Incidental Mutation 'R7017:Gnpat'
ID 545383
Institutional Source Beutler Lab
Gene Symbol Gnpat
Ensembl Gene ENSMUSG00000031985
Gene Name glyceronephosphate O-acyltransferase
Synonyms D1Ertd819e
MMRRC Submission 045118-MU
Accession Numbers
Essential gene? Possibly non essential (E-score: 0.387) question?
Stock # R7017 (G1)
Quality Score 225.009
Status Validated
Chromosome 8
Chromosomal Location 125589772-125616796 bp(+) (GRCm39)
Type of Mutation missense
DNA Base Change (assembly) T to C at 125590014 bp (GRCm39)
Zygosity Heterozygous
Amino Acid Change Valine to Alanine at position 13 (V13A)
Ref Sequence ENSEMBL: ENSMUSP00000125323 (fasta)
Gene Model predicted gene model for transcript(s): [ENSMUST00000034465] [ENSMUST00000034466] [ENSMUST00000161986]
AlphaFold P98192
Predicted Effect probably benign
Transcript: ENSMUST00000034465
SMART Domains Protein: ENSMUSP00000034465
Gene: ENSMUSG00000031984

DomainStartEndE-ValueType
low complexity region 39 49 N/A INTRINSIC
Pfam:DUF4602 119 243 1e-32 PFAM
Predicted Effect probably benign
Transcript: ENSMUST00000034466
AA Change: V13A

PolyPhen 2 Score 0.326 (Sensitivity: 0.90; Specificity: 0.89)
SMART Domains Protein: ENSMUSP00000034466
Gene: ENSMUSG00000031985
AA Change: V13A

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 probably benign
Transcript: ENSMUST00000161986
AA Change: V13A

PolyPhen 2 Score 0.326 (Sensitivity: 0.90; Specificity: 0.89)
SMART Domains Protein: ENSMUSP00000125323
Gene: ENSMUSG00000031985
AA Change: V13A

DomainStartEndE-ValueType
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: 99.5%
Validation Efficiency 100% (75/75)
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: 76 list
GeneRefVarChr/LocMutationPredicted EffectZygosity
2410137M14Rik A G 17: 37,288,926 (GRCm39) probably benign Het
Acot3 A T 12: 84,100,077 (GRCm39) probably benign Het
Add3 T A 19: 53,222,284 (GRCm39) V297E possibly damaging Het
Arfgap1 C G 2: 180,618,097 (GRCm39) probably null Het
Cacna1i T C 15: 80,264,671 (GRCm39) F1500L probably damaging Het
Cacna1s T C 1: 136,023,596 (GRCm39) I945T probably damaging Het
Ccdc180 T A 4: 45,940,934 (GRCm39) N1334K possibly damaging Het
Cd5l C A 3: 87,273,368 (GRCm39) Y112* probably null Het
Cracd GAGGCAGCGCGAGGCCGAGAGGCAGGAGGAGGAAGCAAGACAACGCGAGGCCGAGAGGCAGG GAGACAACGCGAGGCCGAGAGGCAGG 5: 77,004,795 (GRCm39) probably benign Het
Cyp2d40 A T 15: 82,644,234 (GRCm39) F297Y unknown Het
Ddx4 C T 13: 112,738,022 (GRCm39) V546I probably damaging Het
Dgkg T C 16: 22,391,463 (GRCm39) M332V probably benign Het
Dnah12 T C 14: 26,456,835 (GRCm39) I867T probably benign Het
Dnah2 T A 11: 69,382,373 (GRCm39) K1246* probably null Het
Drd2 G A 9: 49,312,129 (GRCm39) V161I probably benign Het
Dsp A G 13: 38,370,683 (GRCm39) D862G probably benign Het
Ephx4 T C 5: 107,553,980 (GRCm39) F10S probably damaging Het
Fabp9 C A 3: 10,259,756 (GRCm39) A76S possibly damaging Het
Fat4 G A 3: 38,945,692 (GRCm39) M1528I probably benign Het
Fbxl12 A G 9: 20,529,616 (GRCm39) S84P unknown Het
Fbxo40 T C 16: 36,790,732 (GRCm39) D126G probably damaging Het
Fpr1 C T 17: 18,097,654 (GRCm39) V112I probably benign Het
Frem2 T C 3: 53,427,023 (GRCm39) N2975S probably benign Het
Gask1a T C 9: 121,795,052 (GRCm39) probably null Het
Gm7945 T C 14: 41,105,610 (GRCm39) Y156C Het
Gpx5 G A 13: 21,475,561 (GRCm39) P55L probably damaging Het
Hbp1 A G 12: 31,993,852 (GRCm39) S59P probably damaging Het
Ighv1-36 T A 12: 114,843,533 (GRCm39) D109V probably damaging Het
Iqcf5 T A 9: 106,392,863 (GRCm39) I40N possibly damaging Het
Kcnma1 T G 14: 23,544,711 (GRCm39) I484L possibly damaging Het
Kera A T 10: 97,444,939 (GRCm39) R99S possibly damaging Het
Kif3b T A 2: 153,171,644 (GRCm39) S707R possibly damaging Het
Lilra6 G T 7: 3,911,707 (GRCm39) T317N possibly damaging Het
Lrrc15 C T 16: 30,091,780 (GRCm39) E520K probably benign Het
Lrrc34 C T 3: 30,699,465 (GRCm39) probably null Het
Lvrn A G 18: 46,983,745 (GRCm39) T163A probably benign Het
Met T A 6: 17,491,286 (GRCm39) L16* probably null Het
Mpzl2 G T 9: 44,958,587 (GRCm39) D108Y probably benign Het
Mrgprb2 T A 7: 48,202,585 (GRCm39) I47F probably benign Het
Muc5ac G C 7: 141,363,424 (GRCm39) probably benign Het
Mybphl T A 3: 108,282,154 (GRCm39) V128E probably damaging Het
Nckap5 A T 1: 126,030,398 (GRCm39) D231E probably damaging Het
Or5g23 T A 2: 85,438,673 (GRCm39) M194L probably benign Het
Orm1 T A 4: 63,263,448 (GRCm39) I87K probably benign Het
Pdgfrb C T 18: 61,214,076 (GRCm39) P954S probably benign Het
Pdzd8 G T 19: 59,333,784 (GRCm39) S79* probably null Het
Pdzd9 T A 7: 120,262,225 (GRCm39) H79L probably benign Het
Plcg1 A T 2: 160,600,017 (GRCm39) I926F probably damaging Het
Plec A T 15: 76,057,741 (GRCm39) F4078L probably damaging Het
Plek G A 11: 17,002,220 (GRCm39) probably benign Het
Pogz T C 3: 94,761,335 (GRCm39) I25T probably damaging Het
Ppfia3 A T 7: 45,008,224 (GRCm39) D215E probably benign Het
Psg22 C A 7: 18,458,366 (GRCm39) S352R probably benign Het
Ptchd4 A G 17: 42,813,626 (GRCm39) Y509C probably damaging Het
Ralgapb C A 2: 158,290,257 (GRCm39) N389K probably benign Het
Rdh1 A G 10: 127,598,906 (GRCm39) D129G probably benign Het
Rimbp3 A G 16: 17,027,610 (GRCm39) T345A probably benign Het
S100a14 T C 3: 90,434,602 (GRCm39) probably null Het
Scamp1 T A 13: 94,361,423 (GRCm39) R152S probably damaging Het
Slc30a2 G A 4: 134,074,726 (GRCm39) R161Q probably damaging Het
Srf T C 17: 46,861,830 (GRCm39) T383A probably benign Het
St6galnac5 T C 3: 152,552,040 (GRCm39) M176V probably damaging Het
St8sia1 C A 6: 142,813,632 (GRCm39) V177F probably damaging Het
Syt12 C T 19: 4,510,895 (GRCm39) probably null Het
Tanc2 A G 11: 105,813,934 (GRCm39) I1793V probably benign Het
Tas2r123 A G 6: 132,824,513 (GRCm39) I137V probably benign Het
Tenm2 T A 11: 36,062,236 (GRCm39) Y543F probably damaging Het
Tent5b T C 4: 133,213,545 (GRCm39) S139P possibly damaging Het
Tgfbr1 T C 4: 47,410,728 (GRCm39) I488T probably damaging Het
Tgm1 T A 14: 55,942,398 (GRCm39) Y651F possibly damaging Het
Thbs3 A T 3: 89,131,722 (GRCm39) D698V probably damaging Het
Tpra1 T A 6: 88,885,294 (GRCm39) I82N probably damaging Het
Ubr4 T A 4: 139,120,401 (GRCm39) D275E probably damaging Het
Vmn2r111 T C 17: 22,778,032 (GRCm39) N549S possibly damaging Het
Wwp1 T C 4: 19,623,124 (GRCm39) Y787C probably damaging Het
Znfx1 T C 2: 166,890,454 (GRCm39) S677G probably damaging 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
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
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'- TCGGGATGCGTTTCACTGTC -3'
(R):5'- TGGATACCAAGCCACGTACC -3'

Sequencing Primer
(F):5'- CCTCGGGCCTGGTTAAGATG -3'
(R):5'- GCCACGTACCCAACTGG -3'
Posted On 2019-05-13