Incidental Mutation 'R8878:Pgap3'
ID 676712
Institutional Source Beutler Lab
Gene Symbol Pgap3
Ensembl Gene ENSMUSG00000038208
Gene Name post-GPI attachment to proteins 3
Synonyms CAB2, Perld1, D430035D22Rik
MMRRC Submission 068746-MU
Accession Numbers
Essential gene? Possibly non essential (E-score: 0.402) question?
Stock # R8878 (G1)
Quality Score 225.009
Status Validated
Chromosome 11
Chromosomal Location 98279503-98291316 bp(-) (GRCm39)
Type of Mutation missense
DNA Base Change (assembly) A to T at 98281924 bp (GRCm39)
Zygosity Heterozygous
Amino Acid Change Valine to Aspartic acid at position 129 (V129D)
Ref Sequence ENSEMBL: ENSMUSP00000119668 (fasta)
Gene Model predicted gene model for transcript(s): [ENSMUST00000041301] [ENSMUST00000090827] [ENSMUST00000128897]
AlphaFold A2A559
Predicted Effect noncoding transcript
Transcript: ENSMUST00000041218
Predicted Effect probably benign
Transcript: ENSMUST00000041301
SMART Domains Protein: ENSMUSP00000035549
Gene: ENSMUSG00000038216

DomainStartEndE-ValueType
Pfam:NNMT_PNMT_TEMT 25 290 1.2e-94 PFAM
Predicted Effect probably benign
Transcript: ENSMUST00000090827
AA Change: V180D

PolyPhen 2 Score 0.108 (Sensitivity: 0.93; Specificity: 0.86)
SMART Domains Protein: ENSMUSP00000088337
Gene: ENSMUSG00000038208
AA Change: V180D

DomainStartEndE-ValueType
signal peptide 1 23 N/A INTRINSIC
Pfam:Per1 54 306 6.3e-96 PFAM
Predicted Effect noncoding transcript
Transcript: ENSMUST00000124527
Predicted Effect noncoding transcript
Transcript: ENSMUST00000128058
Predicted Effect probably benign
Transcript: ENSMUST00000128897
AA Change: V129D

PolyPhen 2 Score 0.162 (Sensitivity: 0.92; Specificity: 0.87)
SMART Domains Protein: ENSMUSP00000119668
Gene: ENSMUSG00000038208
AA Change: V129D

DomainStartEndE-ValueType
signal peptide 1 23 N/A INTRINSIC
Pfam:Per1 51 96 6.2e-14 PFAM
Pfam:Per1 93 256 7.3e-59 PFAM
Meta Mutation Damage Score 0.6467 question?
Coding Region Coverage
  • 1x: 100.0%
  • 3x: 99.9%
  • 10x: 99.7%
  • 20x: 98.9%
Validation Efficiency 99% (73/74)
MGI Phenotype FUNCTION: [Summary is not available for the mouse gene. This summary is for the human ortholog.] This gene encodes a glycosylphosphatidylinositol (GPI)-specific phospholipase that primarily localizes to the Golgi apparatus. This ubiquitously expressed gene is predicted to encode a seven-transmembrane protein that removes unsaturated fatty acids from the sn-2 position of GPI. The remodeling of the constituent fatty acids on GPI is thought to be important for the proper association between GPI-anchored proteins and lipid rafts. The tethering of proteins to plasma membranes via posttranslational GPI-anchoring is thought to play a role in protein sorting and trafficking. Mutations in this gene cause the autosomal recessive neurologic disorder hyperphosphatasia with mental retardation syndrome 4 (HPMRS4). Alternative splicing results in multiple transcript variants encoding distinct isoforms. [provided by RefSeq, Apr 2014]
PHENOTYPE: Mice homozygous for a targeted allele exhibit abnormal head and tail morphology, growth retardation, limb glasping, altered T cell proliferation response and increased susceptibility to EAE. [provided by MGI curators]
Allele List at MGI
Other mutations in this stock
Total: 75 list
GeneRefVarChr/LocMutationPredicted EffectZygosity
Acss2 C A 2: 155,398,324 (GRCm39) H348Q probably benign Het
Ago1 T A 4: 126,357,516 (GRCm39) Y53F probably benign Het
Arrdc5 A G 17: 56,601,342 (GRCm39) L261P probably benign Het
Asb2 C A 12: 103,290,138 (GRCm39) W551L possibly damaging Het
Atl2 T C 17: 80,160,232 (GRCm39) I452V probably benign Het
Atxn7l3 T C 11: 102,183,545 (GRCm39) S203G probably benign Het
Bche A G 3: 73,608,506 (GRCm39) F307L probably benign Het
C6 T C 15: 4,826,454 (GRCm39) V679A probably benign Het
Cd163 A T 6: 124,297,469 (GRCm39) N872Y probably damaging Het
Cdkal1 C A 13: 29,658,607 (GRCm39) V380F probably damaging Het
Ceacam11 A T 7: 17,709,536 (GRCm39) I245L probably benign Het
Ceacam16 G T 7: 19,592,656 (GRCm39) T84K possibly damaging Het
Ceacam2 T A 7: 25,227,351 (GRCm39) Q172L probably benign Het
Chga T G 12: 102,527,720 (GRCm39) S125A possibly damaging Het
Col9a1 T C 1: 24,236,048 (GRCm39) probably null Het
Crybg3 C A 16: 59,380,547 (GRCm39) A236S probably benign Het
Csmd1 A G 8: 15,960,528 (GRCm39) Y3296H probably damaging Het
Cyp2j8 C A 4: 96,358,807 (GRCm39) V371L possibly damaging Het
Des C A 1: 75,337,137 (GRCm39) L26M unknown Het
Edc3 A G 9: 57,623,484 (GRCm39) S140G possibly damaging Het
Fam161a C T 11: 22,970,092 (GRCm39) T90I probably benign Het
Fancm T C 12: 65,173,522 (GRCm39) Y1945H probably damaging Het
Fbn2 C T 18: 58,257,318 (GRCm39) V350I probably benign Het
Git2 A G 5: 114,899,649 (GRCm39) C235R possibly damaging Het
Gk2 T C 5: 97,604,341 (GRCm39) K166E probably benign Het
Gm12258 G A 11: 58,750,112 (GRCm39) R429H unknown Het
Gm7247 T G 14: 51,666,210 (GRCm39) probably benign Het
Gmppa A G 1: 75,414,932 (GRCm39) Y59C probably damaging Het
Has1 G T 17: 18,070,321 (GRCm39) A200E possibly damaging Het
Hbs1l T C 10: 21,234,711 (GRCm39) I588T possibly damaging Het
Helz2 A G 2: 180,874,560 (GRCm39) V1978A possibly damaging Het
Hoxb9 T C 11: 96,165,557 (GRCm39) Y209H probably damaging Het
Hps5 T C 7: 46,421,345 (GRCm39) D706G probably benign Het
Hydin T C 8: 111,035,720 (GRCm39) V137A probably benign Het
Ifngr2 T C 16: 91,359,847 (GRCm39) I318T probably benign Het
Iqgap3 C T 3: 88,020,532 (GRCm39) T1290I probably damaging Het
Jrk A T 15: 74,578,988 (GRCm39) V99E probably benign Het
Kalrn G A 16: 34,018,830 (GRCm39) P1311S probably benign Het
Kalrn G A 16: 34,025,696 (GRCm39) T931M probably damaging Het
Kirrel3 A G 9: 34,850,561 (GRCm39) probably benign Het
Klk1b9 T C 7: 43,443,782 (GRCm39) F99L possibly damaging Het
Lamb3 T C 1: 193,013,124 (GRCm39) C450R probably damaging Het
Lyst T A 13: 13,815,661 (GRCm39) S1182T probably benign Het
Map1a T C 2: 121,138,125 (GRCm39) V2933A probably damaging Het
Map2k5 A T 9: 63,250,667 (GRCm39) probably null Het
Mcm6 A G 1: 128,283,248 (GRCm39) probably null Het
Mmp17 G A 5: 129,683,378 (GRCm39) V505M probably damaging Het
Mpped2 A G 2: 106,575,065 (GRCm39) D50G probably damaging Het
Mtf1 T A 4: 124,715,023 (GRCm39) L216* probably null Het
Niban2 A T 2: 32,811,105 (GRCm39) M372L probably benign Het
Obscn T C 11: 58,890,638 (GRCm39) E7298G unknown Het
Or52ab7 A T 7: 102,978,212 (GRCm39) H173L possibly damaging Het
Or56a3 T C 7: 104,735,763 (GRCm39) L280P probably damaging Het
Or6c205 T C 10: 129,086,883 (GRCm39) L160P probably benign Het
Or7d9 A G 9: 20,197,358 (GRCm39) D129G probably damaging Het
Otulinl T A 15: 27,664,884 (GRCm39) H24L probably benign Het
Pax2 G A 19: 44,777,215 (GRCm39) probably null Het
Pcnt T A 10: 76,244,675 (GRCm39) E1135V probably damaging Het
Polq A G 16: 36,860,869 (GRCm39) N497S probably benign Het
Ppfia4 T C 1: 134,227,122 (GRCm39) T1138A Het
Prickle4 A G 17: 48,001,587 (GRCm39) L32P Het
Prl2c2 C T 13: 13,171,896 (GRCm39) G158R probably damaging Het
Psd3 A G 8: 68,210,750 (GRCm39) I752T probably benign Het
Sag A T 1: 87,756,158 (GRCm39) Y255F probably benign Het
Scn7a A T 2: 66,506,199 (GRCm39) D1563E probably damaging Het
Secisbp2 A G 13: 51,837,404 (GRCm39) N855S probably benign Het
Setd2 T C 9: 110,421,467 (GRCm39) V2011A probably benign Het
Slc30a6 T C 17: 74,730,112 (GRCm39) V334A probably damaging Het
Spen A G 4: 141,204,520 (GRCm39) V1369A unknown Het
Stac2 T C 11: 97,932,373 (GRCm39) T207A probably benign Het
Syne2 T C 12: 75,952,067 (GRCm39) V445A probably benign Het
Tas2r131 C A 6: 132,934,467 (GRCm39) W114L probably damaging Het
Tgfbrap1 G A 1: 43,088,959 (GRCm39) R815* probably null Het
Trpv2 A T 11: 62,481,112 (GRCm39) I404L probably benign Het
Zfp236 G A 18: 82,617,122 (GRCm39) T1791M probably damaging Het
Other mutations in Pgap3
AlleleSourceChrCoordTypePredicted EffectPPH Score
IGL01942:Pgap3 APN 11 98,288,780 (GRCm39) missense probably damaging 1.00
IGL03409:Pgap3 APN 11 98,289,764 (GRCm39) missense possibly damaging 0.95
R0053:Pgap3 UTSW 11 98,281,924 (GRCm39) missense probably benign 0.16
R0053:Pgap3 UTSW 11 98,281,924 (GRCm39) missense probably benign 0.16
R1185:Pgap3 UTSW 11 98,281,960 (GRCm39) missense probably damaging 1.00
R1185:Pgap3 UTSW 11 98,281,960 (GRCm39) missense probably damaging 1.00
R1185:Pgap3 UTSW 11 98,281,960 (GRCm39) missense probably damaging 1.00
R1579:Pgap3 UTSW 11 98,280,879 (GRCm39) missense probably benign
R1938:Pgap3 UTSW 11 98,291,040 (GRCm39) critical splice donor site probably null
R2117:Pgap3 UTSW 11 98,281,933 (GRCm39) missense probably damaging 0.99
R2367:Pgap3 UTSW 11 98,281,985 (GRCm39) splice site probably null
R3854:Pgap3 UTSW 11 98,281,638 (GRCm39) missense possibly damaging 0.49
R4820:Pgap3 UTSW 11 98,281,300 (GRCm39) missense probably damaging 1.00
R5208:Pgap3 UTSW 11 98,288,874 (GRCm39) missense probably damaging 1.00
R5493:Pgap3 UTSW 11 98,281,540 (GRCm39) missense possibly damaging 0.87
R5783:Pgap3 UTSW 11 98,281,290 (GRCm39) missense probably benign
R7722:Pgap3 UTSW 11 98,281,610 (GRCm39) missense probably benign 0.00
R7943:Pgap3 UTSW 11 98,281,227 (GRCm39) missense probably damaging 1.00
R8347:Pgap3 UTSW 11 98,281,575 (GRCm39) small deletion probably benign
R8888:Pgap3 UTSW 11 98,281,602 (GRCm39) missense possibly damaging 0.73
R8895:Pgap3 UTSW 11 98,281,602 (GRCm39) missense possibly damaging 0.73
R9466:Pgap3 UTSW 11 98,289,796 (GRCm39) missense probably benign 0.01
R9531:Pgap3 UTSW 11 98,288,823 (GRCm39) missense probably damaging 1.00
X0026:Pgap3 UTSW 11 98,281,305 (GRCm39) missense possibly damaging 0.80
Predicted Primers PCR Primer
(F):5'- AAAGGGTTGAAGGCTCCCTG -3'
(R):5'- GACACAGTGAAACAGCCATG -3'

Sequencing Primer
(F):5'- TTGAAGGCTCCCTGAAGCCAC -3'
(R):5'- AGGTAGGGCTCCTGATGAC -3'
Posted On 2021-07-15