RBP3 (retinol binding protein 3)

Gene

• Entrez ID: 5949
• Gene name: Retinol binding protein 3
• Gene symbol: RBP3
• Synonyms (NCBI Gene): D10S64, D10S65, D10S66, IRBP, RBPI, RP66
• Chromosome: 10
• Chromosome location: 10q11.22
• Summary: Interphotoreceptor retinol-binding protein is a large glycoprotein known to bind retinoids and found primarily in the interphotoreceptor matrix of the retina between the retinal pigment epithelium and the photoreceptor cells. It is thought to transport re

SNPs

SNP ID	Visualize variation	Clinical significance	Consequence
rs34932849	G>A	Conflicting-interpretations-of-pathogenicity	Missense variant, coding sequence variant
rs143076262	C>A,G,T	Conflicting-interpretations-of-pathogenicity	Missense variant, coding sequence variant
rs146038948	C>T	Conflicting-interpretations-of-pathogenicity	Coding sequence variant, synonymous variant
rs146150511	G>A	Pathogenic	Coding sequence variant, missense variant
rs146175391	G>A,T	Conflicting-interpretations-of-pathogenicity	Coding sequence variant, synonymous variant
rs148591757	C>A,T	Uncertain-significance, conflicting-interpretations-of-pathogenicity	Coding sequence variant, missense variant
rs782215106	C>A,T	Likely-pathogenic	Synonymous variant, coding sequence variant, missense variant
rs782469310	C>G,T	Likely-pathogenic	Coding sequence variant, missense variant
rs782604129	TTC>-	Likely-pathogenic	Coding sequence variant, inframe deletion
rs917821437	C>A,G	Likely-pathogenic	Missense variant, coding sequence variant
rs1588865728	C>T	Pathogenic	Coding sequence variant, stop gained

miRNA

miRTarBase ID	miRNA	Experiments	Reference
MIRT1297372	hsa-miR-146b-3p	CLIP-seq
MIRT1297373	hsa-miR-1913	CLIP-seq
MIRT1297374	hsa-miR-3120-5p	CLIP-seq
MIRT1297375	hsa-miR-3173-5p	CLIP-seq
MIRT1297376	hsa-miR-3194-3p	CLIP-seq
MIRT1297377	hsa-miR-324-3p	CLIP-seq
MIRT1297378	hsa-miR-346	CLIP-seq
MIRT1297379	hsa-miR-4283	CLIP-seq
MIRT1297380	hsa-miR-4288	CLIP-seq
MIRT1297381	hsa-miR-4292	CLIP-seq
MIRT1297382	hsa-miR-4489	CLIP-seq
MIRT1297383	hsa-miR-632	CLIP-seq
MIRT1297384	hsa-miR-760	CLIP-seq
MIRT1297385	hsa-miR-874	CLIP-seq
MIRT2088387	hsa-miR-1292	CLIP-seq
MIRT2088388	hsa-miR-1343	CLIP-seq
MIRT2088389	hsa-miR-3121-5p	CLIP-seq
MIRT2088390	hsa-miR-4268	CLIP-seq
MIRT2088391	hsa-miR-4448	CLIP-seq
MIRT2088392	hsa-miR-4471	CLIP-seq
MIRT2088393	hsa-miR-4646-5p	CLIP-seq

Transcription factors

Transcription factor	Regulation	Reference
CRX	Activation	12409453
CRX	Repression	15277472
CRX	Unknown	11934446
KLF15	Repression	15277472;15963234
NRL	Repression	15277472
OTX2	Activation	10354480;10372988
OTX2	Unknown	18628516
ZNF239	Repression	12409453

Gene ontology (GO)

GO ID	Ontology	Definition	Evidence	Reference
GO:0001523	Process	Retinoid metabolic process	TAS
GO:0005501	Function	Retinoid binding	TAS	2542268
GO:0005515	Function	Protein binding	IPI	32296183
GO:0005576	Component	Extracellular region	IEA
GO:0005576	Component	Extracellular region	TAS
GO:0005615	Component	Extracellular space	IDA	23486466
GO:0006508	Process	Proteolysis	IEA
GO:0006629	Process	Lipid metabolic process	TAS	2542268
GO:0007601	Process	Visual perception	TAS	2542268
GO:0008236	Function	Serine-type peptidase activity	IEA
GO:0016918	Function	Retinal binding	IEA
GO:0019841	Function	Retinol binding	IBA
GO:0019841	Function	Retinol binding	IEA
GO:0033165	Component	Interphotoreceptor matrix	IEA
GO:0090658	Component	Cone matrix sheath	IBA
GO:1903561	Component	Extracellular vesicle	HDA	24769233

Other IDs

• MIM: 180290
• HGNC: 9921
• e!Ensembl: ENSG00000265203

Protein

• UniProt ID: P10745
• Protein name: Retinol-binding protein 3 (Interphotoreceptor retinoid-binding protein) (IRBP) (Interstitial retinol-binding protein)
• Protein function: IRBP shuttles 11-cis and all trans retinoids between the retinol isomerase in the pigment epithelium and the visual pigments in the photoreceptor cells of the retina.
• Family and domains:

  Pfam

  Accession	ID	Position in sequence	Description	Type
  PF11918	Peptidase_S41_N	21 → 127		Domain
  PF03572	Peptidase_S41	129 → 307	Peptidase family S41	Family
  PF11918	Peptidase_S41_N	309 → 436		Domain
  PF03572	Peptidase_S41	438 → 617	Peptidase family S41	Family
  PF11918	Peptidase_S41_N	619 → 740		Domain
  PF03572	Peptidase_S41	742 → 918	Peptidase family S41	Family
  PF11918	Peptidase_S41_N	920 → 1039		Domain
  PF03572	Peptidase_S41	1041 → 1217	Peptidase family S41	Family

• Sequence:

  MMREWVLLMSVLLCGLAGPTHLFQPSLVLDMAKVLLDNYCFPENLLGMQEAIQQAIKSHE
  ILSISDPQTLASVLTAGVQSSLNDPRLVISYEPSTPEPPPQVPALTSLSEEELLAWLQRG
  LRHEVLEGNVGYLRVDSVPGQEVLSMMGEFLVAHVWGNLMGTSALVLDLRHCTGGQVSGI
  PYIISYLHPGNTILHVDTIYNRPSNTTTEIWTLPQVLGERYGADKDVVVLTSSQTRGVAE
  DIAHILKQMRRAIVVGERTGGGALDLRKLRIGESDFFFTVPVSRSLGPLGGGSQTWEGSG
  VLPCVGTPAEQALEKALAILTLRSALPGVVHCLQEVLKDYYTLVDRVPTLLQHLASMDFS
  TVVSEEDLVTKLNAGLQAASEDPRLLVRAIGPTETPSWPAPDAAAEDSPGVAPELPEDEA
  IRQALVDSVFQVSVLPGNVGYLRFDSFADASVLGVLAPYVLRQVWEPLQDTEHLIMDLRH
  NPGGPSSAVPLLLSYFQGPEAGPVHLFTTYDRRTNITQEHFSHMELPGPRYSTQRGVYLL
  TSHRTATAAEEFAFLMQSLGWATLVGEITAGNLLHTRTVPLLDTPEGSLALTVPVLTFID
  NHGEAWLGGGVVPDAIVLAEEALDKAQEVLEFHQSLGALVEGTGHLLEAHYARPEVVGQT
  SALLRAKLAQGAYRTAVDLESLASQLTADLQEVSGDHRLLVFHSPGELVVEEAPPPPPAV
  PSPEELTYLIEALFKTEVLPGQLGYLRFDAMAELETVKAVGPQLVRLVWQQLVDTAALVI
  DLRYNPGSYSTAIPLLCSYFFEAEPRQHLYSVFDRATSKVTEVWTLPQVAGQRYGSHKDL
  YILMSHTSGSAAEAFAHTMQDLQRATVIGEPTAGGALSVGIYQVGSSPLYASMPTQMAMS
  ATTGKAWDLAGVEPDITVPMSEALSIAQDIVALRAKVPTVLQTAGKLVADNYASAELGAK
  MATKLSGLQSRYSRVTSEVALAEILGADLQMLSGDPHLKAAHIPENAKDRIPGIVPMQIP
  SPEVFEELIKFSFHTNVLEDNIGYLRFDMFGDGELLTQVSRLLVEHIWKKIMHTDAMIID
  MRFNIGGPTSSIPILCSYFFDEGPPVLLDKIYSRPDDSVSELWTHAQVVGERYGSKKSMV
  ILTSSVTAGTAEEFTYIMKRLGRALVIGEVTSGGCQPPQTYHVDDTNLYLTIPTARSVGA
  SDGSSWEGVGVTPHVVVPAEEALARAKEMLQHNQLRVKRSPGLQDHL

• Sequence length: 1247

Pathways

Reactome:

The retinoid cycle in cones (daylight vision)
The canonical retinoid cycle in rods (twilight vision)

Associated diseases

Evidence Score:

• ★☆☆☆☆  Gene-disease association found in Text Mining only
• ★★☆☆☆  Found in Text Mining and Unknown/Other Associations
• ★★★☆☆  Reported in Unknown/Other Associations across ≥2 Sources
• ★★★★☆  ClinVar: Pathogenic/Likely Pathogenic (<5 Variants)
• ★★★★★  ClinVar: Pathogenic/Likely Pathogenic (≥5 Variants)

Causal
Phenotype Name	Clinical Significance	dbSNP ID	RCV Accession	Evidence Score
Autosomal recessive retinitis pigmentosa	Pathogenic	rs782245537	RCV001257783	★★★★☆ ClinVar: Pathogenic / Likely Pathogenic (<5 Variants)
Cone-rod dystrophy	Pathogenic	rs1588865728	RCV002267760	★★★★☆ ClinVar: Pathogenic / Likely Pathogenic (<5 Variants)
RBP3-related disorder	Likely pathogenic	rs781793052	RCV003391342	★★★★☆ ClinVar: Pathogenic / Likely Pathogenic (<5 Variants)
Retinal dystrophy	Pathogenic; Likely pathogenic	rs2549027726, rs1392992564, rs2132257029, rs1565767178, rs781881541, rs782463303	RCV004817057 RCV003889523 RCV003889525 RCV003889528 RCV001073631 RCV003890354	★★★★★ ClinVar: Pathogenic / Likely Pathogenic (≥5 Variants)
Retinitis pigmentosa	Pathogenic	rs1555210929, rs1836974640	RCV001199531 RCV001199530	★★★★☆ ClinVar: Pathogenic / Likely Pathogenic (<5 Variants)
Retinitis pigmentosa 66	Likely pathogenic; Pathogenic	rs1555211286, rs2549028615, rs146150511, rs1836931186, rs782574616, rs782245537	RCV001376430 RCV002468771 RCV000043517 RCV001078178 RCV001810002 RCV001376320	★★★★★ ClinVar: Pathogenic / Likely Pathogenic (≥5 Variants)

Unknown / Other Associations
Phenotype Name	Clinical Significance	Source	Evidence Score
ANKYLOSING SPONDYLITIS AND OTHER INFLAMMATORY SPONDYLOPATHIES	—	Disgenet	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
AUTOIMMUNE DISEASES	—	CTD	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
CONE-ROD DYSTROPHIES	—	Disgenet	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Congenital stationary night blindness	Uncertain significance	ClinVar	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Hypercholesterolemia, familial, 1	Uncertain significance	ClinVar	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
NIGHT BLINDNESS, CONGENITAL STATIONARY	—	Disgenet	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Optic atrophy	Uncertain significance	ClinVar Disgenet	★★★☆☆ Reported in Unknown/Other Associations (≥2 sources)
RETINITIS PIGMENTOSA 1	—	CTD, Disgenet CTD, Disgenet	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Retinitis Pigmentosa, Recessive	Uncertain significance; Conflicting classifications of pathogenicity	ClinVar	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
UVEITIS	—	CTD, Disgenet CTD, Disgenet	★★☆☆☆ Found in Text Mining + Unknown/Other Associations

Associations from Text Mining
Disease Name	Disease (Merged)	Source	PMID	Relationship Type	Evidence Score
Adrenal Gland Pheochromocytoma	Adrenal Gland Pheochromocytoma	BEFREE	1978560		★☆☆☆☆ Found in Text Mining only
Amaurosis congenita of Leber, type 1	Leber congenital amaurosis	BEFREE	29721936		★☆☆☆☆ Found in Text Mining only
Autoimmune Diseases	Autoimmune Diseases	BEFREE	10903340		★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Autoimmune Diseases	Autoimmune disease	Pubtator	16030131	Associate	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Autoimmune Diseases	Autoimmune Diseases	CTD_human_DG	20007828, 21850155		★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Brain Neoplasms	Brain Neoplasms	BEFREE	1334963		★☆☆☆☆ Found in Text Mining only
Carcinoma Hepatocellular	Hepatocellular carcinoma	Pubtator	33845647	Associate	★☆☆☆☆ Found in Text Mining only
Cataract	Cataract	HPO_DG			★☆☆☆☆ Found in Text Mining only
Colorectal Carcinoma	Colorectal Cancer	UNIPROT_DG			★☆☆☆☆ Found in Text Mining only
Conductive hearing loss	Hearing Loss	HPO_DG			★☆☆☆☆ Found in Text Mining only
Congenital hypoplasia of penis	Congenital Hypoplasia Of Penis	HPO_DG			★☆☆☆☆ Found in Text Mining only
Diabetes	Diabetes	BEFREE	31270273		★☆☆☆☆ Found in Text Mining only
Diabetes Mellitus	Diabetes Mellitus	BEFREE	31270273		★☆☆☆☆ Found in Text Mining only
Diabetes Mellitus, Non-Insulin-Dependent	Diabetes Mellitus	HPO_DG			★☆☆☆☆ Found in Text Mining only
Diabetic Retinopathy	Diabetic Retinopathy	BEFREE	19823802, 31270273		★☆☆☆☆ Found in Text Mining only
Disorder of eye	Disorder Of Eye	GENOMICS_ENGLAND_DG			★☆☆☆☆ Found in Text Mining only
Exfoliation Syndrome	Exfoliation Syndrome	BEFREE	30842085		★☆☆☆☆ Found in Text Mining only
Familial medullary thyroid carcinoma	Thyroid cancer	Pubtator	2576939	Associate	★☆☆☆☆ Found in Text Mining only
Glaucoma	Glaucoma	HPO_DG			★☆☆☆☆ Found in Text Mining only
Hirschsprung Disease	Hirschsprung Disease	BEFREE	8467706		★☆☆☆☆ Found in Text Mining only
Hyperglycemia	Hyperglycemia	BEFREE	31270273		★☆☆☆☆ Found in Text Mining only
Hyperinsulinism	Hyperinsulinism	HPO_DG			★☆☆☆☆ Found in Text Mining only
Hypogonadism	Hypogonadism	HPO_DG			★☆☆☆☆ Found in Text Mining only
Intellectual Disability	Mental retardation	HPO_DG			★☆☆☆☆ Found in Text Mining only
Juvenile arthritis	Arthritis	BEFREE	8739566		★☆☆☆☆ Found in Text Mining only
Keratoconus	Keratoconus	HPO_DG			★☆☆☆☆ Found in Text Mining only
Medullary carcinoma of thyroid	Megalencephaly, Polymicrogyria, Polydactyly, Hydrocephalus Syndrome	BEFREE	1978560		★☆☆☆☆ Found in Text Mining only
Mucocutaneous Lymph Node Syndrome	Kawasaki disease	Pubtator	37550746	Associate	★☆☆☆☆ Found in Text Mining only
Multiple Endocrine Neoplasia Type 2a	Multiple Endocrine Neoplasia	BEFREE	1968709, 2567278, 2906045, 7902324, 8094065		★☆☆☆☆ Found in Text Mining only
Myopia	Myopia	Pubtator	37806543	Associate	★☆☆☆☆ Found in Text Mining only
Neoplasms	Neoplasms	BEFREE	1606838		★☆☆☆☆ Found in Text Mining only
Night blindness, congenital stationary	Night blindness	CLINVAR_DG			★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Nyctalopia	Nyctalopia	HPO_DG			★☆☆☆☆ Found in Text Mining only
Nystagmus	Nystagmus	HPO_DG			★☆☆☆☆ Found in Text Mining only
Obesity	Obesity	HPO_DG			★☆☆☆☆ Found in Text Mining only
Optic Atrophy	Optic Atrophy	HPO_DG			★★★☆☆ Reported in Unknown/Other Associations (≥2 sources)
Parathyroid Neoplasms	Parathyroid Neoplasms	BEFREE	1978560		★☆☆☆☆ Found in Text Mining only
Parathyroid Neoplasms	Parathyroid neoplasm	Pubtator	1978560	Associate	★☆☆☆☆ Found in Text Mining only
Pheochromocytoma	Pheochromocytoma	BEFREE	1978560		★☆☆☆☆ Found in Text Mining only
Pheochromocytoma	Pheochromocytoma	Pubtator	1978560	Associate	★☆☆☆☆ Found in Text Mining only
PIGMENTARY DISORDER, RETICULATE, WITH SYSTEMIC MANIFESTATIONS	Pigmentary Disorder, Reticulate, With Systemic Manifestations	BEFREE	19823802		★☆☆☆☆ Found in Text Mining only
Posterior subcapsular cataract	Capsular cataract	HPO_DG			★☆☆☆☆ Found in Text Mining only
Retinal Diseases	Retinal Diseases	BEFREE	19823802		★☆☆☆☆ Found in Text Mining only
Retinal Dystrophies	Retinal Dystrophy	BEFREE	25766589		★☆☆☆☆ Found in Text Mining only
Retinal Dystrophies	Retinal Dystrophy	CLINVAR_DG	26872967		★☆☆☆☆ Found in Text Mining only
Retinitis Pigmentosa	Retinitis Pigmentosa	ORPHANET_DG	19074801		★★★★☆ ClinVar: Pathogenic / Likely Pathogenic (<5 Variants)
Retinitis Pigmentosa	Retinitis pigmentosa	Pubtator	19074801	Associate	★★★★☆ ClinVar: Pathogenic / Likely Pathogenic (<5 Variants)
Retinitis Pigmentosa	Retinitis Pigmentosa	BEFREE	1974891, 21067480, 23486466, 23849777, 25766589, 9895244		★★★★☆ ClinVar: Pathogenic / Likely Pathogenic (<5 Variants)
Retinitis pigmentosa	Retinitis Pigmentosa	Orphanet			★★★★☆ ClinVar: Pathogenic / Likely Pathogenic (<5 Variants)
Retinitis Pigmentosa	Retinitis Pigmentosa	CTD_human_DG	23486466		★★★★☆ ClinVar: Pathogenic / Likely Pathogenic (<5 Variants)
Retinitis Pigmentosa	Retinitis Pigmentosa	GENOMICS_ENGLAND_DG			★★★★☆ ClinVar: Pathogenic / Likely Pathogenic (<5 Variants)
RETINITIS PIGMENTOSA 66	Retinitis Pigmentosa	CLINVAR_DG	19074801		★★★★★ ClinVar: Pathogenic / Likely Pathogenic (≥5 Variants)
RETINITIS PIGMENTOSA 66	Retinitis Pigmentosa	UNIPROT_DG	19074801, 23486466		★★★★★ ClinVar: Pathogenic / Likely Pathogenic (≥5 Variants)
RETINITIS PIGMENTOSA 66	Retinitis Pigmentosa	CTD_human_DG			★★★★★ ClinVar: Pathogenic / Likely Pathogenic (≥5 Variants)
RETINITIS PIGMENTOSA 66	Retinitis Pigmentosa	GENOMICS_ENGLAND_DG			★★★★★ ClinVar: Pathogenic / Likely Pathogenic (≥5 Variants)
Retinoblastoma	Retinoblastoma	BEFREE	10372988, 11134581, 11597600, 11934446, 1606838, 19823802, 7928191		★☆☆☆☆ Found in Text Mining only
Retinoblastoma	Retinoblastoma	Pubtator	11134581, 11934446	Associate	★☆☆☆☆ Found in Text Mining only
Retinoschisis	Retinoschisis	Pubtator	34991515	Associate	★☆☆☆☆ Found in Text Mining only
Rod-Cone Dystrophy	Rod-cone dystrophy	HPO_DG			★☆☆☆☆ Found in Text Mining only
Sensorineural Hearing Loss (disorder)	Hearing Loss	HPO_DG			★☆☆☆☆ Found in Text Mining only
Severe myopia	Myopia	BEFREE	25766589		★☆☆☆☆ Found in Text Mining only
Squamous cell carcinoma of the head and neck	Carcinoma Of The Head And Neck	BEFREE	22494072		★☆☆☆☆ Found in Text Mining only
Thyroid cancer medullary	Medullary thyroid cancer	Pubtator	1978560	Associate	★☆☆☆☆ Found in Text Mining only
Uveitis	Uveitis	BEFREE	10903340, 17911600, 24015215, 25367119, 28261206, 28846213, 29467002		★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Uveitis	Uveitis	CTD_human_DG	21850155		★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Uveitis, Posterior	Uveitis	BEFREE	28763100		★☆☆☆☆ Found in Text Mining only