25 Matching Annotations
  1. Oct 2026
    1. Like other membrane guanylyl cyclases, the 1101 aa retGC is predicted to have a hydrophobic amino-terminal signal sequence followed by a large extracelluiar domain, a single membrane spanning domain, a kinase homology domain, and a guanylyl cyclase catalytic domain. In contrast to other membrane guanylyl cylases, such as natriuretic peptide receptors, retGC has a relatively high basal level of activity when expressed in human 293 cells. cGMP production by retGC is unaffected by any of the known natriuretic peptides. In situ hybridization analysis of a variety of rhesus monkey tissues showed retGC transcripts to be localized exclusively along the retinal outer nuclear layer, corresponding to the nuclei of the rod and cone photoreceptor cells. Our results suggest that retGC may synthesize cGMP required for recovery of the dark state after phototransduction.

      Selection B - Gene function is consistent with phenotype.

      GOterm: GO:0007168 (receptor guanylyl cyclase signaling pathway)

      FunctionalEvidence: Exogenous expression of the gene product in 293 cells exhibits a high level of cGMP production activity. When combined with the in situ hybridization evidence showing its expression along the retinal outer nuclear layer (coinciding with the rod and cone photoreceptor cell nuclei), this biochemical evidence indicates a function in synthesizing cGMP to promote recovery of the dark state following phototransduction.

      FunctionalHPO: HP:0000662 (Nyctalopia), HP:0007663 (Reduced visual acuity), HP:0007688 (Undetectable light- and dark-adapted electroretinogram), HP:0007703 (Abnormality of retinal pigmentation)

      PhenotypeEvidence: The ability of the exogenously expressed enzyme to efficiently catalyze cGMP production (Figure) is consistent with the loss of photoreceptor function that is characteristic of the disease, as abnormalities in cGMP levels have long been associated with photoreceptor degeneration (PMID: 4369896).

    1. AAV-mediated expression of human L-opsin promoted cone outer segment regeneration and rescued cone-mediated function when mice were injected subretinally at 2 months of age or younger. Cone-mediated function and visually guided behavior were maintained for at least 8 months post-treatment. However, when mice were treated at 5 and 7 months of age, the chance and effectiveness of rescue was significantly reduced, although cones were still present in the retina. Crossing Opn1mw−/−/Opn1sw−/− mice with proteasomal activity reporter mice (UbG76V–GFP) did not reveal GFP accumulation in Opn1mw−/−/Opn1sw−/− cones eliminating impaired degradation of ubiquitinated proteins as stress factor contributing to cone loss. Our results demonstrate that AAV-mediated gene augmentation therapy can rescue cone structure and function in a mouse model with a congenital opsin deletion

      Selection B- Gene function is consistent with phenotype.

      ExperimentName: OPN1LW encodes a long-wave-sensitive opsin and can rescue cone-mediated function when subretinally injected in Opn1mw−/−/Opn1sw−/− mice.

      GOterm: GO:0007602 (phototransduction)

      FunctionalEvidence: Subretinal injection of AAV carrying the OPN1LW gene encoding human L-opsin into mice at age 2 months or younger promoted cone outer segment regeneration () and rescued cone functions such as the b-wave amplitude of the long wavelength-mediated electroretinogram response (Figures 2A, 2B, 4D) and visually guided behavior (Figure 4E).

      FunctionalHPO: Protanopia HP:0011522

    1. To determine if LRP-5 has any effect on the canonical Wnt signaling pathway in mammalian cells, we coexpressed LRP-5 with Wnt-1 in NIH 3T3 cells. In these cells, Wnt-1 has been shown to elevate the levels of cytosolic β-catenin and activate LEF-1-dependent transcriptional activity (Li et al. 1999aLi L Yuan H Weaver C Mao J Farr III, G.H Sussman D.J Jonkers J Kimelman D Wu D Axin and Frat-1 interact with Dvl and GSK, bridging Dvl to GSK in Wnt-mediated regulation of LEF-1.EMBO J. 1999; 18 (a): 4233-4240Crossref PubMed Scopus (358) Google Scholar, Li et al. 1999bLi L Yuan H Xie W Mao J McMahon E Sussman D Wu D Dishevelled proteins lead to two different signaling pathways; regulation of the JNK and b-catenin pathways.J. Biol. Chem. 1999; 274 (b): 129-134Crossref PubMed Scopus (255) Google Scholar). Expression of LRP-5 alone had no effect on LEF-1 activity (Figure 1A), as determined using a LEF-1-dependent luciferase reporter gene assay (Hsu et al. 1998Hsu S.C Galceran J Grosschedl R Modulation of Transcriptional Regulation By Lef-1 in Response to Wnt-1 Signaling and Association With Beta-Catenin.Mol. Cell. Biol. 1998; 18: 4807-4818Crossref PubMed Scopus (338) Google Scholar), but enhanced the effect of Wnt-1 (Figure 1A) or Wnt-3a (data not shown). To confirm that LRP-5 acted with secreted Wnt-1 protein, a paracrine coculture approach was used (Li et al. 1999aLi L Yuan H Weaver C Mao J Farr III, G.H Sussman D.J Jonkers J Kimelman D Wu D Axin and Frat-1 interact with Dvl and GSK, bridging Dvl to GSK in Wnt-mediated regulation of LEF-1.EMBO J. 1999; 18 (a): 4233-4240Crossref PubMed Scopus (358) Google Scholar), in which LRP-5 and the reporter luciferase were transfected into one group of cells and Wnt-1 was transfected into a separate group of cells. These two groups were combined after transfection, and luciferase activities were determined after the cells were cocultured for 24 hr. Since Wnt-1 and the reporter gene were produced in different cells, any effect of Wnt-1 could be attributed only to the interaction of secreted Wnt-1 protein with cells expressing LRP-5 and containing the reporter gene. As shown in Figure 1B, LRP-5 and Wnt-1 acted synergistically in the activation of LEF-1-dependent transcription in the paracrine assay, demonstrating that LRP-5 potentiates the signaling of secreted Wnt-1. The same results were also observed for Wnt-3a in similar coculture assays (data not shown).

      Selection B - Gene function is consistent with phenotype.

      Title: LRP5 is a canonical Wnt signaling pathway co-receptor.

      GOterm: GO:0060070 (canonical Wnt signaling pathway)

      FunctionalEvidence: Exogenous LRP5 expression in NIH3T3 cells increases the activity of the canonical Wnt signaling transcription factor LEF1 only when combined with exogenous expression of the Wnt-1 ligand in a separate population of cells grown in co-culture (Figure 1). This function is related to the phenotype in that canonical Wnt signaling is known to mediate bone formation.

      FunctionalHPO: HP:0004349 (reduced bone mineral density), osteoporosis (HP:0000939), HP:0020110 (bone fracture)

    1. We demonstrate that the 60 and 90kD tri-snRNP proteins specifically associate with the U4/U6 snRNP at salt concentrations where the tri-snRNP complex has dissociated. The primary structures of the 60kD and 90kD proteins were determined by cloning and sequencing their respective cDNAs. The U4/U6-60kD protein possesses a C-terminal WD domain that contains seven WD repeats and thus belongs to the WD-protein family, whose best-characterized members include the Gbeta subunits of heterotrimeric G proteins. A database homology search revealed a significant degree of overall homology (57.8% similarity, 33.9% identity) between the human 60kD protein and the Saccharomyces cerevisiae U4/U6 snRNP protein Prp4p. Two additional, previously undetected WD repeats (with seven in total) were also identified in Prp4p, consistent with the possibility that 60kD/Prp4p, like beta-transducin, may adopt a propeller-like structure. The U4/U6-90kD protein was shown to exhibit significant homology, particularly in its C-terminal half, with the S. cerevisiae splicing factor Prp3p, which also associates with the yeast U4/U6 snRNP. Interestingly, U4/U6-90kD shares short regions of homology with E. coli RNase III, including a region encompassing its double-stranded RNA binding domain. Based on their structural similarity with essential splicing factors in yeast, the human U4/U6-60kD and 90kD proteins are likely also to play important roles in the mammalian splicing process.

      Selection A- Gene with same function implicated in disease

      ExperimentName: PRPF4 is a U4/U6 small nuclear ribonucleoprotein component that functions in mRNA splicing.

      GOterm: GO:0000398 (mRNA splicing, via spliceosome)

      FunctionalEvidence: PRPF4, PRPF3, PRPF31, and PRPF8 are all splicing factors involved in mRNA processing and are encoded by genes that harbor variants associated with retinitis pigmentosa.

      HGNC: HGNC:17348 (PRPF3, retinitis pigmentosa 18), HGNC:15446 (PRPF31, retinitis pigmentosa 11), HGNC:17340 (PRPF8, retinitis pigmentosa 13)

      GeneEvidence: PRPF3 harbors variants that cause retinitis pigmentosa 18 (PMID: 11773002), PRPF31 harbors variants that cause retinitis pigmentosa 11 (PMID: 12444105), and PRPF8 harbors variants that cause retinitis pigmentosa 13 (PMID: 7951236).

      SharedGeneImplication: PRPF4, PRPF3, PRPF31, and PRPF8 are encode splicing factors involved in mRNA processing.

    1. Our results revealed that the PRPF31 deficiency causes mis-splicing of genes involved in RNA processing (PRPF3, PRPF8, PRPF4, and PRPF19) and phototransduction (RHO, ROM1, FSCN2, GNAT2, and GNAT1) in the retina in the PRPF31 reduced samples. Mis-splicing of genes implicated in phototransduction was associated with photoreceptor degeneration observed in RP patients.

      PRPF4, PRPF3, PRPF31, and PRPF8 are all splicing factors involved in mRNA processing and are encoded by genes that harbor variants associated with retinitis pigmentosa.

    1. Impg2

      ExperimentName: Morpholino-based disruption of Impg2 in medaka fish

      NonHumanModel: Oryzias latipes

      GeneAlteration: Model animals were subjected to targeted disruption of Impg2 by morpholino-based silencing.

      ModelPhenotype: HP:0030610 (Photoreceptor outer segment loss on macular OCT).

      HumanPhenotype: HP:0000529 (Progressive visual loss), HP:0000662 (Nyctalopia), HP:0000551 (Color vision defect), HP:0008002 (Abnormality of macular pigmentation), HP:0000543 (Optic disc pallor), HP:0007843 (Attenuation of retinal blood vessels), HP:0000533 (Chorioretinal atrophy), HP:0000518 (Cataract), HP:0008323 (Abnormal light- and dark-adapted electroretinogram), HP:0007737 (Bone spicule pigmentation of the retina), HP:0007994 (Peripheral visual field loss), HP:0000603 (Central scotoma)

      ModelEvidence: Morpholino-injected animals exhibit decreased photoreceptor outer segment length, especially for cones (Figures 4I, 4J).

      ModelVariant: The model does not introduce a variant previously observed in human patients, but rather disrupts the expression of the Impg2 ortholog using a morpholino.

    2. Using morpholino-mediated ablation of Impg1 and its paralog Impg2 in medaka fish, we confirmed a phenotype consistent with that observed in the families, including a decreased length of rod and cone photoreceptor outer segments.

      ExperimentName: Morpholino-based disruption of Impg1 in medaka fish

      NonHumanModel: Oryzias latipes

      GeneAlteration: Model animals were subjected to targeted disruption of Impg1 by morpholino-based silencing.

      ModelPhenotype: HP:0030610 (Photoreceptor outer segment loss on macular OCT).

      HumanPhenotype: HP:0007754 (Macular dystrophy), HP:0007769 (Peripheral retinal degeneration), HP:0032037 (Mildly reduced visual acuity, progressive), HP:0008179 (Decreased Arden ratio of electrooculogram)

      ModelEvidence: Morpholino-injected animals exhibit decreased photoreceptor outer segment length, especially for cones (Figures 4I, 4J).

      ModelVariant: The model does not introduce a variant previously observed in human patients, but rather disrupts the expression of the Impg1 ortholog using a morpholino.

    1. we expressed chimeric homodimeric enzymes, enhanced GFP (EGFP)-PDE6C-A and EGFP-PDE6C-B, containing the PDE6A and PDE6B catalytic domains, respectively, in transgenic Xenopus laevis. Similar to EGFP-PDE6C, EGFP-PDE6C-A and EGFP-PDE6C-B were targeted to the rod outer segments and concentrated at the disc rims. PDE6C, PDE6C-A, and PDE6C-B were isolated following selective immunoprecipitation of the EGFP fusion proteins. All three enzymes, PDE6C, PDE6C-A, and PDE6C-B, hydrolyzed cGMP with similar Km (20–23 μm) and kcat (4200–5100 s−1) values. Likewise, the Ki values for PDE6C, PDE6C-A, and PDE6C-B inhibition by the cone- and rod-specific PDE6 γ-subunits (Pγ) were comparable. Recombinant cone transducin-α (Gαt2) and native rod Gαt1 fully and potently activated PDE6C, PDE6C-A, and PDE6C-B. In contrast, the half-maximal activation of bovine rod PDE6 required markedly higher concentrations of Gαt2 or Gαt1. Our results suggest that PDE6A and PDE6B are enzymatically equivalent.

      Selection B- Gene function is consistent with phenotype.

      GOterm: GO:0047555 (3',5'-cyclic-GMP phosphodiesterase activity)

      FunctionalEvidence: Purified PDE6A fusion protein tagged with EGFP and fused with sequences from PDE6C catalyzes cGMP hydrolysis comparably to the known phosphodiesterase enzymes PDE6B and PDE6C (Fig. 4), confirming that PDE6a is a rod-associated phosphodiesterase that hydrolyzes cGMP.

      FunctionalHPO: HP:0000662 (Nyctalopia), HP:0007994 (Peripheral visual field loss), HP:0000543 (Optic disc pallor), HP:0007843 (Attenuation of retinal blood vessels), HP:0007737 (Bone spicule pigmentation of the retina), HP:0000654 (Decreased light- and dark-adapted electroretinogram amplitude)

    1. PDE6C hydrolyzed cGMP with a Km of 65 ± 6 μm and kcat of 4400 ± 300 s−1 (Fig. 7A).

      Selection B- Gene function is consistent with phenotype.

      GOterm: GO:0047555 (3',5'-cyclic-GMP phosphodiesterase activity)

      FunctionalEvidence: Purified PDE6C hydrolyzed cGMP with a Km and kcat slightly lower than trypsin-activated bovine rod PDE6 (Figure 7A).

      FunctionalHPO: HP:0000551 (Color vision defect), HP:0030465 (Undetectable light-adapted electroretinogram)

    1. Generation of Bbs1M390R/M390R Knockin Mice. We targeted the Bbs1 gene in mice by constructing a vector containing regions of the mouse Bbs1 gene that replaced the normal methionine codon at position 390 in exon 12 with an arginine codon on homologous recombination (Fig. 1A). RT-PCR of cDNA amplified from the knockin mice confirmed that the M390R allele was spliced correctly without inclusion of the intronic neomycin cassette. Sequencing of the Bbs1M390R/M390R cDNA confirmed that the Bbs1 gene was modified with the incorporation of the homozygous methionine to arginine (ATG to AGG) change in the knockin line (Fig. 1B).

      ExperimentName: Knock-in of the p.M390R variant into the mouse Bbs1 gene.

      NonHumanModel: Mus musculus

      GeneAlteration: The model animals have been subjected to homologous recombination-based knock-in of the p.M390R variant into exon 12 of the endogenous mouse Bbs1 gene. The variant has been studied in the homozygous state.

      ModelPhenotype: HP:0032558 (Absent sperm flagella), HP:0010633 (Partial anosmia), HP:0012433 (Abnormal social behavior), HP:0030469 (Abnormal dark-adapted electroretinogram), HP:0030610 (Photoreceptor outer segment loss on macular OCT), HP:0030609 (Photoreceptor layer loss on macular OCT), HP:0001513 (Obesity), HP:0002119 (Ventriculomegaly),

      HumanPhenotype: HP:0000639 (Nystagmus), HP:0000510 (Rod-cone dystrophy), HP:0007663 (Reduced visual acuity), HP:0000662 (Nyctalopia), HP:0000518 (Cataract), HP:0008323 (Abnormal light- and dark-adapted electroretinogram), HP:0000107 (Renal cyst), HP:0001513 (Obesity), HP:0010442 (Polydactyly), HP:0002463 (Language impairment), HP:0000026 (Male hypogonadism)

      ModelEvidence: Sperm flagella were absent (Figures 2A, 2B). Loss of the outer nuclear layer and degeneration of the photoreceptor inner and outer segments were observed in older mice (Figures 2C, 2D). Photoreceptor morphology in the outer segment was also disrupted in TEM images (Figure 2E). Scotopic responses showed a- and b-wave attenuation (Figure 2G), while photopic responses were not significantly different (Figure 2H). Homozygous mice showed obesity relative to wild-type and heterozygous mice (Figure 3). Brain sections showed neuroanatomical defects, especially ventriculomegaly (Figure 4). Brain cilia were morphologically abnormal (Figure 5). Renal cysts and polydactyly were investigated but not observed.

      ModelVariant: This model introduced a disease-associated variant known from affected human patients (NM_024649.5(BBS1):c.1169T>G (p.Met390Arg), ClinVar ID: 12143).

    1. To determine the subcellular localization of Rp1L1 in rods, we double stained Rp1L1 and rhodopsin, Rp1, or γ-tubulin in dissociated OS preparations (Fig. 2B). Rhodopsin localizes to OS discs, Rp1 localizes to the axoneme of the basal OS (Zhao et al., 2003; Liu et al., 2004), and γ-tubulin localizes to the basal bodies of the CCs (Hong et al., 2001). We found that Rp1L1 localized to the axoneme of both the OS and CCs but not to the axoneme of the IS or on the basal bodies (Figs. 1E, 2B). Recent photoreceptor sensory cilium complex proteome revealed Rp1L1 expression in the OS but not in the IS, consistent with our observations (Liu et al., 2007). Furthermore, Rp1L1 coexisted with Rp1 only in the OS axoneme but not in the CCs; Rp1L1 and Rp1 appeared localized along the entire length of OS axoneme but were more concentrated at the basal third OS, consistent with previous findings (Fig. 2B, bottom) (Zhao et al., 2003; Liu et al., 2004). To determine whether Rp1L1 was colocalized with microtubules in the axoneme, we stained Rp1L1 in retinal sections with α-acetylated tubulin, which is a marker of polymerized microtubules, including those of the axoneme (Fig. 2C). All Rp1L1 signals were colocalized with axoneme-positive signals. Only a small amount of α-acetylated tubulin-positive axoneme did not appear to include Rp1L1. These were probably the axonemes of cones, which lack Rp1L1 (Fig. 2C, long arrowhead). These findings suggest that both Rp1L1 and Rp1 are expressed in the rod photoreceptor axoneme.

      Selection B- Gene function is consistent with phenotype.

      ExperimentName: RP1L1 protein localizes to the axoneme of the outer segment of rod photoreceptor cells, but not to the connecting cilium, inner segment, or basal bodies (and from cone cells altogether).

      GOterm: GO:0120200 (rod photoreceptor outer segment)

      FunctionalEvidence: Immunofluorescent staining of Rp1l1 was performed in retinal sections, with staining of rhodopsin, Rp1, and gamma-tubulin for comparison (Figures 1E, 2A, 2B, 2C).

      FunctionalHPO: Macular dystrophy HP:0007754, Reduced visual acuity HP:0007663

    1. It shares several biochemical properties with other metalloproteinase inhibitors, including evidence of intrachain disulfide bonds and resistance to cleavage by trypsin. An electrophoretic assay employing a metal ion-dependent gelatinase from conditioned cell culture medium demonstrates inhibitor activity for purified 21-kDa protein. The 21-kDa protein is the major inhibitor in the extracellular matrix and appears unique in solubility properties among inhibitors with a TIMP-like sequence.

      Selection B- Gene function is consistent with phenotype.

      GOterm: GO:0008191 (metalloendoproteinase inhibitor activity)

      FunctionalEvidence: The functional evidence consists of an electrophoretic assay in which the 21-kDa chicken ortholog of human TIMP3 shows inhibitory activity towards a metalloproteinase.

      FunctionalHPO: Abnormal extracellular matrix turnover in the inner aspect of Bruch's membrane

      PhenotypeEvidence: This metalloproteinase inhibitor activity and ECM localization of the gene product indicate that it functions in ECM remodeling, balancing the activity of matrix metalloproteinases. This is consistent with the disease phenotype of abnormal thickening of the inner aspect of Bruch's membrane (PMID:11879143). The inhibitor evidence is shown in Figure 2B, where a 21-kDa band protects a gelatin substrate from enzymatic metalloproteinase activity. The purification of the gene product from the extracellular matrix is depicted in Figure 1. A later study showed that the human ortholog of this chicken gene is the TIMP3 gene, mapped to the region on chromosome 22 between q12.1-q13.2 (PMID:8188246).

    1. MLSN Is a Plasma Membrane Protein Mediating Ca2+ Entry. To obtain additional evidence that members of the TRPM subfamily promote cation influx, we expressed the founding member of the TRPM subfamily, MLSN, in HEK293 cells and performed Ca2+ imaging. Expression of MLSN in these cells led to a pronounced Ca2+ entry upon switching the cells from the Ca2+-free to the Ca2+-containing solution; however, alterations in osmolarity had no effect (Fig. ​(Fig.44A, n = 280). Nontransfected cells or cells cotransfected with pYFP and the empty pcDNA3 vector did not display changes in Ca2+ concentration upon switching from the Ca2+-free to the Ca2+-containing bath solutions (Fig. ​(Fig.33D). As was the case with TRPM4, Ca2+ entry mediated by MLSN was blocked by La3+. There was no Sr2+ permeation, and Ba2+ entry was considerably slower than Ca2+ entry (Fig. ​(Fig.44B, n = 32), indicating that MLSN channels have a divalent cation selectivity with Ca2+ > Ba2+ ≫ Sr2+. To determine the subcellular localization of MLSN, we performed immunofluorescent microscopy on transfected HEK293 cells. The confocal images indicated that the MLSN protein was localized at or in close proximity to the plasma membrane (Fig. ​(Fig.44 C and D).

      Selection B- Gene function is consistent with phenotype.

      Title: TRPM1 (MLSN) is a plasma membrane protein that mediates the cellular influx of calcium and other divalent cations, leading to depolarization, as part of the depolarizing photoresponse within ON-bipolar cells of the retina.

      GOterm: GO:0005261 (cation channel activity), GO:0005262 (calcium channel activity)

      FunctionalEvidence: Exogenous expression of TRPM1 (MLSN) in HEK293 cells conferred the ability to allow entry of calcium, barium, and strontium ions, unlike the pYFP or empty vector controls (Figures 4A, 4B, 3C). Confocal microscopy also showed localization to the plasma membrane (Figures 4C, 4D).

      FunctionalHPO: HP:0000662 (Nyctalopia), HP:0000545 (Myopia), HP:0000572 (Visual loss), HP:0007984 (Electronegative electroretinogram)

      PhenotypeEvidence: This evidence is consistent with the view of congenital stationary night blindness 1C as a channelopathy caused by a defect in divalent cation influx, signal transduction, and the polarization / depolarization of ON-bipolar cells.

    1. To identify and characterize the anti-angiogenic domain of TIMP-3, structure function analyses and synthetic peptide studies were performed using VEGF-mediated receptor binding, signaling, migration and proliferation. In addition, the ability of TIMP-3 peptides to inhibit CNV in a mouse model was evaluated.

      Selection B- Gene function is consistent with phenotype.

      GOterm: GO:0016525 (negative regulation of angiogenesis)

      FunctionalEvidence: The previously known ability of TIMP3 protein to block the binding of VEGF to the VEGFR-2 receptor (PMID:12652295, PMID:19478078) is mapped to the C-terminal region of TIMP3 consisting of amino acids 160-211 (Figures 1c, 2b). This region is relevant to disease in that nonsense variants (PMID:10854443) and splice site disrupting variants (PMID:9760202) of TIMP3 are predicted to remove most or all of this domain. This region is not only necessary and sufficient to block VEGF binding to VEGFR-2 in ELISA assays (Figure 2b), but also can block VEGF-stimulated endothelial migration (Figure 4) and proliferation (Figure 6). In an animal model of choroidal neovascularization (CNV) with lesions induced by laser, the injection of C-terminal TIMP3 peptides can limit CNV-based lesion size (Figure 7). This introduces the possibility that some phenotypes of Sorsby fundus dystrophy such as CNV may be mediated by loss of normal TIMP3 function rather than gain of an abnormal TIMP3 function.

      FunctionalHPO: HP:0011506 (Choroidal neovascularization)

    1. We identified the TULP3-associated proteins by tandem affinity purification followed by mass spectrometry. In both lines (A and B), we found all known components of the IFT-A complex to be associated with TULP3, but not in the control LAP line (Fig. 1A–C). The IFT-A complex proteins recovered were WDR19, IFT140, IFT122, THM1, and WDR35 (Fig. 1A,C, see ​seeDD and Supplemental Fig. S1B for homologs in other organisms and a comment on the nomenclature). Peptide coverage for all of the IFT-A complex proteins was at least 39%, supporting the high significance of the identifications. IFT43 (C14orf179), reported recently to be a part of the IFT-A complex (Cole and Snell 2009), was also recovered (peptide coverage 9%). The IFT-A complex was similarly associated with LAPTULP3 in murine NIH 3T3 fibroblasts and kidney inner medullary-collecting duct IMCD-3 cells (Supplemental Figs. S1A,B, S2A). Tandem affinity purification of the IFT-A complex using a clonal line expressing IFT140LAP in RPE cells likewise copurified with endogenous TULP3 (Fig. 1A–C).

      Selection B- Gene function is consistent with phenotype.

      GOterm: GO:0030991 (intraciliary transport particle A)

      FunctionalEvidence: Mass spectrometry analysis of IFT-A complex components co-purifying with the TULP3 protein identified the IFT140 protein along with several other known components such as WDR19, IFT122, THM1, and WDR35 (Figure 1C). These other IFT-A components were also confirmed by mass spectrometry to co-purify with IFT140 itself (Figure 1C).

      FunctionalHPO: Absence of primary cilia in a high number of cells from the affected patients (shown using acetylated alpha-tubulin staining of cultured fibroblasts)

      PhenotypeEvidence: Primary cilia from the affected patients are known to be absent from a high proportion of cells in the affected individuals, while the gene product functions in a complex known to participate in retrograde ciliary transport (Figure 1A, 1C). This trafficking process is known to be mediated by the IFT-A complex and is critical to the assembly and maintenance of cilia.

    1. Although it is known that RPE65 is critical for regeneration of 11-cis retinol in the visual cycle, the function of RPE65 is elusive. Here we show that recombinant RPE65, when expressed in QBI-293A and COS-1 cells, has robust enzymatic activity of the previous unidentified isomerohydrolase, an enzyme converting all-trans retinyl ester to 11-cis retinol in the visual cycle.

      Selection B - Gene function is consistent with phenotype.

      GOterm: GO:0052885 (all-trans-retinyl-ester hydrolase, 11-cis retinol forming activity)

      FunctionalEvidence: Exogenous co-expression of RPE65 and the LRAT enzyme in QBI-293A or COS-1 cells provides these cells with the enzymatic ability to generate 11-cis retinol from all-trans retinyl ester, identifying RPE65 as the human isomerohydrolase enzyme (Figures 4B-4F).

      FunctionalHPO: HP:0007688 (Undetectable light- and dark-adapted electroretinogram), HP:0000529 (Progressive visual loss), HP:0000618 (Blindness)

      PhenotypeEvidence: Maintenance of vision is dependent upon the visual retinoid cycle to enzymatically regenerate 11-cis retinal following the light-induced isomerization of this pigment to all-trans retinal. Isomerohydrolase is an enzymatic activity known to be responsible for this conversion and known to localize to the retinal pigment epithelium, but not previously mapped to a human gene prior to this study. The present paper identifies the RPE65 protein as the human isomerohydrolase enzyme, linking its biallelic loss to congenital blindness (Figures 4B-4F).

    1. (f) Presynaptic localization of mouse CaBP4 (red) demonstrated by covisualization with a presynaptic protein (PSD95; green). Arrows indicate rod spherules and cone pedicles. (g) Colocalization of synaptic vesicle proteins SV2 and synaptophysin (green) with mouse CaBP4 (red).

      Biochemical evidence showing mouse CaBP4 (red) localization to the presynaptic region based on co-localization with the PSD95 marker (green).

    1. RPGR was found in the connecting cilia of rods and cones with no evidence for species-dependent variation. RPGR ORF15 was the predominant variant in photoreceptor connecting cilia whereas constitutive RPGR (default) was the sole variant in the transitional zone of motile cilia in airway epithelia. Removal of soluble materials in the interphotoreceptor matrix facilitated detection of RPGR in the connecting cilia in photoreceptors. conclusions. RPGR localizes in photoreceptor connecting cilia and in a homologous structure, the transitional zone of motile cilia. These data are important for understanding the multitude of clinical manifestations associated with mutations in RPGR.

      Selection B - Gene function is consistent with phenotype.

      GOterm: GO:0032391 (photoreceptor connecting cilium)

      FunctionalEvidence: This study uses a RPGR antibody to stain mouse retinal sections, showing localization of RPGR to the region between the outer segment and inner segment associated with the connecting cilia of rod and cone photoreceptors (Figure 2A). A similar experiment was performed in earlier studies with similar results (PMID: 11104772 Figure 4A, PMID: 10725384 Figure 2D upper). Within mouse airway epithelium tissue sections, RPGR antibody stained a narrow band across the apical domains of multi-ciliated cells (Figure 7A), corresponding with the basal parts of the motile cilia adjacent to the basal bodies (Figures 7B, 7C). This transitional zone of the motile cilia is the structural equivalent of the connecting cilia of photoreceptors, consistent with a biochemical role for RPGR in regulating ciliary organization and/or transport in both the retina and the respiratory tract.

      FunctionalHPO: HP:0007642 (Congenital stationary night blindness), HP:0007994 (Peripheral visual field loss), HP:0000529 (Progressive visual loss), HP:0000365 (Hearing impairment), HP:0002205 (Recurrent respiratory infections), HP:0011109 (Chronic sinusitis), HP:0000388 (Otitis media), HP:0002837 (Recurrent bronchitis), HP:0012263 (Immotile cilia), HP:0005938 (Abnormal respiratory motile cilium morphology)

      PhenotypeEvidence: This identification of RPGR as a potential regulator of ciliary organization and/or transport in multiple tissues is consistent with the diverse phenotypes associated with RPGR loss-of-function, ranging from visual defects associated with rod and cone dysfunction to respiratory defects associated with dysfunction of the respiratory motile cilia.

    1. In cell-based assays, the overexpression of ADAM9 enhanced the ectodomain shedding of EphB4, Tie-2, Flk-1, CD40, VCAM, and VE-cadherin, so the enhanced expression of ADAM9 could potentially affect pathological neovascularization by increasing the shedding of these and other membrane proteins from endothelial cells. Finally, we provide the first evidence for the upregulation of ADAM9-dependent shedding by reactive oxygen species, which in turn are known to play a critical role in OIR.

      Selection B- Gene function is consistent with phenotype.

      Title: ADAM9 enhances protelytic shedding of membrane protein ectodomains.

      GOterm: GO:0006509 (membrane protein ectodomain proteolysis), GO:0045765 (regulation of angiogenesis)

      FunctionalEvidence: ADAM9 over-expression in COS-7 cells enhances proteolytic shedding of membrane proteins involved in angiogenesis (Figure 5). This effect is further enhanced by reactive oxygen species (Figures 6, 7).

      FunctionalHPO: HP:0007843 (Attenuation of retinal blood vessels), HP:0000546 (Retinal degeneration)

      PhenotypeEvidence: This evidence is consistent with attenuation of retinal blood vessels observed in human patients as well as the finding from this same paper that Adam9 knockout mice exhibit reduced ocular neovascularization (Figures 1, 3).

    1. The interphotoreceptor matrix (IPM) occupies the extracellular space between the apical surface of the retinal pigmented epithelium and the external limiting membrane of the neural retina. This space contains two chondroitin sulfate proteoglycans, designated IPM 150 and IPM 200

      Selection B- Gene function is consistent with phenotype.

      GOterm: GO:0033165 (interphotoreceptor matrix)

      FunctionalEvidence: IMPG1 protein can be purified as a component of an insoluble extracellular layer that is located between apical side of the RPE and the external limiting membrane of the neural retina, known as the interphotoreceptor matrix (Figure 1). This layer is known to support the function and maintenance of photoreceptor cells (PMID: 7344830).

      FunctionalHPO: HP:0030612 (Abnormal retinal morphology on macular OCT, specifically photoreceptor outer segment elongation), HP:0007677 (Vitelliform-like macular lesions)

      PhenotypeEvidence: The article provides an example of the function of IMPG1 (here referred to as IPM150) as a component of the interphotoreceptor matrix, an insoluble extracellular layer that is located between apical side of the RPE and the external limiting membrane of the neural retina, and which supports the adhesion, function, and maintenance of photoreceptor cells.

    1. The disintegrin domain of MDC-9 lacks an RGD motif but has recently been reported to bind the alpha(6)beta(1) integrin; however, it is unclear whether MDC-9 can bind other integrins. In the present study myeloma cells, but not lymphoblastoid cells, were shown to bind to immobilised, recombinantly expressed MDC-9 disintegrin domain (A9dis). Binding was divalent cation-dependent, being supported by Mn(2+) and Ca(2+). Adhesion of myeloma cells to A9dis was completely inhibited by an antibody to the alpha(v)beta(5) integrin but not by antibodies to other subunits. RGD-containing peptides had no effect on binding, suggesting that MDC-9 interacts with alpha(v)beta(5) in an RGD-independent manner. Flow cytometric analyses demonstrated that myeloma cells, but not lymphoblastoid cells, expressed alpha(v)beta(5) on the cell membrane. These data indicated that the disintegrin domain of MDC-9 can function as an adhesion molecule by interacting with an alpha(v)beta(5) integrin.

      Selection B- Gene function is consistent with phenotype.

      Title: ADAM9 (MDC-9) functions as an adhesion molecule by interacting with integrins.

      GOterm: GO:0033630 (positive regulation of cell adhesion mediated by integrin)

      FunctionalEvidence: Melanoma cells bind to they the immobilized recombinant ADAM9 disintegrin domain in a manner that is dependent on divalent cations (Mn2+ or Ca2+). The interaction can also be disrupted by an antibody to the alpha(v)beta(5) integrin, indicating that the cell-cell adhesion function of ADAM9 is mediated by an interaction with this molecule.

      FunctionalHPO: HP:0000546 (Retinal degeneration), HP:0007703 (Abnormality of retinal pigmentation), HP:0030610 (Photoreceptor outer segment loss on macular OCT

      PhenotypeEvidence: This evidence is consistent with evidence that Adam9 knockout mice exhibit a gap between the photoreceptor outer nuclear segment and the retinal pigment epithelium, indicating that loss of this adhesion molecule may impair the integrity of retinal organization.

    1. We provide here structural evidence that the protein product of the ocular albinism type 1 gene (OA1), a pigment cell-specific integral membrane glycoprotein, represents a novel member of the GPCR superfamily and demonstrate that it binds heterotrimeric G proteins. Moreover, we show that OA1 is not found at the plasma membrane, being instead targeted to specialized intracellular organelles, the melanosomes. Our data suggest that OA1 represents the first example of an exclusively intracellular GPCR

      Selection B- Gene function is consistent with phenotype.

      Title: GPR143 binds heterotrimeric G proteins and shows subcellular localization to melanosomes.

      GOterm: GO:0032402 (melanosome transport)

      FunctionalEvidence: Exogenously expressed GPR143 in COS-7 cells forms protein-protein interactions with heterotrimeric G-proteins that can be co-immunoprecipitated (Figure 2). This was validated with endogenous GPR143 (Figure 3). GPR143 shows subcellular localization not to the plasma membrane but to melanosomes (Figures 4, 6).

      FunctionalHPO: HP:0005592 (Giant melanosomes in melanocytes), severely reduced microtubule-based motility in melanosomes

      HumanPhenotype: HP:0005592 (Giant melanosomes in melanocytes), HP:0007894 (Hypopigmentation of the fundus), severely reduced microtubule-based motility in melanosomes, Giant melanosomes in retinal pigment epithelial cells

      PhenotypeEvidence: This evidence is consistent with the melanocyte trafficking defects characteristic of human patients.

    1. Protein extracts from wild-type and LAP-BBS4 transgenic testes were subjected to tandem affinity purification. In LAP-BBS4 transgenic testis, all BBSome subunits (Bbs1, Bbs2, Bbs5, Bbs7, Bbs8, and Bbs9) were co-purified with LAP-BBS4, while no BBS proteins were purified when wild-type testes were used (Figure 1A and Table S1).

      Selection B- Gene function is consistent with phenotype.

      GOterm: GO:0034464 (BBSome)

      FunctionalEvidence: Affinity-purified human BBS4 expressed from a transgene in mouse testes resulted in co-purification of all BBSome subunits, including Bbs1, as identified by mass spectrometry (Figure 1A).

      FunctionalHPO: HP:0000026 (Male hypogonadism), HP:0000510 (Rod-cone dystrophy), HP:0001513 (Obesity)

    1. Subcellular localization of spam to the outer segment of mature porcine retina using antibody to spam (green) and antibody to rhodopsin (red). The overlay shows the localization of spam in the same region as rhodopsin (yellow) in the outer segment of the photoreceptor cell layer.

      Selection B- Gene function is consistent with phenotype.

      GOterm: GO:0001750 (cellular component of the photoreceptor outer segment)

      FunctionalEvidence: Immunofluorescent staining of mature porcine retina tissues with an antibody to the EYS protein shows subcellular localization to the outer segment specifically (Figure 2b). This region of the retina holds the light-absorbing, ciliated part of the photoreceptor cells, and localization / function in this region is consistent with the rod and cone photoreceptor dysfunction phenotypes found in the human patients.

      FunctionalHPO: Nyctalopia HP:0000662, Undetectable electroretinogram HP:0000550, Reduced visual acuity HP:0007663

    1. Glycosaminoglycans: KS and C6S

      ExperimentName: Accumulation of glycosaminoglycans

      GOterm:

      FunctionalEvidence: Patient cells assayed with artificial substrates for the N-acetylgalactosamine-6-sulfate sulfatase encoded by GALNS, depending on the severity of the coding sequence alteration, are either unable to break down the substrate or are hindered. Further, in mucopolysaccharidosis IVA patients with known variants, elevated levels of keratan sulfate and chondroitin-6-sulfate can be found in their urine where levels in unaffected individuals are much lower.

      HGNC:

      GeneEvidence:

      SharedGeneImplication: