Incidental Mutation 'R0109:Pgap1'
ID 64180
Institutional Source Beutler Lab
Gene Symbol Pgap1
Ensembl Gene ENSMUSG00000073678
Gene Name post-GPI attachment to proteins 1
Synonyms 9030223K07Rik, D230012E17Rik, oto, 5033403E17Rik, PGAP1
MMRRC Submission 038395-MU
Accession Numbers
Essential gene? Probably essential (E-score: 0.764) question?
Stock # R0109 (G1)
Quality Score 165
Status Not validated
Chromosome 1
Chromosomal Location 54512159-54596843 bp(-) (GRCm39)
Type of Mutation missense
DNA Base Change (assembly) A to T at 54533984 bp (GRCm39)
Zygosity Heterozygous
Amino Acid Change Valine to Glutamic Acid at position 643 (V643E)
Ref Sequence ENSEMBL: ENSMUSP00000095346 (fasta)
Gene Model predicted gene model for transcript(s): [ENSMUST00000097739]
AlphaFold Q3UUQ7
Predicted Effect probably damaging
Transcript: ENSMUST00000097739
AA Change: V643E

PolyPhen 2 Score 1.000 (Sensitivity: 0.00; Specificity: 1.00)
SMART Domains Protein: ENSMUSP00000095346
Gene: ENSMUSG00000073678
AA Change: V643E

DomainStartEndE-ValueType
transmembrane domain 7 29 N/A INTRINSIC
Pfam:PGAP1 82 302 7.2e-83 PFAM
transmembrane domain 597 619 N/A INTRINSIC
transmembrane domain 678 700 N/A INTRINSIC
transmembrane domain 737 759 N/A INTRINSIC
transmembrane domain 819 838 N/A INTRINSIC
low complexity region 854 866 N/A INTRINSIC
low complexity region 871 884 N/A INTRINSIC
transmembrane domain 902 921 N/A INTRINSIC
Meta Mutation Damage Score 0.3337 question?
Coding Region Coverage
  • 1x: 99.2%
  • 3x: 98.5%
  • 10x: 96.9%
  • 20x: 93.6%
Validation Efficiency
MGI Phenotype FUNCTION: [Summary is not available for the mouse gene. This summary is for the human ortholog.] The protein encoded by this gene functions early in the glycosylphosphatidylinositol (GPI) biosynthetic pathway, catalyzing the inositol deacylation of GPI. The encoded protein is required for the production of GPI that can attach to proteins, and this may be an important factor in the transport of GPI-anchored proteins from the endoplasmic reticulum to the Golgi. Defects in this gene are a cause of mental retardation, autosomal recessive 42. [provided by RefSeq, Mar 2016]
PHENOTYPE: Mutations in this gene result in a variety of forebrain, eye, jaw, craniofacial, ear, and vertebra defects that are background sensitive. [provided by MGI curators]
Allele List at MGI
Other mutations in this stock
Total: 50 list
GeneRefVarChr/LocMutationPredicted EffectZygosity
Abca14 A T 7: 119,917,985 (GRCm39) K1496* probably null Het
Anapc1 C A 2: 128,476,613 (GRCm39) R1335L probably damaging Het
Arhgef10l A T 4: 140,305,605 (GRCm39) S203T probably benign Het
Astn1 C T 1: 158,491,674 (GRCm39) T41I possibly damaging Het
Avil A G 10: 126,849,513 (GRCm39) N603S probably benign Het
Brca1 T C 11: 101,421,916 (GRCm39) D149G possibly damaging Het
Col19a1 A C 1: 24,598,849 (GRCm39) probably null Het
Cps1 T C 1: 67,268,577 (GRCm39) V1435A possibly damaging Het
Cyp2j6 A T 4: 96,406,394 (GRCm39) I459N probably damaging Het
Cyth1 T C 11: 118,073,132 (GRCm39) E242G probably damaging Het
Dclk3 T G 9: 111,296,738 (GRCm39) L94R possibly damaging Het
Dsg3 T C 18: 20,673,191 (GRCm39) V954A probably damaging Het
Dync2h1 T A 9: 7,111,487 (GRCm39) D309V probably damaging Het
Efhd2 A G 4: 141,601,878 (GRCm39) F101L probably benign Het
Fgd5 T A 6: 91,965,216 (GRCm39) M325K possibly damaging Het
Fras1 T C 5: 96,857,936 (GRCm39) S2077P probably benign Het
Frmpd1 A T 4: 45,279,340 (GRCm39) E688D probably benign Het
Hspg2 T C 4: 137,289,512 (GRCm39) V3824A probably benign Het
Kctd16 A G 18: 40,392,204 (GRCm39) E264G probably benign Het
Mapk15 A T 15: 75,867,926 (GRCm39) K153* probably null Het
Miox G A 15: 89,219,784 (GRCm39) V91I probably benign Het
Nfyb G A 10: 82,590,836 (GRCm39) A65V possibly damaging Het
Or4a69 A G 2: 89,313,147 (GRCm39) F111L probably benign Het
Or52d1 T C 7: 103,755,812 (GRCm39) S109P probably damaging Het
Or5b94 C A 19: 12,652,224 (GRCm39) F218L probably benign Het
Parp9 T C 16: 35,768,711 (GRCm39) I64T probably damaging Het
Pfkfb4 T C 9: 108,827,957 (GRCm39) V43A probably benign Het
Pip5k1b T A 19: 24,356,411 (GRCm39) M176L probably benign Het
Ppfia4 A T 1: 134,251,955 (GRCm39) probably null Het
Prdx2 G A 8: 85,696,880 (GRCm39) G4S probably benign Het
Rin3 A G 12: 102,279,340 (GRCm39) I50V possibly damaging Het
Rtl1 G A 12: 109,561,841 (GRCm39) probably benign Het
Sgsm3 G C 15: 80,893,667 (GRCm39) D434H probably damaging Het
Shank2 T C 7: 143,964,314 (GRCm39) S634P possibly damaging Het
Sik2 A G 9: 50,810,775 (GRCm39) M447T possibly damaging Het
Sla2 A G 2: 156,725,507 (GRCm39) probably null Het
Spata16 T A 3: 26,967,416 (GRCm39) F389I probably damaging Het
Srebf1 G A 11: 60,092,630 (GRCm39) A793V probably benign Het
Tmed11 T A 5: 108,925,278 (GRCm39) D178V probably damaging Het
Traf7 A G 17: 24,732,900 (GRCm39) F110L probably benign Het
Ttn T A 2: 76,555,908 (GRCm39) I30366F probably damaging Het
Ubqlnl C T 7: 103,799,399 (GRCm39) V33M probably damaging Het
Vmn1r194 A G 13: 22,429,217 (GRCm39) Y278C probably damaging Het
Vmn2r100 C A 17: 19,742,382 (GRCm39) P252Q possibly damaging Het
Vmn2r114 A T 17: 23,529,549 (GRCm39) Y184* probably null Het
Vmn2r53 C T 7: 12,315,993 (GRCm39) A609T probably damaging Het
Vps13b A G 15: 35,572,265 (GRCm39) T961A probably benign Het
Xirp2 T A 2: 67,349,622 (GRCm39) N3272K probably damaging Het
Zfp217 C T 2: 169,957,382 (GRCm39) A539T probably benign Het
Zfp454 T A 11: 50,774,602 (GRCm39) T24S possibly damaging Het
Other mutations in Pgap1
AlleleSourceChrCoordTypePredicted EffectPPH Score
IGL00846:Pgap1 APN 1 54,531,180 (GRCm39) splice site probably benign
IGL01111:Pgap1 APN 1 54,570,102 (GRCm39) missense probably benign 0.17
IGL01406:Pgap1 APN 1 54,572,573 (GRCm39) splice site probably null
IGL01592:Pgap1 APN 1 54,560,470 (GRCm39) missense probably damaging 1.00
IGL02005:Pgap1 APN 1 54,590,214 (GRCm39) missense probably damaging 0.99
IGL02026:Pgap1 APN 1 54,533,978 (GRCm39) missense probably benign 0.05
IGL02086:Pgap1 APN 1 54,587,147 (GRCm39) missense probably damaging 1.00
IGL02354:Pgap1 APN 1 54,551,975 (GRCm39) missense probably benign 0.02
IGL02361:Pgap1 APN 1 54,551,975 (GRCm39) missense probably benign 0.02
IGL02995:Pgap1 APN 1 54,532,509 (GRCm39) missense probably benign 0.19
IGL03012:Pgap1 APN 1 54,572,572 (GRCm39) splice site probably benign
R0044:Pgap1 UTSW 1 54,532,527 (GRCm39) missense probably damaging 1.00
R0109:Pgap1 UTSW 1 54,533,984 (GRCm39) missense probably damaging 1.00
R0241:Pgap1 UTSW 1 54,575,110 (GRCm39) splice site probably null
R0241:Pgap1 UTSW 1 54,575,110 (GRCm39) splice site probably null
R0352:Pgap1 UTSW 1 54,525,617 (GRCm39) splice site probably benign
R1297:Pgap1 UTSW 1 54,567,682 (GRCm39) missense possibly damaging 0.94
R1429:Pgap1 UTSW 1 54,534,020 (GRCm39) missense probably benign 0.01
R1465:Pgap1 UTSW 1 54,567,714 (GRCm39) missense probably benign 0.11
R1465:Pgap1 UTSW 1 54,567,714 (GRCm39) missense probably benign 0.11
R1542:Pgap1 UTSW 1 54,531,249 (GRCm39) missense probably benign 0.16
R1816:Pgap1 UTSW 1 54,531,216 (GRCm39) missense probably damaging 0.99
R1817:Pgap1 UTSW 1 54,575,128 (GRCm39) missense probably benign 0.15
R1905:Pgap1 UTSW 1 54,551,120 (GRCm39) missense probably benign 0.26
R2006:Pgap1 UTSW 1 54,590,220 (GRCm39) missense possibly damaging 0.76
R3551:Pgap1 UTSW 1 54,569,302 (GRCm39) missense possibly damaging 0.89
R3833:Pgap1 UTSW 1 54,596,624 (GRCm39) missense probably damaging 0.99
R3901:Pgap1 UTSW 1 54,532,507 (GRCm39) missense probably benign
R4487:Pgap1 UTSW 1 54,567,751 (GRCm39) missense probably benign 0.26
R4874:Pgap1 UTSW 1 54,569,296 (GRCm39) missense probably damaging 0.96
R5184:Pgap1 UTSW 1 54,521,015 (GRCm39) missense probably damaging 1.00
R6181:Pgap1 UTSW 1 54,551,936 (GRCm39) missense probably benign 0.05
R6212:Pgap1 UTSW 1 54,554,052 (GRCm39) missense probably damaging 0.99
R6269:Pgap1 UTSW 1 54,587,167 (GRCm39) nonsense probably null
R6525:Pgap1 UTSW 1 54,521,048 (GRCm39) missense probably benign 0.00
R6944:Pgap1 UTSW 1 54,569,320 (GRCm39) missense probably damaging 1.00
R7214:Pgap1 UTSW 1 54,582,220 (GRCm39) missense possibly damaging 0.47
R7256:Pgap1 UTSW 1 54,532,366 (GRCm39) critical splice donor site probably null
R7290:Pgap1 UTSW 1 54,587,225 (GRCm39) missense possibly damaging 0.45
R7356:Pgap1 UTSW 1 54,569,293 (GRCm39) missense probably benign 0.10
R7525:Pgap1 UTSW 1 54,570,081 (GRCm39) missense probably benign 0.26
R7602:Pgap1 UTSW 1 54,582,345 (GRCm39) missense probably damaging 1.00
R7897:Pgap1 UTSW 1 54,590,167 (GRCm39) missense probably damaging 1.00
R8278:Pgap1 UTSW 1 54,529,430 (GRCm39) missense probably benign
R9189:Pgap1 UTSW 1 54,519,908 (GRCm39) missense probably benign 0.31
R9238:Pgap1 UTSW 1 54,550,570 (GRCm39) missense probably benign
R9428:Pgap1 UTSW 1 54,575,206 (GRCm39) missense probably damaging 1.00
R9479:Pgap1 UTSW 1 54,582,275 (GRCm39) nonsense probably null
X0025:Pgap1 UTSW 1 54,521,029 (GRCm39) missense probably benign 0.26
X0060:Pgap1 UTSW 1 54,575,193 (GRCm39) missense probably damaging 1.00
Predicted Primers PCR Primer
(F):5'- AGCAGCTCAAAGTCAGGAAGTCAAC -3'
(R):5'- GCAGTGAACCTTCCAAGAGAACTGTC -3'

Sequencing Primer
(F):5'- GTCAGGAAGTCAACAGCTATTTG -3'
(R):5'- AAGCTATAGACCCTTGCAGTTTGG -3'
Posted On 2013-08-06