Domains

Protein: ENSMUSP00000105763
Gene: ENSMUSG00000027346
AA Change: H60Q

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

Predicted Effect

probably benign
Transcript: ENSMUST00000110142
AA Change: H244Q

PolyPhen 2 Score 0.170 (Sensitivity: 0.92; Specificity: 0.87)

SMART Domains

Protein: ENSMUSP00000105769
Gene: ENSMUSG00000027346
AA Change: H244Q

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: ENSMUST00000124107

SMART Domains

Protein: ENSMUSP00000122751
Gene: ENSMUSG00000027346

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

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

0.0898

Coding Region Coverage

1x: 99.2%
3x: 98.4%
10x: 96.5%
20x: 93.2%

Validation Efficiency

93% (65/70)

Allele List at MGI

Other mutations in this stock

Total: 57 list
Gene	Ref	Var	Chr/Loc	Mutation	Predicted Effect	Zygosity
Agbl5	G	A	5: 30,903,059	R141Q	probably damaging	Het
AI593442	TGAGGAGGAGGAGGAGGA	TGAGGAGGAGGAGGA	9: 52,677,814		probably benign	Het
Aig1	A	G	10: 13,801,900	I116T	probably benign	Het
Alox12	A	T	11: 70,255,314		probably null	Het
Ap3s1	T	A	18: 46,754,430	D43E	probably benign	Het
Arhgap35	A	G	7: 16,565,134	M2T	possibly damaging	Het
Asah2	T	A	19: 32,014,308	E451V	probably benign	Het
Ash1l	T	G	3: 88,984,717	I1301S	probably damaging	Het
Ass1	G	A	2: 31,488,653		probably null	Het
Ccpg1	A	G	9: 72,999,078	T39A	possibly damaging	Het
Cd101	T	A	3: 101,003,705	Y879F	possibly damaging	Het
Cdc23	C	A	18: 34,651,689	V7L	unknown	Het
Cdh23	T	C	10: 60,436,807	T530A	possibly damaging	Het
Cep68	G	T	11: 20,238,477	Q643K	probably damaging	Het
Ces1c	A	G	8: 93,127,569	S113P	probably damaging	Het
Cnga4	T	C	7: 105,407,025	I278T	probably benign	Het
Col1a1	A	G	11: 94,951,576	D1440G	unknown	Het
Cspp1	A	G	1: 10,047,466	I48V	possibly damaging	Het
Ctsj	T	A	13: 61,003,850	S85C	possibly damaging	Het
Cyp39a1	C	A	17: 43,746,597	D442E	probably damaging	Het
Dock3	A	T	9: 106,991,093	F664Y	probably damaging	Het
Gtf3a	T	A	5: 146,951,282	V131E	probably benign	Het
Gtpbp3	A	T	8: 71,490,382	R147W	probably damaging	Het
H2-Ke6	G	A	17: 34,027,578		probably benign	Het
H2-Oa	A	T	17: 34,094,370	I132F	probably damaging	Het
Idi1	T	A	13: 8,887,927	C91*	probably null	Het
Itga11	A	G	9: 62,755,196	I484V	probably benign	Het
Kpna3	C	T	14: 61,391,245	S101N	probably damaging	Het
Larp4	G	A	15: 99,973,017		probably benign	Het
Mink1	T	C	11: 70,605,144	L390P	probably damaging	Het
Morc1	T	G	16: 48,502,352	S337R	probably benign	Het
Myo10	A	G	15: 25,785,940	R1236G	probably damaging	Het
Nkx3-1	T	C	14: 69,191,947	I138T	possibly damaging	Het
Nnt	T	C	13: 119,366,400	N489S	probably damaging	Het
Nrcam	A	T	12: 44,570,353	I711F	probably benign	Het
Ntrk3	A	G	7: 78,577,774	S4P	probably damaging	Het
Obsl1	T	C	1: 75,487,963	T1605A	possibly damaging	Het
Olfr346	A	G	2: 36,688,643	I214V	possibly damaging	Het
Olfr851	A	G	9: 19,497,261	E171G	probably benign	Het
Pank1	T	C	19: 34,878,916	H54R	probably benign	Het
Pgm2l1	A	G	7: 100,268,265	I530V	probably benign	Het
Psmd2	A	G	16: 20,661,655	T709A	probably benign	Het
Qsox1	G	T	1: 155,812,835		probably benign	Het
Rbm14	A	G	19: 4,802,795	S520P	probably benign	Het
Rbm15b	G	A	9: 106,884,921	R683C	probably benign	Het
Rhbdd2	T	A	5: 135,636,022	V69D	probably damaging	Het
Sart1	T	C	19: 5,388,548	E27G	possibly damaging	Het
Scn4a	G	A	11: 106,348,727	P153L	probably damaging	Het
Serpinb6d	A	T	13: 33,671,247	R301S	probably benign	Het
Sf3a2	C	A	10: 80,804,441		probably benign	Het
Syne1	T	C	10: 5,047,767	D400G	probably benign	Het
Tenm2	T	C	11: 36,024,633	S2025G	possibly damaging	Het
Ttc16	A	T	2: 32,767,976	D476E	probably damaging	Het
Ttc9c	A	T	19: 8,816,032	C81*	probably null	Het
Ulk2	G	A	11: 61,803,662	P474L	probably damaging	Het
Vmn1r66	A	G	7: 10,274,795	C104R	probably damaging	Het
Vwa2	C	T	19: 56,909,320	H686Y	probably damaging	Het

Other mutations in Gpcpd1

Allele	Source	Chr	Coord	Type	Predicted Effect	PPH Score
IGL00542:Gpcpd1	APN	2	132556983	splice site	probably null
IGL00672:Gpcpd1	APN	2	132530548	utr 3 prime	probably benign
IGL00676:Gpcpd1	APN	2	132554011	missense	probably damaging	1.00
IGL00832:Gpcpd1	APN	2	132546850	missense	probably damaging	1.00
IGL00931:Gpcpd1	APN	2	132538118	missense	probably benign	0.00
IGL01309:Gpcpd1	APN	2	132550324	missense	probably damaging	0.97
IGL01960:Gpcpd1	APN	2	132539898	critical splice donor site	probably null
IGL02110:Gpcpd1	APN	2	132530610	nonsense	probably null
IGL02267:Gpcpd1	APN	2	132568710	missense	probably damaging	1.00
IGL02570:Gpcpd1	APN	2	132547685	missense	probably benign	0.01
IGL02588:Gpcpd1	APN	2	132534753	missense	probably damaging	1.00
IGL03306:Gpcpd1	APN	2	132534073	critical splice donor site	probably null
Baependi	UTSW	2	132544435	missense	probably damaging	1.00
R0413:Gpcpd1	UTSW	2	132564623	splice site	probably benign
R1876:Gpcpd1	UTSW	2	132534753	missense	probably damaging	1.00
R4276:Gpcpd1	UTSW	2	132540287	missense	probably damaging	0.99
R4571:Gpcpd1	UTSW	2	132550350	missense	probably benign	0.05
R4849:Gpcpd1	UTSW	2	132534099	missense	probably damaging	1.00
R4930:Gpcpd1	UTSW	2	132546874	missense	probably damaging	1.00
R5060:Gpcpd1	UTSW	2	132544435	missense	probably damaging	1.00
R5148:Gpcpd1	UTSW	2	132534190	nonsense	probably null
R5189:Gpcpd1	UTSW	2	132553972	missense	probably damaging	1.00
R5344:Gpcpd1	UTSW	2	132558677	intron	probably benign
R5623:Gpcpd1	UTSW	2	132534717	missense	probably damaging	1.00
R6086:Gpcpd1	UTSW	2	132538114	missense	probably damaging	1.00
R6787:Gpcpd1	UTSW	2	132537838	intron	probably benign
R6885:Gpcpd1	UTSW	2	132554074	missense	possibly damaging	0.56
R7223:Gpcpd1	UTSW	2	132534056	missense	probably benign	0.00
R7261:Gpcpd1	UTSW	2	132568699	missense	probably damaging	0.97
R7900:Gpcpd1	UTSW	2	132534739	missense	probably damaging	0.99
R8120:Gpcpd1	UTSW	2	132554023	missense	probably damaging	1.00
R8494:Gpcpd1	UTSW	2	132544435	missense	probably damaging	0.97
X0018:Gpcpd1	UTSW	2	132534769	missense	probably damaging	1.00
X0060:Gpcpd1	UTSW	2	132534781	missense	probably damaging	1.00
X0066:Gpcpd1	UTSW	2	132544395	missense	probably benign	0.33

Predicted Primers

PCR Primer
(F):5'- TAAGGGCCTAGCTGCTTCTC -3'
(R):5'- CCAAGTTCACTTTGAAGGTTTTAGG -3'

Sequencing Primer
(F):5'- AGCTGCTTCTCCCCAACTTAC -3'
(R):5'- GTCCTCTGACCTCTACATAC -3'

Posted On

2016-06-06