Incidental Mutation 'R4669:Ppfia3'
ID 352265
Institutional Source Beutler Lab
Gene Symbol Ppfia3
Ensembl Gene ENSMUSG00000003863
Gene Name protein tyrosine phosphatase, receptor type, f polypeptide (PTPRF), interacting protein (liprin), alpha 3
Synonyms 2410127E16Rik, Liprin-alpha3
MMRRC Submission 041925-MU
Accession Numbers
Essential gene? Possibly non essential (E-score: 0.252) question?
Stock # R4669 (G1)
Quality Score 225
Status Not validated
Chromosome 7
Chromosomal Location 44988550-45016443 bp(-) (GRCm39)
Type of Mutation missense
DNA Base Change (assembly) T to C at 45001517 bp (GRCm39)
Zygosity Heterozygous
Amino Acid Change Glutamic Acid to Glycine at position 465 (E465G)
Gene Model predicted gene model for transcript(s): [ENSMUST00000003961] [ENSMUST00000210248] [ENSMUST00000211067]
AlphaFold P60469
Predicted Effect probably damaging
Transcript: ENSMUST00000003961
AA Change: E616G

PolyPhen 2 Score 0.996 (Sensitivity: 0.55; Specificity: 0.98)
SMART Domains Protein: ENSMUSP00000003961
Gene: ENSMUSG00000003863
AA Change: E616G

DomainStartEndE-ValueType
coiled coil region 27 129 N/A INTRINSIC
coiled coil region 167 426 N/A INTRINSIC
coiled coil region 448 500 N/A INTRINSIC
low complexity region 534 550 N/A INTRINSIC
coiled coil region 597 642 N/A INTRINSIC
low complexity region 651 672 N/A INTRINSIC
low complexity region 707 719 N/A INTRINSIC
SAM 835 904 1.46e-10 SMART
SAM 950 1017 8.22e-5 SMART
SAM 1038 1110 3.58e-5 SMART
low complexity region 1156 1169 N/A INTRINSIC
Predicted Effect probably damaging
Transcript: ENSMUST00000107779
AA Change: E616G

PolyPhen 2 Score 0.996 (Sensitivity: 0.55; Specificity: 0.98)
SMART Domains Protein: ENSMUSP00000103408
Gene: ENSMUSG00000003863
AA Change: E616G

DomainStartEndE-ValueType
coiled coil region 27 129 N/A INTRINSIC
coiled coil region 167 426 N/A INTRINSIC
coiled coil region 448 500 N/A INTRINSIC
low complexity region 534 550 N/A INTRINSIC
coiled coil region 597 642 N/A INTRINSIC
low complexity region 651 672 N/A INTRINSIC
low complexity region 707 719 N/A INTRINSIC
SAM 835 904 1.46e-10 SMART
SAM 950 1017 8.22e-5 SMART
SAM 1038 1110 3.58e-5 SMART
low complexity region 1156 1169 N/A INTRINSIC
Predicted Effect probably damaging
Transcript: ENSMUST00000137578
AA Change: E465G

PolyPhen 2 Score 0.999 (Sensitivity: 0.14; Specificity: 0.99)
SMART Domains Protein: ENSMUSP00000118183
Gene: ENSMUSG00000003863
AA Change: E465G

DomainStartEndE-ValueType
coiled coil region 16 275 N/A INTRINSIC
coiled coil region 297 349 N/A INTRINSIC
low complexity region 383 399 N/A INTRINSIC
coiled coil region 446 491 N/A INTRINSIC
low complexity region 500 521 N/A INTRINSIC
low complexity region 556 568 N/A INTRINSIC
SAM 684 753 1.46e-10 SMART
SAM 790 857 8.22e-5 SMART
SAM 878 950 3.58e-5 SMART
low complexity region 996 1009 N/A INTRINSIC
Predicted Effect probably benign
Transcript: ENSMUST00000210248
AA Change: E465G

PolyPhen 2 Score 0.213 (Sensitivity: 0.92; Specificity: 0.88)
Predicted Effect noncoding transcript
Transcript: ENSMUST00000210479
Predicted Effect noncoding transcript
Transcript: ENSMUST00000210586
Predicted Effect probably damaging
Transcript: ENSMUST00000211067
AA Change: E616G

PolyPhen 2 Score 0.996 (Sensitivity: 0.55; Specificity: 0.98)
Coding Region Coverage
  • 1x: 99.2%
  • 3x: 98.6%
  • 10x: 97.3%
  • 20x: 95.4%
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 is a member of the LAR protein-tyrosine phosphatase-interacting protein (liprin) family. Liprins interact with members of LAR family of transmembrane protein tyrosine phosphatases, which are known to be important for axon guidance and mammary gland development. Liprin family protein has been shown to localize phosphatase LAR to cell focal adhesions and may be involved in the molecular organization of presynaptic active zones. [provided by RefSeq, Jul 2008]
Allele List at MGI
Other mutations in this stock
Total: 98 list
GeneRefVarChr/LocMutationPredicted EffectZygosity
Acad8 A G 9: 26,901,923 (GRCm39) L147P probably damaging Het
Acan A G 7: 78,750,890 (GRCm39) E464G probably benign Het
Agap1 A G 1: 89,765,528 (GRCm39) probably null Het
Akap13 A G 7: 75,378,842 (GRCm39) T2128A probably damaging Het
Ap2a1 A T 7: 44,552,343 (GRCm39) probably benign Het
Arap3 T C 18: 38,129,307 (GRCm39) D217G probably benign Het
Arl2 C A 19: 6,184,716 (GRCm39) R179L probably damaging Het
Atg2a T A 19: 6,309,017 (GRCm39) probably null Het
B3gat1 T A 9: 26,663,052 (GRCm39) L6Q probably benign Het
Bcl10 A G 3: 145,636,327 (GRCm39) N75S probably damaging Het
Bmpr2 T C 1: 59,906,875 (GRCm39) L656S probably damaging Het
Brms1l A G 12: 55,888,356 (GRCm39) E48G possibly damaging Het
C2cd2l A T 9: 44,226,322 (GRCm39) N414K possibly damaging Het
Capn2 C T 1: 182,298,345 (GRCm39) C640Y probably benign Het
Ccdc153 G T 9: 44,157,021 (GRCm39) R99M probably damaging Het
Ccdc51 A G 9: 108,920,030 (GRCm39) N142S probably benign Het
Cdipt A G 7: 126,577,578 (GRCm39) H108R possibly damaging Het
Ceacam20 T C 7: 19,719,952 (GRCm39) Y495H probably damaging Het
Celf2 T C 2: 6,726,339 (GRCm39) I47V probably benign Het
Cts3 C T 13: 61,714,637 (GRCm39) E223K probably benign Het
Cyp2a22 T C 7: 26,637,280 (GRCm39) D168G possibly damaging Het
Cyp2c67 T A 19: 39,632,098 (GRCm39) H90L probably benign Het
Ddx4 T C 13: 112,758,778 (GRCm39) Y261C probably damaging Het
Dnah17 T C 11: 117,965,119 (GRCm39) T2308A probably benign Het
Dnah6 T C 6: 73,014,671 (GRCm39) T3587A probably damaging Het
Dpy19l1 C T 9: 24,343,664 (GRCm39) V494I possibly damaging Het
Dse T G 10: 34,029,008 (GRCm39) Y694S probably damaging Het
Emilin3 T C 2: 160,752,717 (GRCm39) I78V probably benign Het
Esam T A 9: 37,447,952 (GRCm39) Y195* probably null Het
Extl3 T A 14: 65,313,745 (GRCm39) N479I possibly damaging Het
Fat2 A G 11: 55,202,441 (GRCm39) V211A probably benign Het
Ganc G T 2: 120,261,548 (GRCm39) V343F probably benign Het
Ggt5 T C 10: 75,438,865 (GRCm39) L121P probably damaging Het
Gnmt A T 17: 47,037,225 (GRCm39) C186* probably null Het
Gpr75 A T 11: 30,842,072 (GRCm39) I326F probably damaging Het
Gsdme C T 6: 50,185,102 (GRCm39) V451M probably damaging Het
H2-T23 G T 17: 36,342,690 (GRCm39) D149E probably damaging Het
Hmcn2 G T 2: 31,325,804 (GRCm39) R4277L probably benign Het
Irf9 C A 14: 55,843,223 (GRCm39) H94N probably benign Het
Jhy T C 9: 40,872,449 (GRCm39) N20S probably benign Het
Klf17 C A 4: 117,617,568 (GRCm39) C263F probably damaging Het
Lama5 T C 2: 179,822,430 (GRCm39) Y2881C probably damaging Het
Lig1 T G 7: 13,044,953 (GRCm39) I882S probably damaging Het
Ltn1 A T 16: 87,215,375 (GRCm39) M420K possibly damaging Het
Mael T C 1: 166,063,077 (GRCm39) E125G probably damaging Het
Mib2 C T 4: 155,741,872 (GRCm39) D275N possibly damaging Het
Mical3 C T 6: 120,934,664 (GRCm39) R1805Q probably damaging Het
Mix23 A G 16: 35,903,089 (GRCm39) D27G probably damaging Het
Mllt10 A G 2: 18,208,444 (GRCm39) D158G probably damaging Het
Mocs1 A G 17: 49,761,613 (GRCm39) D569G possibly damaging Het
Msh6 T C 17: 88,292,234 (GRCm39) S330P possibly damaging Het
Mtmr2 T C 9: 13,707,260 (GRCm39) S199P probably damaging Het
Ndufaf5 T C 2: 140,029,675 (GRCm39) V164A probably benign Het
Nek9 T C 12: 85,360,978 (GRCm39) E518G probably benign Het
Nfatc2 T C 2: 168,413,410 (GRCm39) I72V probably benign Het
Nlrp9c C T 7: 26,074,793 (GRCm39) A746T possibly damaging Het
Nup42 A G 5: 24,387,415 (GRCm39) R402G probably benign Het
Ogdh G T 11: 6,290,600 (GRCm39) C406F probably benign Het
Or3a1d A G 11: 74,237,789 (GRCm39) V207A probably benign Het
Or4c120 G A 2: 89,001,245 (GRCm39) H104Y probably damaging Het
Or8b35 A T 9: 37,904,381 (GRCm39) I198F possibly damaging Het
Or8g17 T A 9: 38,930,675 (GRCm39) Y54F probably benign Het
Or8j3 A T 2: 86,028,277 (GRCm39) M273K possibly damaging Het
Otof A G 5: 30,578,318 (GRCm39) probably null Het
Pcdhb17 T C 18: 37,619,259 (GRCm39) S350P probably damaging Het
Phf3 T C 1: 30,869,027 (GRCm39) T674A probably damaging Het
Pikfyve T A 1: 65,289,432 (GRCm39) C1235S probably damaging Het
Prkg1 T A 19: 31,641,639 (GRCm39) I15F probably damaging Het
Rab5c A G 11: 100,610,843 (GRCm39) F22L probably damaging Het
Raf1 A G 6: 115,609,880 (GRCm39) S220P probably damaging Het
Rgl1 T G 1: 152,397,122 (GRCm39) R716S probably damaging Het
Rhbg C A 3: 88,153,273 (GRCm39) W205L probably damaging Het
Rimbp3 A G 16: 17,027,053 (GRCm39) E159G possibly damaging Het
Ryr1 T C 7: 28,759,256 (GRCm39) D3338G probably null Het
Sash1 T C 10: 8,606,149 (GRCm39) N747S probably benign Het
Serpina3g A T 12: 104,205,479 (GRCm39) I73F probably damaging Het
Sfxn2 C A 19: 46,574,213 (GRCm39) N134K probably damaging Het
Slc12a6 A G 2: 112,184,640 (GRCm39) H853R probably damaging Het
Slc16a12 C T 19: 34,649,965 (GRCm39) D357N probably damaging Het
Slc39a8 T C 3: 135,561,772 (GRCm39) Y164H probably benign Het
Snx9 A G 17: 5,977,499 (GRCm39) K518E probably damaging Het
Spdye4c G A 2: 128,434,273 (GRCm39) V5I possibly damaging Het
Spef2 A G 15: 9,676,459 (GRCm39) V704A probably benign Het
Stard3nl T A 13: 19,560,689 (GRCm39) N29Y probably damaging Het
Strap C A 6: 137,712,384 (GRCm39) S11* probably null Het
Synpo2 A G 3: 122,906,712 (GRCm39) L868P probably damaging Het
Tenm2 A G 11: 35,901,314 (GRCm39) V2474A probably damaging Het
Tm9sf4 T A 2: 153,029,228 (GRCm39) V92D probably damaging Het
Tmf1 A T 6: 97,147,388 (GRCm39) M526K probably benign Het
Top2b T G 14: 16,409,189 (GRCm38) I777M probably damaging Het
Ttc39d A G 17: 80,525,068 (GRCm39) I576V probably benign Het
Upk1a T G 7: 30,304,554 (GRCm39) T193P probably benign Het
Vmn2r67 A T 7: 84,799,732 (GRCm39) V502E probably benign Het
Wdr17 A G 8: 55,143,083 (GRCm39) V189A possibly damaging Het
Wrap73 A T 4: 154,236,153 (GRCm39) S161C probably benign Het
Zfp568 A G 7: 29,722,702 (GRCm39) H549R probably damaging Het
Zfp605 T A 5: 110,275,227 (GRCm39) M115K possibly damaging Het
Zp1 T A 19: 10,896,269 (GRCm39) H152L probably benign Het
Other mutations in Ppfia3
AlleleSourceChrCoordTypePredicted EffectPPH Score
IGL01783:Ppfia3 APN 7 45,009,481 (GRCm39) splice site probably null
IGL02086:Ppfia3 APN 7 44,989,996 (GRCm39) unclassified probably benign
IGL02160:Ppfia3 APN 7 45,009,475 (GRCm39) splice site probably benign
IGL02373:Ppfia3 APN 7 45,008,273 (GRCm39) missense probably damaging 0.98
IGL02417:Ppfia3 APN 7 44,991,141 (GRCm39) missense probably damaging 0.98
IGL02501:Ppfia3 APN 7 45,004,362 (GRCm39) splice site probably benign
IGL02638:Ppfia3 APN 7 45,006,092 (GRCm39) missense probably damaging 1.00
IGL03084:Ppfia3 APN 7 44,989,651 (GRCm39) missense probably benign 0.00
R0207:Ppfia3 UTSW 7 44,997,958 (GRCm39) missense probably damaging 1.00
R0962:Ppfia3 UTSW 7 44,997,146 (GRCm39) splice site probably benign
R1086:Ppfia3 UTSW 7 45,011,182 (GRCm39) missense probably damaging 1.00
R1146:Ppfia3 UTSW 7 45,001,639 (GRCm39) missense probably benign 0.19
R1146:Ppfia3 UTSW 7 45,001,639 (GRCm39) missense probably benign 0.19
R1566:Ppfia3 UTSW 7 44,990,112 (GRCm39) missense probably damaging 1.00
R1677:Ppfia3 UTSW 7 45,006,090 (GRCm39) missense probably benign 0.03
R1876:Ppfia3 UTSW 7 45,001,631 (GRCm39) missense possibly damaging 0.75
R2219:Ppfia3 UTSW 7 45,004,314 (GRCm39) nonsense probably null
R2336:Ppfia3 UTSW 7 45,006,121 (GRCm39) splice site probably null
R2843:Ppfia3 UTSW 7 45,005,852 (GRCm39) missense probably damaging 1.00
R2844:Ppfia3 UTSW 7 45,005,852 (GRCm39) missense probably damaging 1.00
R2846:Ppfia3 UTSW 7 45,005,852 (GRCm39) missense probably damaging 1.00
R4777:Ppfia3 UTSW 7 44,990,581 (GRCm39) missense probably damaging 1.00
R4787:Ppfia3 UTSW 7 44,990,050 (GRCm39) missense possibly damaging 0.89
R4994:Ppfia3 UTSW 7 44,990,542 (GRCm39) missense probably damaging 1.00
R5042:Ppfia3 UTSW 7 44,991,765 (GRCm39) missense probably damaging 1.00
R5821:Ppfia3 UTSW 7 45,003,040 (GRCm39) missense probably damaging 0.96
R6116:Ppfia3 UTSW 7 45,004,127 (GRCm39) missense probably damaging 1.00
R6515:Ppfia3 UTSW 7 44,989,657 (GRCm39) missense possibly damaging 0.94
R6868:Ppfia3 UTSW 7 45,003,036 (GRCm39) missense probably damaging 1.00
R6920:Ppfia3 UTSW 7 45,008,231 (GRCm39) missense possibly damaging 0.46
R6935:Ppfia3 UTSW 7 45,001,631 (GRCm39) missense possibly damaging 0.47
R6978:Ppfia3 UTSW 7 44,996,272 (GRCm39) missense probably benign 0.02
R7017:Ppfia3 UTSW 7 45,008,224 (GRCm39) missense probably benign
R7027:Ppfia3 UTSW 7 45,004,160 (GRCm39) missense possibly damaging 0.80
R7078:Ppfia3 UTSW 7 45,010,019 (GRCm39) missense probably damaging 1.00
R7256:Ppfia3 UTSW 7 44,991,167 (GRCm39) missense probably benign 0.43
R7378:Ppfia3 UTSW 7 45,010,870 (GRCm39) splice site probably null
R7570:Ppfia3 UTSW 7 44,990,172 (GRCm39) critical splice acceptor site probably null
R7814:Ppfia3 UTSW 7 45,001,686 (GRCm39) missense probably benign
R8298:Ppfia3 UTSW 7 45,009,618 (GRCm39) missense probably damaging 1.00
R8712:Ppfia3 UTSW 7 45,011,129 (GRCm39) missense probably benign 0.43
R8781:Ppfia3 UTSW 7 44,997,953 (GRCm39) missense possibly damaging 0.94
R8843:Ppfia3 UTSW 7 44,997,941 (GRCm39) missense probably benign 0.02
R8901:Ppfia3 UTSW 7 44,991,141 (GRCm39) missense probably damaging 1.00
R8984:Ppfia3 UTSW 7 44,990,100 (GRCm39) missense probably damaging 1.00
R9149:Ppfia3 UTSW 7 44,999,717 (GRCm39) critical splice acceptor site probably null
R9284:Ppfia3 UTSW 7 45,011,222 (GRCm39) missense probably damaging 1.00
R9427:Ppfia3 UTSW 7 45,008,213 (GRCm39) missense possibly damaging 0.46
R9683:Ppfia3 UTSW 7 45,005,999 (GRCm39) missense probably benign 0.29
R9803:Ppfia3 UTSW 7 44,990,539 (GRCm39) missense probably benign 0.01
Predicted Primers PCR Primer
(F):5'- ACACACTGTTTGGTATAGGTGC -3'
(R):5'- TACAGGACAGGACTGGGATC -3'

Sequencing Primer
(F):5'- GCTTAGGGTCACTGATCAGAC -3'
(R):5'- ACAGGACTGGGATCGGTCTG -3'
Posted On 2015-10-08