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Table 1 Ciliary proteins with a nuclear presence

From: Nuclear roles for cilia-associated proteins

Nuclear + cytoplasmic >0.2 Ambiguous between 0.2 and 0.1 Cytoplasmic >0.1
ARL3 ADP-ribosylation factor-like protein 3 RNC = 0.51 (nuc + cyto)
Interactor with RP2 and PDEδ. Involved in trafficking of vesicles from the Golgi to the cilium, especially; farnesylated cargo in association with PDEδ and RPGR; and myristoylated cargo in association with UNC119 and RP2
ARL6 ADP-ribosylation factor-like protein 6 RNC = 0.49 (nuc + cyto)
Mutated in Bardet–Biedl syndrome (type 3) and retinitis pigmentosa (type 55). At the ciliary gate, it regulates Wnt signaling. Functions with BBSome to coat proteins for trafficking to the cilium basal body, cilium, cytosol, transition zone
ATXN10 Ataxin 10 RNC = 0.48 (nuc + cyto)
Mutated in 1 NPHP family (splice-site mutation). Forms complex with NPHP5 and 6 at the basal body  
C21orf59 a Jaffe et al. [42] c21orf59/kurly controls both cilia motility and polarization RNS = 0.48 (nuc + cyto)
C8orf37 Mutated in cone–rod dystrophy (type 16) and retinitis pigmentosa (type 64). Localizes to basal body in cultured RPE cells and Basal body and ciliary rootlet in mouse photoreceptors
Basal body, ciliary root
RNS = 0.36 (nuc + cyto)
CETN2 a Centrin-2 RNS = 0.55/0.58 (nuc + cyto)
CETN3 a Centrin-3 RNS = 0.33 (nuc + cyto)
CTNNB1 Catenin beta-1 RNS = 0.031 (cytoplasmic a )
Involved in regulation of PKD1 and PKD2 expression. Nek2 substrate involved in centrosome separation, along with rootletin (CROCC). Facilitator of canonical Wnt signalling pathway. Many links between cilia and Wnt signaling centrosome
DNAL1 Dynein light chain 1, axonemal RNS = 0.49 (nuc + cyto)
Mutated in primary ciliary dyskinesia (type 16) Component of outer dynein arms. Axoneme
DPCD Deleted in primary ciliary dyskinesia RNS = 0.29 (nuc + cyto)
Deleted in a mouse model of primary ciliary dyskinesia
EFHC2 a EF-hand domain-containing family member C2 RNS = 0.47 (nuc + cyto)
HEATR2 HEAT repeat-containing protein 2 RNS = 0.63 (nuc + cyto)
Mutation linked to premature centromere division (PCD), presumably involved in dynein arm transport or assembly
HSPA8 Heat shock cognate 71 kDa protein RNS = 0.49 (nuc + cyto)
Chaperone of the IFT together with DnajB6
HSPB11 Heat shock protein beta-11 RNS = 0.48 (nuc + cyto)
IFT25, part of IFT-B complex. Forms a complex with IFT27.
External submission. Cilium, IFT
IFT27 Intraflagellar transport protein 27 RNS = 0.45 (nuc + cyto)
Component of IFT complex B. Rab-like small G protein basal body, cilium, IFT
KIF17 Kinesin-like protein KIF17 RNS = 0.21 (nuc + cyto)
Kinesin 2 motor, active in antergrade IFT ciliary tip
LRRC6 Protein TILB homolog RNS = 0.34 (nuc + cyto)
Essential for proper axonemal assembly of inner and outer dynein arms, causes PCD. Cilium
MAPRE1 (EB1) MT-associated protein RP/EB family 1 RNS = 0.38 (nuc + cyto)
MT plus-end-tracking protein. promotes ciliogenesis. Centrosome, golgi
MNS1 Meiosis-specific nuclear structural protein 1 RNS = 0.37 (nuc + cyto)
Mns1−/− mice have short, immotile sperm flagella, situs defects, and hydrocephalus. Protein localized along flagellum. Knockdown in IMCD3 and 3T3 cells causes Hh signaling defects axoneme
NME7 Nucleoside diphosphate kinase 7 RNS = 0.21 (nuc + cyto)
IFT transport and signaling defects after knockdown
NME8 Thioredoxin domain-containing protein 3 RNS = 0.39 (nuc + cyto)
The sea urchin ortholog of this gene encodes a component of sperm outer dynein arms, and the protein is implicated in ciliary function. Mutations in this gene are implicated in primary ciliary dyskinesia type 6
NPHP1 Nephrocystin-1 RNS = 0.36 (nuc + cyto)
Known ciliopathy gene JBTS4, NPHP1, SLS1 transition zone
NUP214 Nuclear pore complex protein Nup214 RNS = 0.45 (nuc + cyto)
Part of ciliary pore complex transition zone
NUP35 Nucleoporin NUP35 RNS = 0.47 (nuc + cyto)
Nucleoporin 35 kDa, part of ciliary pore complex transition zone
NUP37 Nucleoporin NUP37 RNS = 0.56 (nuc + cyto)
Part of ciliary pore complex transition zone
NUP62 Nuclear pore glycoprotein p62 RNS = 0.38 (nuc + cyto)
Part of ciliary pore complex transition zone
NUP93 Nuclear pore complex protein Nup93 RNS − 0.45 (nuc + cyto)
Part of ciliary pore complex
transition zone
OCRL Oculocerebrorenal syndrome of Lowe RNS = 0.24 (nuc + cyto)
Linked to Lowe Syndrome. Involved in assembly of primary cilia, involved in Rab8n-dependent protein trafficking to the cilium
ORC1 Origin recognition complex subunit 1 RNS = 0.23 (nuc + cyto)
Linked to Meier–Gorlin syndrome (MGS), a disorder conferring microcephaly, primordial dwarfism, underdeveloped ears, and skeletal abnormalities. knockdown affects ciliogenesis and Hh signaling
PAFAH1B1 Platelet-activating factor acetylhydrolase IB alpha RNS = 0.28 (nuc + cyto)
LIS1 Mammalian Lis1 localizes to motile cilia in trachea and oviduct, but is absent from non-motile primary cilia axoneme
PDE6D cGMP 3′,5′-cyclic phosphodiesterase subunit delta RNS = 0.40 (nuc + cyto)p
Part of the ARL13B, INPP5E, and CEP164 network
PLK1 Serine/threonine-protein kinase PLK1 RNS = 0.39 (nuc + cyto)
Localizes to TZ and induces phosphorylation of NPHP1 transition zone
RABL5 Rab-like protein 5 RNS = 0.33 (nuc + cyto)
IFT22, component of IFT complex B cilium, IFT
RILPL2 RILP-like protein 2 RNS = 0.50 (nuc + cyto)
Rab effector. Regulates cilium membrane content. Cilium, basal body
RSPH4A Radial spoke head protein 4 homolog A RNS = 0.90 (most nuclear)
Defective Hh signaling but no structural cilia defects after knockdown. Mutations in RSPH4A cause primary ciliary dyskinesia, with typical respiratory features, but without situs abnormalities. These findings suggest that radial spoke proteins are not essential for embryonic nodal ciliary function, which is important in the determination of left–right axis development cilium, axoneme
RSPH9 Radial spoke head protein 9 homolog RNS = 0.44 (nuc + cyto)
Mutations in RSPH9 linked to primary ciliary dyskinesia, with typical respiratory features, but without situs abnormalities. These findings suggest that radial spoke proteins are not essential for embryonic nodal ciliary function, which is important in the determination of left–right axis development structural cilia defects of primary cilia after knockdown in 3 different murine cell lines cilium, axoneme
SNX10 Sorting nexin-10 (Fragment) RNS = 0.51 (nuc + cyto)
Regulates ciliogenesis Centrosome
SSNA1 Sjoegren syndrome nuclear autoantigen 1 RNA + 0.50 (nuc + cyto)
siRNA knockdown in 3 mouse cell lines perturbs receptor transport into cilium and HH signaling
STK38L Serine/threonine-protein kinase 38-like RNA = 0.34 (nuc + cyto)
Phosphorylates Rabin8. Mutated in canine retinal degeneration. Cytosol
SUFU Suppressor of fused homolog RNS = 0.24 (nuc + cyto)
Localizes to ciliary tip together with GLI transcription factors. Role in Hh signaling ciliary tip
TEKT4 Tektin-4 RNS = 0.35 (nuc + cyto)
Axonemal protein required for flagella motility in mouse sperm. Expression reduced in inasthenozoospermic men. Cilium
TNPO1 Transportin-1 RNS = 0.44 (nuc + cyto)
Importin beta 2. Regulates entry of RP2 and kinesin motor into cilium axoneme
TRAPPC3 Trafficking protein particle complex subunit 3 RNS = 0.30 (nuc + cyto).
Required for Rabin8 centrosome trafficking and ciliogenesis basal body, centrosome
TTK Dual specificity protein kinase TTK RNS = 0.33 (nuc + cyto)
Negatively regulates ciliogenesis. Centrosome
WDR19 WD repeat-containing protein 19 RNS = 0.22 (nuc + cyto)
Mutations in WDR19 associated with ciliopathies nephronophthisis (NPHP13), Jeune and Sensenbrenner syndromes (ATD5), IFT complex A component (aka IFT144) cilium, IFT
  1. Xenopus Proteomic data from Wuhr et al. ciliary proteins (and curator notes) from: http://www.syscilia.org/goldstandard.shtml
  2. aIndicates known ciliary protein added to list of ciliary proteins