RPGRIP1L

gene
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Also known as KIAA1005CORS3JBTS7MKS5NPHP8FTMPPP1R134

Summary

RPGRIP1L (RPGRIP1 like, HGNC:29168) is a protein-coding gene on chromosome 16q12.2, encoding Protein fantom (Q68CZ1). Negatively regulates signaling through the G-protein coupled thromboxane A2 receptor (TBXA2R).

The protein encoded by this gene can localize to the basal body-centrosome complex or to primary cilia and centrosomes in ciliated cells. The encoded protein has been found to interact with nephrocystin-4. Defects in this gene are a cause of Joubert syndrome type 7 (JBTS7) and Meckel syndrome type 5 (MKS5).

Source: NCBI Gene 23322 — RefSeq curated summary.

At a glance

  • Gene–disease (curated): ciliopathy (Definitive, ClinGen) — +5 more curated relationships
  • GWAS associations: 23
  • Clinical variants (ClinVar): 2,164 total — 159 pathogenic, 132 likely-pathogenic
  • Phenotypes (HPO): 121
  • MANE Select transcript: NM_015272

Identifiers

Gene identifiers

FieldValue
HGNC IDHGNC:29168
Approved symbolRPGRIP1L
NameRPGRIP1 like
Location16q12.2
Locus typegene with protein product
StatusApproved
AliasesKIAA1005, CORS3, JBTS7, MKS5, NPHP8, FTM, PPP1R134
Ensembl geneENSG00000103494
Ensembl biotypeprotein_coding
OMIM610937
Entrez23322

Gene structure

Transcript identifiers

Ensembl transcripts: 18 — 12 protein_coding, 2 retained_intron, 2 protein_coding_CDS_not_defined, 2 nonsense_mediated_decay

ENST00000262135, ENST00000562230, ENST00000562588, ENST00000563746, ENST00000564374, ENST00000565343, ENST00000566096, ENST00000568009, ENST00000568653, ENST00000569716, ENST00000621565, ENST00000647211, ENST00000679110, ENST00000680193, ENST00000680907, ENST00000681587, ENST00000935860, ENST00000944945

RefSeq mRNA: 6 — MANE Select: NM_015272 NM_001127897, NM_001308334, NM_001328422, NM_001328423, NM_001330538, NM_015272

CCDS: CCDS32447, CCDS45486, CCDS76868, CCDS81980, CCDS86526, CCDS86527

Canonical transcript exons

ENST00000647211 — 27 exons

ExonStartEnd
ENSE000006841885360548153605614
ENSE000006841895361096753611051
ENSE000006841915361902553619208
ENSE000008526435367501753675122
ENSE000008526445367287053673016
ENSE000008526455367151053671583
ENSE000011083265364896453649115
ENSE000011083285364103353641116
ENSE000011083305365253553652987
ENSE000011083375364128553641475
ENSE000011083385364562553646003
ENSE000011410515365877253658878
ENSE000011410595366487053665009
ENSE000011410835368643353686576
ENSE000014830545362221953622356
ENSE000014830585363831053638411
ENSE000014830765368786353687965
ENSE000016187735369206653692364
ENSE000017468745369615153696295
ENSE000026294865359815353602188
ENSE000027136545370063953700730
ENSE000034848275365745353657632
ENSE000035693935363643953636512
ENSE000035852355363769553637854
ENSE000035895355365841453658464
ENSE000036526895365647253656589
ENSE000037191605370380353703859

Expression profiles

Bgee: expression breadth ubiquitous, 207 present calls, max score 89.39.

FANTOM5 (CAGE): breadth ubiquitous, TPM avg 13.7780 / max 588.4982, expressed in 1660 samples.

FANTOM5 promoters (2 alternative TSS)

Promoter IDTPM avgSamples expressed
15740713.15931653
1574080.6186363

Top tissues by expression

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

TissueAnatomy IDExpression scoreQuality
bronchial epithelial cellCL:000232889.39gold quality
primordial germ cell in gonadCL:0000670 ∩ UBERON:000099186.17gold quality
male germ line stem cell (sensu Vertebrata) in testisCL:0000089 ∩ UBERON:000047385.68gold quality
epithelium of bronchusUBERON:000203183.93gold quality
ventricular zoneUBERON:000305382.69gold quality
right testisUBERON:000453482.69gold quality
bronchusUBERON:000218582.54gold quality
left testisUBERON:000453382.42gold quality
testisUBERON:000047382.08gold quality
right uterine tubeUBERON:000130280.94gold quality
calcaneal tendonUBERON:000370180.52gold quality
cortical plateUBERON:000534380.03gold quality
stromal cell of endometriumCL:000225579.81gold quality
ganglionic eminenceUBERON:000402379.52gold quality
mucosa of paranasal sinusUBERON:000503078.89gold quality
tibiaUBERON:000097978.76gold quality
adrenal tissueUBERON:001830377.48gold quality
adenohypophysisUBERON:000219677.31gold quality
pituitary glandUBERON:000000776.91gold quality
olfactory segment of nasal mucosaUBERON:000538676.35gold quality
choroid plexus epitheliumUBERON:000391175.72gold quality
prefrontal cortexUBERON:000045175.43gold quality
islet of LangerhansUBERON:000000675.37gold quality
right adrenal gland cortexUBERON:003582775.29gold quality
right adrenal glandUBERON:000123374.52gold quality
Brodmann (1909) area 23UBERON:001355474.31gold quality
left adrenal glandUBERON:000123474.17gold quality
left adrenal gland cortexUBERON:003582573.73gold quality
embryoUBERON:000092273.67gold quality
right frontal lobeUBERON:000281072.89gold quality

Single-cell (SCXA)

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

ExperimentMarker?Max mean expression
E-ANND-3yes8.18

Regulation

Is transcription factor: no

miRNA regulators (miRDB)

169 targeting RPGRIP1L, top 30 by miRDB confidence (max_score; target_count = how many genes the miRNA targets in total — lower means more specific):

miRNAMax scoreAvg scoremiRNA target_count
HSA-MIR-3646100.0073.565283
HSA-MIR-3924100.0072.092394
HSA-MIR-3163100.0077.238605
HSA-MIR-30A-5P100.0076.313233
HSA-MIR-30B-5P100.0076.293248
HSA-MIR-30C-5P100.0076.293248
HSA-MIR-30D-5P100.0076.323233
HSA-MIR-30E-5P100.0076.323242
HSA-MIR-513A-5P100.0069.772465
HSA-MIR-4668-3P100.0068.742635
HSA-MIR-3613-3P100.0076.367965
HSA-MIR-548C-3P99.9974.017587
HSA-MIR-34A-5P99.9971.211784
HSA-MIR-449A99.9971.051776
HSA-MIR-366299.9973.825684
HSA-MIR-27A-3P99.9872.132955
HSA-MIR-27B-3P99.9872.132955
HSA-MIR-998599.9872.112939
HSA-MIR-548N99.9871.944170
HSA-MIR-480399.9871.993117
HSA-MIR-1213699.9872.815713
HSA-MIR-616-5P99.9875.584775
HSA-MIR-34C-5P99.9770.451577
HSA-MIR-449B-5P99.9770.261580
HSA-MIR-3065-5P99.9771.563281
HSA-MIR-495-3P99.9672.814197
HSA-MIR-568899.9673.234504
HSA-MIR-365899.9673.874379
HSA-MIR-548AJ-3P99.9673.385345
HSA-MIR-548X-3P99.9673.385345

Literature-anchored findings (GeneRIF, showing 27)

  • Responsible for Joubert syndrome, affecting cilia and basal bodies. (PMID:17558407)
  • Mutations can cause the multiorgan phenotypic abnormalities found in cerebello-oculo-renal syndrome or Meckel syndrome. (PMID:17558409)
  • T615P mutation represents the most common mutation in the RPGRIP1L gene causing disease in about 8-10% of Joubert syndrome type B patients negative for NPHP1, NPHP6, or AHI1 mutations (PMID:17960139)
  • Discuss Fto/Ftm gene expression regulation via CUTL1. (PMID:18256137)
  • Mutations in RPGRIP1L: extending the clinical spectrum of ciliopathies. Review. (PMID:18281315)
  • RPGRIP1L mutations are largely confined to the cerebello-renal subgroup, while they overall represent a rare cause of JSRD (<2%). (PMID:18565097)
  • data suggest that RPGRIP1L suppresses anchorage-independent growth partly through the mitotic checkpoint protein Mad2. (PMID:19410446)
  • RPGRIP1L interacts with retinitis pigmentosa GTPase, loss of which causes retinal degeneration. (PMID:19430481)
  • Mutations in MKS3 are responsible for the majority of COACH syndrome, with minor contributions from CC2D2A and RPGRIP1L. (PMID:19574260)
  • CSPP isoforms require their common C-terminal domain to interact with Nephrocystin 8 (NPHP8/RPGRIP1L) and to form a ternary complex with NPHP8 and NPHP4. (PMID:20519441)
  • Insulin was identified as a key factor regulating FTM expression during human preadipocyte differentiation. (PMID:20865646)
  • Nek4 interaction with both RPGRIP1 and the RPGRIP1L is involved in cilium assembly. (PMID:21685204)
  • Data show that the minor allele (N) of I393N in IQCB1 and the common allele (R) of R744Q in RPGRIP1L were associated with severe disease in XlRP with RPGR mutations. (PMID:21857984)
  • Genetic variation may affect severity of disease for X-linked retinitis pigmentosa. (PMID:22183348)
  • First evidence of the association between RPGRIP1L gene and susceptibility of Vascular Dementia. (PMID:22425971)
  • All Spanish families with Alstrom syndrome were homozygous for 229A allele of RPGRIP1L, with the exception of a p.A229T heterozygous patient. (PMID:22876109)
  • KIAA1005 (rs3213758)is associated with single nucleotide polymorphisms in Korean patients, either non-segmental or segmental type. (PMID:23678272)
  • Importantly, one Japanese and one Omani families carried compound biallelic mutations in two distinct genes (TMEM67/RPGRIP1L and TMEM138/BBS1, respectively). (PMID:27434533)
  • our studies revealed RPGRIP1L as a novel MyoVa-binding protein - the first to be demonstrated to interact with MyoVa at the centrosome - and uncover an unprecedented link between MyoVa and ciliogenesis, providing new perspectives for studies aiming to better understand why defects in MyoVa cause neurological disorders in Griscelli syndrome patients. (PMID:28266547)
  • Loss of Rpgrip1l expression is associated with Ciliopathy. (PMID:29650680)
  • we didn’t found the significant association between RPGRIP1L and BMI in Chinese women (PMID:29657248)
  • T allele in RPGRIP1L gene might increase the risk of vitiligo in a Chinese Han population. (PMID:30539925)
  • it might be reasonable to consider RPGRIP1L as an important gene whose variations could be associated with obesity risk factors. (PMID:30597647)
  • Biotinylation assays on cell surface proteins not only reinforced the role of RPGRIP1L in desmoglein endocytosis, but also suggested that RPGRIP1L may be more broadly involved in endocytosis. Thus, data obtained from this study advanced our understanding of the biological functions of RPGRIP1L by identifying its role in the cellular endocytic pathway. (PMID:30689641)
  • Rpgrip1l controls ciliary gating by ensuring the proper amount of Cep290 at the vertebrate transition zone. (PMID:33625872)
  • The Major Ciliary Isoforms of RPGR Build Different Interaction Complexes with INPP5E and RPGRIP1L. (PMID:33808286)
  • Identification of Pathogenic Variants in RPGRIP1L with Meckel Syndrome and Preimplantation Genetic Testing in a Chinese Family. (PMID:35233738)

Cross-species orthologs

5 orthologs

OrganismSymbolGene ID
danio_reriorpgrip1lENSDARG00000051754
mus_musculusRpgrip1lENSMUSG00000033282
rattus_norvegicusRpgrip1lENSRNOG00000011829
caenorhabditis_elegansWBGENE00007490
caenorhabditis_elegansWBGENE00206538

Paralogs (1): RPGRIP1 (ENSG00000092200)

Protein

Protein identifiers

Protein fantomQ68CZ1 (reviewed: Q68CZ1)

Alternative names: Nephrocystin-8, RPGR-interacting protein 1-like protein

All UniProt accessions (10): Q68CZ1, A0A087WX34, A0A7P0TB06, H3BPF5, H3BPS4, H3BS47, H3BV03, I3L1B5, I3L2P2, J3QLR9

UniProt curated annotations — full annotation on UniProt →

Function. Negatively regulates signaling through the G-protein coupled thromboxane A2 receptor (TBXA2R). May be involved in mechanisms like programmed cell death, craniofacial development, patterning of the limbs, and formation of the left-right axis. Involved in the organization of apical junctions; the function is proposed to implicate a NPHP1-4-8 module. Does not seem to be strictly required for ciliogenesis. Involved in establishment of planar cell polarity such as in cochlear sensory epithelium and is proposed to implicate stabilization of disheveled proteins. Involved in regulation of proteasomal activity at the primary cilium probably implicating association with PSDM2.

Subunit / interactions. Interacts with NPHP4 and NPHP1; NPHP1, NPHP4 and RPGRIP1L are proposed to form a functional NPHP1-4-8 module localized to cell-cell contacts and the ciliary transition zone; NPHP4 mediates the interaction between NPHP1 and RPGRIP1L. Interacts with IQCB1; the interaction likely requires additional interactors. Interacts with TBXA2R (via C-terminus). Interacts with RPGR. Interacts with NEK4. Interacts with NPHP4, INVS and DVL2; the complex is proposed to be involved in DVL2 stabilization.

Subcellular location. Cytoplasm. Cytoskeleton. Cilium basal body. Cilium axoneme. Microtubule organizing center. Centrosome. Cell junction. Tight junction.

Tissue specificity. Ubiquitously expressed with relatively high level of expression in hypothalamus and islet. During early development, expressed in multiple organs including brain, eye, forelimb and kidney.

Disease relevance. Ciliary dysfunction leads to a broad spectrum of disorders, collectively termed ciliopathies. Overlapping clinical features include retinal degeneration, renal cystic disease, skeletal abnormalities, fibrosis of various organ, and a complex range of anatomical and functional defects of the central and peripheral nervous system. The ciliopathy range of diseases includes Meckel-Gruber syndrome, Bardet-Biedl syndrome, Joubert syndrome, nephronophtisis, Senior-Loken syndrome, and Jeune asphyxiating thoracic dystrophy among others. Single-locus allelism is insufficient to explain the variable penetrance and expressivity of such disorders, leading to the suggestion that variations across multiple sites of the ciliary proteome, including RPGRIP1L, influence the clinical outcome. Joubert syndrome 7 (JBTS7) [MIM:611560] A disorder presenting with cerebellar ataxia, oculomotor apraxia, hypotonia, neonatal breathing abnormalities and psychomotor delay. Neuroradiologically, it is characterized by cerebellar vermian hypoplasia/aplasia, thickened and reoriented superior cerebellar peduncles, and an abnormally large interpeduncular fossa, giving the appearance of a molar tooth on transaxial slices (molar tooth sign). Additional variable features include retinal dystrophy and renal disease. The disease is caused by variants affecting the gene represented in this entry. Meckel syndrome 5 (MKS5) [MIM:611561] A disorder characterized by a combination of renal cysts and variably associated features including developmental anomalies of the central nervous system (typically encephalocele), hepatic ductal dysplasia and cysts, and polydactyly. The disease is caused by variants affecting the gene represented in this entry. COACH syndrome 3 (COACH3) [MIM:619113] A form of COACH syndrome, a disorder characterized by cerebellar vermis hypoplasia, developmental delay, impaired intellectual development, ataxia, and hepatic fibrosis. Patients present the molar tooth sign, a midbrain-hindbrain malformation pathognomonic for Joubert syndrome and related disorders. Other features, such as coloboma and renal cysts, may be variable. COACH3 inheritance is autosomal recessive. The disease is caused by variants affecting the gene represented in this entry.

Similarity. Belongs to the RPGRIP1 family.

Isoforms (2)

UniProt IDNamesCanonical?
Q68CZ1-11yes
Q68CZ1-22

RefSeq proteins (6): NP_001121369, NP_001295263, NP_001315351, NP_001315352, NP_001317467, NP_056087* (*=MANE)

Domains & families (InterPro)

IDNameType
IPR000008C2_domDomain
IPR021656C2-C2_1Domain
IPR031139RPGRIP1_famFamily
IPR035892C2_domain_sfHomologous_superfamily
IPR041091RPGRIP1_CDomain

Pfam: PF00168, PF11618, PF18111

UniProt features (47 total): sequence variant 19, strand 9, sequence conflict 5, helix 3, coiled-coil region 3, domain 2, splice variant 2, compositionally biased region 2, chain 1, region of interest 1

Structure

Experimental structures (PDB)

1 structures.

PDBMethodResolution (Å)
2YRBSOLUTION NMR

Predicted structure (AlphaFold)

ModelpLDDTFraction very-high
AF-Q68CZ1-F171.020.29

Function

Pathways and Gene Ontology

Reactome pathways

2 pathways

IDPathway
R-HSA-5610787Hedgehog ‘off’ state
R-HSA-5620912Anchoring of the basal body to the plasma membrane

MSigDB gene sets: 493 (showing top): GOBP_MORPHOGENESIS_OF_AN_EPITHELIUM, GOBP_HINDBRAIN_DEVELOPMENT, GOBP_HEPATICOBILIARY_SYSTEM_DEVELOPMENT, GOBP_EMBRYO_DEVELOPMENT_ENDING_IN_BIRTH_OR_EGG_HATCHING, AAGCAAT_MIR137, GOBP_EPITHELIUM_DEVELOPMENT, GOBP_METENCEPHALON_DEVELOPMENT, GOBP_ESTABLISHMENT_OR_MAINTENANCE_OF_CELL_POLARITY, GOBP_HINDLIMB_MORPHOGENESIS, GOBP_PROTEIN_LOCALIZATION_TO_CILIUM, GOBP_NEUROGENESIS, GOBP_NEURAL_TUBE_DEVELOPMENT, GOBP_NEURAL_RETINA_DEVELOPMENT, GOBP_FORELIMB_MORPHOGENESIS, GOBP_VENTRICULAR_SYSTEM_DEVELOPMENT

GO Biological Process (27): in utero embryonic development (GO:0001701), establishment of planar polarity (GO:0001736), kidney development (GO:0001822), liver development (GO:0001889), establishment or maintenance of cell polarity (GO:0007163), determination of left/right symmetry (GO:0007368), regulation of smoothened signaling pathway (GO:0008589), neural tube patterning (GO:0021532), cerebellum development (GO:0021549), lateral ventricle development (GO:0021670), olfactory bulb development (GO:0021772), corpus callosum development (GO:0022038), embryonic forelimb morphogenesis (GO:0035115), embryonic hindlimb morphogenesis (GO:0035116), nose development (GO:0043584), negative regulation of G protein-coupled receptor signaling pathway (GO:0045744), retinal rod cell development (GO:0046548), pericardium development (GO:0060039), cochlea development (GO:0090102), non-motile cilium assembly (GO:1905515), brain development (GO:0007420), regulation of signal transduction (GO:0009966), telencephalon development (GO:0021537), limb morphogenesis (GO:0035108), camera-type eye development (GO:0043010), cilium assembly (GO:0060271), head development (GO:0060322)

GO Molecular Function (2): thromboxane A2 receptor binding (GO:0031870), protein binding (GO:0005515)

GO Cellular Component (15): cytoplasm (GO:0005737), centrosome (GO:0005813), cytosol (GO:0005829), plasma membrane (GO:0005886), cell-cell junction (GO:0005911), bicellular tight junction (GO:0005923), cilium (GO:0005929), axoneme (GO:0005930), nuclear speck (GO:0016607), photoreceptor connecting cilium (GO:0032391), ciliary transition zone (GO:0035869), ciliary basal body (GO:0036064), cytoskeleton (GO:0005856), cell projection (GO:0042995), anchoring junction (GO:0070161)

Reactome top-level categories

Rollup of top-2 pathways:

CategoryPathways
Signaling by Hedgehog1
Assembly of the 9+0 primary cilium1

GO top-level categories

Rollup of top GO terms by namespace:

CategoryTerms
anatomical structure development5
cellular anatomical structure5
telencephalon development2
embryonic limb morphogenesis2
microtubule organizing center2
cilium2
chordate embryonic development1
morphogenesis of a polarized epithelium1
establishment of tissue polarity1
animal organ development1
renal system development1
gland development1
hepaticobiliary system development1
cellular process1
determination of bilateral symmetry1
left/right pattern formation1
smoothened signaling pathway1
regulation of signal transduction1
regionalization1
neural tube development1
metencephalon development1
ventricular system development1
olfactory lobe development1
forelimb morphogenesis1
hindlimb morphogenesis1
sensory organ development1
respiratory system development1
G protein-coupled receptor signaling pathway1
regulation of G protein-coupled receptor signaling pathway1
negative regulation of signal transduction1
eye photoreceptor cell development1
retinal rod cell differentiation1
heart development1
epithelium development1
inner ear development1
cilium assembly1
prostanoid receptor binding1
binding1
intracellular anatomical structure1
centriole1

Protein interactions and networks

STRING

1720 interactions, top by confidence (×1000):

Protein AProtein BPartner UniProtScore
RPGRIP1LNPHP4O75161998
RPGRIP1LNPHP1O15259993
RPGRIP1LCEP290O15078977
RPGRIP1LTMEM67Q5HYA8970
RPGRIP1LCC2D2AQ9P2K1969
RPGRIP1LTMEM216Q9P0N5957
RPGRIP1LRPGRQ92834943
RPGRIP1LNPHP3Q7Z494940
RPGRIP1LAHI1Q8N157939
RPGRIP1LPSMD2Q13200916
RPGRIP1LARL13BQ3SXY8899
RPGRIP1LMKS1Q9NXB0892
RPGRIP1LTMEM231Q9H6L2879
RPGRIP1LB9D1Q9UPM9868
RPGRIP1LTMEM237Q96Q45866

IntAct

68 interactions, top by confidence:

ABTypeScore
NPHP1NPHP4psi-mi:“MI:2364”(proximity)0.930
NPHP1NPHP4psi-mi:“MI:0914”(association)0.930
RPGRIP1LNPHP4psi-mi:“MI:0915”(physical association)0.760
RPGRNPHP4psi-mi:“MI:2364”(proximity)0.730
RPGRNPHP1psi-mi:“MI:0914”(association)0.560
RpgrRPGRIP1Lpsi-mi:“MI:0915”(physical association)0.510
RPGRIP1LRpgrpsi-mi:“MI:0915”(physical association)0.510
RPGRIP1LPPP1CApsi-mi:“MI:0407”(direct interaction)0.440
PCM1CEP162psi-mi:“MI:0914”(association)0.420
RPGRIP1LCCP110psi-mi:“MI:0914”(association)0.420
CEP162CCP110psi-mi:“MI:2364”(proximity)0.420
RPGRIP1LLAS1Lpsi-mi:“MI:0915”(physical association)0.400
RPGRIP1LKIF2Apsi-mi:“MI:0914”(association)0.350
SPATA7CFAP410psi-mi:“MI:0914”(association)0.350
NEK4E2F8psi-mi:“MI:0914”(association)0.350
NEK4QSOX1psi-mi:“MI:0914”(association)0.350
RPGRNPHP1psi-mi:“MI:0914”(association)0.350
ZSCAN29GSDMEpsi-mi:“MI:0914”(association)0.350
Mpsi-mi:“MI:0914”(association)0.350
FTLSH3PXD2Bpsi-mi:“MI:0914”(association)0.350
PNMA2TARS3psi-mi:“MI:0914”(association)0.350
TRIM52MEIOCpsi-mi:“MI:0914”(association)0.350
INSYN1CCDC85Cpsi-mi:“MI:0914”(association)0.350
WHAMMP3EXOC5psi-mi:“MI:0914”(association)0.350
SPMAP2PRICKLE3psi-mi:“MI:0914”(association)0.350
WHAMMP3CCDC22psi-mi:“MI:0914”(association)0.350
TTC8psi-mi:“MI:0914”(association)0.350

BioGRID (239): RPGRIP1L (Affinity Capture-RNA), RPGRIP1L (Affinity Capture-RNA), RPGRIP1L (Affinity Capture-Western), CCP110 (Affinity Capture-Western), CEP170 (Affinity Capture-Western), CEP192 (Affinity Capture-Western), KIAA0753 (Affinity Capture-Western), OFD1 (Affinity Capture-Western), PCM1 (Affinity Capture-Western), PCNT (Affinity Capture-MS), CSPP1 (Affinity Capture-MS), MPRIP (Affinity Capture-MS), PCM1 (Affinity Capture-MS), CEP170B (Affinity Capture-MS), IPO7 (Affinity Capture-MS)

ESM2 similar proteins: A0JN62, A2RT67, A2RUS2, A2VDU2, A4IFB6, A4IIM3, A7MBL8, B1H2P5, B4F779, O94967, P48553, Q08CL8, Q0VEJ0, Q14161, Q15650, Q3TLI0, Q4R350, Q5RAQ5, Q5RCP7, Q5RDV5, Q5TKA1, Q5XIA4, Q5ZIW2, Q5ZJK1, Q68CZ1, Q6AYF1, Q6QD73, Q7TSG1, Q7ZYH1, Q8BH15, Q8BIK4, Q8BKH7, Q8C735, Q8CG73, Q8CGF6, Q8IWR0, Q8IZQ1, Q8N6S4, Q8N960, Q8NEU8

Diamond homologs: A0A096LPI5, A6NIU2, A6NJG6, F2Z398, P0DTE4, P51957, Q09FC8, Q5H9K5, Q5T7P6, Q68CZ1, Q6B4Z3, Q6UX73, Q86U02, Q8IV13, Q8N7M2, Q8N9N2, Q8NDZ0, Q8NEM8, Q8TDM0, Q92918, Q96J02, Q96MD7, Q9BUA6, Q9NXG0, Q8N2A0, A7MB40, P78312, Q8CGI1, A2RRD8, A6NHJ4, P0CJ79, P17035, P51522, Q08AN1, Q0VGE8, Q3MIS6, Q5HY98, Q5R8X1, Q5RER9, Q5VIY5

SIGNOR signaling

2 interactions.

AEffectBMechanism
RPGRIP1Ldown-regulatesRELAdemethylation
RPGRIP1Ldown-regulatesNfKb-p65/p50demethylation

Enriched among interaction partners

Reactome pathways and GO biological processes over-represented among this gene’s 61 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:

PathwayPartnersFoldFDR
Anchoring of the basal body to the plasma membrane1035.3×3e-11
Loss of Nlp from mitotic centrosomes734.7×8e-08
Loss of proteins required for interphase microtubule organization from the centrosome734.7×8e-08
AURKA Activation by TPX2733.3×8e-08
Recruitment of mitotic centrosome proteins and complexes729.7×1e-07
Regulation of PLK1 Activity at G2/M Transition727.8×2e-07
Recruitment of NuMA to mitotic centrosomes725.5×3e-07
Amplification of signal from unattached kinetochores via a MAD2 inhibitory signal518.2×2e-04

GO biological processes:

GO termPartnersFoldFDR
cilium assembly79.5×3e-03

Disease & clinical

Clinical variants and AI predictions

ClinVar

2164 variants total. Per-class counts are floors (≥ shown; pagination cap):

ClassificationCount (floor)
Pathogenic159
Likely pathogenic132
Uncertain significance800
Likely benign824
Benign50

Top pathogenic / likely-pathogenic (30)

Variant IDHGVSClassification
1032670NM_015272.5(RPGRIP1L):c.2581_2582insG (p.Leu861fs)Pathogenic
1066451NC_000016.9:g.(?53639383)(53698931_?)delPathogenic
1068NM_015272.5(RPGRIP1L):c.697A>T (p.Lys233Ter)Pathogenic
1068465NM_015272.5(RPGRIP1L):c.676G>T (p.Glu226Ter)Pathogenic
1068561NM_015272.5(RPGRIP1L):c.2711del (p.Lys904fs)Pathogenic
1068738NM_015272.5(RPGRIP1L):c.2582dup (p.Ser862fs)Pathogenic
1069NM_015272.5(RPGRIP1L):c.1843A>C (p.Thr615Pro)Pathogenic
1069111NM_015272.5(RPGRIP1L):c.663_664dup (p.Ile222fs)Pathogenic
1069496NM_015272.5(RPGRIP1L):c.496G>T (p.Glu166Ter)Pathogenic
1070NM_015272.5(RPGRIP1L):c.757C>T (p.Gln253Ter)Pathogenic
1070007NM_015272.5(RPGRIP1L):c.1225A>T (p.Arg409Ter)Pathogenic
1070105NM_015272.5(RPGRIP1L):c.1252G>T (p.Glu418Ter)Pathogenic
1071499NM_015272.5(RPGRIP1L):c.2397C>A (p.Cys799Ter)Pathogenic
1072NM_015272.5(RPGRIP1L):c.394A>T (p.Arg132Ter)Pathogenic
1072338NM_015272.5(RPGRIP1L):c.1920dup (p.Glu641Ter)Pathogenic
1073NM_015272.5(RPGRIP1L):c.1033C>T (p.Gln345Ter)Pathogenic
1073461NM_015272.5(RPGRIP1L):c.149del (p.Leu50fs)Pathogenic
1074159NM_015272.5(RPGRIP1L):c.421C>T (p.Gln141Ter)Pathogenic
1075586NM_015272.5(RPGRIP1L):c.528del (p.Gly177fs)Pathogenic
1076236NC_000016.9:g.(?53729213)(53730217_?)delPathogenic
1076237NC_000016.9:g.(?53652917)(53656288_?)delPathogenic
1076238NC_000016.9:g.(?53720335)(53721887_?)delPathogenic
1077NM_015272.5(RPGRIP1L):c.2269del (p.Thr757fs)Pathogenic
1080NM_015272.5(RPGRIP1L):c.1975T>C (p.Ser659Pro)Pathogenic
1185042NM_015272.5(RPGRIP1L):c.427C>T (p.Gln143Ter)Pathogenic
1323533NM_015272.5(RPGRIP1L):c.3545del (p.Pro1182fs)Pathogenic
1323535NM_015272.5(RPGRIP1L):c.2921del (p.Lys974fs)Pathogenic
1370102NC_000016.9:g.(?53698772)(53734645_?)delPathogenic
1384547NM_015272.5(RPGRIP1L):c.988C>T (p.Gln330Ter)Pathogenic
1391379NM_015272.5(RPGRIP1L):c.3605_3608del (p.Asn1202fs)Pathogenic

SpliceAI

4756 predictions. Top by Δscore:

VariantEffectΔscore
16:53602040:A:ACdonor_gain1.0000
16:53602041:C:CCdonor_gain1.0000
16:53602189:C:CCacceptor_gain1.0000
16:53605513:T:Adonor_gain1.0000
16:53605610:GAAGG:Gacceptor_gain1.0000
16:53605612:AGG:Aacceptor_gain1.0000
16:53605613:GG:Gacceptor_gain1.0000
16:53605614:GC:Gacceptor_loss1.0000
16:53605615:C:CAacceptor_loss1.0000
16:53605615:C:CCacceptor_gain1.0000
16:53619023:A:ACdonor_gain1.0000
16:53619023:A:Tdonor_loss1.0000
16:53619023:AC:Adonor_gain1.0000
16:53619024:C:CCdonor_gain1.0000
16:53619024:CC:Cdonor_gain1.0000
16:53619024:CCA:Cdonor_gain1.0000
16:53619024:CCATT:Cdonor_gain1.0000
16:53619204:GATGG:Gacceptor_gain1.0000
16:53619205:ATGG:Aacceptor_gain1.0000
16:53619206:TGG:Tacceptor_gain1.0000
16:53619207:GG:Gacceptor_gain1.0000
16:53619208:GC:Gacceptor_loss1.0000
16:53619208:GCTGT:Gacceptor_gain1.0000
16:53619209:C:CCacceptor_gain1.0000
16:53619211:G:Cacceptor_gain1.0000
16:53619212:T:TCacceptor_gain1.0000
16:53619213:T:Cacceptor_gain1.0000
16:53619213:T:TCacceptor_gain1.0000
16:53619221:C:CTacceptor_gain1.0000
16:53619222:A:Tacceptor_gain1.0000

AlphaMissense

8773 scored. Top likely-pathogenic:

VariantProtein changeam_pathogenicity
16:53641413:A:GW916R0.999
16:53641413:A:TW916R0.999
16:53657487:A:GL516P0.998
16:53657508:A:GL509P0.998
16:53692341:A:GL85P0.998
16:53645741:A:GL856P0.997
16:53692344:C:GR84P0.997
16:53692360:C:GA79P0.997
16:53605606:A:GF1237S0.996
16:53641411:C:AW916C0.996
16:53641411:C:GW916C0.996
16:53692251:A:GL115P0.996
16:53602149:A:GL1292P0.995
16:53619126:A:GL1172P0.995
16:53619174:A:GL1156P0.995
16:53645714:A:TV865D0.995
16:53692350:A:GL82S0.995
16:53641412:C:GW916S0.994
16:53652969:G:TA573D0.994
16:53657527:C:GA503P0.994
16:53692230:A:GL122P0.994
16:53619122:A:CF1173L0.993
16:53619122:A:TF1173L0.993
16:53619124:A:GF1173L0.993
16:53645864:A:TV815D0.993
16:53645933:A:GL792P0.993
16:53664938:A:GL392P0.993
16:53671549:C:GR355P0.993
16:53692352:C:AK81N0.993
16:53692352:C:GK81N0.993

dbSNP variants (sampled 300 via entrez): RS1000004866 (16:53702021 T>C), RS1000015985 (16:53659580 G>A,T), RS1000048595 (16:53655919 A>G), RS1000075018 (16:53700486 A>C), RS1000078215 (16:53610087 A>G), RS1000174022 (16:53694765 G>A,C), RS1000227750 (16:53694563 C>T), RS1000233828 (16:53647137 A>G,T), RS1000247094 (16:53671032 G>A), RS1000282366 (16:53650435 T>A), RS1000324090 (16:53644430 A>G), RS1000332868 (16:53636356 T>G), RS1000347369 (16:53671269 T>C,G), RS1000362900 (16:53624911 G>A), RS1000389519 (16:53644128 A>C)

Disease associations

OMIM: gene MIM:610937 | disease phenotypes: MIM:213300, MIM:249000, MIM:611560, MIM:611561, MIM:619113, MIM:216360, MIM:256100, MIM:209900, MIM:204000

GenCC curated gene-disease

DiseaseClassificationInheritance
Meckel syndrome, type 5DefinitiveAutosomal recessive
Joubert syndrome 7StrongAutosomal recessive
ciliopathyStrongAutosomal recessive
COACH syndrome 1SupportiveAutosomal recessive
Joubert syndrome with renal defectSupportiveAutosomal recessive
Meckel syndromeSupportiveAutosomal recessive

ClinGen Gene-Disease Validity (1)

Expert-panel classifications — Definitive > Strong > Moderate > Limited > Disputed > Refuted.

DiseaseClassificationInheritance
ciliopathyDefinitiveAR

Mondo (18): Joubert syndrome (MONDO:0018772), Meckel syndrome (MONDO:0018921), Joubert syndrome 7 (MONDO:0012694), Meckel syndrome, type 5 (MONDO:0012695), COACH syndrome 3 (MONDO:0030862), COACH syndrome 1 (MONDO:0800103), Joubert syndrome and related disorders (MONDO:0015369), nephronophthisis (MONDO:0019005), focal segmental glomerulosclerosis (MONDO:0100313), kidney disorder (MONDO:0005240), optic atrophy (MONDO:0003608), Bardet-Biedl syndrome (MONDO:0015229), Leber congenital amaurosis (MONDO:0018998), inherited retinal dystrophy (MONDO:0019118), ciliopathy (MONDO:0005308)

Orphanet (10): Isolated Joubert syndrome (Orphanet:475), Meckel syndrome (Orphanet:564), Joubert syndrome with renal defect (Orphanet:220497), Joubert syndrome with hepatic defect (Orphanet:1454), Joubert syndrome and related disorders (Orphanet:140874), Nephronophthisis (Orphanet:655), Bardet-Biedl syndrome (Orphanet:110), Leber congenital amaurosis (Orphanet:65), OBSOLETE: Inherited retinal disorder (Orphanet:71862), Ciliopathy (Orphanet:363250)

HPO phenotypes

121 total (30 of 121 shown, HPO-id order):

HPOTerm
HP:0000003Multicystic kidney dysplasia
HP:0000007Autosomal recessive inheritance
HP:0000023Inguinal hernia
HP:0000028Cryptorchidism
HP:0000037Male pseudohermaphroditism
HP:0000062Ambiguous genitalia
HP:0000068Urethral atresia
HP:0000073Ureteral duplication
HP:0000083Renal insufficiency
HP:0000090Nephronophthisis
HP:0000092Renal tubular atrophy
HP:0000107Renal cyst
HP:0000112Nephropathy
HP:0000175Cleft palate
HP:0000202Orofacial cleft
HP:0000204Cleft upper lip
HP:0000221Furrowed tongue
HP:0000238Hydrocephalus
HP:0000252Microcephaly
HP:0000256Macrocephaly
HP:0000276Long face
HP:0000293Full cheeks
HP:0000316Hypertelorism
HP:0000340Sloping forehead
HP:0000347Micrognathia
HP:0000358Posteriorly rotated ears
HP:0000369Low-set ears
HP:0000426Prominent nasal bridge
HP:0000457Depressed nasal ridge
HP:0000463Anteverted nares

GWAS associations

23 associations (top):

StudyTraitp-value
GCST000961_23Bipolar disorder2.000000e-06
GCST001992_1Vitiligo (non-segmental)6.000000e-11
GCST003476_1Eyebrow thickness3.000000e-06
GCST004766_20Triglyceride change in response to fenofibrate in statin-treated type 2 diabetes2.000000e-07
GCST006190_40Diastolic blood pressure x smoking status (ever vs never) interaction (2df test)2.000000e-10
GCST006190_66Diastolic blood pressure x smoking status (ever vs never) interaction (2df test)4.000000e-08
GCST006192_13Systolic blood pressure x smoking status (ever vs never) interaction (2df test)4.000000e-20
GCST006192_27Systolic blood pressure x smoking status (ever vs never) interaction (2df test)1.000000e-13
GCST006193_23Diastolic blood pressure x smoking status (current vs non-current) interaction (2df test)3.000000e-11
GCST006193_64Diastolic blood pressure x smoking status (current vs non-current) interaction (2df test)6.000000e-09
GCST006195_5Systolic blood pressure x smoking status (current vs non-current) interaction (2df test)6.000000e-14
GCST006195_53Systolic blood pressure x smoking status (current vs non-current) interaction (2df test)1.000000e-20
GCST008129_87Body mass index5.000000e-11
GCST008152_151Weight6.000000e-06
GCST008369_24Plasma anti-thyroglobulin levels5.000000e-06
GCST009371_9Bipolar disorder or body mass index6.000000e-09
GCST009464_2Facial morphology7.000000e-09
GCST009464_21Facial morphology4.000000e-08
GCST009464_3Facial morphology3.000000e-09
GCST90011900_125Serum alkaline phosphatase levels8.000000e-11
GCST90016670_7Kidney volume2.000000e-09
GCST90016671_5Visceral adipose tissue volume3.000000e-08
GCST90016672_1Abdominal subcutaneous adipose tissue volume2.000000e-21

EFO canonical traits (7, from GWAS)

EFO IDTrait name
EFO:0007681triglyceride change measurement
EFO:0006336diastolic blood pressure
EFO:0006527smoking status measurement
EFO:0006335systolic blood pressure
EFO:0004340body mass index
EFO:0004338body weight
EFO:0004533alkaline phosphatase measurement

MeSH disease descriptors (10)

DescriptorNameTree numbers
D020788Bardet-Biedl SyndromeC10.228.140.617.200; C11.270.684.624; C16.131.077.245.125; C16.320.184.125
D005923Glomerulosclerosis, Focal SegmentalC12.050.351.968.419.570.363.640; C12.200.777.419.570.363.660; C12.950.419.570.363.640
D007674Kidney DiseasesC12.050.351.968.419; C12.200.777.419; C12.950.419
D057130Leber Congenital AmaurosisC11.270.516; C11.768.364
D008831MicrocephalyC05.660.207.620; C10.500.507.400.500; C16.131.621.207.620; C16.131.666.507.400.500
D009896Optic AtrophyC10.292.700.225; C11.640.451
D058499Retinal DystrophiesC11.768.585.658
C566916Joubert Syndrome 7 (supp.)
C536296Joubert syndrome 4 (supp.)
C566915Meckel Syndrome, Type 5 (supp.)

Drugs & pharmacology

Drug and pharmacology data

Is drug target: no

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

CTD chemical–gene interactions

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

ChemicalActions (top 5)PubMed papers
Benzo(a)pyreneaffects methylation, decreases expression3
Air Pollutantsaffects cotreatment, increases abundance, increases expression2
Tetrachlorodibenzodioxindecreases expression2
Tobacco Smoke Pollutiondecreases expression, increases expression2
Valproic Acidaffects expression, decreases expression2
Cyclosporineaffects expression, decreases expression2
Aflatoxin B1affects expression, decreases methylation2
aristolochic acid Idecreases expression1
methylmercuric chloridedecreases expression1
triphenyl phosphateaffects expression1
alpha-pineneaffects cotreatment, increases expression, increases abundance1
bisphenol Adecreases methylation1
beta-lapachoneincreases expression1
sodium arsenitedecreases expression1
butyraldehydedecreases expression1
potassium chromate(VI)affects cotreatment, decreases expression1
aflatoxin B2increases methylation1
methacrylaldehydeaffects cotreatment, increases expression, increases abundance1
epigallocatechin gallateaffects cotreatment, decreases expression1
abrinedecreases expression1
Resveratrolaffects cotreatment, increases expression1
Sunitinibincreases expression1
Acroleinaffects cotreatment, increases expression, increases abundance1
Doxorubicindecreases expression1
Latexdecreases expression1
Methyl Methanesulfonateincreases expression1
Ouabaindecreases expression1
Ozoneincreases expression, increases abundance, affects cotreatment1
Plant Extractsaffects cotreatment, increases expression1
Quercetinincreases expression1

Clinical trials (associated diseases)

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

TrialPhaseStatusTitle
NCT01129557PHASE4TERMINATEDAldosterone Breakthrough During Diovan, Tekturna, and Combination Therapy in Patients With Proteinuric Kidney Disease
NCT02399462PHASE4WITHDRAWNActhar for Treatment of Post-transplant FSGS
NCT02585804PHASE4COMPLETEDTreating to Reduce Albuminuria and Normalize Hemodynamic Function in Focal ScLerosis With dApagliflozin Trial Effects
NCT02633046PHASE4COMPLETEDActhar for Treatment-Resistant or Treatment-Intolerant Proteinuria
NCT07219121PHASE4RECRUITINGSparsentan in Posttransplant Immunoglobulin A Nephropathy or Focal Segmental Glomerulosclerosis
NCT00067990PHASE4COMPLETEDAngiotensin II Blockade for Chronic Allograft Nephropathy
NCT00117078PHASE4COMPLETEDAranesp® Monthly Preference Study - 2
NCT00117130PHASE4COMPLETEDStudy to Evaluate Effectiveness of Aranesp®
NCT00132431PHASE4COMPLETEDSTART: Sensipar Treatment Algorithm to Reach K/DOQI Targets in Chronic Kidney Disease Subjects With Secondary Hyperparathyroidism
NCT00140985PHASE4COMPLETEDAntiproteinuric Efficacy of Losartan Potassium in Patients With Non-Diabetic Proteinuric Renal Diseases (0954-213)
NCT00246129PHASE4COMPLETEDCamTac Trial:Campath-Tacrolimus vs IL2R MoAb/Tacrolimus/MMF in Renal Transplantation
NCT00275535PHASE4COMPLETEDThe Comparison of Tacrolimus and Sirolimus Immunosuppression Based Drug Regimens in Kidney Transplant Recipients
NCT00282217PHASE4COMPLETEDStudy Evaluating Sirolimus in the Treatment of Kidney Transplant
NCT00289614PHASE4COMPLETEDPatients With Renal Impairment and Diabetes Undergoing Computed Tomography (CT)
NCT00290069PHASE4UNKNOWNRenal Function Optimization With Mycophenolate Mofetil (MMF) Immunosuppressor Regimes (ALHAMBRA)
NCT00338468PHASE4TERMINATEDA Study to Assess Disability in Anemic Elderly Patients With Kidney Disease Receiving PROCRIT (Epoetin Alfa)
NCT00368901PHASE4COMPLETEDSTAAR-2 Clinical Study
NCT00369733PHASE4COMPLETEDSTAAR-3 Clinical Study
NCT00369772PHASE4COMPLETEDSTAAR-1 Clinical Study
NCT00379899PHASE4COMPLETEDADVANCE: Study to Evaluate Cinacalcet Plus Low Dose Vitamin D on Vascular Calcification in Subjects With Chronic Kidney Disease Receiving Hemodialysis
NCT00443508PHASE4UNKNOWNReduction or Discontinuation of CNI’s With Conversion to Everolimus-Based Immunosuppresion
NCT00452478PHASE4TERMINATEDConversion From Standard Phosphate Binder Therapy to Fosrenol® (Lanthanum Carbonate) in Chronic Kidney Disease Stage 5
NCT00492518PHASE4COMPLETEDAcetylcysteine, Theophylline, and a Combination of Both in the Prophylaxis of Contrast-Induced Nephropathy
NCT00505102PHASE4UNKNOWNSafe Renal Function In Long Term Heart Transplanted Patients
NCT00526331PHASE4COMPLETEDEvaluation of Arterial Pressure Based Cardiac Output for Goal-Directed Perioperative Therapy
NCT00688480PHASE4COMPLETEDDo Xanthine Oxidase Inhibitors Reduce Both Left Ventricular Hypertrophy and Endothelial Dysfunction in Cardiovascular Patients With Renal Dysfunction?
NCT00863707PHASE4COMPLETEDA Study of the Safety and Tolerance of Regadenoson in Subjects With Renal Impairment
NCT01101698PHASE4UNKNOWNVitamin K2 and Vessel Calcification in Chronic Kidney Disease Patients
NCT01150201PHASE4COMPLETEDAliskiren Combined With Losartan in Proteinuric, Non-diabetic Chronic Kidney Disease
NCT01155141PHASE4COMPLETEDIdiopathic Focal Segmental Glomerulosclerosis (FSGS) and Treatment With ACTH
NCT01228279PHASE4COMPLETEDSympathetic Activity in Patients With End-stage Renal Disease on Peritoneal Dialysis
NCT01334333PHASE4COMPLETEDComparison of Medication Adherence Between Once and Twice Daily Tacrolimus in Stable Renal Transplant Recipients
NCT01437943PHASE4TERMINATEDEffect of Short Term Aliskiren Treatment in Kidney Transplant Patients
NCT01545479PHASE4COMPLETEDIncreased Renal Oxygenation and Angiotensin Converting Enzyme Inhibition
NCT01614431PHASE4COMPLETEDN Acetyl Cysteine for Cystinosis Patients
NCT01631149PHASE4COMPLETEDEffect of Deep BLock on Intraoperative Surgical Conditions
NCT01722513PHASE4UNKNOWNEfficacy and Safety of Alprostadil Prevent Contrast Induced Nephropathy
NCT01985360PHASE4COMPLETEDISCHEMIA-Chronic Kidney Disease Trial
NCT02311010PHASE4UNKNOWNPractical Use of Advagraf de Novo After Kidney Transplantation According to Recipient Genetic Polymorphism
NCT02413073PHASE4COMPLETEDWhole Body Vibration in Kidney Disease