Incidental Mutation 'R0394:Gnpat'
ID 31870
Institutional Source Beutler Lab
Gene Symbol Gnpat
Ensembl Gene ENSMUSG00000031985
Gene Name glyceronephosphate O-acyltransferase
Synonyms D1Ertd819e
MMRRC Submission 038600-MU
Accession Numbers
Essential gene? Possibly non essential (E-score: 0.387) question?
Stock # R0394 (G1)
Quality Score 225
Status Validated
Chromosome 8
Chromosomal Location 125589772-125616796 bp(+) (GRCm39)
Type of Mutation missense
DNA Base Change (assembly) C to A at 125606964 bp (GRCm39)
Zygosity Heterozygous
Amino Acid Change Serine to Arginine at position 373 (S373R)
Ref Sequence ENSEMBL: ENSMUSP00000125323 (fasta)
Gene Model predicted gene model for transcript(s): [ENSMUST00000034466] [ENSMUST00000161986]
AlphaFold P98192
Predicted Effect possibly damaging
Transcript: ENSMUST00000034466
AA Change: S383R

PolyPhen 2 Score 0.817 (Sensitivity: 0.84; Specificity: 0.93)
SMART Domains Protein: ENSMUSP00000034466
Gene: ENSMUSG00000031985
AA Change: S383R

DomainStartEndE-ValueType
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 noncoding transcript
Transcript: ENSMUST00000161628
Predicted Effect possibly damaging
Transcript: ENSMUST00000161986
AA Change: S373R

PolyPhen 2 Score 0.817 (Sensitivity: 0.84; Specificity: 0.93)
SMART Domains Protein: ENSMUSP00000125323
Gene: ENSMUSG00000031985
AA Change: S373R

DomainStartEndE-ValueType
low complexity region 5 20 N/A INTRINSIC
PlsC 145 274 8.3e-21 SMART
Blast:PlsC 298 326 2e-6 BLAST
Predicted Effect noncoding transcript
Transcript: ENSMUST00000162455
Meta Mutation Damage Score 0.4243 question?
Coding Region Coverage
  • 1x: 99.1%
  • 3x: 98.2%
  • 10x: 96.0%
  • 20x: 92.0%
Validation Efficiency 99% (79/80)
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: 78 list
GeneRefVarChr/LocMutationPredicted EffectZygosity
1110002E22Rik C A 3: 137,773,065 (GRCm39) S751R probably damaging Het
Abca8a A G 11: 109,917,169 (GRCm39) V1610A probably damaging Het
Actl10 A T 2: 154,394,957 (GRCm39) H202L probably benign Het
Alox12 A T 11: 70,136,761 (GRCm39) V489E probably damaging Het
Ap4m1 T A 5: 138,170,465 (GRCm39) F5I probably benign Het
Atn1 T C 6: 124,726,696 (GRCm39) probably benign Het
Atrnl1 T A 19: 57,661,608 (GRCm39) N529K probably benign Het
B3gntl1 C T 11: 121,510,541 (GRCm39) G336D probably damaging Het
Bmp1 G A 14: 70,727,474 (GRCm39) A703V probably damaging Het
Brat1 T G 5: 140,704,141 (GRCm39) L798R probably damaging Het
Cacna1c C T 6: 118,602,458 (GRCm39) G1302R probably damaging Het
Cdr2 A T 7: 120,557,954 (GRCm39) D190E probably benign Het
Cenpe T C 3: 134,922,186 (GRCm39) probably benign Het
Clstn1 A G 4: 149,728,635 (GRCm39) D687G probably benign Het
Coro1a A G 7: 126,299,812 (GRCm39) F337L probably benign Het
Ddx49 T A 8: 70,749,575 (GRCm39) I252F probably damaging Het
Dennd2a T A 6: 39,499,746 (GRCm39) D273V possibly damaging Het
Derl2 A T 11: 70,905,387 (GRCm39) F32I probably benign Het
Dmrta1 A G 4: 89,580,276 (GRCm39) Y412C probably damaging Het
Dsg1a A G 18: 20,466,807 (GRCm39) N559S probably damaging Het
Dusp26 G T 8: 31,581,987 (GRCm39) R27L probably benign Het
Eif2ak3 T C 6: 70,862,202 (GRCm39) I492T probably benign Het
Exoc7 G T 11: 116,191,224 (GRCm39) Q219K probably damaging Het
F2r T C 13: 95,740,984 (GRCm39) T184A probably damaging Het
Fbf1 G A 11: 116,043,288 (GRCm39) probably benign Het
Fbxo28 A G 1: 182,144,580 (GRCm39) M328T probably benign Het
Fsip2 T A 2: 82,821,419 (GRCm39) D5717E possibly damaging Het
Golgb1 G T 16: 36,695,941 (GRCm39) probably benign Het
Greb1l T C 18: 10,523,374 (GRCm39) V844A probably damaging Het
Hps1 G T 19: 42,759,338 (GRCm39) probably null Het
Inppl1 G T 7: 101,477,402 (GRCm39) probably benign Het
Isca1 C T 13: 59,906,699 (GRCm39) probably null Het
Itgb2 T A 10: 77,378,309 (GRCm39) C46S probably damaging Het
Kifc5b C T 17: 27,142,056 (GRCm39) T178M probably benign Het
Krt80 T C 15: 101,250,180 (GRCm39) T22A probably damaging Het
L3mbtl2 C T 15: 81,552,942 (GRCm39) A125V probably damaging Het
Ltbp2 C T 12: 84,853,198 (GRCm39) probably benign Het
Mettl18 A G 1: 163,823,910 (GRCm39) D77G probably benign Het
Mfsd2a A G 4: 122,843,961 (GRCm39) L336P probably benign Het
Mgat4b A G 11: 50,121,746 (GRCm39) probably null Het
Mtmr14 C T 6: 113,257,649 (GRCm39) R233* probably null Het
Nbea T C 3: 55,937,328 (GRCm39) Y761C probably damaging Het
Neb A T 2: 52,067,571 (GRCm39) probably null Het
Nup85 T G 11: 115,455,357 (GRCm39) M1R probably null Het
Obi1 T C 14: 104,716,289 (GRCm39) R695G possibly damaging Het
Or6c70 T A 10: 129,709,811 (GRCm39) I272L probably benign Het
Oxr1 T A 15: 41,680,593 (GRCm39) M177K probably damaging Het
Pgm2l1 A G 7: 99,901,405 (GRCm39) Y98C probably damaging Het
Pi4kb G T 3: 94,904,115 (GRCm39) probably benign Het
Pi4kb G A 3: 94,904,116 (GRCm39) probably benign Het
Pirb T A 7: 3,722,247 (GRCm39) S199C probably benign Het
Prss23 A C 7: 89,159,055 (GRCm39) I338S probably damaging Het
Rapgef3 A T 15: 97,655,700 (GRCm39) probably benign Het
Rdh7 T A 10: 127,720,539 (GRCm39) T278S probably benign Het
Rrp1b A G 17: 32,277,538 (GRCm39) D606G probably benign Het
Rxfp1 T A 3: 79,559,684 (GRCm39) Y379F possibly damaging Het
Rxfp2 T C 5: 149,990,853 (GRCm39) V514A probably benign Het
Scel A T 14: 103,799,954 (GRCm39) E202V probably benign Het
Slc25a36 G A 9: 96,962,257 (GRCm39) A244V probably benign Het
Slc2a13 T G 15: 91,400,595 (GRCm39) Q209P probably damaging Het
Slc38a6 A G 12: 73,399,304 (GRCm39) N456S probably benign Het
Slc6a12 G T 6: 121,323,957 (GRCm39) probably null Het
Spag6l T C 16: 16,598,493 (GRCm39) I333V probably benign Het
Spen G A 4: 141,201,514 (GRCm39) A2371V probably benign Het
St6galnac1 T C 11: 116,657,466 (GRCm39) D366G probably damaging Het
Stk33 T C 7: 108,940,696 (GRCm39) S5G probably benign Het
Tex56 T C 13: 35,116,636 (GRCm39) probably benign Het
Tle2 T C 10: 81,413,482 (GRCm39) L84P probably damaging Het
Tmem14a T C 1: 21,296,876 (GRCm39) M78T probably damaging Het
Top2b T A 14: 16,413,556 (GRCm38) probably null Het
Trmt13 A G 3: 116,376,299 (GRCm39) F364S probably damaging Het
Unkl T A 17: 25,449,751 (GRCm39) probably null Het
Uvrag A G 7: 98,653,926 (GRCm39) probably benign Het
Vmn2r8 T A 5: 108,949,938 (GRCm39) N303I probably benign Het
Vsig10l A G 7: 43,114,879 (GRCm39) N360S probably damaging Het
Zdhhc25 T C 15: 88,485,123 (GRCm39) Y153H probably damaging Het
Zfp646 T C 7: 127,482,434 (GRCm39) V1537A possibly damaging Het
Zfp664 T A 5: 124,963,129 (GRCm39) Y174* probably null Het
Other mutations in Gnpat
AlleleSourceChrCoordTypePredicted EffectPPH 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
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
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'- GGCATTTTCGGTACAGACCCATCTC -3'
(R):5'- GTGCATCCCATATACGTACCAGGC -3'

Sequencing Primer
(F):5'- TGCACCAATTGACTGAAGCTG -3'
(R):5'- TATACGTACCAGGCCAAAGCAG -3'
Posted On 2013-04-24