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WormBase Tree Display for Variation: WBVar00093499

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Name Class

WBVar00093499NamePublic_nameok2346
Other_nameF39B1.1.1:c.1983+11_3178-14del
HGVSgCHROMOSOME_X:g.15239181_15240777del
Sequence_detailsSMapS_parentSequenceF39B1
Flanking_sequencescgcatgtcatcgtcacgctggaaagcatcataacacttacataaaggtccaatggaatcc
Mapping_targetF39B1
Type_of_mutationDeletion
PCR_productok2346_external
ok2346_internal
SeqStatusSequenced
Variation_typeAllele
OriginSpeciesCaenorhabditis elegans
StrainWBStrain00032504
LaboratoryRB
PersonWBPerson46
KO_consortium_allele
StatusLive
AffectsGeneWBGene00009552
TranscriptF39B1.1.1VEP_consequencesplice_acceptor_variant,splice_donor_variant,coding_sequence_variant,intron_variant
VEP_impactHIGH
HGVScF39B1.1.1:c.1983+11_3178-14del
Intron_number12-15/24
Exon_number13-15/25
Interactor (25)
IsolationMutagenEMS
DescriptionPhenotypeWBPhenotype:0000241Paper_evidenceWBPaper00035284
Curator_confirmedWBPerson2021
RemarkMutations resulted in the accumulation of cell corpses at several embryonic stagesPaper_evidenceWBPaper00035284
Curator_confirmedWBPerson2021
WBPhenotype:0000243Paper_evidenceWBPaper00044390
Curator_confirmedWBPerson2987
RemarkThe piki-1(ok2346) mutation resulted in a significant increase in the duration time of cell corpses observed in embryos (Figure S1D)Paper_evidenceWBPaper00044390
Curator_confirmedWBPerson2987
WBPhenotype:0000679Paper_evidenceWBPaper00044390
Curator_confirmedWBPerson2987
RemarkCell corpse phagosomal labeling by the lysosomal membrane marker LAAT-1::mCHERRY was reduced in piki-1(ok2346) mutants (Figure 2G).Paper_evidenceWBPaper00044390
Curator_confirmedWBPerson2987
Authors found that cell corpse phagosomal association of GFP-RAB-5, which is recruited at early phagosome maturation stages, decreased significantly in piki-1(ok2346) mutants (Figure 2E).Paper_evidenceWBPaper00044390
Curator_confirmedWBPerson2987
Authors found that cell corpse phagosomal association of GFP-RAB-7, which is recruited at late phagosome maturation stages, decreased significantly in piki-1(ok2346) mutants (Figure 2F).Paper_evidenceWBPaper00044390
Curator_confirmedWBPerson2987
Phenotype_assayGenotypeLAAT-1-mCHERRYPaper_evidenceWBPaper00044390
Curator_confirmedWBPerson2987
GFP-RAB-5Paper_evidenceWBPaper00044390
Curator_confirmedWBPerson2987
GFP-RAB-7Paper_evidenceWBPaper00044390
Curator_confirmedWBPerson2987
WBPhenotype:0001180Paper_evidenceWBPaper00048406
Curator_confirmedWBPerson17560
RemarkTable S1Paper_evidenceWBPaper00048406
Curator_confirmedWBPerson17560
WBPhenotype:0001181Paper_evidenceWBPaper00044390
Curator_confirmedWBPerson2987
RemarkThe piki-1(ok2346) mutation resulted in a significant increase in the number of cell corpses observed in 1.5f stage embryos (Figure 2I)Paper_evidenceWBPaper00044390
Curator_confirmedWBPerson2987
WBPhenotype:0001846Paper_evidenceWBPaper00044390
WBPaper00048406
Curator_confirmedWBPerson2987
WBPerson17560
RemarkAuthors found that cell corpse phagosomal association of GFP-RAB-5, which is recruited at early phagosome maturation stages, decreased significantly in piki-1(ok2346) mutants (Figure 2E).Paper_evidenceWBPaper00044390
Curator_confirmedWBPerson2987
Authors found that cell corpse phagosomal association of GFP-RAB-7, which is recruited at late phagosome maturation stages, decreased significantly in piki-1(ok2346) mutants (Figure 2F).Paper_evidenceWBPaper00044390
Curator_confirmedWBPerson2987
Cell corpse phagosomal labeling by the lysosomal membrane marker LAAT-1::mCHERRY was reduced in piki-1(ok2346) mutants (Figure 2G).Paper_evidenceWBPaper00044390
Curator_confirmedWBPerson2987
piki-1(ok2346) mutants exhibited a significant delay in the recruitment of phosphatidylinositol 3-phosphate (PI3P) to corpse-engulfing phagosomes, as determined by the PI3P marker YFP-2xFYVE (Figure 3C,H S3C,D)Paper_evidenceWBPaper00044390
Curator_confirmedWBPerson2987
"As previously reported (Lu et_al, 2012), loss of piki-1, which affects PtdIns3P generation, abolished phagosomal association of LST-4, suggesting that PtdIns3P is important for recruiting LST-4 to phagosomes (Fig 6 D)."Paper_evidenceWBPaper00048406
Curator_confirmedWBPerson17560
Phenotype_assayGenotypeGFP-RAB-5Paper_evidenceWBPaper00044390
Curator_confirmedWBPerson2987
GFP-RAB-7Paper_evidenceWBPaper00044390
Curator_confirmedWBPerson2987
LAAT-1-mCHERRYPaper_evidenceWBPaper00044390
Curator_confirmedWBPerson2987
YFP-2xFYVE, a marker for phosphatidylinositol 3-phosphatePaper_evidenceWBPaper00044390
Curator_confirmedWBPerson2987
WBPhenotype:0002349Paper_evidenceWBPaper00044390
Curator_confirmedWBPerson2987
RemarkAuthors found significantly reduced YFP-2xFYVE labeling of cell corpses in piki-1(ok2346) mutants, suggesting that phosphatidylinositol 3-phosphate (PtdIns3P) generation and/or accumulation on phagosomes is affected (Figure 2C, D).Paper_evidenceWBPaper00044390
Curator_confirmedWBPerson2987
Phenotype_assayGenotypeYFP-2xFYVE, a marker for phosphatidylinositol 3-phosphatePaper_evidenceWBPaper00044390
Curator_confirmedWBPerson2987
WBPhenotype:0002394Paper_evidenceWBPaper00048406
Curator_confirmedWBPerson17560
RemarkFigure 3, unsealed phagosomes can be labeled by PLCδ1-PH and the membrane impermeable dye FM4-64. Loss of mtm-1, piki-1, lst-4, dyn-1 or ocrl-1 shows phagosome sealing defective; "As in mtm-1(lf), persistent phagosomes in piki-1 or piki-1;vps-34 RNAi worms were labeled by both FM4-64 and PLCδ1-PH, indicating that phagosomal sealing is defective (Fig 3, H-I'', L, and M; and Fig S3, F-F''', H, and I)."Paper_evidenceWBPaper00048406
Curator_confirmedWBPerson17560
Phenotype_not_observedWBPhenotype:0000436Paper_evidenceWBPaper00035284
WBPaper00040857
Curator_confirmedWBPerson2021
WBPerson712
RemarkThe plasma membrane localization of MTM-1 was not obviously affected in piki-1(ok2346) mutantsPaper_evidenceWBPaper00035284
Curator_confirmedWBPerson2021
Mutation did not cause SNB-1::VENUS localization defects.Paper_evidenceWBPaper00040857
Curator_confirmedWBPerson712
WBPhenotype:0000736Paper_evidenceWBPaper00044390
Curator_confirmedWBPerson2987
RemarkThe piki-1(ok2346) mutation did not cause autophagy defects, as determined by antibody staining for LGG-1 and SEPA-1 (Figure S4)Paper_evidenceWBPaper00044390
Curator_confirmedWBPerson2987
Authors examined phosphatidylinositol 3-phosphate (PtdIns3P) on autophagic structures by quantifying the percentage of LGG-1 puncta that were positive for YFP-2xFYVE. In wild-type embryos, very few LGG-1 puncta (17%) were positive for YFP-2xFYVE (Fig. 4A and E). Authors found that loss of piki-1 did not significantly reduce PtdIns3P on LGG-1 puncta in epg-6(bp242) embryos, suggesting that piki-1 is not required for producing PtdIns3P on autophagic structures (Fig. 4C-E).Paper_evidenceWBPaper00044390
Curator_confirmedWBPerson2987
Phenotype_assayGenotypeepg-6(bp242)Paper_evidenceWBPaper00044390
Curator_confirmedWBPerson2987
WBPhenotype:0001346Paper_evidenceWBPaper00044390
Curator_confirmedWBPerson2987
RemarkActin ring formation on corpse-engulfing phagosomes was not affected by the piki-1(ok2346) mutation (Figure S3A,B)Paper_evidenceWBPaper00044390
Curator_confirmedWBPerson2987
Phenotype_assayGenotypeGFP-ACT-1Paper_evidenceWBPaper00044390
Curator_confirmedWBPerson2987
WBPhenotype:0001846Paper_evidenceWBPaper00044390
Curator_confirmedWBPerson2987
RemarkActin ring formation on corpse-engulfing phagosomes was not affected by the piki-1(ok2346) mutation (Figure S3A,B)Paper_evidenceWBPaper00044390
Curator_confirmedWBPerson2987
Phenotype_assayGenotypeGFP-ACT-1Paper_evidenceWBPaper00044390
Curator_confirmedWBPerson2987
ReferenceWBPaper00040857
WBPaper00035284
WBPaper00044390
WBPaper00048406
RemarkSequenced by the C. elegans Gene Knockout ConsortiumPaper_evidenceWBPaper00041807
MethodKO_consortium_allele