Gene Details | GeDiPNet - Complete Gene Info, Disease Associations & Pathways

Gene Gene SNPs miRNA Gene ontology Other IDs Protein Pathways Associated diseases
Entrez ID Entrez Gene ID - the GENE ID in NCBI Gene database.	6121
Gene name Gene Name - the full gene name approved by the HGNC.	Retinoid isomerohydrolase RPE65
Gene symbol Gene Symbol - the official gene symbol approved by the HGNC.	RPE65
Synonyms (NCBI Gene) Gene synonyms aliases	BCO3, LCA2, RP20, mRPE65, p63, rd12, sRPE65
Chromosome Chromosome number	1
Chromosome location Chromosomal Location - indicates the cytogenetic location of the gene or region on the chromosome.	1p31.3
Summary Summary of gene provided in NCBI Entrez Gene.	The protein encoded by this gene is a component of the vitamin A visual cycle of the retina which supplies the 11-cis retinal chromophore of the photoreceptors opsin visual pigments. It is a member of the carotenoid cleavage oxygenase superfamily. All mem

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SNP ID	Visualize variation	Clinical significance	Consequence
rs61751276	C>T	Pathogenic-likely-pathogenic, pathogenic, likely-pathogenic	Intron variant
rs61751279	T>A	Not-provided, pathogenic	Splice acceptor variant, intron variant
rs61751281	C>T	Pathogenic	Missense variant, coding sequence variant, intron variant
rs61751282	C>T	Not-provided, likely-pathogenic	Missense variant, coding sequence variant, intron variant
rs61752871	G>A	Pathogenic	5 prime UTR variant, coding sequence variant, missense variant
rs61752877	G>A,T	Not-provided, pathogenic	Stop gained, coding sequence variant, synonymous variant
rs61752883	C>A	Uncertain-significance, likely-pathogenic	Missense variant, coding sequence variant
rs61752895	G>A	Pathogenic, not-provided	Stop gained, coding sequence variant
rs61752896	A>C,G	Not-provided, pathogenic	Missense variant, coding sequence variant
rs61752902	T>-	Pathogenic	Coding sequence variant, frameshift variant
rs61752904	T>A	Pathogenic	Stop gained, coding sequence variant
rs61752908	C>T	Not-provided, likely-pathogenic	Missense variant, coding sequence variant
rs61752909	A>G	Pathogenic, not-provided	Missense variant, coding sequence variant
rs62636300	T>C	Pathogenic, not-provided	Missense variant, coding sequence variant
rs62637004	A>C	Pathogenic, not-provided	Missense variant, coding sequence variant
rs62642583	AAATTCTGTTATGACGATCC>-	Not-provided, pathogenic	Coding sequence variant, frameshift variant
rs62642584	C>A,T	Pathogenic, likely-pathogenic, not-provided	Missense variant, stop gained, coding sequence variant
rs62653011	A>G	Pathogenic, not-provided	Missense variant, coding sequence variant
rs62653015	C>A,T	Likely-pathogenic	Missense variant, coding sequence variant
rs121917744	G>A,T	Pathogenic	Missense variant, coding sequence variant
rs121917745	G>A	Likely-pathogenic, pathogenic, not-provided	Missense variant, coding sequence variant
rs121918844	A>-,AA	Pathogenic	Frameshift variant, coding sequence variant
rs146357166	G>T	Conflicting-interpretations-of-pathogenicity	Intron variant, synonymous variant, coding sequence variant
rs150260489	T>C	Conflicting-interpretations-of-pathogenicity	Intron variant, synonymous variant, coding sequence variant
rs192907397	C>A,T	Likely-pathogenic	Missense variant, coding sequence variant
rs199683808	G>A,C	Likely-pathogenic	Missense variant, coding sequence variant, 5 prime UTR variant
rs281865520	T>-,TT	Pathogenic, not-provided	Coding sequence variant, frameshift variant
rs368088025	G>A,T	Pathogenic, likely-pathogenic	Intron variant, coding sequence variant, synonymous variant, stop gained
rs747393487	G>-	Pathogenic	Coding sequence variant, frameshift variant, 5 prime UTR variant
rs752058510	C>T	Likely-pathogenic	Coding sequence variant, missense variant
rs768445391	A>G	Likely-pathogenic	Missense variant, coding sequence variant
rs774130993	C>T	Pathogenic	Coding sequence variant, stop gained
rs777879312	C>A,T	Conflicting-interpretations-of-pathogenicity	Intron variant
rs786205444	C>-	Likely-pathogenic	Coding sequence variant, frameshift variant
rs886042807	AA>-	Pathogenic	Intron variant, coding sequence variant, stop gained
rs988133284	G>A,C	Pathogenic	Stop gained, synonymous variant, coding sequence variant
rs1057518922	C>A,T	Pathogenic	Splice donor variant
rs1064795255	G>A	Likely-pathogenic	Missense variant, coding sequence variant
rs1191496583	C>T	Likely-pathogenic, uncertain-significance	Missense variant, coding sequence variant
rs1193631220	C>A	Pathogenic	Missense variant, coding sequence variant
rs1420672586	C>A	Likely-pathogenic	Missense variant, coding sequence variant
rs1429137932	C>A	Likely-pathogenic	Missense variant, intron variant, coding sequence variant
rs1553152989	T>C	Pathogenic	Synonymous variant, coding sequence variant
rs1553153243	C>T	Likely-pathogenic	Coding sequence variant, missense variant
rs1557595199	T>G	Likely-pathogenic	Splice acceptor variant
rs1557600322	T>A,C	Pathogenic, uncertain-significance	Coding sequence variant, missense variant
rs1571158279	T>C	Pathogenic	Coding sequence variant, missense variant
rs1571158755	C>T	Likely-pathogenic	Coding sequence variant, missense variant
rs1571164333	G>A	Pathogenic	Coding sequence variant, stop gained
rs1571164534	T>A	Likely-pathogenic	Coding sequence variant, missense variant
rs1571165140	->CCA	Likely-pathogenic	Coding sequence variant, inframe insertion
rs1571172233	T>G	Pathogenic	Coding sequence variant, intron variant, missense variant

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miRTarBase ID	miRNA	Experiments	Reference
MIRT018146	hsa-miR-335-5p	Microarray	18185580
MIRT028349	hsa-miR-32-5p	Sequencing	20371350
MIRT1315590	hsa-miR-3140-3p	CLIP-seq
MIRT1315591	hsa-miR-3658	CLIP-seq
MIRT1315592	hsa-miR-935	CLIP-seq
MIRT2093904	hsa-miR-4468	CLIP-seq
MIRT1315592	hsa-miR-935	CLIP-seq
MIRT2614219	hsa-miR-127-5p	CLIP-seq
MIRT2614220	hsa-miR-4264	CLIP-seq
MIRT2614221	hsa-miR-4328	CLIP-seq
MIRT2614222	hsa-miR-4797-3p	CLIP-seq
MIRT2614219	hsa-miR-127-5p	CLIP-seq
MIRT2614220	hsa-miR-4264	CLIP-seq
MIRT2614221	hsa-miR-4328	CLIP-seq
MIRT2614222	hsa-miR-4797-3p	CLIP-seq

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GO ID	Ontology	Definition	Evidence	Reference
GO:0001523	Process	Retinoid metabolic process	IDA	25112876
GO:0001523	Process	Retinoid metabolic process	TAS
GO:0001786	Function	Phosphatidylserine binding	ISS
GO:0001895	Process	Retina homeostasis	IMP	15557452
GO:0003407	Process	Neural retina development	IEA
GO:0003834	Function	Beta-carotene 15,15'-dioxygenase activity	IBA
GO:0005515	Function	Protein binding	IPI	28514442, 33961781
GO:0005634	Component	Nucleus	IEA
GO:0005737	Component	Cytoplasm	IEA
GO:0005783	Component	Endoplasmic reticulum	IEA
GO:0005789	Component	Endoplasmic reticulum membrane	IDA	29659842
GO:0005886	Component	Plasma membrane	IEA
GO:0005886	Component	Plasma membrane	TAS
GO:0006629	Process	Lipid metabolic process	IEA
GO:0006776	Process	Vitamin A metabolic process	TAS	9326941
GO:0007601	Process	Visual perception	IEA
GO:0007601	Process	Visual perception	TAS	9326941
GO:0007623	Process	Circadian rhythm	IEA
GO:0009416	Process	Response to light stimulus	IEA
GO:0016020	Component	Membrane	IEA
GO:0016020	Component	Membrane	ISS
GO:0016702	Function	Oxidoreductase activity, acting on single donors with incorporation of molecular oxygen, incorporation of two atoms of oxygen	IEA
GO:0016787	Function	Hydrolase activity	IEA
GO:0016853	Function	Isomerase activity	IDA	28874556
GO:0016853	Function	Isomerase activity	IEA
GO:0031210	Function	Phosphatidylcholine binding	ISS
GO:0042572	Process	Retinol metabolic process	IEA
GO:0042574	Process	Retinal metabolic process	IBA
GO:0042574	Process	Retinal metabolic process	IEA
GO:0043010	Process	Camera-type eye development	IEA
GO:0044297	Component	Cell body	IEA
GO:0046872	Function	Metal ion binding	IEA
GO:0050251	Function	Retinol isomerase activity	IBA
GO:0050908	Process	Detection of light stimulus involved in visual perception	IMP	15557452
GO:0052884	Function	All-trans-retinyl-palmitate hydrolase, 11-cis retinol forming activity	IDA	25112876
GO:0052884	Function	All-trans-retinyl-palmitate hydrolase, 11-cis retinol forming activity	IEA
GO:0052884	Function	All-trans-retinyl-palmitate hydrolase, 11-cis retinol forming activity	TAS
GO:0052885	Function	All-trans-retinyl-ester hydrolase, 11-cis retinol forming activity	IBA
GO:0052885	Function	All-trans-retinyl-ester hydrolase, 11-cis retinol forming activity	IEA
GO:0052885	Function	All-trans-retinyl-ester hydrolase, 11-cis retinol forming activity	ISS
GO:1901612	Function	Cardiolipin binding	ISS
GO:1901827	Process	Zeaxanthin biosynthetic process	IBA
GO:1901827	Process	Zeaxanthin biosynthetic process	IDA	28874556

MIM	HGNC	e!Ensembl
180069	10294	ENSG00000116745

Protein

UniProt ID

Q16518

Protein name

Retinoid isomerohydrolase (EC 3.1.1.64) (All-trans-retinyl-palmitate hydrolase) (Lutein isomerase) (Meso-zeaxanthin isomerase) (EC 5.3.3.22) (Retinal pigment epithelium-specific 65 kDa protein) (Retinol isomerase)

Protein function

Critical isomerohydrolase in the retinoid cycle involved in regeneration of 11-cis-retinal, the chromophore of rod and cone opsins. Catalyzes the cleavage and isomerization of all-trans-retinyl fatty acid esters to 11-cis-retinol which is furthe

Family and domains

Pfam

Accession	ID	Position in sequence	Description	Type
PF03055	RPE65	15 → 532	Retinal pigment epithelial membrane protein	Family

Tissue specificity

TISSUE SPECIFICITY: Retina (at protein level). Retinal pigment epithelium specific. {ECO:0000269|PubMed:17848510, ECO:0000269|PubMed:21493626}.

Sequence

MSIQVEHPAGGYKKLFETVEELSSPLTAHVTGRIPLWLTGSLLRCGPGLFEVGSEPFYHL
FDGQALLHKFDFKEGHVTYHRRFIRTDAYVRAMTEKRIVITEFGTCAFPDPCKNIFSRFF
SYFRGVEVTDNALVNVYPVGEDYYACTETNFITKINPETLETIKQVDLCNYVSVNGATAH
PHIENDGTVYNIGNCFGKNFSIAYNIVKIPPLQADKEDPISKSEIVVQFPCSDRFKPSYV
HSFGLTPNYIVFVETPVKINLFKFLSSWSLWGANYMDCFESNETMGVWLHIADKKRKKYL
NNKYRTSPFNLFHHINTYEDNGFLIVDLCCWKGFEFVYNYLYLANLRENWEEVKKNARKA
PQPEVRRYVLPLNIDKADTGKNLVTLPNTTATAILCSDETIWLEPEVLFSGPRQAFEFPQ
INYQKYCGKPYTYAYGLGLNHFVPDRLCKLNVKTKETWVWQEPDSYPSEPIFVSHPDALE
EDDGVVLSVVVSPGAGQKPAYLLILNAKDLSEVARAEVEINIPVTFHGLFKKS

Sequence length

533

Interactions

View interactions

	KEGG		Reactome
	Retinol metabolism Metabolic pathways		The canonical retinoid cycle in rods (twilight vision)

Show/Hide Causal Diseases (4)

Disease merge term	Disease name	dbSNP ID	References
Causal Diseases caused by PATHOGENIC or LIKELY PATHOGENIC variants from ClinVar only
Leber Congenital Amaurosis	Leber congenital amaurosis 2, leber congenital amaurosis	rs61751282, rs1571164534, rs199683808, rs281865292, rs34627040, rs62653011, rs61752896, rs1057518922, rs774309607, rs61751281, rs752058510, rs61752909, rs61752883, rs61752866, rs61752904 View all (56 more)	N/A
retinal dystrophy	Retinal dystrophy	rs281865285, rs61752906, rs1645824260, rs61752895, rs1057518922, rs562037932, rs62642584, rs61751281, rs61752871, rs774130993, rs886042220, rs368088025, rs62636295, rs878853372, rs1444234037 View all (13 more)	N/A
Retinitis Pigmentosa	retinitis pigmentosa 20, retinitis pigmentosa, Autosomal recessive retinitis pigmentosa	rs61752909, rs61752883, rs1429137932, rs61752895, rs281865520, rs61751282, rs752058510, rs199683808, rs61752871, rs1571170561, rs121917745, rs368088025, rs1557600322, rs61752884, rs786205444 View all (17 more)	N/A
cone-rod dystrophy	Cone-rod dystrophy	rs767528365	N/A

Show/Hide Unknown Diseases (2)

Disease merge term	Disease name	Evidence	References	Source
Unknown Includes: (1) ClinVar NON-pathogenic variants (Uncertain, Benign, Conflicting, VUS), (2) GenCC associations, (3) GWAS associations, (4) CBGDA evidence-based associations. NOTE: Diseases with pathogenic evidence are excluded to avoid conflicts.
Glaucoma	Glaucoma	N/A	N/A	GWAS
Joubert Syndrome	Joubert syndrome 9	N/A	N/A	ClinVar

Show/Hide Text Mining Associations (48)

Disease Name	Relationship Type	References
Associations from Text Mining Disease associations identified through Pubtator
Adenomatous Polyposis Coli	Associate	33952291
Amaurosis congenita of Leber type 1	Associate	34289237
Amaurosis congenita of Leber type 2	Associate	18441370, 21606598, 22171060, 23474247, 36225124, 38631180
Atrophy	Associate	11264131, 32014860, 36142423
Autoimmune Diseases	Associate	16030131
Blindness	Associate	14611946, 19583479, 20043869, 22323828, 27375040, 32034665, 32879773, 35129589
Bone Diseases	Associate	11264131, 33952291
Choroideremia	Associate	27307694, 29947567
Color Vision Defects	Associate	29332120
Cone Dystrophy	Associate	18599565
Cone Rod Dystrophies	Associate	32014860, 33684911
Conversion Disorder	Associate	18599565
Diabetic Retinopathy	Associate	37318461
Epiretinal Membrane	Associate	40725401
Eye Diseases	Associate	36950921
Friedreich Ataxia 1	Associate	31273949
Fundus Albipunctatus	Associate	31273949
Genetic Diseases Inborn	Associate	22171060, 25383945
Hyperopia	Associate	31273949
Hypertensive Retinopathy	Associate	35129589, 37058101, 38002999
Ichthyosis prematurity syndrome	Associate	31595490
Leber Congenital Amaurosis	Associate	10615133, 11062306, 11264131, 14611946, 15024725, 16272259, 16828753, 18055820, 18539930, 18682808, 18809924, 18936139, 19117922, 19431183, 19583479 View all (51 more)
Leber Congenital Amaurosis	Inhibit	19953081
Leber congenital amaurosis type 3	Associate	29414951
Lung Neoplasms	Associate	36224547
Macular Degeneration	Associate	11264131, 23404124
Mobility Limitation	Associate	36123082
Muscular Disorders Atrophic	Associate	37322672
Night Blindness	Associate	26364624, 36950921
Nystagmus Pathologic	Associate	11264131, 18599565, 36950921
Oculocerebrorenal Syndrome	Associate	36950921
Ovarian Neoplasms	Associate	36224547
Patterned dystrophy of retinal pigment epithelium	Associate	32014860
Pigmentation Disorders	Associate	36429068
Pseudoinflammatory fundus dystrophy Finnish type	Associate	36950921
Refsum Disease Infantile	Associate	32033431, 35456422, 36460718, 36878196
Retinal Cone Dystrophy 1	Associate	29332120
Retinal Degeneration	Associate	11727200, 14611946, 26352687, 26427455, 28130426, 28945494, 29033008, 31273949, 32879773, 33684911, 35129589, 36878196, 36950921, 37660736, 37704110, 38002999, 39828244, 40384766 View all (3 more)
Retinal Diseases	Associate	25752820, 27307694, 30658988, 30711060, 31877759, 32423767, 33798654, 33952291, 34088339, 35765055, 36352427, 36429068, 37547722, 40384766
Retinal Drusen	Associate	11264131
Retinal Dystrophies	Associate	11062306, 11264131, 11727200, 16828753, 18441371, 18599565, 23878505, 25383945, 27307694, 27375040, 27874104, 28712537, 29681726, 30025081, 30268864 View all (23 more)
Retinal Dystrophy Early Onset Severe	Associate	14611946, 25383945, 34289237, 40384766
Retinitis	Associate	30025081
Retinitis Pigmentosa	Associate	11264131, 16272259, 26626312, 29947567, 32014860, 35569774, 35726567, 35748082, 36142423, 36950921, 37322672, 37578425, 38627549, 40384766, 9501220
Sveinsson Chorioretinal Atrophy	Associate	33838313
Vision Disorders	Associate	16828753, 18441371, 22171060, 27307694, 28237426, 29133760, 30025081, 30658988, 30711060, 32879773, 33952291, 36429068, 36950921, 40384766
Vision Low	Associate	35129589
Vitelliform Macular Dystrophy	Associate	27307694

RPE65 (retinoid isomerohydrolase RPE65)