RILP

gene
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Also known as FLJ31193

Summary

RILP (Rab interacting lysosomal protein, HGNC:30266) is a protein-coding gene on chromosome 17p13.3, encoding Rab-interacting lysosomal protein (Q96NA2). Rab effector playing a role in late endocytic transport to degradative compartments.

This gene encodes a lysosomal protein that interacts with RAB7, a small GTPase that controls transport to endocytic degradative compartments. Studies using mutant forms of the two proteins suggest that this protein represents a downstream effector for RAB7, and both proteins act together in the regulation of late endocytic traffic. A unique region of this protein has also been shown to be involved in the regulation of lysosomal morphology.

Source: NCBI Gene 83547 — RefSeq curated summary.

At a glance

  • Clinical variants (ClinVar): 64 total
  • MANE Select transcript: NM_031430

Identifiers

Gene identifiers

FieldValue
HGNC IDHGNC:30266
Approved symbolRILP
NameRab interacting lysosomal protein
Location17p13.3
Locus typegene with protein product
StatusApproved
AliasesFLJ31193
Ensembl geneENSG00000167705
Ensembl biotypeprotein_coding
OMIM607848
Entrez83547

Gene structure

Transcript identifiers

Ensembl transcripts: 11 — 9 protein_coding, 2 retained_intron

ENST00000301336, ENST00000570858, ENST00000573398, ENST00000574810, ENST00000898468, ENST00000898469, ENST00000898470, ENST00000898471, ENST00000931214, ENST00000946792, ENST00000946793

RefSeq mRNA: 1 — MANE Select: NM_031430 NM_031430

CCDS: CCDS11009

Canonical transcript exons

ENST00000301336 — 8 exons

ExonStartEnd
ENSE0000119871016487991649044
ENSE0000119871316492001649306
ENSE0000119871716494121649505
ENSE0000130743316461501646619
ENSE0000131293316495771649866
ENSE0000359049516469061646989
ENSE0000359643216478351647957
ENSE0000369052116483501648495

Expression profiles

Bgee: expression breadth ubiquitous, 135 present calls, max score 97.87.

FANTOM5 (CAGE): breadth ubiquitous, TPM avg 8.6203 / max 143.3783, expressed in 1662 samples.

FANTOM5 promoters (9 alternative TSS)

Promoter IDTPM avgSamples expressed
1637593.65981349
1637631.5084371
1637601.0293598
1637670.6591247
1637640.5697195
1637610.5361232
1637620.4188176
1637660.148551
1637650.090445

Top tissues by expression

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

TissueAnatomy IDExpression scoreQuality
apex of heartUBERON:000209897.87gold quality
hindlimb stylopod muscleUBERON:000425295.02gold quality
heart left ventricleUBERON:000208494.83gold quality
right lobe of thyroid glandUBERON:000111993.36gold quality
gastrocnemiusUBERON:000138892.72gold quality
left lobe of thyroid glandUBERON:000112092.44gold quality
muscle of legUBERON:000138392.33gold quality
thyroid glandUBERON:000204692.00gold quality
bloodUBERON:000017891.69gold quality
right atrium auricular regionUBERON:000663191.67gold quality
heartUBERON:000094891.47gold quality
mucosa of transverse colonUBERON:000499191.30gold quality
skeletal muscle tissueUBERON:000113490.84gold quality
right lobe of liverUBERON:000111490.47gold quality
duodenumUBERON:000211490.18gold quality
right adrenal gland cortexUBERON:003582788.60gold quality
liverUBERON:000210788.33gold quality
muscle tissueUBERON:000238588.11gold quality
left adrenal gland cortexUBERON:003582588.06gold quality
right adrenal glandUBERON:000123387.95gold quality
transverse colonUBERON:000115787.58gold quality
left adrenal glandUBERON:000123487.50gold quality
right lungUBERON:000216787.00gold quality
subcutaneous adipose tissueUBERON:000219086.59gold quality
adipose tissueUBERON:000101386.56gold quality
omental fat padUBERON:001041486.53gold quality
monocyteCL:000057686.38gold quality
male germ line stem cell (sensu Vertebrata) in testisCL:0000089 ∩ UBERON:000047386.21gold quality
upper lobe of left lungUBERON:000895286.21gold quality
spleenUBERON:000210686.19gold quality

Single-cell (SCXA)

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

ExperimentMarker?Max mean expression
E-ANND-3yes12.03

Regulation

Is transcription factor: no

miRNA regulators (miRDB)

12 targeting RILP, 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-6758-5P100.0066.211470
HSA-MIR-6856-5P100.0065.471298
HSA-MIR-556-3P99.7468.751203
HSA-MIR-7112-5P99.5965.76104
HSA-MIR-223-5P99.2468.821206
HSA-MIR-6791-5P99.1665.921844
HSA-MIR-197297.6767.381172
HSA-MIR-490-5P96.7565.81661
HSA-MIR-6726-5P95.9763.72841
HSA-MIR-92095.9763.95811
HSA-MIR-430095.8564.561003
HSA-MIR-5591-5P95.8564.761002

Literature-anchored findings (GeneRIF, showing 20)

  • Unique region in RILP responsible for its specific role in regulating lysosomal morphology as well as in its interaction with Rab7 and Rab34. (PMID:14668488)
  • The crystal structure of Rab7-GTP in complex with the Rab7 binding domain of RILP reveals that Rab7 interacts with RILP specifically via two distinct areas. (PMID:15933719)
  • The data together indicate that RILP, as already demonstrated for several other Rab effector proteins, is capable of self-association, thus probably forming a homo-dimer. (PMID:15996637)
  • RILP indeed prenylated, while phosphorylation analysis showed that the two protein kinase A sites are phosphorylated. (PMID:16417580)
  • Hence, RILPsv provides an extra dimension to the control of vesicle fusion and transport by the small GTPase Rab7. (PMID:16631113)
  • we have isolated, using the yeast two-hybrid system, the EAP30/SNF8/VPS22 subunit of the ESCRT-II complex as a RILP interacting protein. (PMID:16857164)
  • These results establish that RILP is required for biogenesis of multivesicular endosomes and degradative trafficking of EGFRs but not for trafficking of transferrin receptors through early endosomes. (PMID:17959629)
  • REST/NRSF, dynactin p150(Glued), huntingtin, HAP1, and RILP form a complex involved in the translocation of REST/NRSF into the nucleus and HAP1 controls REST/NRSF cellular localization in neurons (PMID:18922795)
  • Results describe how ORP1L contacts VAP to control Rab7-RILP-p150 Glued and late endosome positioning. (PMID:19564404)
  • RILP directly and concomitantly binds the tethering HOPS complex and the p150(Glued) subunit of the dynein motor. ORP1L then functions as a cholesterol-sensing switch controlling RILP-HOPS-p150(Glued) interactions. (PMID:23729732)
  • RILP regulates the activity of the V-ATPase through its interaction with V1G1. (PMID:24762812)
  • VPS41 subunit of HOPS complex was defined to be the major partner for interacting with RILP. (PMID:25445562)
  • RILP regulates vacuolar ATPase through interaction with the V1G1 subunit (PMID:26180254)
  • RILP suppresses the invasion of breast cancer cells by interacting with RalGDS to inhibit its guanine nucleotide exchange factor activity for RalA. (PMID:26469971)
  • Hepatitis C virus (HCV) modifies cellular trafficking by cleaving Rab interacting lysosomal protein (RILP), which serves to redirect ras-related protein Rab-7 (Rab7)-containing vesicles to a kinesin-dependent trafficking mode promoting virion secretion. (PMID:27791088)
  • structural and biochemical investigation of the Rab7-ORP1L interaction revealed architecture that leaves the canonical effector-interacting switch regions available for RILP binding and thus allows formation of the ORP1L-Rab7-RILP tripartite complex. (PMID:30012887)
  • Caspase-1 regulates cellular trafficking via cleavage of the Rab7 adaptor protein RILP in cultured neoplastic epithelial cells has been reported. (PMID:30100068)
  • Methylation of RILP in lung cancer promotes tumor cell proliferation and invasion. (PMID:33128214)
  • RILP inhibits proliferation, migration, and invasion of PC3 prostate cancer cells. (PMID:35981451)
  • RILP Induces Cholesterol Accumulation in Lysosomes by Inhibiting Endoplasmic Reticulum-Endolysosome Interactions. (PMID:39195203)

Cross-species orthologs

5 orthologs

OrganismSymbolGene ID
danio_reriorilpENSDARG00000074660
mus_musculusRilpENSMUSG00000038195
rattus_norvegicusRilpENSRNOG00000003784
drosophila_melanogasterRilplFBGN0024985
caenorhabditis_elegansWBGENE00007860

Paralogs (4): DZIP1 (ENSG00000134874), RILPL2 (ENSG00000150977), DZIP1L (ENSG00000158163), RILPL1 (ENSG00000188026)

Protein

Protein identifiers

Rab-interacting lysosomal proteinQ96NA2 (reviewed: Q96NA2)

All UniProt accessions (2): Q96NA2, I3L1U0

UniProt curated annotations — full annotation on UniProt →

Function. Rab effector playing a role in late endocytic transport to degradative compartments. Involved in the regulation of lysosomal morphology and distribution. Induces recruitment of dynein-dynactin motor complexes to Rab7A-containing late endosome and lysosome compartments. Promotes centripetal migration of phagosomes and the fusion of phagosomes with the late endosomes and lysosomes.

Subunit / interactions. Homodimer. Interacts with RAB7A. Interacts with RAB34. Identified in a complex with MREG and DCTN1; interacts directly with MREG. Interacts with CLN3. Interacts with FLCN; the interaction is direct and promotes association between RILP and RAB34.

Subcellular location. Late endosome membrane. Lysosome membrane. Cytoplasmic vesicle. Phagosome membrane.

Tissue specificity. Ubiquitous. Strongly expressed in fetal heart, heart, stomach, spleen, adrenal gland, thyroid gland, salivary gland, fetal liver, liver and lung. Poorly expressed in brain.

Isoforms (2)

UniProt IDNamesCanonical?
Q96NA2-11yes
Q96NA2-22

RefSeq proteins (1): NP_113618* (*=MANE)

Domains & families (InterPro)

IDNameType
IPR021563RILP_dimerDomain
IPR034743RH1Domain
IPR034744RH2Domain
IPR051241DZIP_RILPLFamily

Pfam: PF09744, PF11461

UniProt features (27 total): mutagenesis site 8, modified residue 3, region of interest 3, domain 2, splice variant 2, sequence variant 2, helix 2, compositionally biased region 2, chain 1, sequence conflict 1, coiled-coil region 1

Structure

Experimental structures (PDB)

1 structures.

PDBMethodResolution (Å)
1YHNX-RAY DIFFRACTION3

Predicted structure (AlphaFold)

ModelpLDDTFraction very-high
AF-Q96NA2-F171.720.38

Functional residue map

Curated UniProt residues grouped by drug-discovery relevance — catalytic, ligand-binding, modification, and mutation-validated positions. Source: UniProtKB sequence features.

Post-translational modifications (3): 314, 315, 308

Mutagenesis-validated functional residues (8):

PositionPhenotype
248strongly reduces dimerization and localization to late endosomal/lysosomal compartments.
251abolishes dimerization, interaction with rab7a and localization to late endosomal/lysosomal compartments.
252abolishes interaction with rab7a and localization to late endosomal/lysosomal compartments.
255abolishes dimerization, interaction with rab7a and localization to late endosomal/lysosomal compartments.
258reduces dimerization, interaction with rab7a and localization to late endosomal/lysosomal compartments.
304abolishes interaction with rab7a and localization to late endosomal/lysosomal compartments.
305abolishes interaction with rab7a and localization to late endosomal/lysosomal compartments.
306abolishes interaction with rab7a and localization to late endosomal/lysosomal compartments.

Function

Pathways and Gene Ontology

Reactome pathways

1 pathways

IDPathway
R-HSA-2132295MHC class II antigen presentation

MSigDB gene sets: 108 (showing top): GSE18804_SPLEEN_MACROPHAGE_VS_COLON_TUMORAL_MACROPHAGE_DN, GOBP_LYSOSOMAL_TRANSPORT, GOBP_ENDOSOME_ORGANIZATION, REACTOME_ADAPTIVE_IMMUNE_SYSTEM, GOCC_VACUOLAR_MEMBRANE, GOBP_VESICLE_ORGANIZATION, GOBP_ENDOSOME_TO_LYSOSOME_TRANSPORT, GOBP_POSITIVE_REGULATION_OF_PROTEIN_CATABOLIC_PROCESS, GOBP_MACROMOLECULE_CATABOLIC_PROCESS, GOBP_VACUOLAR_TRANSPORT, TGACCTY_ERR1_Q2, GOBP_VESICLE_MEDIATED_TRANSPORT, GOMF_GTPASE_BINDING, GOBP_NEGATIVE_REGULATION_OF_PROTEIN_CATABOLIC_PROCESS, GOCC_MICROTUBULE_ORGANIZING_CENTER

GO Biological Process (8): endosome to lysosome transport (GO:0008333), protein transport (GO:0015031), endosome transport via multivesicular body sorting pathway (GO:0032509), negative regulation of protein catabolic process (GO:0042177), early endosome to late endosome transport (GO:0045022), positive regulation of protein catabolic process (GO:0045732), cilium assembly (GO:0060271), intralumenal vesicle formation (GO:0070676)

GO Molecular Function (4): small GTPase binding (GO:0031267), protein dimerization activity (GO:0046983), dynein light intermediate chain binding (GO:0051959), protein binding (GO:0005515)

GO Cellular Component (11): cytoplasm (GO:0005737), lysosome (GO:0005764), lysosomal membrane (GO:0005765), late endosome (GO:0005770), phagocytic vesicle membrane (GO:0030670), late endosome membrane (GO:0031902), protein-containing complex (GO:0032991), ciliary basal body (GO:0036064), endosome (GO:0005768), membrane (GO:0016020), cytoplasmic vesicle (GO:0031410)

Reactome top-level categories

Rollup of top-1 pathways:

CategoryPathways
Adaptive Immune System1

GO top-level categories

Rollup of top GO terms by namespace:

CategoryTerms
protein catabolic process2
regulation of protein catabolic process2
cytoplasm2
endosome membrane2
protein binding2
cellular anatomical structure2
lysosomal transport1
intercellular transport1
vesicle-mediated transport1
transport1
intracellular protein localization1
establishment of protein localization1
endosomal transport1
multivesicular body sorting pathway1
negative regulation of catabolic process1
negative regulation of protein metabolic process1
vesicle-mediated transport between endosomal compartments1
positive regulation of catabolic process1
positive regulation of protein metabolic process1
axoneme assembly1
intraciliary transport involved in cilium assembly1
cilium organization1
protein localization to cilium1
organelle assembly1
trans-Golgi to periciliary membrane compartment transport1
plasma membrane bounded cell projection assembly1
ciliary transition zone assembly1
vesicle budding from membrane1
endosome organization1
GTPase binding1
binding1
intracellular anatomical structure1
lytic vacuole1
lysosome1
lytic vacuole membrane1
endosome1
endocytic vesicle membrane1
phagocytic vesicle1
late endosome1
cellular_component1

Protein interactions and networks

STRING

743 interactions, top by confidence (×1000):

Protein AProtein BPartner UniProtScore
RILPRAB34Q9BZG1922
RILPRAB7AP51149788
RILPDCTN1Q14203765
RILPOSBPL1AQ9BXW6703
RILPRDXP35241689
RILPMSNP26038674
RILPRAB36O95755656
RILPRILPL2Q969X0623
RILPFYCO1Q9BQS8619
RILPEZRP15311588
RILPMREGQ8N565587
RILPATP6V1G1O75348573
RILPSNAP29O95721557
RILPVAMP8Q9BV40552
RILPARL8BQ9NVJ2524

IntAct

44 interactions, top by confidence:

ABTypeScore
RILPRAB7Apsi-mi:“MI:0407”(direct interaction)0.930
RILPRAB7Apsi-mi:“MI:0915”(physical association)0.930
RAB7ARILPpsi-mi:“MI:0915”(physical association)0.930
EIF2S1EIF2S3psi-mi:“MI:0914”(association)0.820
OSBPL1ARAB7Apsi-mi:“MI:0915”(physical association)0.670
RILPVPS41psi-mi:“MI:0915”(physical association)0.570
RILPVPS41psi-mi:“MI:0403”(colocalization)0.570
RILPVPS41psi-mi:“MI:0407”(direct interaction)0.570
TGFBR2RILPpsi-mi:“MI:0915”(physical association)0.560
SPRED1RILPpsi-mi:“MI:0915”(physical association)0.560
INSRACTBpsi-mi:“MI:0914”(association)0.530
RILPVPS16psi-mi:“MI:0915”(physical association)0.460
RILPVPS18psi-mi:“MI:0915”(physical association)0.460
RILPVPS11psi-mi:“MI:0915”(physical association)0.460
RILPVPS39psi-mi:“MI:0915”(physical association)0.460
RILPVPS18psi-mi:“MI:0403”(colocalization)0.460
VPS39RILPpsi-mi:“MI:0403”(colocalization)0.460
RILPVPS16psi-mi:“MI:0403”(colocalization)0.460
RILPVPS11psi-mi:“MI:0403”(colocalization)0.460
RAB7Apsi-mi:“MI:0407”(direct interaction)0.440

BioGRID (41): RILP (Two-hybrid), VPS11 (Reconstituted Complex), VPS16 (Reconstituted Complex), VPS18 (Reconstituted Complex), VPS39 (Reconstituted Complex), VPS41 (Reconstituted Complex), RILP (Reconstituted Complex), RAB7A (Reconstituted Complex), RILP (Affinity Capture-MS), RAB7A (Affinity Capture-Western), RILP (Affinity Capture-Western), RAB7A (Affinity Capture-Western), RILP (Two-hybrid), RAB7A (Affinity Capture-Western), RILP (Two-hybrid)

ESM2 similar proteins: A0A140LIT1, A0A1B0GVG4, A0A494C0Y3, A0JNH6, A0JNN8, A1A5D9, A2ARS0, A5A769, A5PJP1, A6NC98, A7YWC8, C9JTQ0, O15049, O35764, O95502, P0C7N4, P0DPE3, P58660, Q0P5D1, Q1HCM0, Q2TAC2, Q3LUD3, Q3LUD4, Q3TMW1, Q3UMT1, Q4QRL3, Q5BLP8, Q5JTB6, Q6QNY0, Q6QZQ4, Q8BP01, Q8C7U1, Q8CHW5, Q8K262, Q8N283, Q8N6Y0, Q8TAT2, Q8TER5, Q8TF21, Q91XV7

Diamond homologs: A0PJT0, Q17QG3, Q5EBL4, Q5ND29, Q96NA2

SIGNOR signaling

0 interactions.

Enriched among interaction partners

Reactome pathways and GO biological processes over-represented among this gene’s 25 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.

GO biological processes:

GO termPartnersFoldFDR
endosomal vesicle fusion5244.2×2e-09
endosome to lysosome transport687.9×6e-09

Disease & clinical

Clinical variants and AI predictions

ClinVar

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

ClassificationCount (floor)
Pathogenic0
Likely pathogenic0
Uncertain significance53
Likely benign3
Benign0

Top pathogenic / likely-pathogenic (0)

SpliceAI

0 predictions. Top by Δscore:

AlphaMissense

2547 scored. Top likely-pathogenic:

VariantProtein changeam_pathogenicity
17:1648407:C:GR255P0.992
17:1648398:A:GL258P0.991
17:1647865:A:GM305T0.990
17:1649031:A:GL148P0.988
17:1649710:G:TA32D0.986
17:1649689:A:GL39P0.985
17:1647877:A:GI301T0.983
17:1648365:A:GL269P0.983
17:1649282:A:GL116P0.983
17:1649022:A:GL151P0.982
17:1649001:A:GL158P0.980
17:1648382:G:CF263L0.979
17:1648382:G:TF263L0.979
17:1648384:A:GF263L0.979
17:1648377:A:GL265P0.978
17:1648394:T:AK259N0.978
17:1648394:T:GK259N0.978
17:1649244:C:GA129P0.978
17:1647877:A:CI301S0.976
17:1649258:C:GR124P0.975
17:1646915:A:GI340T0.974
17:1648395:T:AK259I0.974
17:1649249:A:GL127P0.974
17:1649620:A:GL62P0.972
17:1647873:C:AK302N0.969
17:1647873:C:GK302N0.969
17:1647872:C:GA303P0.968
17:1647898:A:TV294D0.968
17:1648371:T:AE267V0.968
17:1648350:C:GR274P0.967

dbSNP variants (sampled 300 via entrez): RS1000325663 (17:1649427 G>A,T), RS1000464998 (17:1647198 G>A), RS1000532766 (17:1648243 T>C), RS1000648800 (17:1648011 T>C,G), RS1001010739 (17:1650260 C>G), RS1001289560 (17:1647276 A>G), RS1001590531 (17:1647510 GAAT>G), RS1002205595 (17:1647094 G>A), RS1002318513 (17:1646891 C>T), RS1002586045 (17:1645832 G>A,T), RS1002769236 (17:1650774 G>A), RS1004418082 (17:1649137 G>A,C), RS1004445334 (17:1649894 T>G), RS1004498685 (17:1650008 C>A,G), RS1004778492 (17:1648600 G>C)

Disease associations

OMIM: gene MIM:607848 | disease phenotypes:

GenCC curated gene-disease

Mondo (0):

Orphanet (0):

HPO phenotypes

0 total (0 of 0 shown, HPO-id order):

GWAS associations

0 associations (top):

Drugs & pharmacology

Drug and pharmacology data

Is drug target: no

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

CTD chemical–gene interactions

28 total (human), top 28 by PubMed support.

ChemicalActions (top 5)PubMed papers
Tobacco Smoke Pollutiondecreases methylation, decreases expression2
aristolochic acid Iincreases expression1
FR900359increases phosphorylation1
triphenyl phosphateaffects expression1
propionaldehydeincreases expression1
hydroxyhydroquinonedecreases expression, decreases reaction1
tris(2-butoxyethyl) phosphateaffects expression1
sodium arseniteincreases expression1
butyraldehydeincreases expression1
4-aminobenzhydrazidedecreases expression, decreases reaction1
2-palmitoylglycerolincreases expression1
entinostatincreases expression1
jinfukangaffects cotreatment, increases expression1
Acetaminophendecreases expression1
Benzo(a)pyrenedecreases methylation1
Cisplatinaffects cotreatment, increases expression1
Dichlorodiphenyl Dichloroethylenedecreases expression1
Diazinonincreases methylation1
Silicon Dioxideincreases expression1
Smokedecreases expression1
Triclosandecreases expression1
Urethaneincreases expression1
Valproic Aciddecreases expression, increases methylation1
8-Bromo Cyclic Adenosine Monophosphateincreases expression1
1-Methyl-4-phenylpyridiniumincreases expression1
Aflatoxin B1decreases expression1
Cadmium Chloridedecreases expression1
Copper Sulfatedecreases expression1

Clinical trials (associated diseases)

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

No linked Atlas pages yet — the cross-entity mesh grows as the corpus expands.