RBP3

retinol binding protein 3

Basic information

Region (hg38): 10:47348362-47357881

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 (852 variants)
• Retinitis pigmentosa (103 variants)
• Inborn genetic diseases (67 variants)
• Retinitis pigmentosa 66 (41 variants)
• not specified (9 variants)
• Retinal dystrophy (7 variants)
• Retinitis Pigmentosa, Recessive (4 variants)
• Retinitis pigmentosa 66;Retinitis pigmentosa (2 variants)
• Retinitis pigmentosa;Retinitis pigmentosa 66 (2 variants)
• RBP3-related condition (1 variants)
• Autosomal recessive retinitis pigmentosa (1 variants)
• Congenital stationary night blindness (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.

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.

Variant type	Pathogenic	Likely pathogenic	VUS	Likely benign	Benign	Sum
synonymous			8	234	6	248
missense	3		536	5	4	548
nonsense	14	1	1			16
start loss			1			1
frameshift	8	5	3			16
inframe indel			4			4
splice donor/acceptor (+/-2bp)			1			1
splice region			2	3		5
non coding			9	11	2	22
Total	25	6	563	250	12

Highest pathogenic variant AF is 0.0000460

Variants in RBP3

This is a list of pathogenic ClinVar variants found in the RBP3 region.

You can filter this list by clicking the number of variants in the Variants pathogenicity by type table.

Position	Type	Phenotype	Significance	ClinVar
10-47348383-GAGA-G		Retinitis Pigmentosa, Recessive	Uncertain significance (Jun 14, 2016)
10-47348402-G-A		Retinitis pigmentosa	Uncertain significance (Jan 13, 2018)
10-47348472-C-T		Retinitis pigmentosa • Retinitis pigmentosa 66	Benign (Nov 07, 2021)
10-47348486-T-C			Uncertain significance (Dec 15, 2021)
10-47348489-T-C			Uncertain significance (Jul 11, 2022)
10-47348517-G-A			Likely benign (Aug 11, 2021)
10-47348525-G-A		Inborn genetic diseases	Uncertain significance (Nov 18, 2022)
10-47348526-T-C			Likely benign (Jun 15, 2023)
10-47348537-G-T		Retinitis pigmentosa 66	Uncertain significance (Jun 27, 2013)
10-47348538-C-A			Likely benign (Nov 20, 2019)
10-47348541-C-T			Likely benign (Nov 27, 2023)
10-47348547-C-T			Conflicting classifications of pathogenicity (Jan 15, 2024)
10-47348557-C-A			Uncertain significance (Oct 04, 2022)
10-47348559-A-C			Likely benign (Mar 26, 2023)
10-47348562-C-T		Retinitis pigmentosa	Benign/Likely benign (Jan 24, 2024)
10-47348563-C-T			Likely benign (Jun 13, 2022)
10-47348564-T-G			Uncertain significance (Jul 05, 2022)
10-47348577-G-A			Uncertain significance (Aug 30, 2021)
10-47348581-A-G			Uncertain significance (Apr 24, 2023)
10-47348585-T-G			Uncertain significance (Jun 26, 2020)
10-47348602-T-G			Uncertain significance (Sep 06, 2022)
10-47348604-C-T		Retinitis pigmentosa	Conflicting classifications of pathogenicity (Dec 30, 2023)
10-47348610-G-A		Retinitis pigmentosa	Conflicting classifications of pathogenicity (Dec 11, 2023)
10-47348616-C-A		Inborn genetic diseases	Uncertain significance (Jan 11, 2023)
10-47348616-C-G			Uncertain significance (Feb 14, 2022)

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