Mutagenetix > Incidental Mutation

Incidental Mutation 'R1604:Gnpat'

176337

Institutional Source

Beutler Lab

Gene Symbol

Gnpat

Ensembl Gene

ENSMUSG00000031985

Gene Name

glyceronephosphate O-acyltransferase

Synonyms

D1Ertd819e

MMRRC Submission

039641-MU

Accession Numbers

Essential gene?

Possibly non essential (E-score: 0.387) question?

Stock #

R1604 (G1)

Quality Score

225

Status

Not validated

Chromosome

Chromosomal Location

125589772-125616796 bp(+) (GRCm39)

Type of Mutation

missense

DNA Base Change (assembly)

T to C at 125603700 bp (GRCm39)

Zygosity

Heterozygous

Amino Acid Change

Serine to Proline at position 193 (S193P)

Ref Sequence

ENSEMBL: ENSMUSP00000125323 (fasta)

Gene Model

predicted gene model for transcript(s): [ENSMUST00000034466] [ENSMUST00000161986]

AlphaFold

P98192

Predicted Effect

probably damaging
Transcript: ENSMUST00000034466
AA Change: S203P

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

SMART Domains

Protein: ENSMUSP00000034466
Gene: ENSMUSG00000031985
AA Change: S203P

Domain	Start	End	E-Value	Type
low complexity region	5	20	N/A	INTRINSIC
SCOP:d1dbha1	27	146	6e-3	SMART
PlsC	155	284	8.3e-21	SMART
Blast:PlsC	308	336	1e-6	BLAST
low complexity region	638	652	N/A	INTRINSIC

Predicted Effect

probably damaging
Transcript: ENSMUST00000161986
AA Change: S193P

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

SMART Domains

Protein: ENSMUSP00000125323
Gene: ENSMUSG00000031985
AA Change: S193P

Domain	Start	End	E-Value	Type
low complexity region	5	20	N/A	INTRINSIC
PlsC	145	274	8.3e-21	SMART
Blast:PlsC	298	326	2e-6	BLAST

Coding Region Coverage

1x: 99.0%
3x: 98.0%
10x: 95.3%
20x: 89.1%

Validation Efficiency

MGI Phenotype

FUNCTION: [Summary is not available for the mouse gene. This summary is for the human ortholog.] This gene encodes an enzyme located in the peroxisomal membrane which is essential to the synthesis of ether phospholipids. Mutations in this gene are associated with rhizomelic chondrodysplasia punctata. Two transcript variants encoding different isoforms have been found for this gene. [provided by RefSeq, Oct 2015]
PHENOTYPE: Homozygous mutant mice lack plasmalogens due to inactivation of ether lipid synthesis. Mutant mice exhibit dwarfism, male infertility, defects in eye development, and optic nerve hypoplasia. While some mice die prematurely, others, particularly females, are long-lived. [provided by MGI curators]

Allele List at MGI

Other mutations in this stock

Total: 62 list
Gene	Ref	Var	Chr/Loc	Mutation	Predicted Effect	Zygosity
Aldoart2	A	G	12: 55,612,405 (GRCm39)	D110G	probably damaging	Het
Angptl2	T	C	2: 33,133,785 (GRCm39)	M369T	possibly damaging	Het
Anks3	C	T	16: 4,766,117 (GRCm39)	V151M	probably damaging	Het
Arl6ip6	T	C	2: 53,082,508 (GRCm39)	L125P	probably damaging	Het
Bmp1	T	C	14: 70,745,444 (GRCm39)	Q247R	possibly damaging	Het
Ccdc30	A	G	4: 119,188,793 (GRCm39)	I491T	probably damaging	Het
Cdhr1	T	A	14: 36,817,050 (GRCm39)	I104F	probably benign	Het
Cdk17	G	T	10: 93,068,360 (GRCm39)	M372I	probably damaging	Het
Cyp2c54	A	G	19: 40,058,787 (GRCm39)	V215A	probably benign	Het
D430041D05Rik	T	A	2: 104,035,487 (GRCm39)	I1614F	probably damaging	Het
Ddx55	A	G	5: 124,697,369 (GRCm39)	N244D	probably damaging	Het
Dop1b	G	T	16: 93,559,458 (GRCm39)	V617F	probably benign	Het
Erbb4	G	T	1: 68,385,728 (GRCm39)	A287E	possibly damaging	Het
Fmnl2	A	G	2: 52,995,549 (GRCm39)	E424G	probably damaging	Het
Gad2	T	C	2: 22,513,852 (GRCm39)		probably null	Het
Gm17421	G	A	12: 113,333,155 (GRCm39)		noncoding transcript	Het
Gm9894	T	A	13: 67,913,008 (GRCm39)		noncoding transcript	Het
Gpr20	C	T	15: 73,567,853 (GRCm39)	V179M	probably damaging	Het
Hdgf	T	A	3: 87,821,347 (GRCm39)		probably null	Het
Itgb8	A	T	12: 119,166,265 (GRCm39)	L89M	probably damaging	Het
Lnx2	T	C	5: 146,966,135 (GRCm39)	D328G	probably benign	Het
Lrguk	A	G	6: 34,049,305 (GRCm39)	T341A	possibly damaging	Het
Map1b	A	G	13: 99,566,080 (GRCm39)	S2214P	unknown	Het
Mms22l	T	C	4: 24,502,804 (GRCm39)	F131L	probably damaging	Het
Msmo1	A	G	8: 65,180,689 (GRCm39)	I75T	probably damaging	Het
Or10d1c	A	T	9: 38,893,914 (GRCm39)	M142K	probably benign	Het
Or2a56	G	A	6: 42,932,650 (GRCm39)	A73T	possibly damaging	Het
Or51k1	G	T	7: 103,661,162 (GRCm39)	A249E	probably damaging	Het
Or8c13	A	G	9: 38,091,645 (GRCm39)	V158A	probably benign	Het
Or8d2	T	G	9: 38,760,000 (GRCm39)	F197V	probably benign	Het
Pkhd1l1	C	T	15: 44,330,763 (GRCm39)	R113*	probably null	Het
Polr2m	T	C	9: 71,390,959 (GRCm39)	D81G	probably damaging	Het
Ppp1r15b	T	A	1: 133,060,287 (GRCm39)	M268K	probably benign	Het
Ptprcap	T	A	19: 4,206,073 (GRCm39)	L52*	probably null	Het
Rasgrp2	C	T	19: 6,457,087 (GRCm39)	T277I	possibly damaging	Het
Rrbp1	T	C	2: 143,831,310 (GRCm39)	N286D	probably damaging	Het
Scml2	G	T	X: 160,014,442 (GRCm39)	E566D	possibly damaging	Het
Scrib	A	C	15: 75,920,089 (GRCm39)	S1557A	probably damaging	Het
Sergef	C	A	7: 46,092,783 (GRCm39)	V409L	probably benign	Het
Shisal1	T	C	15: 84,290,672 (GRCm39)	M212V	probably benign	Het
Slc6a13	A	G	6: 121,309,328 (GRCm39)	M280V	probably benign	Het
Slc9a8	C	T	2: 167,313,352 (GRCm39)	P409S	probably benign	Het
Smarca4	CGAGGAGGAGGAGGAGG	CGAGGAGGAGGAGG	9: 21,612,239 (GRCm39)		probably benign	Het
Spc25	T	C	2: 69,035,498 (GRCm39)	D4G	probably damaging	Het
Specc1	C	T	11: 61,933,883 (GRCm39)	R88C	probably damaging	Het
Srsf11	C	T	3: 157,724,948 (GRCm39)		probably null	Het
Stt3b	T	C	9: 115,079,995 (GRCm39)	E639G	probably damaging	Het
Sult3a1	A	C	10: 33,742,616 (GRCm39)	E81A	probably damaging	Het
Taf1b	G	A	12: 24,606,623 (GRCm39)	G481D	probably benign	Het
Tgm4	T	C	9: 122,874,129 (GRCm39)	V123A	probably benign	Het
Tie1	G	T	4: 118,331,604 (GRCm39)	H973N	probably damaging	Het
Tmem117	C	T	15: 94,992,425 (GRCm39)	R362W	probably damaging	Het
Txnip	A	T	3: 96,466,277 (GRCm39)	Q107L	probably benign	Het
Ubap2	C	T	4: 41,199,872 (GRCm39)	A752T	probably benign	Het
Vcan	A	G	13: 89,837,780 (GRCm39)	V1628A	probably benign	Het
Vmn2r115	T	A	17: 23,564,245 (GRCm39)	M139K	probably benign	Het
Wwp1	A	G	4: 19,659,709 (GRCm39)	V193A	probably benign	Het
Zcchc8	C	T	5: 123,838,721 (GRCm39)	A606T	probably benign	Het
Zfp131	G	A	13: 120,230,316 (GRCm39)	L371F	probably damaging	Het
Zfp518b	T	C	5: 38,830,949 (GRCm39)	D352G	probably damaging	Het
Zfp784	A	G	7: 5,039,453 (GRCm39)		probably benign	Het
Zfp940	A	T	7: 29,545,500 (GRCm39)	F136I	probably benign	Het

Other mutations in Gnpat

Allele	Source	Chr	Coord	Type	Predicted Effect	PPH Score
IGL00089:Gnpat	APN	8	125,603,653 (GRCm39)	splice site	probably benign
IGL00422:Gnpat	APN	8	125,611,752 (GRCm39)	missense	probably damaging	1.00
IGL01327:Gnpat	APN	8	125,605,372 (GRCm39)	missense	probably damaging	1.00
IGL02257:Gnpat	APN	8	125,613,587 (GRCm39)	unclassified	probably benign
IGL02951:Gnpat	APN	8	125,597,644 (GRCm39)	missense	probably benign	0.01
IGL03084:Gnpat	APN	8	125,605,638 (GRCm39)	missense	probably damaging	0.99
R0114:Gnpat	UTSW	8	125,610,096 (GRCm39)	missense	probably benign	0.06
R0394:Gnpat	UTSW	8	125,606,964 (GRCm39)	missense	possibly damaging	0.82
R1023:Gnpat	UTSW	8	125,597,519 (GRCm39)	missense	probably benign	0.28
R1052:Gnpat	UTSW	8	125,605,255 (GRCm39)	missense	probably damaging	1.00
R1052:Gnpat	UTSW	8	125,604,246 (GRCm39)	missense	probably benign	0.00
R1537:Gnpat	UTSW	8	125,597,555 (GRCm39)	missense	probably damaging	0.97
R1711:Gnpat	UTSW	8	125,613,691 (GRCm39)	splice site	probably null
R1754:Gnpat	UTSW	8	125,603,745 (GRCm39)	missense	probably damaging	1.00
R2118:Gnpat	UTSW	8	125,603,680 (GRCm39)	missense	probably damaging	0.99
R2278:Gnpat	UTSW	8	125,603,659 (GRCm39)	missense	probably benign	0.35
R2429:Gnpat	UTSW	8	125,603,758 (GRCm39)	missense	probably damaging	1.00
R4579:Gnpat	UTSW	8	125,605,241 (GRCm39)	splice site	probably null
R6176:Gnpat	UTSW	8	125,605,593 (GRCm39)	missense	probably damaging	1.00
R7017:Gnpat	UTSW	8	125,590,014 (GRCm39)	missense	probably benign	0.33
R7081:Gnpat	UTSW	8	125,590,008 (GRCm39)	missense	possibly damaging	0.53
R7388:Gnpat	UTSW	8	125,614,553 (GRCm39)	missense	probably benign	0.32
R7716:Gnpat	UTSW	8	125,603,673 (GRCm39)	missense	probably benign	0.32
R7848:Gnpat	UTSW	8	125,613,630 (GRCm39)	missense	possibly damaging	0.89
R8169:Gnpat	UTSW	8	125,606,869 (GRCm39)	missense	probably benign	0.02
R8355:Gnpat	UTSW	8	125,597,579 (GRCm39)	missense	probably benign	0.11
R8363:Gnpat	UTSW	8	125,590,038 (GRCm39)	missense	probably benign	0.28
R8851:Gnpat	UTSW	8	125,601,004 (GRCm39)	missense	probably damaging	1.00
R9234:Gnpat	UTSW	8	125,610,179 (GRCm39)	missense	probably damaging	1.00
R9276:Gnpat	UTSW	8	125,614,524 (GRCm39)	missense	probably benign	0.45
R9701:Gnpat	UTSW	8	125,613,678 (GRCm39)	missense	probably benign	0.01
X0025:Gnpat	UTSW	8	125,600,138 (GRCm39)	missense	probably null	0.99
Z1177:Gnpat	UTSW	8	125,590,035 (GRCm39)	missense	probably benign	0.02

Predicted Primers

PCR Primer
(F):5'- ACCACGGAGCCAAGAGAGATACA -3'
(R):5'- TCCTGAGGGAAGGCAGTCAGAG -3'

Sequencing Primer
(F):5'- gtcctgctgccattgcc -3'
(R):5'- GCAGTCAGAGGTCTATCTAGAGTG -3'

Posted On

2014-04-24