Table 1 Ciliary proteins with a nuclear presence

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