RLBP1

retinaldehyde binding protein 1

Basic information

Region (hg38): 15:89209868-89221614

Links

ENSG00000140522 ∙ NCBI:6017 ∙ OMIM:180090 ∙ HGNC:10024 ∙ Uniprot:P12271 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

Phenotypes

GenCC

Source: genCC

• retinitis pigmentosa (Supportive), mode of inheritance: AD
• retinitis punctata albescens (Supportive), mode of inheritance: AD
• Bothnia retinal dystrophy (Supportive), mode of inheritance: AR
• fundus albipunctatus (Supportive), mode of inheritance: AD
• Bothnia retinal dystrophy (Definitive), mode of inheritance: AR
• Newfoundland cone-rod dystrophy (Strong), mode of inheritance: AR
• Bothnia retinal dystrophy (Strong), mode of inheritance: AR
• fundus albipunctatus (Strong), mode of inheritance: AR
• Newfoundland cone-rod dystrophy (Strong), mode of inheritance: AR
• RLBP1-related retinopathy (Definitive), mode of inheritance: AR

Clinical Genomic Database

Source: CGD

Condition	Inheritance	Intervention Categories	Intervention/Rationale	Manifestation Categories	References
Newfoundland rod-cone dystrophy; Bothnia retinal dystrophy; Retinitis punctata albescens; Fundus albipunctatus	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	10102298; 11176989; 11868161; 14718298; 18344446; 20301590; 21447491; 22551409

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the RLBP1 gene.

• not provided (250 variants)
• Retinitis pigmentosa (55 variants)
• Pigmentary retinal dystrophy (55 variants)
• Newfoundland cone-rod dystrophy (53 variants)
• not specified (15 variants)
• Inborn genetic diseases (7 variants)
• Retinitis punctata albescens (5 variants)
• Retinal dystrophy (4 variants)
• RLBP1-Related Disorders (3 variants)
• Bothnia retinal dystrophy (3 variants)
• Retinitis Pigmentosa, Recessive (2 variants)
• Autosomal recessive retinitis pigmentosa (2 variants)
• Progressive sclerosing poliodystrophy (1 variants)
• Congenital stationary night blindness (1 variants)
• RLBP1-related condition (1 variants)
• Newfoundland cone-rod dystrophy;Bothnia retinal dystrophy;Pigmentary retinal dystrophy (1 variants)
• Abnormality of the eye (1 variants)
• Pigmentary retinal dystrophy;Newfoundland cone-rod dystrophy;Bothnia retinal dystrophy (1 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the RLBP1 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			3	55	2	60
missense	1	4	97	3		105
nonsense	5	2	2			9
start loss	1					1
frameshift	6		1			7
inframe indel		1	2			3
splice donor/acceptor (+/-2bp)		4	1			5
splice region	1		8	12		21
non coding			14	25	13	52
Total	13	11	120	83	15

Highest pathogenic variant AF is 0.0000263

Variants in RLBP1

This is a list of pathogenic ClinVar variants found in the RLBP1 region.

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

Position	Type	Phenotype	Significance	ClinVar
15-89209882-A-G		Retinitis pigmentosa • Newfoundland cone-rod dystrophy • Pigmentary retinal dystrophy	Uncertain significance (Jan 13, 2018)
15-89209905-G-A		Pigmentary retinal dystrophy • Retinitis pigmentosa • Newfoundland cone-rod dystrophy	Benign/Likely benign (Jan 12, 2018)
15-89209929-C-T		Retinitis pigmentosa • Newfoundland cone-rod dystrophy • Pigmentary retinal dystrophy	Conflicting classifications of pathogenicity (Jan 12, 2018)
15-89209951-A-G		Newfoundland cone-rod dystrophy • Retinitis pigmentosa • Pigmentary retinal dystrophy	Uncertain significance (Jan 13, 2018)
15-89209963-G-A		Retinitis pigmentosa • Newfoundland cone-rod dystrophy • Pigmentary retinal dystrophy	Benign (Apr 13, 2018)
15-89209984-A-T		Newfoundland cone-rod dystrophy • Pigmentary retinal dystrophy • Retinitis pigmentosa	Uncertain significance (Jan 12, 2018)
15-89209989-C-T		Pigmentary retinal dystrophy • Newfoundland cone-rod dystrophy • Retinitis pigmentosa	Benign (May 14, 2021)
15-89210029-C-T		Retinitis pigmentosa • Pigmentary retinal dystrophy • Newfoundland cone-rod dystrophy	Uncertain significance (Jan 13, 2018)
15-89210043-T-G		Pigmentary retinal dystrophy • Retinitis pigmentosa • Newfoundland cone-rod dystrophy	Benign/Likely benign (May 25, 2021)
15-89210068-T-G		Pigmentary retinal dystrophy • Retinitis pigmentosa • Newfoundland cone-rod dystrophy	Conflicting classifications of pathogenicity (Jan 12, 2018)
15-89210073-C-T		Pigmentary retinal dystrophy • Newfoundland cone-rod dystrophy • Retinitis pigmentosa	Uncertain significance (Jan 12, 2018)
15-89210118-A-C		Newfoundland cone-rod dystrophy • Retinitis pigmentosa • Pigmentary retinal dystrophy	Benign (May 14, 2021)
15-89210150-C-T		Retinitis pigmentosa • Newfoundland cone-rod dystrophy • Pigmentary retinal dystrophy	Uncertain significance (Jan 13, 2018)
15-89210303-A-T			Likely benign (Jan 25, 2024)
15-89210308-G-A			Uncertain significance (Aug 23, 2022)
15-89210312-C-T			Likely benign (Dec 06, 2023)
15-89210314-G-A		not specified	Uncertain significance (Oct 13, 2022)
15-89210315-G-C		Pigmentary retinal dystrophy • Newfoundland cone-rod dystrophy • Retinitis pigmentosa	Conflicting classifications of pathogenicity (Feb 01, 2024)
15-89210315-G-T		Newfoundland cone-rod dystrophy • Retinitis pigmentosa • Pigmentary retinal dystrophy	Conflicting classifications of pathogenicity (Oct 25, 2023)
15-89210318-G-T			Likely benign (May 13, 2023)
15-89210322-A-G			Uncertain significance (Sep 24, 2021)
15-89210330-C-T			Likely benign (Mar 08, 2023)
15-89210332-C-G			Uncertain significance (Feb 25, 2020)
15-89210333-A-G			Likely benign (Dec 24, 2023)
15-89210338-C-A			Uncertain significance (Mar 12, 2022)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
RLBP1	protein_coding	protein_coding	ENST00000268125	7	11883

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.0000113	0.826	125701	0	47	125748	0.000187

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	-0.308	195	183	1.06	0.0000121	2081
Missense in Polyphen		79	78.134	1.0111		821
Synonymous	0.326	70	73.6	0.952	0.00000487	596
Loss of Function	1.33	10	15.7	0.637	8.55e-7	171

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000165	0.000152
Ashkenazi Jewish	0.00	0.00
East Asian	0.00141	0.00141
Finnish	0.0000462	0.0000462
European (Non-Finnish)	0.0000970	0.0000967
Middle Eastern	0.00141	0.00141
South Asian	0.000131	0.000131
Other	0.000327	0.000326

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Soluble retinoid carrier essential the proper function of both rod and cone photoreceptors. Participates in the regeneration of active 11-cis-retinol and 11-cis-retinaldehyde, from the inactive 11-trans products of the rhodopsin photocycle and in the de novo synthesis of these retinoids from 11-trans metabolic precursors. The cycling of retinoids between photoreceptor and adjacent pigment epithelium cells is known as the 'visual cycle'. {ECO:0000269|PubMed:19846785}.
• Disease: DISEASE: Rod-cone dystrophy Newfoundland (NFRCD) [MIM:607476]: A rod-cone dystrophy reminiscent of retinitis punctata albescens but with a substantially lower age at onset and more-rapid and distinctive progression. Rod-cone dystrophies results from initial loss of rod photoreceptors, later followed by cone photoreceptors loss. {ECO:0000269|PubMed:11868161}. Note=The disease is caused by mutations affecting the gene represented in this entry.; DISEASE: Retinitis punctata albescens (RPA) [MIM:136880]: A form of fleck retina disease characterized by aggregation of white flecks posteriorly in the retina, causing night blindness and delayed dark adaptation. It differs from fundus albipunctatus in being progressive and evolving to generalized atrophy of the retina. {ECO:0000269|PubMed:10102299, ECO:0000269|PubMed:11453974, ECO:0000269|PubMed:9326942}. Note=The disease is caused by mutations affecting the gene represented in this entry.
• Pathway: Vitamin A and Carotenoid Metabolism;Signaling by GPCR;Signal Transduction;The canonical retinoid cycle in rods (twilight vision);The retinoid cycle in cones (daylight vision);G alpha (i) signalling events;Visual phototransduction;the visual cycle I (vertebrates);GPCR downstream signalling (Consensus)

Recessive Scores

• pRec: 0.216

Intolerance Scores

• loftool: 0.332
• rvis_EVS: 0.17
• rvis_percentile_EVS: 65.96

Haploinsufficiency Scores

• pHI: 0.257
• hipred: N
• hipred_score: 0.350
• ghis: 0.512

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.502

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Rlbp1
• Phenotype: integument phenotype (the observable morphological and physiological characteristics of the skin and its associated structures, such as the hair, nails, sweat glands, sebaceous glands and other secretory glands that are manifested through development and lifespan); skeleton 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); vision/eye phenotype; cardiovascular system phenotype (the observable morphological and physiological characteristics of the mammalian heart, blood vessels, or circulatory system that are manifested through development and lifespan); pigmentation phenotype

Zebrafish Information Network

• Gene name: rlbp1b
• Affected structure: pigmentation
• Phenotype tag: abnormal
• Phenotype quality: decreased intensity

Gene ontology

• Biological process: retinoid metabolic process;vitamin A metabolic process;visual perception;response to stimulus
• Cellular component: cellular_component;cytosol;cell body
• Molecular function: 11-cis retinal binding;retinol binding