RILPL2

gene
On this page

Also known as MGC7036FLJ30380FLJ32372

Summary

RILPL2 (Rab interacting lysosomal protein like 2, HGNC:28787) is a protein-coding gene on chromosome 12q24.31, encoding RILP-like protein 2 (Q969X0). Involved in cell shape and neuronal morphogenesis, positively regulating the establishment and maintenance of dendritic spines.

This gene encodes a protein that contains a rab-interacting lysosomal protein-like domain. This protein may be involved in regulating lysosome morphology. This protein may also be a target for the Hepatitis C virus and assist in viral replication. Alternate splicing results in multiple transcript variants.

Source: NCBI Gene 196383 — RefSeq curated summary.

At a glance

  • GWAS associations: 25
  • Clinical variants (ClinVar): 40 total
  • MANE Select transcript: NM_145058

Identifiers

Gene identifiers

FieldValue
HGNC IDHGNC:28787
Approved symbolRILPL2
NameRab interacting lysosomal protein like 2
Location12q24.31
Locus typegene with protein product
StatusApproved
AliasesMGC7036, FLJ30380, FLJ32372
Ensembl geneENSG00000150977
Ensembl biotypeprotein_coding
OMIM614093
Entrez196383

Gene structure

Transcript identifiers

Ensembl transcripts: 7 — 6 protein_coding, 1 nonsense_mediated_decay

ENST00000280571, ENST00000718482, ENST00000718483, ENST00000718484, ENST00000718485, ENST00000884090, ENST00000884091

RefSeq mRNA: 1 — MANE Select: NM_145058 NM_145058

CCDS: CCDS9248

Canonical transcript exons

ENST00000280571 — 4 exons

ExonStartEnd
ENSE00000996988123423044123423157
ENSE00001100430123415039123415921
ENSE00001432183123430508123430659
ENSE00004035230123436082123436684

Expression profiles

Bgee: expression breadth ubiquitous, 254 present calls, max score 97.60.

FANTOM5 (CAGE): breadth ubiquitous, TPM avg 35.8441 / max 3220.8405, expressed in 1806 samples.

FANTOM5 promoters (5 alternative TSS)

Promoter IDTPM avgSamples expressed
13394619.87671707
1339477.48391097
1339486.08281543
1339491.6371822
1339500.7637515

Top tissues by expression

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

TissueAnatomy IDExpression scoreQuality
parotid glandUBERON:000183197.60gold quality
vena cavaUBERON:000408795.53gold quality
pharyngeal mucosaUBERON:000035595.15gold quality
pancreatic ductal cellCL:000207995.01gold quality
cauda epididymisUBERON:000436094.95gold quality
nasal cavity epitheliumUBERON:000538494.66gold quality
body of tongueUBERON:001187694.66gold quality
saphenous veinUBERON:000731894.64gold quality
tongueUBERON:000172394.62gold quality
ponsUBERON:000098894.16gold quality
superior surface of tongueUBERON:000737194.15gold quality
trabecular bone tissueUBERON:000248394.08gold quality
kidney epitheliumUBERON:000481993.94silver quality
esophagus squamous epitheliumUBERON:000692093.79gold quality
tibiaUBERON:000097993.78gold quality
tracheaUBERON:000312693.73gold quality
bronchusUBERON:000218593.35gold quality
bronchial epithelial cellCL:000232893.32gold quality
lower lobe of lungUBERON:000894993.13gold quality
pericardiumUBERON:000240793.00gold quality
epithelium of nasopharynxUBERON:000195192.83gold quality
urethraUBERON:000005792.80gold quality
myocardiumUBERON:000234992.15silver quality
palpebral conjunctivaUBERON:000181291.83gold quality
monocyteCL:000057691.57gold quality
middle temporal gyrusUBERON:000277191.53gold quality
buccal mucosa cellCL:000233691.46gold quality
caput epididymisUBERON:000435891.34gold quality
superficial temporal arteryUBERON:000161491.28gold quality
seminal vesicleUBERON:000099891.18gold quality

Single-cell (SCXA)

Detected in 4 experiment(s), a significant marker in 4.

ExperimentMarker?Max mean expression
E-HCAD-4yes34.96
E-MTAB-9467yes17.75
E-ANND-3yes15.13
E-GEOD-135922yes10.49

Regulation

Is transcription factor: no

miRNA regulators (miRDB)

51 targeting RILPL2, 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-LET-7A-3P100.0074.033932
HSA-LET-7B-3P100.0074.083913
HSA-LET-7F-1-3P100.0074.023928
HSA-MIR-98-3P100.0074.083907
HSA-MIR-8485100.0077.574731
HSA-MIR-548C-3P99.9974.017587
HSA-MIR-4789-5P99.9870.762721
HSA-MIR-4666A-3P99.9671.713434
HSA-MIR-551B-5P99.9671.283493
HSA-MIR-314399.9371.963104
HSA-MIR-10523-5P99.9169.222038
HSA-MIR-806399.9169.763146
HSA-MIR-394199.8670.542735
HSA-MIR-374C-5P99.8072.062910
HSA-MIR-655-3P99.8072.192909
HSA-MIR-4699-3P99.7170.153142
HSA-MIR-4755-5P99.7170.342716
HSA-MIR-5006-3P99.7170.262728
HSA-MIR-449999.6267.291470
HSA-MIR-444199.4966.563216
HSA-MIR-6740-3P99.4868.491392
HSA-MIR-608199.4866.071446
HSA-MIR-5009-3P99.4569.431341
HSA-MIR-103A-1-5P99.3967.781545
HSA-MIR-103A-2-5P99.3967.721577
HSA-MIR-145-3P99.3367.66764
HSA-MIR-751599.3168.221795
HSA-MIR-488-5P99.2868.12821
HSA-MIR-3160-5P99.2869.071938
HSA-MIR-452899.1869.771936

Literature-anchored findings (GeneRIF, showing 3)

  • Structural Basis for Rab8a Recruitment of RILPL2 via LRRK2 Phosphorylation of Switch 2. (PMID:32017888)
  • LRRK2-phosphorylated Rab10 sequesters Myosin Va with RILPL2 during ciliogenesis blockade. (PMID:33727250)
  • Prognostic value of RILPL2 and its correlation with tumor immune microenvironment and glycolysis in non-small cell lung cancer. (PMID:36536539)

Cross-species orthologs

5 orthologs

OrganismSymbolGene ID
danio_reriorilpl2ENSDARG00000024818
mus_musculusRilpl2ENSMUSG00000029401
rattus_norvegicusRilpl2ENSRNOG00000001061
drosophila_melanogasterRilplFBGN0024985
caenorhabditis_elegansWBGENE00007860

Paralogs (4): DZIP1 (ENSG00000134874), DZIP1L (ENSG00000158163), RILP (ENSG00000167705), RILPL1 (ENSG00000188026)

Protein

Protein identifiers

RILP-like protein 2Q969X0 (reviewed: Q969X0)

Alternative names: Rab-interacting lysosomal protein-like 2, p40phox-binding protein

All UniProt accessions (1): Q969X0

UniProt curated annotations — full annotation on UniProt →

Function. Involved in cell shape and neuronal morphogenesis, positively regulating the establishment and maintenance of dendritic spines. Plays a role in cellular protein transport, including protein transport away from primary cilia. May function via activation of RAC1 and PAK1.

Subunit / interactions. Homodimer. Interacts with RAC1. Interacts (via N-terminus) with MYO5A, the interaction is required for its role in dendrite formation. Interacts with RAB8A; interaction is dependent on the phosphorylation of RAB8A on ‘Thr-72’. Interacts with RAB10 and RAB12; interaction is dependent on the phosphorylation of ‘Thr-73’ on RAB10 and ‘Ser-105’ on RAB12.

Subcellular location. Cytoplasm. Cytosol. Cytoskeleton. Microtubule organizing center. Centrosome. Cell projection. Cilium.

Tissue specificity. Widely expressed. Expressed at higher level in lung.

Similarity. Belongs to the RILPL family.

RefSeq proteins (1): NP_659495* (*=MANE)

Domains & families (InterPro)

IDNameType
IPR021563RILP_dimerDomain
IPR034743RH1Domain
IPR034744RH2Domain
IPR051241DZIP_RILPLFamily

Pfam: PF09744, PF11461

UniProt features (12 total): mutagenesis site 3, domain 2, region of interest 2, chain 1, helix 1, coiled-coil region 1, compositionally biased region 1, modified residue 1

Structure

Experimental structures (PDB)

3 structures.

PDBMethodResolution (Å)
6SQ2X-RAY DIFFRACTION1.68
6RIRX-RAY DIFFRACTION1.77
7LWBX-RAY DIFFRACTION1.9

Predicted structure (AlphaFold)

ModelpLDDTFraction very-high
AF-Q969X0-F177.730.47

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 (1): 107

Mutagenesis-validated functional residues (3):

PositionPhenotype
149loss of interaction with rab8a, rab10 and rab12.
130loss of interaction with rab8a, rab10 and rab12.
132loss of interaction with rab8a, rab10 and rab12.

Function

Pathways and Gene Ontology

Reactome pathways

0 pathways

MSigDB gene sets: 224 (showing top): GOBP_EPITHELIUM_DEVELOPMENT, GOBP_INTRACELLULAR_PROTEIN_TRANSPORT, GOBP_EPITHELIAL_CELL_DEVELOPMENT, GRAESSMANN_APOPTOSIS_BY_DOXORUBICIN_DN, GRAESSMANN_RESPONSE_TO_MC_AND_DOXORUBICIN_DN, GOMF_GTPASE_BINDING, CHANDRAN_METASTASIS_DN, GOBP_PROTEIN_LOCALIZATION_TO_CELL_PERIPHERY, GOCC_MICROTUBULE_ORGANIZING_CENTER, MARTINEZ_RB1_TARGETS_DN, KOYAMA_SEMA3B_TARGETS_UP, GOBP_CILIUM_ORGANIZATION, KINSEY_TARGETS_OF_EWSR1_FLII_FUSION_DN, GOCC_CENTROSOME, GOBP_ESTABLISHMENT_OF_PROTEIN_LOCALIZATION_TO_MEMBRANE

GO Biological Process (4): epithelial cell morphogenesis (GO:0003382), cilium assembly (GO:0060271), protein transport from ciliary membrane to plasma membrane (GO:1903445), protein transport (GO:0015031)

GO Molecular Function (5): small GTPase binding (GO:0031267), identical protein binding (GO:0042802), protein dimerization activity (GO:0046983), dynein light intermediate chain binding (GO:0051959), protein binding (GO:0005515)

GO Cellular Component (8): cytoplasm (GO:0005737), centrosome (GO:0005813), cytosol (GO:0005829), cilium (GO:0005929), membrane (GO:0016020), ciliary basal body (GO:0036064), cytoskeleton (GO:0005856), cell projection (GO:0042995)

GO top-level categories

Rollup of top GO terms by namespace:

CategoryTerms
cellular anatomical structure4
protein binding3
microtubule organizing center2
cell morphogenesis1
epithelial cell development1
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
protein transport within lipid bilayer1
establishment of protein localization to plasma membrane1
protein localization to plasma membrane1
transport1
intracellular protein localization1
establishment of protein localization1
GTPase binding1
binding1
intracellular anatomical structure1
centriole1
cytoplasm1
intraciliary transport particle1
membrane-bounded organelle1
plasma membrane bounded cell projection1
cilium1
intracellular membraneless organelle1

Protein interactions and networks

STRING

522 interactions, top by confidence (×1000):

Protein AProtein BPartner UniProtScore
RILPL2RAB8AP24407928
RILPL2RAB10P61026919
RILPL2RAB36O95755731
RILPL2RAB29O14966714
RILPL2PPM1HQ9ULR3707
RILPL2RAB12Q6IQ22668
RILPL2RILPQ96NA2623
RILPL2RAB35Q15286602
RILPL2RHAGQ02094564
RILPL2MYO5AQ9Y4I1521
RILPL2EHBP1L1Q8N3D4501
RILPL2RAB3AP20336484
RILPL2RAB8BQ92930479
RILPL2MITD1Q8WV92471
RILPL2MAPK8IP3Q9UPT6452

IntAct

28 interactions, top by confidence:

ABTypeScore
RAB8ARILPL2psi-mi:“MI:0915”(physical association)0.720
RILPL2RAB8Apsi-mi:“MI:0914”(association)0.720
RILPL2RAB8Apsi-mi:“MI:0915”(physical association)0.720
RILPL2RAB8Apsi-mi:“MI:0407”(direct interaction)0.720
RAB8Apsi-mi:“MI:0407”(direct interaction)0.680
RILPL2RILPL2psi-mi:“MI:0407”(direct interaction)0.660
RILPL2RILPL2psi-mi:“MI:0915”(physical association)0.660
RAB8AWDR91psi-mi:“MI:0914”(association)0.600
RILPL2RAB10psi-mi:“MI:0915”(physical association)0.560
RILPL2psi-mi:“MI:0915”(physical association)0.490
RILPL2psi-mi:“MI:0915”(physical association)0.490
RILPL2psi-mi:“MI:0915”(physical association)0.370
RILPL2psi-mi:“MI:0915”(physical association)0.370
CAND1GTPBP10psi-mi:“MI:0914”(association)0.350
WHAMMP3EXOC5psi-mi:“MI:0914”(association)0.350
FRAT2GSK3Apsi-mi:“MI:0914”(association)0.350
WHAMMP3CCDC22psi-mi:“MI:0914”(association)0.350
NRILPL2psi-mi:“MI:2364”(proximity)0.270
RILPL2psi-mi:“MI:0915”(physical association)0.000
sgrRRILPL2psi-mi:“MI:0915”(physical association)0.000
TUBB4ARILPL2psi-mi:“MI:0915”(physical association)0.000
HEXDRILPL2psi-mi:“MI:0915”(physical association)0.000

BioGRID (11): RILPL2 (Affinity Capture-RNA), RILPL2 (Two-hybrid), RILPL2 (Affinity Capture-Western), RILPL2 (Synthetic Growth Defect), RILPL2 (Two-hybrid), RILPL2 (Two-hybrid), RILPL2 (Proximity Label-MS), RILPL2 (Affinity Capture-MS), RILPL2 (Affinity Capture-MS), RILPL2 (Affinity Capture-MS), RILPL2 (Affinity Capture-MS)

ESM2 similar proteins: A0PJP4, A0PJT0, A2VDP1, A4IFK7, D3ZUQ0, E9PSL7, O14578, O75665, P0C219, P49025, P97817, Q01850, Q0IHE5, Q14BN4, Q17QG3, Q28623, Q3LGD4, Q3SYW5, Q3URD3, Q3V079, Q4R3X1, Q4R7Y8, Q58A65, Q5DTM8, Q5EBL4, Q5R5R4, Q5VTR2, Q5ZJA3, Q5ZLS3, Q62172, Q62796, Q68CZ1, Q6AYA0, Q6DFC2, Q6DH86, Q6NRH3, Q6ZUS6, Q7Z3E2, Q86VS8, Q8BR07

Diamond homologs: A0PJP4, A0PJT0, A4IFK7, A4IGC3, D3ZUQ0, O76878, Q0IHE5, Q0P4J3, Q17QG3, Q5EBL4, Q6AYA0, Q6IP02, Q969X0, Q99LE1, Q9JJC6, Q5ND29

SIGNOR signaling

0 interactions.

Disease & clinical

Clinical variants and AI predictions

ClinVar

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

ClassificationCount (floor)
Pathogenic0
Likely pathogenic0
Uncertain significance32
Likely benign2
Benign0

Top pathogenic / likely-pathogenic (0)

SpliceAI

661 predictions. Top by Δscore:

VariantEffectΔscore
12:123423039:CTTA:Cdonor_loss1.0000
12:123423041:TA:Tdonor_loss1.0000
12:123423042:A:ACdonor_gain1.0000
12:123423042:A:Cdonor_loss1.0000
12:123423042:ACAG:Adonor_gain1.0000
12:123423043:C:CGdonor_gain1.0000
12:123423043:CA:Cdonor_gain1.0000
12:123423043:CAG:Cdonor_gain1.0000
12:123423043:CAGC:Cdonor_gain1.0000
12:123423043:CAGCT:Cdonor_gain1.0000
12:123423153:GGCCA:Gacceptor_gain1.0000
12:123423154:GCCA:Gacceptor_gain1.0000
12:123423155:CCA:Cacceptor_gain1.0000
12:123423155:CCAC:Cacceptor_gain1.0000
12:123423156:CA:Cacceptor_gain1.0000
12:123423156:CAC:Cacceptor_gain1.0000
12:123423157:AC:Aacceptor_loss1.0000
12:123423158:C:CCacceptor_gain1.0000
12:123423166:C:CTacceptor_gain1.0000
12:123423167:G:Tacceptor_gain1.0000
12:123430509:T:TAdonor_gain1.0000
12:123430529:T:TAdonor_gain1.0000
12:123430536:C:CTdonor_gain1.0000
12:123436080:ACCT:Adonor_gain1.0000
12:123436080:ACCTC:Adonor_gain1.0000
12:123436081:CCT:Cdonor_gain1.0000
12:123436081:CCTC:Cdonor_gain1.0000
12:123436081:CCTCC:Cdonor_gain1.0000
12:123436125:T:TAdonor_gain1.0000
12:123423037:CACT:Cdonor_loss0.9900

AlphaMissense

1368 scored. Top likely-pathogenic:

VariantProtein changeam_pathogenicity
12:123430600:G:CF133L0.999
12:123430600:G:TF133L0.999
12:123430602:A:GF133L0.999
12:123430601:A:GF133S0.998
12:123430565:C:GR145P0.997
12:123430586:A:GL138P0.996
12:123430556:A:GL148P0.994
12:123430601:A:CF133C0.993
12:123430566:G:TR145S0.990
12:123430574:A:GL142P0.989
12:123436223:G:CF66L0.989
12:123436223:G:TF66L0.989
12:123436225:A:GF66L0.989
12:123430544:A:GL152P0.987
12:123430602:A:TF133I0.987
12:123436266:A:GL52P0.986
12:123430602:A:CF133V0.985
12:123436275:C:TG49D0.985
12:123430552:C:AK149N0.984
12:123430552:C:GK149N0.984
12:123436197:A:GL75P0.984
12:123436215:A:TV69D0.984
12:123436276:C:GG49R0.984
12:123436230:A:GL64P0.983
12:123436287:G:AS45F0.982
12:123430523:A:GL159P0.980
12:123436206:A:GL72P0.979
12:123436299:A:TV41E0.978
12:123436314:A:GL36P0.976
12:123436209:A:TV71D0.975

dbSNP variants (sampled 300 via entrez): RS1000040163 (12:123413593 G>A), RS1000058549 (12:123435052 C>G,T), RS1000114010 (12:123419160 A>G), RS1000122889 (12:123425863 A>G), RS1000186067 (12:123420625 C>A,T), RS1000240873 (12:123425540 G>A), RS1000306582 (12:123431118 A>G), RS1000335617 (12:123431438 G>A), RS1000460951 (12:123424813 G>A), RS1000508748 (12:123414394 G>A), RS1000550861 (12:123419318 C>T), RS1000642430 (12:123430340 C>A,T), RS1000673547 (12:123430377 C>T), RS1000725896 (12:123438034 G>A), RS1000744524 (12:123435260 C>T)

Disease associations

OMIM: gene MIM:614093 | disease phenotypes:

GenCC curated gene-disease

Mondo (0):

Orphanet (0):

HPO phenotypes

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

GWAS associations

25 associations (top):

StudyTraitp-value
GCST002149_20Schizophrenia2.000000e-08
GCST002539_19Schizophrenia2.000000e-14
GCST002598_15Educational attainment7.000000e-08
GCST004521_72Autism spectrum disorder or schizophrenia8.000000e-12
GCST004627_145Lymphocyte count6.000000e-13
GCST005956_10Waist-to-hip ratio adjusted for BMI6.000000e-08
GCST005958_11Waist-to-hip ratio adjusted for BMI (age >50)4.000000e-07
GCST005962_22Waist-to-hip ratio adjusted for BMI x sex x age interaction (4df test)1.000000e-08
GCST006005_21High density lipoprotein cholesterol levels2.000000e-09
GCST006803_10Schizophrenia6.000000e-16
GCST007277_17Tourette syndrome2.000000e-06
GCST008163_151Height5.000000e-08
GCST010703_43Brain morphology (MOSTest)1.000000e-08
GCST012227_570Hip circumference adjusted for BMI4.000000e-09
GCST90011898_12Alanine aminotransferase levels2.000000e-15
GCST90020024_447A body shape index1.000000e-15
GCST90020024_448A body shape index7.000000e-09
GCST90020025_412Waist-to-hip ratio adjusted for BMI4.000000e-09
GCST90020025_418Waist-to-hip ratio adjusted for BMI1.000000e-20
GCST90020025_419Waist-to-hip ratio adjusted for BMI1.000000e-13
GCST90020025_420Waist-to-hip ratio adjusted for BMI4.000000e-10
GCST90020027_1218Waist-hip index3.000000e-19
GCST90020027_1219Waist-hip index5.000000e-13
GCST90020027_1220Waist-hip index4.000000e-10
GCST90020029_370Waist circumference adjusted for body mass index3.000000e-13

EFO canonical traits (9, from GWAS)

EFO IDTrait name
EFO:0004784self reported educational attainment
EFO:0004587lymphocyte count
EFO:0007788BMI-adjusted waist-hip ratio
EFO:0008007age at assessment
EFO:0008343sex interaction measurement
EFO:0004612high density lipoprotein cholesterol measurement
EFO:0004346neuroimaging measurement
EFO:0008039BMI-adjusted hip circumference
EFO:0007789BMI-adjusted waist circumference

Drugs & pharmacology

Drug and pharmacology data

Is drug target: no

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

CTD chemical–gene interactions

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

ChemicalActions (top 5)PubMed papers
Estradiolaffects cotreatment, increases expression, decreases expression, affects expression4
Valproic Acidincreases expression, affects expression4
Cyclosporinedecreases expression3
Acetaminophendecreases expression, affects response to substance2
aristolochic acid Iincreases expression1
triphenyl phosphateaffects expression1
tris(2-butoxyethyl) phosphateaffects expression1
sodium arsenitedecreases expression1
perfluorooctanoic acidaffects cotreatment, increases expression1
aflatoxin B2decreases methylation1
di-n-butylphosphoric acidaffects expression1
entinostatincreases expression1
K 7174decreases expression1
nutlin 3affects cotreatment, increases expression1
ICG 001decreases expression1
abrinedecreases expression1
jinfukangaffects cotreatment, increases expression1
NSC 689534affects binding, decreases expression1
(+)-JQ1 compounddecreases expression1
Leflunomidedecreases expression1
Norethindrone Acetateincreases expression, affects cotreatment1
Cisplatinaffects cotreatment, increases expression1
Copperaffects binding, decreases expression1
Cosmeticsaffects cotreatment, increases expression1
Dactinomycinaffects cotreatment, increases expression1
Doxorubicinincreases expression1
Flame Retardantsaffects cotreatment, increases expression1
Plasticizersaffects cotreatment, increases expression1
Progesteroneaffects cotreatment, decreases expression1
Quercetindecreases 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.