IFT88

Summary

IFT88 (intraflagellar transport 88, HGNC:20606) is a protein-coding gene on chromosome 13q12.11, encoding Intraflagellar transport protein 88 homolog (Q13099). Positively regulates primary cilium biogenesis.

This gene encodes a member of the tetratrico peptide repeat (TPR) family. The encoded protein is involved in cilium biogenesis. Mutations of a similar gene in mouse can cause polycystic kidney disease. Several transcript variants encoding distinct isoforms have been identified for this gene.

Source: NCBI Gene 8100 — RefSeq curated summary.

At a glance

• Gene–disease (curated): retinitis pigmentosa (Supportive, GenCC)
• GWAS associations: 4
• Clinical variants (ClinVar): 591 total
• Phenotypes (HPO): 31
• MANE Select transcript: NM_006531

Identifiers

Gene identifiers

Field	Value
HGNC ID	HGNC:20606
Approved symbol	IFT88
Name	intraflagellar transport 88
Location	13q12.11
Locus type	gene with protein product
Status	Approved
Aliases	hTg737, Tg737, D13S1056E, MGC26259
Ensembl gene	ENSG00000032742
Ensembl biotype	protein_coding
OMIM	600595
Entrez	8100

Gene structure

Transcript identifiers

Ensembl transcripts: 52 — 49 protein_coding, 3 protein_coding_CDS_not_defined

ENST00000319980, ENST00000351808, ENST00000389373, ENST00000461115, ENST00000470695, ENST00000482172, ENST00000537103, ENST00000894238, ENST00000894239, ENST00000894240, ENST00000894241, ENST00000894242, ENST00000894243, ENST00000894244, ENST00000894245, ENST00000894246, ENST00000894247, ENST00000894248, ENST00000894249, ENST00000894250, ENST00000894251, ENST00000894252, ENST00000894253, ENST00000894254, ENST00000894255, ENST00000894256, ENST00000894257, ENST00000894258, ENST00000894259, ENST00000894260, ENST00000894261, ENST00000927832, ENST00000950099, ENST00000950100, ENST00000950101, ENST00000950102, ENST00000950103, ENST00000950104, ENST00000950105, ENST00000950106, ENST00000950107, ENST00000950108, ENST00000950109, ENST00000950110, ENST00000950111, ENST00000950112, ENST00000950113, ENST00000950114, ENST00000950115, ENST00000950116, ENST00000950117, ENST00000950118

RefSeq mRNA: 19 — MANE Select: NM_006531 NM_001318491, NM_001318493, NM_001353565, NM_001353566, NM_001353567, NM_001353568, NM_001353569, NM_001353570, NM_001353571, NM_001353572, NM_001353573, NM_001353574, NM_001353575, NM_001353576, NM_001353577, NM_001353578, NM_001353579, NM_006531, NM_175605

CCDS: CCDS31944, CCDS31945

Canonical transcript exons

ENST00000351808 — 26 exons

Exon	Start	End
ENSE00000994969	20605035	20605105
ENSE00000994970	20589811	20589867
ENSE00000994972	20591618	20591681
ENSE00000994975	20599451	20599565
ENSE00000994976	20597015	20597119
ENSE00000994978	20644843	20644958
ENSE00000994980	20601705	20601933
ENSE00000994982	20592335	20592404
ENSE00000994983	20596150	20596240
ENSE00000994985	20643455	20643605
ENSE00000994986	20590967	20591020
ENSE00000994987	20598651	20598753
ENSE00001162827	20567157	20567256
ENSE00002712977	20641290	20641398
ENSE00002726528	20582957	20583019
ENSE00003501965	20574380	20574475
ENSE00003528150	20653876	20653928
ENSE00003556850	20625750	20625849
ENSE00003595969	20638332	20638518
ENSE00003599771	20691054	20691444
ENSE00003604510	20663498	20663604
ENSE00003625094	20615793	20615879
ENSE00003628874	20690705	20690815
ENSE00003650108	20656365	20656430
ENSE00003650622	20670973	20671039
ENSE00003666195	20631016	20631102

Expression profiles

Bgee: expression breadth ubiquitous, 284 present calls, max score 97.21.

FANTOM5 (CAGE): breadth ubiquitous, TPM avg 11.1806 / max 190.2305, expressed in 1738 samples.

FANTOM5 promoters (3 alternative TSS)

Promoter ID	TPM avg	Samples expressed
134308	10.2720	1726
134307	0.7024	453
134309	0.2061	87

Top tissues by expression

293 total, by Bgee expression score (0-100, higher = more expressed):

Tissue	Anatomy ID	Expression score	Quality
bronchial epithelial cell	CL:0002328	97.21	gold quality
sperm	CL:0000019	96.99	gold quality
epithelium of bronchus	UBERON:0002031	96.62	gold quality
bronchus	UBERON:0002185	96.04	gold quality
left testis	UBERON:0004533	95.67	gold quality
right testis	UBERON:0004534	95.63	gold quality
male germ cell	CL:0000015	95.55	gold quality
right uterine tube	UBERON:0001302	95.43	gold quality
testis	UBERON:0000473	94.71	gold quality
mucosa of paranasal sinus	UBERON:0005030	94.69	gold quality
caput epididymis	UBERON:0004358	92.91	gold quality
tibia	UBERON:0000979	92.30	gold quality
calcaneal tendon	UBERON:0003701	92.20	gold quality
male germ line stem cell (sensu Vertebrata) in testis	CL:0000089 ∩ UBERON:0000473	92.17	gold quality
adenohypophysis	UBERON:0002196	90.66	gold quality
corpus callosum	UBERON:0002336	90.46	gold quality
pituitary gland	UBERON:0000007	90.43	gold quality
epithelium of nasopharynx	UBERON:0001951	90.08	gold quality
cranial nerve II	UBERON:0000941	89.67	gold quality
tendon	UBERON:0000043	89.66	gold quality
olfactory segment of nasal mucosa	UBERON:0005386	89.63	gold quality
right lobe of thyroid gland	UBERON:0001119	88.78	gold quality
left lobe of thyroid gland	UBERON:0001120	88.71	gold quality
thyroid gland	UBERON:0002046	88.65	gold quality
germinal epithelium of ovary	UBERON:0001304	88.60	gold quality
adult organism	UBERON:0007023	88.49	gold quality
nephron tubule	UBERON:0001231	88.21	gold quality
cauda epididymis	UBERON:0004360	87.87	gold quality
tendon of biceps brachii	UBERON:0008188	87.82	gold quality
metanephros cortex	UBERON:0010533	87.65	gold quality

Single-cell (SCXA)

Detected in 1 experiment(s), a significant marker in 1.

Experiment	Marker?	Max mean expression
E-ANND-3	yes	9.47

Regulation

Is transcription factor: no

Upstream regulators (CollecTRI, top): GLI3

miRNA regulators (miRDB)

12 targeting IFT88, top 30 by miRDB confidence (max_score; target_count = how many genes the miRNA targets in total — lower means more specific):

miRNA	Max score	Avg score	miRNA target_count
HSA-MIR-302C-5P	99.97	72.56	3642
HSA-MIR-3605-5P	99.96	67.12	932
HSA-MIR-6875-3P	99.82	70.26	2983
HSA-MIR-5700	99.64	69.88	2280
HSA-MIR-5689	99.50	71.26	1154
HSA-MIR-3176	99.25	64.35	954
HSA-MIR-3922-3P	99.25	64.96	1136
HSA-MIR-548L	99.06	70.90	2560
HSA-MIR-3124-3P	98.87	68.95	2123
HSA-MIR-4695-3P	96.71	67.21	836
HSA-MIR-552-3P	96.68	64.12	1026
HSA-MIR-592	96.59	67.59	817

Literature-anchored findings (GeneRIF, showing 18)

• IFT88 is a centrosomal protein regulating G1-S transition in non-ciliated cells. (PMID:17264151)
• The results indicate that loss of heterozygosity of the tumor suppressor gene Tg737 may play an important role in the carcinogenetic mechanism of liver cancer stem cells. (PMID:20300861)
• Data show that IFT88 depletion induces mitotic defects in human cultured cells, in kidney cells from the IFT88 mouse mutant Tg737(orpk) and in zebrafish embryos. (PMID:21441926)
• A mutation in IFT88 causes a hitherto unknown human ciliopathy. (PMID:22941275)
• this work suggests that Tg737 is involved in the invasion and migration of hepatoma cells under hypoxia, with the involvement of the polycystin-1, IL-8, and TGF-beta1 signaling pathway (PMID:22974282)
• subtle regulation of IFT and associated cilia structure, tunes the wnt response controlling stem cell differentiation. (PMID:24346024)
• MiR-548a-5p negatively regulates the tumor inhibitor gene Tg737 and promotes tumorigenesis in vitro and in vivo, indicating its potential as a novel therapeutic target for hepatocellular carcinoma. (PMID:27340352)
• Data suggest that the function of the fusion transcript crystallin, lambda 1 protein - intraflagellar transport 88 (CRYL1-IFT88) is closed to CRYL1 because it contained most of domain of CRYL1. (PMID:28489570)
• multivariate Cox regression analyses demonstrated that Tg737 expression was an independent factor for predicting the overall survival of hepatocellular carcinoma patients (PMID:28663060)
• BFGF also upregulated the mRNA and protein expression of IFT88 in primary cultured chondrocytes. (PMID:28901443)
• IFT88/primary cilia play a role in metabolic reprogramming in thyroid cancer cells. (PMID:29743590)
• TCTN2 Depletion-Induced IFT88 Lumen Leakage and Ciliary Weakening (PMID:29866362)
• These observations suggest that the rare and unique combination of IFT88 alleles observed in this study provide insight into the physiological role of IFT88 in humans and the likely mechanism underlying retinal pathology in the pedigree with inherited retinal degeneration (PMID:29978320)
• Significant association was found between IFT88 rs9509311 and rs2497490 and Nonsyndromic cleft lip with or without cleft palate (NSCLP) in non-Hispanic white families (p = .004 and .005), while nominal associations were found for rs7998361 and rs9509307 (p < .05). Pairwise association analyses also showed nominal associations between NSCLP in both NHW and Hispanic data sets (p < .05). (PMID:30953423)
• IFT88 controls NuMA enrichment at k-fibers minus-ends to facilitate their re-anchoring into mitotic spindles. (PMID:31312011)
• The Intraflagellar Transport Protein IFT88 Is Disrupted in Cystic Fibrosis. (PMID:31891309)
• Multifaceted investigation underlies diverse mechanisms contributing to the downregulation of Hedgehog pathway-associated genes INTU and IFT88 in lung adenocarcinoma and uterine corpus endometrial carcinoma. (PMID:36084949)
• Vinblastine Resistance Is Associated with Nephronophthisis 3-Mediated Primary Cilia via Intraflagellar Transport Protein 88 and Apoptosis-Antagonizing Transcription Factor. (PMID:39408701)

Cross-species orthologs

4 orthologs

Organism	Symbol	Gene ID
danio_rerio	ift88	ENSDARG00000027234
mus_musculus	Ift88	ENSMUSG00000040040
rattus_norvegicus	Ift88	ENSRNOG00000009278
caenorhabditis_elegans		WBGENE00003885

Paralogs (14): TTC7A (ENSG00000068724), TMTC4 (ENSG00000125247), TMTC1 (ENSG00000133687), TMTC3 (ENSG00000139324), TTC6 (ENSG00000139865), BBS4 (ENSG00000140463), TTC13 (ENSG00000143643), OGT (ENSG00000147162), CFAP70 (ENSG00000156042), TTC8 (ENSG00000165533), TTC7B (ENSG00000165914), TTC16 (ENSG00000167094), TMTC2 (ENSG00000179104), TTC34 (ENSG00000215912)

Protein

Protein identifiers

Intraflagellar transport protein 88 homolog — Q13099 (reviewed: Q13099)

Alternative names: Recessive polycystic kidney disease protein Tg737 homolog, Tetratricopeptide repeat protein 10

All UniProt accessions (4): A0A140VJL7, Q13099, F5H6C2, F6SRW8

UniProt curated annotations — full annotation on UniProt →

Function. Positively regulates primary cilium biogenesis. Also involved in autophagy since it is required for trafficking of ATG16L and the expansion of the autophagic compartment.

Subunit / interactions. Component of the IFT complex B, at least composed of IFT20, IFT22, IFT25, IFT27, IFT46, IFT52, TRAF3IP1/IFT54, IFT57, IFT74, IFT80, IFT81, and IFT88. Interacts with IFT20, IFT22, IFT25, IFT27, IFT52, TRAF3IP1, IFT74, IFT80 and IFT81. Interacts with IFT172. Interacts with IFT57. Interacts with IFT46. Interacts with IFT70B. Interacts with C2CD3. Interacts with ENTR1 (via N-terminus). Interacts with LRRC56. Interacts with DZIP1. Interacts with CCDC38. Interacts with CCDC146. Interacts with CFAP53.

Subcellular location. Cytoplasm. Cytoskeleton. Microtubule organizing center. Centrosome. Centriole. Cell projection. Cilium. Cilium basal body. Flagellum.

Tissue specificity. Expressed in the heart, brain, liver, lung, kidney, skeletal muscle and pancreas.

Isoforms (3)

UniProt ID	Names	Canonical?
Q13099-2	2	yes
Q13099-1	1
Q13099-3	3

RefSeq proteins (19): NP_001305420, NP_001305422, NP_001340494, NP_001340495, NP_001340496, NP_001340497, NP_001340498, NP_001340499, NP_001340500, NP_001340501, NP_001340502, NP_001340503, NP_001340504, NP_001340505, NP_001340506, NP_001340507, NP_001340508, NP_006522, NP_783195 (=MANE)

Domains & families (InterPro)

ID	Name	Type
IPR006597	Sel1-like	Repeat
IPR011990	TPR-like_helical_dom_sf	Homologous_superfamily
IPR019734	TPR_rpt	Repeat

Pfam: PF13174, PF13181, PF13424, PF13432

UniProt features (29 total): repeat 12, sequence conflict 6, compositionally biased region 3, sequence variant 3, region of interest 2, splice variant 2, chain 1

Structure

Experimental structures (PDB)

0 structures.

Predicted structure (AlphaFold)

Model	pLDDT	Fraction very-high
AF-Q13099-F1	77.20	0.47

Function

Pathways and Gene Ontology

Reactome pathways

5 pathways

ID	Pathway
R-HSA-5610787	Hedgehog ‘off’ state
R-HSA-5620924	Intraflagellar transport
R-HSA-9613829	Chaperone Mediated Autophagy
R-HSA-9615710	Late endosomal microautophagy
R-HSA-9646399	Aggrephagy

MSigDB gene sets: 219 (showing top): GOBP_VACUOLE_ORGANIZATION, GOBP_NEUROGENESIS, GOBP_REGULATION_OF_VACUOLE_ORGANIZATION, GOBP_POSITIVE_REGULATION_OF_ORGANELLE_ORGANIZATION, GOBP_REGULATION_OF_CELLULAR_COMPONENT_BIOGENESIS, GOCC_MICROTUBULE_ORGANIZING_CENTER, GOBP_MACROAUTOPHAGY, GHO_ATF5_TARGETS_UP, BROWNE_HCMV_INFECTION_48HR_DN, GOBP_POSITIVE_REGULATION_OF_CELLULAR_COMPONENT_BIOGENESIS, GOBP_REGULATION_OF_CELL_PROJECTION_ORGANIZATION, GOBP_EAR_DEVELOPMENT, MODULE_195, GOBP_CILIUM_ORGANIZATION, GOCC_CENTROSOME

GO Biological Process (11): kidney development (GO:0001822), response to silicon dioxide (GO:0034021), intraciliary anterograde transport (GO:0035720), intraciliary transport (GO:0042073), positive regulation of cilium assembly (GO:0045724), inner ear receptor cell stereocilium organization (GO:0060122), cilium assembly (GO:0060271), regulation of cilium assembly (GO:1902017), non-motile cilium assembly (GO:1905515), regulation of autophagosome assembly (GO:2000785), cell projection organization (GO:0030030)

GO Molecular Function (2): kinesin binding (GO:0019894), protein binding (GO:0005515)

GO Cellular Component (25): manchette (GO:0002177), nucleolus (GO:0005730), centrosome (GO:0005813), centriole (GO:0005814), cytosol (GO:0005829), cilium (GO:0005929), microtubule cytoskeleton (GO:0015630), intraciliary transport particle A (GO:0030991), intraciliary transport particle B (GO:0030992), motile cilium (GO:0031514), centriolar satellite (GO:0034451), ciliary basal body (GO:0036064), sperm flagellum (GO:0036126), intercellular bridge (GO:0045171), mitotic spindle (GO:0072686), sperm midpiece (GO:0097225), sperm principal piece (GO:0097228), sperm end piece (GO:0097229), ciliary tip (GO:0097542), ciliary base (GO:0097546), non-motile cilium (GO:0097730), sperm head-tail coupling apparatus (GO:0120212), cytoplasm (GO:0005737), cytoskeleton (GO:0005856), cell projection (GO:0042995)

Reactome top-level categories

Rollup of top-4 pathways:

Category	Pathways
Autophagy	2
Signaling by Hedgehog	1
Assembly of the 9+0 primary cilium	1
Selective autophagy	1

GO top-level categories

Rollup of top GO terms by namespace:

Category	Terms
cellular anatomical structure	9
cilium	5
cilium assembly	3
microtubule organizing center	3
intraciliary transport particle	3
sperm flagellum	3
cilium organization	2
regulation of organelle assembly	2
intracellular membraneless organelle	2
protein-containing complex	2
animal organ development	1
renal system development	1
response to oxygen-containing compound	1
intraciliary transport	1
transport along microtubule	1
positive regulation of plasma membrane bounded cell projection assembly	1
regulation of cilium assembly	1
positive regulation of organelle assembly	1
neuron projection development	1
inner ear receptor cell development	1
axoneme assembly	1
intraciliary transport involved in cilium assembly	1
protein localization to cilium	1
organelle assembly	1
trans-Golgi to periciliary membrane compartment transport	1
plasma membrane bounded cell projection assembly	1
ciliary transition zone assembly	1
regulation of plasma membrane bounded cell projection assembly	1
autophagosome assembly	1
regulation of vacuole organization	1
cellular component organization	1
cytoskeletal protein binding	1
binding	1
microtubule cytoskeleton	1
nuclear lumen	1
centriole	1
cytoplasm	1
membrane-bounded organelle	1
plasma membrane bounded cell projection	1
cytoskeleton	1

Protein interactions and networks

STRING

2988 interactions, top by confidence (×1000):

Protein A	Protein B	Partner UniProt	Score
IFT88	IFT52	Q9Y366	997
IFT88	IFT46	Q9NQC8	996
IFT88	IFT57	Q9NWB7	996
IFT88	IFT70B	Q8N4P2	995
IFT88	IFT27	Q9BW83	994
IFT88	IFT74	Q96LB3	992
IFT88	IFT81	Q8WYA0	991
IFT88	IFT172	Q9UG01	988
IFT88	IFT80	Q9P2H3	978
IFT88	KIF3A	Q9Y496	978
IFT88	IFT25	Q9Y547	975
IFT88	IFT20	Q8IY31	967
IFT88	IFT38	Q96AJ1	967
IFT88	IFT56	A0AVF1	948
IFT88	TTC21B	Q7Z4L5	935

IntAct

92 interactions, top by confidence:

A	B	Type	Score
IFT70A	IFT56	psi-mi:“MI:0914”(association)	0.790
IFT70B	IFT56	psi-mi:“MI:0914”(association)	0.790
IFT27	IFT56	psi-mi:“MI:0914”(association)	0.690
IFT25	IFT56	psi-mi:“MI:0914”(association)	0.690
IFT46	IFT56	psi-mi:“MI:0914”(association)	0.640
IFT88	IFT56	psi-mi:“MI:0914”(association)	0.640
IFT22	IFT56	psi-mi:“MI:0914”(association)	0.640
IFT57	IFT56	psi-mi:“MI:0914”(association)	0.640
IFT88	ENTR1	psi-mi:“MI:0915”(physical association)	0.600
ENTR1	IFT88	psi-mi:“MI:0403”(colocalization)	0.600
IFT172	IFT56	psi-mi:“MI:0914”(association)	0.590

BioGRID (86): IFT88 (Affinity Capture-MS), IFT88 (Affinity Capture-MS), IFT88 (Two-hybrid), IFT80 (Co-fractionation), IFT88 (Affinity Capture-MS), IFT88 (Affinity Capture-MS), IFT88 (Affinity Capture-MS), IFT88 (Affinity Capture-MS), IFT88 (Affinity Capture-MS), IFT88 (Affinity Capture-MS), IFT88 (Affinity Capture-MS), IFT88 (Affinity Capture-MS), IFT88 (Affinity Capture-MS), IFT88 (Affinity Capture-MS), IFT88 (Affinity Capture-MS)

ESM2 similar proteins: A0A644F649, A0AVF1, A1Z8E9, A4III8, A8BS40, A8JA42, A8XBR9, B5X0I6, O17581, O42668, O74458, O76094, O94459, O94474, P11442, P19735, P25870, P29742, P33731, P34574, P41889, P49951, P49965, P53675, P89105, Q00610, Q03560, Q13099, Q16JL4, Q20255, Q29L58, Q4R7Z9, Q57ZL2, Q5CZ52, Q5PR66, Q5U2N8, Q61LA1, Q68FD5, Q6GKV1, Q6INC1

Diamond homologs: Q13099, Q61371

SIGNOR signaling

1 interactions.

A	Effect	B	Mechanism
OFD1	“up-regulates activity”	IFT88	binding

Enriched among interaction partners

Reactome pathways and GO biological processes over-represented among this gene’s 45 IntAct physical interaction partners (hypergeometric vs the genome-wide background, BH-FDR, gene-set size 15–500, ranked by fold). A functional readout of the neighbourhood — distinct from this gene’s own memberships above, and biased toward well-studied / hub proteins, so read it as themes rather than proof.

Reactome pathways:

Pathway	Partners	Fold	FDR
Intraflagellar transport	14	96.7×	9e-24

GO biological processes:

GO term	Partners	Fold	FDR
intraciliary anterograde transport	14	295.6×	1e-31
intraciliary transport	11	147.1×	5e-20
negative regulation of keratinocyte proliferation	5	83.6×	2e-07
keratinocyte proliferation	5	69.2×	4e-07
non-motile cilium assembly	6	41.5×	4e-07
smoothened signaling pathway	9	38.8×	1e-10
cilium assembly	15	26.3×	5e-16

Disease & clinical

Clinical variants and AI predictions

ClinVar

591 variants total. Per-class counts are floors (≥ shown; pagination cap):

Classification	Count (floor)
Pathogenic	0
Likely pathogenic	0
Uncertain significance	345
Likely benign	180
Benign	34

Top pathogenic / likely-pathogenic (0)

SpliceAI

4819 predictions. Top by Δscore:

Variant	Effect	Δscore
13:20573146:GGC:G	donor_gain	1.0000
13:20573147:GC:G	donor_gain	1.0000
13:20582951:TTTTA:T	acceptor_loss	1.0000
13:20582952:TTTAG:T	acceptor_loss	1.0000
13:20582953:TTA:T	acceptor_loss	1.0000
13:20582954:TAG:T	acceptor_loss	1.0000
13:20582955:A:AG	acceptor_gain	1.0000
13:20582956:G:GG	acceptor_gain	1.0000
13:20583016:TCCAG:T	donor_loss	1.0000
13:20583017:CCA:C	donor_gain	1.0000
13:20583017:CCAGT:C	donor_loss	1.0000
13:20583018:CA:C	donor_gain	1.0000
13:20583018:CAGT:C	donor_loss	1.0000
13:20583019:AGTA:A	donor_loss	1.0000
13:20583020:G:GG	donor_gain	1.0000
13:20583020:G:T	donor_loss	1.0000
13:20590965:A:AG	acceptor_gain	1.0000
13:20590966:G:GG	acceptor_gain	1.0000
13:20596148:A:AG	acceptor_gain	1.0000
13:20596149:G:GG	acceptor_gain	1.0000
13:20596149:GCCCA:G	acceptor_gain	1.0000
13:20597009:TTTCA:T	acceptor_loss	1.0000
13:20597012:CAGGC:C	acceptor_loss	1.0000
13:20597013:A:AG	acceptor_gain	1.0000
13:20597014:G:GA	acceptor_gain	1.0000
13:20597116:CTCA:C	donor_gain	1.0000
13:20597117:TCA:T	donor_gain	1.0000
13:20597118:CA:C	donor_gain	1.0000
13:20597118:CAGT:C	donor_loss	1.0000
13:20597119:AGTAA:A	donor_loss	1.0000

AlphaMissense

5457 scored. Top likely-pathogenic:

Variant	Protein change	am_pathogenicity
13:20598702:G:C	A216P	0.999
13:20638416:G:T	G491W	0.999
13:20638452:G:C	A503P	0.999
13:20653892:T:A	W656R	0.999
13:20653892:T:C	W656R	0.999
13:20597027:G:C	A168P	0.998
13:20638473:G:C	A510P	0.998
13:20653908:C:A	A661D	0.998
13:20656379:G:C	A673P	0.998
13:20597036:G:C	A171P	0.997
13:20625800:T:C	L417P	0.997
13:20638416:G:A	G491R	0.997
13:20638416:G:C	G491R	0.997
13:20638417:G:A	G491E	0.997
13:20638453:C:A	A503D	0.997
13:20641290:G:A	G525D	0.997
13:20644924:G:C	A639P	0.997
13:20653915:T:G	C663W	0.997
13:20596205:A:C	S152R	0.996
13:20596207:C:A	S152R	0.996
13:20596207:C:G	S152R	0.996
13:20615840:C:A	A387D	0.996
13:20641325:G:C	A537P	0.996
13:20643550:G:A	G593E	0.996
13:20643585:G:C	A605P	0.996
13:20644886:T:C	L626P	0.996
13:20644925:C:A	A639D	0.996
13:20644946:C:A	A646D	0.996
13:20653913:T:C	C663R	0.996
13:20663499:T:G	C690W	0.996

dbSNP variants (sampled 300 via entrez): RS1000027933 (13:20657761 CAAAATAAATAAA>C), RS1000040951 (13:20670460 G>A,C), RS1000041768 (13:20627495 C>T), RS1000124465 (13:20591044 A>G), RS1000129202 (13:20574074 C>A), RS1000140729 (13:20664060 A>C), RS1000142080 (13:20570405 T>C,G), RS1000161190 (13:20632290 C>T), RS1000176684 (13:20675268 G>A), RS1000192359 (13:20621602 A>G), RS1000240874 (13:20616031 G>A), RS1000293389 (13:20568242 A>ATTAT), RS1000305264 (13:20658152 G>A,C), RS1000331341 (13:20597440 T>C), RS1000369690 (13:20687135 A>G,T)

Disease associations

OMIM: gene MIM:600595 | disease phenotypes: MIM:268000, MIM:208500

GenCC curated gene-disease

Disease	Classification	Inheritance
retinitis pigmentosa	Supportive	Autosomal dominant

Mondo (2): retinitis pigmentosa (MONDO:0019200), Jeune syndrome (MONDO:0018770)

Orphanet (2): Retinitis pigmentosa (Orphanet:791), Jeune syndrome (Orphanet:474)

HPO phenotypes

31 total (30 of 31 shown, HPO-id order):

HPO	Term
HP:0000405	Conductive hearing impairment
HP:0000407	Sensorineural hearing impairment
HP:0000501	Glaucoma
HP:0000505	Visual impairment
HP:0000512	Abnormal electroretinogram
HP:0000543	Optic disc pallor
HP:0000546	Retinal degeneration
HP:0000551	Color vision defect
HP:0000563	Keratoconus
HP:0000602	Ophthalmoplegia
HP:0000613	Photophobia
HP:0000618	Blindness
HP:0000639	Nystagmus
HP:0000648	Optic atrophy
HP:0000662	Nyctalopia
HP:0000842	Hyperinsulinemia
HP:0001105	Retinal atrophy
HP:0007663	Reduced visual acuity
HP:0007675	Progressive night blindness
HP:0007703	Abnormal retinal pigmentation
HP:0007737	Spicular pigmentation of the retina
HP:0007787	Posterior subcapsular cataract
HP:0007843	Attenuation of retinal blood vessels
HP:0007994	Peripheral visual field loss
HP:0008046	Abnormal retinal vascular morphology
HP:0011505	Cystoid macular edema
HP:0012426	Optic disc drusen
HP:0030466	Abnormal full-field electroretinogram
HP:0030488	Abnormal central response of multifocal electroretinogram
HP:0030610	Photoreceptor outer segment loss on macular OCT

GWAS associations

4 associations (top):

Study	Trait	p-value
GCST000774_3	Schizophrenia, bipolar disorder and depression (combined)	3.000000e-06
GCST001713_25	Dental caries	4.000000e-06
GCST002097_17	Coronary artery calcification	5.000000e-06
GCST004781_19	Sulfasalazine-induced agranulocytosis	4.000000e-07

EFO canonical traits (1, from GWAS)

EFO ID	Trait name
EFO:0004723	coronary artery calcification

MeSH disease descriptors (2)

Descriptor	Name	Tree numbers
D012174	Retinitis Pigmentosa	C11.270.684; C11.768.585.658.500; C16.320.290.684
C537571	Jeune syndrome (supp.)

Drugs & pharmacology

Drug and pharmacology data

Is drug target: no

PharmGKB: 1 entry (VIP=true, CPIC=false)

CTD chemical–gene interactions

30 total (human), top 30 by PubMed support.

Chemical	Actions (top 5)	PubMed papers
Valproic Acid	affects expression, increases expression	3
Benzo(a)pyrene	decreases expression, decreases methylation	2
aristolochic acid I	decreases expression	1
GSK-J4	decreases expression	1
dicrotophos	decreases expression	1
methylmercuric chloride	decreases expression	1
potassium chromate(VI)	affects cotreatment, decreases expression	1
3,4,3’,4’-tetrachlorobiphenyl	affects expression	1
nickel sulfate	decreases expression	1
epigallocatechin gallate	affects cotreatment, decreases expression	1
K 7174	increases expression	1
MT19c compound	increases expression	1
Resveratrol	affects cotreatment, increases expression	1
Sunitinib	decreases expression	1
Acetaminophen	decreases expression	1
Air Pollutants	increases abundance, increases expression	1
Arsenic	affects methylation	1
Atrazine	decreases expression	1
Estradiol	decreases expression	1
Hydrogen Peroxide	affects cotreatment, decreases expression	1
Methyl Methanesulfonate	increases expression	1
Plant Extracts	affects cotreatment, increases expression	1
Smoke	increases abundance, increases expression	1
Theophylline	affects cotreatment, decreases expression	1
Tobacco Smoke Pollution	decreases expression	1
Tretinoin	increases expression	1
Urethane	decreases expression	1
Cyclosporine	increases expression	1
Asbestos, Crocidolite	decreases expression	1
Copper Sulfate	decreases expression	1

Cellosaurus cell lines

3 cell lines: 2 induced pluripotent stem cell, 1 cancer cell line

First 10 cell lines (id-ordered, not curated):

Cellosaurus	Name	Category	Sex
CVCL_E3XR	UAB-iPSC-PKD2+IFT88 DKO#1	Induced pluripotent stem cell	Male
CVCL_E3XV	UAB-iPSC-IFT88 KO#1	Induced pluripotent stem cell	Male
CVCL_F1M3	HyCyte A-549 KO-hIFT88	Cancer cell line	Male

Clinical trials (associated diseases)

237 trials via MONDO — disease-level, not drug-specific.

Trial	Phase	Status	Title
NCT00717080	PHASE4	COMPLETED	The Role of Capsular Tension Ring (CTR) in Anterior Capsular Contraction
NCT00000114	PHASE3	COMPLETED	Randomized Trial of Vitamin A and Vitamin E Supplementation for Retinitis Pigmentosa
NCT00000116	PHASE3	COMPLETED	Randomized Trial of DHA for Retinitis Pigmentosa Patients Receiving Vitamin A
NCT00346333	PHASE3	COMPLETED	Clinical Trial of Lutein for Patients With Retinitis Pigmentosa Receiving Vitamin A
NCT01786395	PHASE3	TERMINATED	Phase III Efficacy and Safety Clinical Study of UF-021 for Treatment of Retinitis Pigmentosa
NCT04224207	PHASE3	COMPLETED	Management of Retinitis Pigmentosa by Mesenchymal Stem Cells by Wharton’s Jelly Derived Mesenchymal Stem Cells
NCT04636853	PHASE3	COMPLETED	CB-PRP in Retinitis Pigmentosa and Dry Age-related Macular Degeneration
NCT05537220	PHASE3	ACTIVE_NOT_RECRUITING	Oral N-acetylcysteine for Retinitis Pigmentosa
NCT05800301	PHASE3	COMPLETED	Management of Retinitis Pigmentosa Via Combination of Wharton’s Jelly-derived Mesenchymal Stem Cells and Magnovision
NCT05926583	PHASE3	ACTIVE_NOT_RECRUITING	A Study of AAV5-hRKp.RPGR for the Treatment of Japanese Participants With X-linked Retinitis Pigmentosa
NCT06388200	PHASE3	ACTIVE_NOT_RECRUITING	A Phase 3 Study Of OCU400 Gene Therapy for the Treatment Of Retinitis Pigmentosa
NCT07082855	PHASE3	NOT_YET_RECRUITING	A Multicenter, Randomized, Double-Blind, Controlled Clinical Study of Minocycline for the Treatment of Retinitis Pigmentosa
NCT07290530	PHASE3	NOT_YET_RECRUITING	24-Month Trial of NPI-001 for the Preservation of Photoreceptors in Retinitis Pigmentosa Associated With Usher Syndrome
NCT00100230	PHASE2	COMPLETED	DHA and X-Linked Retinitis Pigmentosa
NCT00447980	PHASE2	COMPLETED	A Study of Encapsulated Cell Technology (ECT) Implant for Participants With Early Stage Retinitis Pigmentosa
NCT00447993	PHASE2	COMPLETED	A Study of Encapsulated Cell Technology (ECT) Implant for Patients With Late Stage Retinitis Pigmentosa
NCT01233609	PHASE2	COMPLETED	Trial of Oral Valproic Acid for Retinitis Pigmentosa
NCT01399515	PHASE2	COMPLETED	Efficacy and Safety of Oral Valproic Acid for Retinitis Pigmentosa
NCT01530659	PHASE2	COMPLETED	Retinal Imaging in CNTF -Releasing Encapsulated Cell Implant Treated Patients for Early-stage Retinitis Pigmentosa
NCT01560715	PHASE2	COMPLETED	Autologous Bone Marrow-Derived Stem Cells Transplantation For Retinitis Pigmentosa
NCT02609165	PHASE2	COMPLETED	Nerve Growth Factor Eye Drops Treatment in Patients With Retinitis Pigmentosa and Cystoid Macular Edema
NCT02661711	PHASE2	COMPLETED	Aflibercept for Macular Oedema With Underlying Retinitis Pigmentosa (AMOUR) Study
NCT02804360	PHASE2	UNKNOWN	Intravitreal Dexamethasone Implant in Retinitis Pigmentosa-related Macular Edema- a Retrospective Study
NCT02837640	PHASE2	UNKNOWN	Studying a Potential Protective Effect of L-Dopa on Retinitis Pigmentosa
NCT03073733	PHASE2	COMPLETED	Safety and Efficacy of Intravitreal Injection of Human Retinal Progenitor Cells in Adults With Retinitis Pigmentosa
NCT04068207	PHASE2	COMPLETED	Minocycline Treatment in Retinitis Pigmentosa
NCT04356716	PHASE2	COMPLETED	Sildenafil for Treatment of Choroidal Ischemia
NCT04604899	PHASE2	COMPLETED	Safety of Repeat Intravitreal Injection of Human Retinal Progenitor Cells (jCell) in Adult Subjects With Retinitis Pigmentosa
NCT04763369	PHASE2	UNKNOWN	Investigation of Therapeutic Efficacy and Safety of UMSCs for the Management of Retinitis Pigmentosa (RP)
NCT04864496	PHASE2	UNKNOWN	Effects of Treatment With N- Acetylcysteine on Visual Outcomes in Patients With Retinitis Pigmentosa
NCT04945772	PHASE2	COMPLETED	Efficacy and Safety of MCO-010 Optogenetic Therapy in Adults With Retinitis Pigmentosa [RESTORE]
NCT05085964	PHASE2	TERMINATED	An Open-Label Extension Study to Evaluate Safety & Tolerability of QR-421a in Subjects With Retinitis Pigmentosa
NCT05392179	PHASE2	COMPLETED	A Study in Subjects With Retinitis Pigmentosa
NCT06627179	PHASE2	RECRUITING	Study to Evaluate Ultevursen in Subjects With Retinitis Pigmentosa (RP) Due to Mutations in Exon 13 of the USH2A Gene
NCT06628947	PHASE2	RECRUITING	A Phase II Study of Intravitreal KIO-301 in Patients With Late-stage Retinitis Pigmentosa
NCT06912633	PHASE2	RECRUITING	Safety of a Single, Intravitreal Injection of 6.0M jCell (Famzeretcel) in Retinitis Pigmentosa (RP)
NCT00063765	PHASE1	COMPLETED	Evaluation of Safety of Ciliary Neurotrophic Factor Implants in the Eye
NCT00065455	PHASE1	COMPLETED	Investigating the Effect of Vitamin A Supplementation on Retinitis Pigmentosa
NCT00458575	PHASE1	TERMINATED	A Study to Evaluate the Safety of CNTO 2476 in Patients With Advanced Retinitis Pigmentosa
NCT01068561	PHASE1	COMPLETED	Autologous Bone Marrow-Derived Stem Cells Transplantation For Retinitis Pigmentosa