Incidental Mutation 'R4837:Pikfyve'
ID 374315
Institutional Source Beutler Lab
Gene Symbol Pikfyve
Ensembl Gene ENSMUSG00000025949
Gene Name phosphoinositide kinase, FYVE type zinc finger containing
Synonyms Pip5k3
MMRRC Submission 042452-MU
Accession Numbers
Essential gene? Essential (E-score: 1.000) question?
Stock # R4837 (G1)
Quality Score 225
Status Validated
Chromosome 1
Chromosomal Location 65186683-65278695 bp(+) (GRCm38)
Type of Mutation missense
DNA Base Change (assembly) A to G at 65246590 bp (GRCm38)
Zygosity Heterozygous
Amino Acid Change Glutamic Acid to Glycine at position 951 (E951G)
Ref Sequence ENSEMBL: ENSMUSP00000079926 (fasta)
Gene Model predicted gene model for transcript(s): [ENSMUST00000081154] [ENSMUST00000097707] [ENSMUST00000190058]
AlphaFold Q9Z1T6
Predicted Effect possibly damaging
Transcript: ENSMUST00000081154
AA Change: E951G

PolyPhen 2 Score 0.921 (Sensitivity: 0.81; Specificity: 0.94)
SMART Domains Protein: ENSMUSP00000079926
Gene: ENSMUSG00000025949
AA Change: E951G

DomainStartEndE-ValueType
low complexity region 58 81 N/A INTRINSIC
FYVE 161 230 5.95e-18 SMART
DEP 376 451 9.05e-27 SMART
Pfam:Cpn60_TCP1 547 822 2e-37 PFAM
low complexity region 1177 1189 N/A INTRINSIC
low complexity region 1516 1536 N/A INTRINSIC
PIPKc 1745 2039 3.03e-162 SMART
Predicted Effect probably benign
Transcript: ENSMUST00000097707
AA Change: E996G

PolyPhen 2 Score 0.000 (Sensitivity: 1.00; Specificity: 0.00)
SMART Domains Protein: ENSMUSP00000095314
Gene: ENSMUSG00000025949
AA Change: E996G

DomainStartEndE-ValueType
low complexity region 58 81 N/A INTRINSIC
FYVE 150 219 5.95e-18 SMART
DEP 365 440 9.05e-27 SMART
Pfam:Cpn60_TCP1 590 864 1.8e-35 PFAM
low complexity region 1222 1234 N/A INTRINSIC
low complexity region 1561 1581 N/A INTRINSIC
PIPKc 1790 2084 3.03e-162 SMART
Predicted Effect probably benign
Transcript: ENSMUST00000190058
SMART Domains Protein: ENSMUSP00000140204
Gene: ENSMUSG00000025949

DomainStartEndE-ValueType
low complexity region 58 81 N/A INTRINSIC
Meta Mutation Damage Score 0.0594 question?
Coding Region Coverage
  • 1x: 99.2%
  • 3x: 98.5%
  • 10x: 96.8%
  • 20x: 93.9%
Validation Efficiency 99% (75/76)
MGI Phenotype FUNCTION: [Summary is not available for the mouse gene. This summary is for the human ortholog.] Phosphorylated derivatives of phosphatidylinositol (PtdIns) regulate cytoskeletal functions, membrane trafficking, and receptor signaling by recruiting protein complexes to cell- and endosomal-membranes. Humans have multiple PtdIns proteins that differ by the degree and position of phosphorylation of the inositol ring. This gene encodes an enzyme (PIKfyve; also known as phosphatidylinositol-3-phosphate 5-kinase type III or PIPKIII) that phosphorylates the D-5 position in PtdIns and phosphatidylinositol-3-phosphate (PtdIns3P) to make PtdIns5P and PtdIns(3,5)biphosphate. The D-5 position also can be phosphorylated by type I PtdIns4P-5-kinases (PIP5Ks) that are encoded by distinct genes and preferentially phosphorylate D-4 phosphorylated PtdIns. In contrast, PIKfyve preferentially phosphorylates D-3 phosphorylated PtdIns. In addition to being a lipid kinase, PIKfyve also has protein kinase activity. PIKfyve regulates endomembrane homeostasis and plays a role in the biogenesis of endosome carrier vesicles from early endosomes. Mutations in this gene cause corneal fleck dystrophy (CFD); an autosomal dominant disorder characterized by numerous small white flecks present in all layers of the corneal stroma. Histologically, these flecks appear to be keratocytes distended with lipid and mucopolysaccharide filled intracytoplasmic vacuoles. Alternative splicing results in multiple transcript variants encoding distinct isoforms.[provided by RefSeq, May 2010]
PHENOTYPE: Mice homozygous for a null allele die prior to implantation with reduced numbers of inner cell mass and trophectoderm cells and blastocoele abnormalities. Mice homozygous for a second null allele show embryonic lethality between somite formation and embryo turning with abnormal visceral endoderm. [provided by MGI curators]
Allele List at MGI

All alleles(16) : Gene trapped(16)

Other mutations in this stock
Total: 73 list
GeneRefVarChr/LocMutationPredicted EffectZygosity
Abca14 A T 7: 120,246,980 (GRCm38) H618L probably benign Het
Adgrl3 A G 5: 81,766,234 (GRCm38) T1230A probably benign Het
Ahnak2 A G 12: 112,785,739 (GRCm38) S203P probably benign Het
Allc A G 12: 28,559,309 (GRCm38) V244A probably benign Het
Ap3m1 G A 14: 21,037,157 (GRCm38) P157L probably damaging Het
Arhgef2 T G 3: 88,632,943 (GRCm38) I97S probably damaging Het
Btaf1 C A 19: 36,966,785 (GRCm38) T398K probably benign Het
Cabp1 T C 5: 115,173,153 (GRCm38) M158V probably damaging Het
Ccdc162 G A 10: 41,673,867 (GRCm38) P340L probably benign Het
Ccdc168 G A 1: 44,061,434 (GRCm38) T168I possibly damaging Het
Clip4 A G 17: 71,834,222 (GRCm38) K524E probably damaging Het
Cltc A G 11: 86,695,648 (GRCm38) V189A probably benign Het
Cmc2 A G 8: 116,894,140 (GRCm38) F34S probably damaging Het
Ctcfl G T 2: 173,113,656 (GRCm38) T271N probably benign Het
Cyp4f16 T A 17: 32,542,764 (GRCm38) F124I possibly damaging Het
Ddx41 C A 13: 55,531,648 (GRCm38) R479L possibly damaging Het
Dgcr6 C A 16: 18,066,846 (GRCm38) N87K possibly damaging Het
Dll1 A G 17: 15,368,859 (GRCm38) L518P probably damaging Het
Dnaja4 G T 9: 54,710,644 (GRCm38) M263I probably benign Het
Dusp13b T A 14: 21,743,525 (GRCm38) probably benign Het
Fam185a T A 5: 21,480,377 (GRCm38) I357N probably benign Het
Fam186a T C 15: 99,940,797 (GRCm38) Y2522C unknown Het
Fam222a T A 5: 114,594,397 (GRCm38) C4* probably null Het
Filip1 T C 9: 79,819,459 (GRCm38) D626G probably damaging Het
Ghrhr C T 6: 55,388,187 (GRCm38) R389C probably damaging Het
Gstm3 T A 3: 107,964,215 (GRCm38) T217S probably benign Het
Gucy2g T C 19: 55,226,053 (GRCm38) T548A probably benign Het
Hectd3 T A 4: 117,002,597 (GRCm38) C744S probably null Het
Hnrnpl T C 7: 28,817,337 (GRCm38) S184P probably benign Het
Il3 G A 11: 54,267,257 (GRCm38) probably benign Het
Itga5 C T 15: 103,354,084 (GRCm38) G330S probably damaging Het
Kl A G 5: 150,980,847 (GRCm38) T355A possibly damaging Het
Lipk A C 19: 34,032,320 (GRCm38) S208R probably damaging Het
Mrs2 T A 13: 24,999,057 (GRCm38) probably null Het
Mutyh A G 4: 116,817,690 (GRCm38) E372G probably damaging Het
Myh4 C A 11: 67,258,992 (GRCm38) A1821D probably benign Het
Nfkb2 G T 19: 46,307,567 (GRCm38) E170D probably benign Het
Nlrp12 T C 7: 3,231,061 (GRCm38) E881G probably damaging Het
Nol9 T C 4: 152,052,095 (GRCm38) probably benign Het
Nwd1 A G 8: 72,657,131 (GRCm38) E52G probably damaging Het
Olfr1025-ps1 A G 2: 85,918,404 (GRCm38) T160A probably benign Het
Opn4 A G 14: 34,596,304 (GRCm38) V242A probably damaging Het
Or4e1 A T 14: 52,463,646 (GRCm38) M121K probably damaging Het
Or4k44 T A 2: 111,537,974 (GRCm38) H105L probably damaging Het
Or6b1 T G 6: 42,837,849 (GRCm38) probably null Het
Or6b2b A G 1: 92,490,975 (GRCm38) V260A probably benign Het
Paxbp1 G A 16: 91,034,978 (GRCm38) Q341* probably null Het
Pcdh7 T C 5: 57,720,411 (GRCm38) V436A possibly damaging Het
Pcdhb18 G A 18: 37,489,814 (GRCm38) V66M probably damaging Het
Plcg1 A G 2: 160,750,986 (GRCm38) N179S probably benign Het
Prr11 A C 11: 87,098,691 (GRCm38) S285A probably benign Het
Ranbp17 A G 11: 33,328,451 (GRCm38) S139P probably damaging Het
Rasa4 G A 5: 136,091,810 (GRCm38) probably null Het
Rnf213 G C 11: 119,442,763 (GRCm38) G2934R probably benign Het
Rpap1 A G 2: 119,778,251 (GRCm38) V210A probably benign Het
Rpn1 T A 6: 88,090,205 (GRCm38) N182K probably benign Het
Rps24 C T 14: 24,491,787 (GRCm38) T14I possibly damaging Het
Rrp12 C T 19: 41,877,505 (GRCm38) probably null Het
Rttn T A 18: 89,090,415 (GRCm38) probably null Het
Rufy1 A G 11: 50,401,493 (GRCm38) S490P probably damaging Het
Sec62 T A 3: 30,809,869 (GRCm38) M100K unknown Het
Spata16 A G 3: 26,732,932 (GRCm38) H253R possibly damaging Het
Srcap T C 7: 127,558,962 (GRCm38) probably benign Het
Srrm1 A G 4: 135,345,512 (GRCm38) probably benign Het
Tbcd G A 11: 121,582,785 (GRCm38) probably null Het
Tedc2 C A 17: 24,220,593 (GRCm38) A25S probably damaging Het
Tnr A T 1: 159,684,788 (GRCm38) probably benign Het
Tnxb A C 17: 34,718,007 (GRCm38) D3730A probably damaging Het
Tor2a G A 2: 32,760,597 (GRCm38) G201D probably damaging Het
Tpp1 T C 7: 105,746,649 (GRCm38) T558A probably benign Het
Vmn1r211 G T 13: 22,852,126 (GRCm38) Q124K probably benign Het
Wasf3 T C 5: 146,460,978 (GRCm38) V185A probably benign Het
Zbtb12 A G 17: 34,896,009 (GRCm38) T257A probably benign Het
Other mutations in Pikfyve
AlleleSourceChrCoordTypePredicted EffectPPH Score
IGL00162:Pikfyve APN 1 65,260,121 (GRCm38) critical splice donor site probably null
IGL01135:Pikfyve APN 1 65,251,635 (GRCm38) missense probably damaging 0.96
IGL01511:Pikfyve APN 1 65,258,869 (GRCm38) nonsense probably null
IGL01759:Pikfyve APN 1 65,253,353 (GRCm38) missense probably benign 0.06
IGL01888:Pikfyve APN 1 65,223,640 (GRCm38) missense probably damaging 1.00
IGL01967:Pikfyve APN 1 65,264,365 (GRCm38) missense possibly damaging 0.89
IGL02055:Pikfyve APN 1 65,238,544 (GRCm38) critical splice donor site probably null
IGL02119:Pikfyve APN 1 65,272,571 (GRCm38) missense probably damaging 1.00
IGL02141:Pikfyve APN 1 65,246,397 (GRCm38) missense probably benign 0.13
IGL02207:Pikfyve APN 1 65,251,678 (GRCm38) critical splice donor site probably null
IGL02380:Pikfyve APN 1 65,256,021 (GRCm38) missense probably damaging 0.99
IGL02400:Pikfyve APN 1 65,252,569 (GRCm38) missense probably damaging 1.00
IGL02403:Pikfyve APN 1 65,244,504 (GRCm38) missense probably damaging 0.99
IGL02426:Pikfyve APN 1 65,251,612 (GRCm38) missense possibly damaging 0.77
IGL02496:Pikfyve APN 1 65,264,376 (GRCm38) missense possibly damaging 0.94
IGL02573:Pikfyve APN 1 65,230,855 (GRCm38) critical splice donor site probably null
IGL02746:Pikfyve APN 1 65,234,272 (GRCm38) missense probably damaging 1.00
IGL02814:Pikfyve APN 1 65,250,194 (GRCm38) nonsense probably null
IGL02890:Pikfyve APN 1 65,230,797 (GRCm38) missense probably benign 0.00
IGL03102:Pikfyve APN 1 65,252,467 (GRCm38) nonsense probably null
IGL03294:Pikfyve APN 1 65,247,067 (GRCm38) missense probably damaging 1.00
falcon UTSW 1 65,196,741 (GRCm38) missense probably damaging 1.00
oompa UTSW 1 65,196,706 (GRCm38) missense probably damaging 1.00
wonka UTSW 1 65,196,706 (GRCm38) missense probably damaging 1.00
G5538:Pikfyve UTSW 1 65,202,916 (GRCm38) missense probably damaging 1.00
R0031:Pikfyve UTSW 1 65,215,929 (GRCm38) splice site probably benign
R0196:Pikfyve UTSW 1 65,256,072 (GRCm38) missense possibly damaging 0.92
R0212:Pikfyve UTSW 1 65,262,905 (GRCm38) missense probably benign 0.41
R0319:Pikfyve UTSW 1 65,246,331 (GRCm38) missense probably benign 0.01
R0332:Pikfyve UTSW 1 65,264,399 (GRCm38) missense probably benign 0.02
R0389:Pikfyve UTSW 1 65,196,706 (GRCm38) missense probably damaging 1.00
R0443:Pikfyve UTSW 1 65,196,706 (GRCm38) missense probably damaging 1.00
R0503:Pikfyve UTSW 1 65,219,899 (GRCm38) missense probably damaging 0.97
R0722:Pikfyve UTSW 1 65,253,523 (GRCm38) missense probably damaging 0.99
R0906:Pikfyve UTSW 1 65,253,397 (GRCm38) missense probably damaging 1.00
R0907:Pikfyve UTSW 1 65,202,830 (GRCm38) missense possibly damaging 0.64
R0970:Pikfyve UTSW 1 65,265,824 (GRCm38) missense probably damaging 0.99
R1188:Pikfyve UTSW 1 65,246,959 (GRCm38) missense possibly damaging 0.46
R1412:Pikfyve UTSW 1 65,202,830 (GRCm38) missense possibly damaging 0.64
R1421:Pikfyve UTSW 1 65,271,311 (GRCm38) missense probably damaging 1.00
R1468:Pikfyve UTSW 1 65,251,666 (GRCm38) missense probably damaging 0.98
R1468:Pikfyve UTSW 1 65,251,666 (GRCm38) missense probably damaging 0.98
R1472:Pikfyve UTSW 1 65,224,201 (GRCm38) missense probably damaging 0.96
R1478:Pikfyve UTSW 1 65,262,977 (GRCm38) critical splice donor site probably null
R1501:Pikfyve UTSW 1 65,265,284 (GRCm38) missense possibly damaging 0.84
R1757:Pikfyve UTSW 1 65,252,548 (GRCm38) missense probably damaging 0.99
R1773:Pikfyve UTSW 1 65,246,370 (GRCm38) missense probably benign
R1773:Pikfyve UTSW 1 65,192,271 (GRCm38) missense probably damaging 0.99
R1795:Pikfyve UTSW 1 65,252,557 (GRCm38) missense probably damaging 1.00
R1855:Pikfyve UTSW 1 65,258,798 (GRCm38) missense probably benign 0.03
R1905:Pikfyve UTSW 1 65,192,295 (GRCm38) critical splice donor site probably null
R1995:Pikfyve UTSW 1 65,246,708 (GRCm38) missense probably damaging 1.00
R2034:Pikfyve UTSW 1 65,222,357 (GRCm38) missense probably damaging 1.00
R2045:Pikfyve UTSW 1 65,253,353 (GRCm38) missense probably benign 0.06
R2229:Pikfyve UTSW 1 65,267,855 (GRCm38) missense probably damaging 1.00
R2295:Pikfyve UTSW 1 65,246,676 (GRCm38) missense probably damaging 0.99
R2913:Pikfyve UTSW 1 65,253,517 (GRCm38) missense probably damaging 1.00
R3818:Pikfyve UTSW 1 65,245,758 (GRCm38) missense probably damaging 1.00
R3832:Pikfyve UTSW 1 65,244,420 (GRCm38) missense probably damaging 0.99
R3850:Pikfyve UTSW 1 65,230,845 (GRCm38) missense probably damaging 1.00
R3946:Pikfyve UTSW 1 65,196,681 (GRCm38) missense probably damaging 1.00
R4105:Pikfyve UTSW 1 65,190,520 (GRCm38) unclassified probably benign
R4542:Pikfyve UTSW 1 65,244,430 (GRCm38) missense probably damaging 1.00
R4574:Pikfyve UTSW 1 65,192,192 (GRCm38) missense probably damaging 1.00
R4601:Pikfyve UTSW 1 65,234,262 (GRCm38) missense probably damaging 1.00
R4667:Pikfyve UTSW 1 65,250,273 (GRCm38) missense probably damaging 1.00
R4668:Pikfyve UTSW 1 65,250,273 (GRCm38) missense probably damaging 1.00
R4669:Pikfyve UTSW 1 65,250,273 (GRCm38) missense probably damaging 1.00
R4707:Pikfyve UTSW 1 65,267,846 (GRCm38) missense probably benign
R4716:Pikfyve UTSW 1 65,246,476 (GRCm38) missense possibly damaging 0.84
R4758:Pikfyve UTSW 1 65,272,515 (GRCm38) missense possibly damaging 0.84
R4784:Pikfyve UTSW 1 65,267,846 (GRCm38) missense probably benign
R4785:Pikfyve UTSW 1 65,267,846 (GRCm38) missense probably benign
R4805:Pikfyve UTSW 1 65,268,800 (GRCm38) missense probably damaging 0.99
R4831:Pikfyve UTSW 1 65,196,741 (GRCm38) missense probably damaging 1.00
R5064:Pikfyve UTSW 1 65,253,407 (GRCm38) missense probably damaging 1.00
R5115:Pikfyve UTSW 1 65,224,117 (GRCm38) intron probably benign
R5265:Pikfyve UTSW 1 65,267,829 (GRCm38) missense possibly damaging 0.72
R5279:Pikfyve UTSW 1 65,196,699 (GRCm38) nonsense probably null
R5384:Pikfyve UTSW 1 65,244,409 (GRCm38) missense probably damaging 1.00
R5387:Pikfyve UTSW 1 65,265,268 (GRCm38) missense possibly damaging 0.94
R5461:Pikfyve UTSW 1 65,235,033 (GRCm38) missense probably damaging 1.00
R5467:Pikfyve UTSW 1 65,252,495 (GRCm38) missense probably damaging 1.00
R5560:Pikfyve UTSW 1 65,253,407 (GRCm38) missense probably damaging 1.00
R5575:Pikfyve UTSW 1 65,273,730 (GRCm38) missense probably damaging 1.00
R5611:Pikfyve UTSW 1 65,256,088 (GRCm38) missense probably damaging 0.96
R5663:Pikfyve UTSW 1 65,216,028 (GRCm38) missense probably benign 0.09
R5891:Pikfyve UTSW 1 65,202,737 (GRCm38) missense probably damaging 1.00
R5960:Pikfyve UTSW 1 65,253,438 (GRCm38) nonsense probably null
R6026:Pikfyve UTSW 1 65,272,697 (GRCm38) missense probably damaging 1.00
R6057:Pikfyve UTSW 1 65,272,571 (GRCm38) missense probably damaging 1.00
R6101:Pikfyve UTSW 1 65,264,345 (GRCm38) critical splice acceptor site probably null
R6105:Pikfyve UTSW 1 65,264,345 (GRCm38) critical splice acceptor site probably null
R6161:Pikfyve UTSW 1 65,216,043 (GRCm38) missense probably benign 0.36
R6287:Pikfyve UTSW 1 65,253,532 (GRCm38) critical splice donor site probably null
R6290:Pikfyve UTSW 1 65,202,925 (GRCm38) critical splice donor site probably null
R6296:Pikfyve UTSW 1 65,262,953 (GRCm38) missense probably damaging 0.99
R6516:Pikfyve UTSW 1 65,265,781 (GRCm38) missense probably benign 0.35
R6835:Pikfyve UTSW 1 65,258,843 (GRCm38) missense probably damaging 0.98
R6994:Pikfyve UTSW 1 65,252,530 (GRCm38) missense probably damaging 1.00
R6997:Pikfyve UTSW 1 65,246,663 (GRCm38) missense probably damaging 1.00
R7038:Pikfyve UTSW 1 65,234,361 (GRCm38) missense probably damaging 1.00
R7044:Pikfyve UTSW 1 65,246,854 (GRCm38) missense probably benign 0.01
R7057:Pikfyve UTSW 1 65,247,205 (GRCm38) missense probably benign 0.00
R7525:Pikfyve UTSW 1 65,244,426 (GRCm38) nonsense probably null
R7558:Pikfyve UTSW 1 65,272,623 (GRCm38) missense probably benign 0.01
R7625:Pikfyve UTSW 1 65,267,877 (GRCm38) missense possibly damaging 0.86
R7807:Pikfyve UTSW 1 65,269,942 (GRCm38) missense probably damaging 1.00
R7961:Pikfyve UTSW 1 65,255,134 (GRCm38) missense probably damaging 1.00
R8009:Pikfyve UTSW 1 65,255,134 (GRCm38) missense probably damaging 1.00
R8154:Pikfyve UTSW 1 65,265,789 (GRCm38) missense probably damaging 1.00
R8192:Pikfyve UTSW 1 65,246,395 (GRCm38) missense possibly damaging 0.93
R8275:Pikfyve UTSW 1 65,253,342 (GRCm38) splice site probably benign
R8307:Pikfyve UTSW 1 65,245,735 (GRCm38) missense possibly damaging 0.77
R8710:Pikfyve UTSW 1 65,215,996 (GRCm38) missense possibly damaging 0.94
R8867:Pikfyve UTSW 1 65,244,417 (GRCm38) missense probably damaging 1.00
R8936:Pikfyve UTSW 1 65,271,268 (GRCm38) missense possibly damaging 0.84
R8940:Pikfyve UTSW 1 65,246,970 (GRCm38) missense probably benign 0.00
R8995:Pikfyve UTSW 1 65,205,587 (GRCm38) critical splice acceptor site probably null
R9092:Pikfyve UTSW 1 65,244,400 (GRCm38) missense probably damaging 1.00
R9131:Pikfyve UTSW 1 65,246,080 (GRCm38) missense probably damaging 1.00
R9151:Pikfyve UTSW 1 65,196,739 (GRCm38) missense probably damaging 1.00
R9210:Pikfyve UTSW 1 65,252,560 (GRCm38) missense probably damaging 1.00
R9212:Pikfyve UTSW 1 65,252,560 (GRCm38) missense probably damaging 1.00
R9235:Pikfyve UTSW 1 65,260,029 (GRCm38) missense probably benign 0.37
R9368:Pikfyve UTSW 1 65,268,742 (GRCm38) missense probably damaging 1.00
R9489:Pikfyve UTSW 1 65,264,402 (GRCm38) missense probably benign
R9605:Pikfyve UTSW 1 65,264,402 (GRCm38) missense probably benign
R9686:Pikfyve UTSW 1 65,252,456 (GRCm38) missense probably damaging 1.00
Predicted Primers PCR Primer
(F):5'- GTTGGAATCAAGGACTGTGC -3'
(R):5'- GGTTCACGGAATGTAATAACTGGAG -3'

Sequencing Primer
(F):5'- TTGGAATCAAGGACTGTGCTAGAG -3'
(R):5'- CTGGAGAGATACAGAGGATTACATC -3'
Posted On 2016-03-01