Mutagenetix > Incidental Mutation

Incidental Mutation 'R7388:Gnpat'

573260

Institutional Source

Beutler Lab

Gene Symbol

Gnpat

Ensembl Gene

ENSMUSG00000031985

Gene Name

glyceronephosphate O-acyltransferase

Synonyms

D1Ertd819e

MMRRC Submission

045470-MU

Accession Numbers

Essential gene?

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

Stock #

R7388 (G1)

Quality Score

225.009

Status

Validated

Chromosome

Chromosomal Location

125589772-125616796 bp(+) (GRCm39)

Type of Mutation

missense

DNA Base Change (assembly)

T to G at 125614553 bp (GRCm39)

Zygosity

Heterozygous

Amino Acid Change

Methionine to Arginine at position 663 (M663R)

Ref Sequence

ENSEMBL: ENSMUSP00000034466 (fasta)

Gene Model

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

AlphaFold

P98192

Predicted Effect

probably benign
Transcript: ENSMUST00000034466
AA Change: M663R

PolyPhen 2 Score 0.320 (Sensitivity: 0.90; Specificity: 0.89)

SMART Domains

Protein: ENSMUSP00000034466
Gene: ENSMUSG00000031985
AA Change: M663R

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 benign
Transcript: ENSMUST00000161986

SMART Domains

Protein: ENSMUSP00000125323
Gene: ENSMUSG00000031985

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: 100.0%
3x: 100.0%
10x: 99.8%
20x: 99.3%

Validation Efficiency

100% (63/63)

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: 63 list
Gene	Ref	Var	Chr/Loc	Mutation	Predicted Effect	Zygosity
Afg3l2	T	C	18: 67,556,023 (GRCm39)	E436G	probably damaging	Het
Agbl5	T	A	5: 31,060,583 (GRCm39)	L759*	probably null	Het
Ankrd13b	T	C	11: 77,363,583 (GRCm39)	D460G	probably benign	Het
Apol10a	A	G	15: 77,373,225 (GRCm39)	D287G	possibly damaging	Het
Arhgap44	A	T	11: 64,915,094 (GRCm39)	Y391*	probably null	Het
Asz1	G	T	6: 18,074,900 (GRCm39)	S271R	probably benign	Het
AW554918	A	G	18: 25,473,170 (GRCm39)	N325D	probably benign	Het
Brinp2	A	T	1: 158,082,579 (GRCm39)	L247Q	probably damaging	Het
Casz1	A	G	4: 149,036,850 (GRCm39)	D1704G	unknown	Het
Cdk5rap1	G	A	2: 154,202,595 (GRCm39)	R212W	probably damaging	Het
Cdkl2	T	A	5: 92,167,318 (GRCm39)	T444S	probably benign	Het
Cers2	T	G	3: 95,228,656 (GRCm39)	F160V	probably benign	Het
Cfap276	T	C	3: 108,450,815 (GRCm39)	F86L	possibly damaging	Het
Cga	T	A	4: 34,907,076 (GRCm39)	M99K	probably benign	Het
Cspp1	C	T	1: 10,135,572 (GRCm39)	R138*	probably null	Het
Dao	T	G	5: 114,153,273 (GRCm39)	*133E	probably null	Het
Ddx1	A	T	12: 13,275,456 (GRCm39)	C544S	probably null	Het
Dgkq	A	T	5: 108,806,112 (GRCm39)	V98E	probably damaging	Het
Dnah6	T	A	6: 73,169,300 (GRCm39)	T434S	possibly damaging	Het
Dntt	A	G	19: 41,027,418 (GRCm39)	N162D	probably benign	Het
Dpysl5	T	C	5: 30,902,805 (GRCm39)	V79A	probably benign	Het
Efcab3	T	C	11: 104,611,871 (GRCm39)	L571P	probably damaging	Het
Ep300	T	C	15: 81,532,567 (GRCm39)	C1602R	unknown	Het
Flrt3	C	T	2: 140,503,672 (GRCm39)		probably null	Het
Gk2	A	G	5: 97,604,757 (GRCm39)	V27A	probably damaging	Het
Hc	A	T	2: 34,874,859 (GRCm39)		probably null	Het
Il12rb1	A	G	8: 71,263,271 (GRCm39)	Y67C	probably damaging	Het
Ints15	G	A	5: 143,297,600 (GRCm39)	A149V	probably benign	Het
Kmt2b	C	T	7: 30,281,385 (GRCm39)	D1229N	probably damaging	Het
Lamc1	T	C	1: 153,124,822 (GRCm39)	T650A	probably damaging	Het
Lrp1	G	A	10: 127,419,766 (GRCm39)	R948*	probably null	Het
Map3k21	T	C	8: 126,654,336 (GRCm39)	I385T	probably damaging	Het
Mmrn1	T	A	6: 60,953,236 (GRCm39)	S506T	probably benign	Het
Nlrp1a	A	G	11: 71,014,023 (GRCm39)	F409S	probably damaging	Het
Nlrp3	T	A	11: 59,455,892 (GRCm39)	I896N	probably benign	Het
Noxred1	C	A	12: 87,273,799 (GRCm39)	V81L	probably damaging	Het
Nrcam	A	T	12: 44,645,272 (GRCm39)	I1225F	probably damaging	Het
Or2z2	C	T	11: 58,346,481 (GRCm39)	C98Y	probably damaging	Het
Otos	T	A	1: 92,572,241 (GRCm39)		probably null	Het
Pcdh20	A	G	14: 88,706,103 (GRCm39)	I399T	probably benign	Het
Pkhd1	C	T	1: 20,309,528 (GRCm39)	V2807I	not run	Het
Prrx2	A	G	2: 30,770,902 (GRCm39)	E235G	probably damaging	Het
Rab13	T	C	3: 90,128,327 (GRCm39)	I41T	probably damaging	Het
Rai1	A	C	11: 60,080,201 (GRCm39)	T1422P	possibly damaging	Het
Rcn1	C	T	2: 105,222,336 (GRCm39)	V217M	probably damaging	Het
Scn2a	T	A	2: 65,518,998 (GRCm39)	V408E	probably damaging	Het
Sec16a	C	T	2: 26,318,376 (GRCm39)	A121T		Het
Slc35d1	A	G	4: 103,046,982 (GRCm39)		probably null	Het
Slc39a6	A	T	18: 24,717,106 (GRCm39)	V642E	probably damaging	Het
Slc6a19	G	A	13: 73,841,203 (GRCm39)	A69V	probably benign	Het
Spink6	A	T	18: 44,215,386 (GRCm39)	T79S	probably damaging	Het
Spire1	T	C	18: 67,652,950 (GRCm39)	D170G	probably damaging	Het
Sugp1	T	C	8: 70,505,269 (GRCm39)	S79P	probably damaging	Het
Syne3	A	G	12: 104,934,167 (GRCm39)	Y201H	probably damaging	Het
Tbc1d10a	T	C	11: 4,155,858 (GRCm39)		probably null	Het
Tmem14a	C	T	1: 21,299,735 (GRCm39)	Q122*	probably null	Het
Tmem161b	C	A	13: 84,370,537 (GRCm39)		probably benign	Het
Trmt61a	A	G	12: 111,645,321 (GRCm39)	I86V	possibly damaging	Het
Tubgcp4	G	A	2: 121,020,447 (GRCm39)		probably null	Het
Vmn1r79	T	A	7: 11,910,668 (GRCm39)	Y183*	probably null	Het
Vmn2r11	A	T	5: 109,202,742 (GRCm39)	W112R	probably benign	Het
Vpreb1a	T	C	16: 16,686,516 (GRCm39)	K125E	probably benign	Het
Wdr6	A	T	9: 108,451,971 (GRCm39)	F637L	probably damaging	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
R1604:Gnpat	UTSW	8	125,603,700 (GRCm39)	missense	probably damaging	1.00
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
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'- CCCCAAGCCTGGAGGATAAAA -3'
(R):5'- CCACCTGCACACTGGTTTT -3'

Sequencing Primer
(F):5'- CCTGGAGGATAAAAAGCAAGCTCC -3'
(R):5'- AAGCTGGCCTTGAACTCATG -3'

Posted On

2019-09-13