RBP3

retinol binding protein 3

Basic information

Region (hg38): 10:47348363-47357881

Links

ENSG00000265203

∙ NCBI:5949 ∙ OMIM:180290 ∙ HGNC:9921 ∙ Uniprot:P10745 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

Phenotypes

GenCC

Source: genCC

retinitis pigmentosa 66 (Strong), mode of inheritance: AR
retinitis pigmentosa (Supportive), mode of inheritance: AD
retinitis pigmentosa 66 (Strong), mode of inheritance: AR

Clinical Genomic Database

Source: CGD

Condition	Inheritance	Intervention Categories	Intervention/Rationale	Manifestation Categories	References
Retinitis pigmentosa 66	AR	General	Genetic knowledge may be beneficial related to issues such as selection of optimal supportive care, informed medical decision-making, prognostic considerations, and avoidance of unnecessary testing	Ophthalmologic	19074801

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the RBP3 gene.

not_provided (920 variants)
Inborn_genetic_diseases (190 variants)
Retinal_dystrophy (104 variants)
Retinitis_pigmentosa (98 variants)
Retinitis_pigmentosa_66 (55 variants)
RBP3-related_disorder (23 variants)
not_specified (10 variants)
Retinitis_Pigmentosa,_Recessive (2 variants)
Cone-rod_dystrophy (1 variants)
Congenital_stationary_night_blindness (1 variants)
Optic_atrophy (1 variants)
Autosomal_recessive_retinitis_pigmentosa (1 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the RBP3 gene is commonly pathogenic or not. These statistics are base on transcript: NM_000002900.3. Only rare variants are included in the table.

In the table, we include only reliable ClinVar variants with their consequences to MANE Select, Mane Plus Clinical transcripts, or transcripts with TSL equals 1. Click the count to view the source variants.

Warning: slight differences between displayed counts and the number of variants in ClinVar may occur, primarily due to (1) the application of a different transcript and/or consequence by our variant effect predictor or (2) differences in clinical significance: we classify Benign/Likely benign variants as Likely benign and Pathogenic/Likely pathogenic variants as Likely pathogenic.

Effect	PathogenicP	Likely pathogenicLP	VUSVUS	Likely benignLB	BenignB	Sum
synonymous		1 clinvar	7 clinvar	325 clinvar	5 clinvar	338
missense	3 clinvar	5 clinvar	619 clinvar	27 clinvar	4 clinvar	658
nonsense	17 clinvar	2 clinvar	2 clinvar			21
start loss			1			1
frameshift	10 clinvar	5 clinvar	2 clinvar			17
splice donor/acceptor (+/-2bp)		1 clinvar				1
Total	30	14	631	352	9

Highest pathogenic variant AF is 0.0000235438

Loading clinvar variants...

GnomAD

Source: gnomAD

dbNSFP

Source: dbNSFP

Function: 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.;
Disease: DISEASE: Retinitis pigmentosa 66 (RP66) [MIM:615233]: A retinal dystrophy belonging to the group of pigmentary retinopathies. Retinitis pigmentosa is characterized by retinal pigment deposits visible on fundus examination and primary loss of rod photoreceptor cells followed by secondary loss of cone photoreceptors. Patients typically have night vision blindness and loss of midperipheral visual field. As their condition progresses, they lose their far peripheral visual field and eventually central vision as well. {ECO:0000269|PubMed:19074801, ECO:0000269|PubMed:23486466}. Note=The disease is caused by mutations affecting the gene represented in this entry.;
Pathway: the visual cycle I (vertebrates) (Consensus)

Recessive Scores

pRec: 0.256

Intolerance Scores

loftool: 0.478
rvis_EVS: -0.96
rvis_percentile_EVS: 9.02

Haploinsufficiency Scores

pHI: 0.372
hipred: Y
hipred_score: 0.544
ghis: 0.450

Essentials

essential_gene_CRISPR: N
essential_gene_CRISPR2: N
essential_gene_gene_trap: N
gene_indispensability_pred: N
gene_indispensability_score: 0.344

Gene Damage Prediction

	All	Recessive	Dominant
Mendelian	Medium	Medium	Medium
Primary Immunodeficiency	Medium	Medium	Medium
Cancer	Medium	Medium	Medium

Mouse Genome Informatics

Gene name: Rbp3
Phenotype: vision/eye phenotype; nervous system phenotype (the observable morphological and physiological characteristics of the extensive, intricate network of electochemical structures in the body that is comprised of the brain, spinal cord, nerves, ganglia and parts of the receptor organs that are manifested through development and lifespan);

Gene ontology

Biological process: retinoid metabolic process;proteolysis;lipid metabolic process;visual perception
Cellular component: extracellular region;extracellular space;cone matrix sheath;extracellular vesicle
Molecular function: retinoid binding;serine-type peptidase activity;retinal binding;retinol binding