Incidental Mutation 'R0053:Pgap3'
ID 64339
Institutional Source Beutler Lab
Gene Symbol Pgap3
Ensembl Gene ENSMUSG00000038208
Gene Name post-GPI attachment to proteins 3
Synonyms CAB2, Perld1, D430035D22Rik
MMRRC Submission 038347-MU
Accession Numbers
Essential gene? Possibly non essential (E-score: 0.391) question?
Stock # R0053 (G1)
Quality Score 225
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: 99.4%
  • 3x: 98.9%
  • 10x: 97.9%
  • 20x: 96.5%
Validation Efficiency 100% (67/67)
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: 53 list
GeneRefVarChr/LocMutationPredicted EffectZygosity
Ada A T 2: 163,574,212 (GRCm39) V148D probably damaging Het
Alpi T C 1: 87,026,512 (GRCm39) D493G probably benign Het
Atp10b A G 11: 43,107,391 (GRCm39) probably benign Het
AY761185 A T 8: 21,434,546 (GRCm39) probably benign Het
Cadm1 C T 9: 47,710,712 (GRCm39) T205I probably damaging Het
Capn3 A G 2: 120,322,318 (GRCm39) I413V possibly damaging Het
Cblb C T 16: 51,963,164 (GRCm39) T369I probably damaging Het
Ccdc54 T A 16: 50,410,597 (GRCm39) N223I probably benign Het
Cdc25c A G 18: 34,868,488 (GRCm39) V294A probably benign Het
Cep170 A T 1: 176,609,946 (GRCm39) S122T possibly damaging Het
Chd1 A G 17: 15,967,451 (GRCm39) N849D probably damaging Het
Cspg4b T C 13: 113,505,023 (GRCm39) W2051R probably benign Het
Dpp3 A G 19: 4,973,154 (GRCm39) C147R probably damaging Het
Dst A G 1: 34,333,631 (GRCm39) probably null Het
Fbxw9 T A 8: 85,791,083 (GRCm39) L250Q probably damaging Het
Gpr75 A T 11: 30,842,571 (GRCm39) Q492L possibly damaging Het
Gramd4 T A 15: 86,014,339 (GRCm39) probably benign Het
Hivep2 T C 10: 14,007,865 (GRCm39) C1488R probably damaging Het
Hjurp G C 1: 88,204,937 (GRCm39) probably benign Het
Inava C T 1: 136,155,288 (GRCm39) V106I probably benign Het
Insr A G 8: 3,205,683 (GRCm39) S1369P probably damaging Het
Insrr A C 3: 87,707,759 (GRCm39) D67A probably damaging Het
Irf2 T A 8: 47,271,886 (GRCm39) Y158N probably benign Het
Katnbl1 A G 2: 112,234,586 (GRCm39) R23G probably benign Het
Lamb2 T A 9: 108,363,936 (GRCm39) C987* probably null Het
Lzts2 T C 19: 45,014,746 (GRCm39) probably benign Het
Mmp14 T A 14: 54,676,109 (GRCm39) probably benign Het
Mycbpap A G 11: 94,402,562 (GRCm39) Y258H probably damaging Het
Nav3 A G 10: 109,602,778 (GRCm39) probably benign Het
Or10j7 T C 1: 173,011,845 (GRCm39) D52G probably benign Het
Or4c100 T A 2: 88,356,507 (GRCm39) N193K probably damaging Het
Parp10 T A 15: 76,126,446 (GRCm39) L247F probably damaging Het
Pcsk6 C T 7: 65,633,451 (GRCm39) probably benign Het
Pibf1 A G 14: 99,377,993 (GRCm39) Y373C probably damaging Het
Plcb1 A G 2: 135,136,835 (GRCm39) E310G probably benign Het
Plin3 T C 17: 56,586,892 (GRCm39) D385G probably damaging Het
Pole A T 5: 110,441,206 (GRCm39) D220V probably damaging Het
Ptprk T A 10: 28,351,105 (GRCm39) F533I probably damaging Het
Resf1 T A 6: 149,229,088 (GRCm39) D711E probably benign Het
Rufy1 A T 11: 50,292,292 (GRCm39) M499K probably benign Het
Scn1a T G 2: 66,130,119 (GRCm39) D1232A probably benign Het
Sec23ip T C 7: 128,346,891 (GRCm39) L49P probably damaging Het
Sf3b1 G A 1: 55,039,532 (GRCm39) Q698* probably null Het
Shprh A T 10: 11,070,116 (GRCm39) probably null Het
Snd1 C A 6: 28,745,334 (GRCm39) probably benign Het
Stab1 C T 14: 30,862,644 (GRCm39) A2260T possibly damaging Het
Stpg2 A G 3: 138,918,082 (GRCm39) Q60R probably benign Het
Strn T C 17: 78,964,363 (GRCm39) H687R possibly damaging Het
Tgfb3 A T 12: 86,124,603 (GRCm39) I35N probably damaging Het
Tnks2 T C 19: 36,852,765 (GRCm39) S166P probably damaging Het
Tyw5 G A 1: 57,440,597 (GRCm39) T55M probably damaging Het
Usp19 A G 9: 108,374,369 (GRCm39) probably null Het
Zfp13 A T 17: 23,795,122 (GRCm39) I483N 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
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
R8878:Pgap3 UTSW 11 98,281,924 (GRCm39) missense probably benign 0.16
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'- CAAAGGGTTGAAGGCTCCCTGAAG -3'
(R):5'- TGCCCTCTCAATGCCATGAACG -3'

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