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GeneBe

RLBP1

retinaldehyde binding protein 1

Basic information

Region (hg38): 15:89209868-89221614

Links

ENSG00000140522NCBI:6017OMIM:180090HGNC:10024Uniprot:P12271AlphaFoldGenCCjaxSfariGnomADPubmedClinVar

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
  • RLBP1-related retinopathy (Definitive), mode of inheritance: AR
  • 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

Clinical Genomic Database

Source: CGD

ConditionInheritanceIntervention CategoriesIntervention/Rationale Manifestation CategoriesReferences
Newfoundland rod-cone dystrophy; Bothnia retinal dystrophy; Retinitis punctata albescens; Fundus albipunctatusARGeneralGenetic knowledge may be beneficial related to issues such as selection of optimal supportive care, informed medical decision-making, prognostic considerations, and avoidance of unnecessary testingOphthalmologic10102298; 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
clinvar
55
clinvar
2
clinvar
60
missense
1
clinvar
4
clinvar
97
clinvar
3
clinvar
105
nonsense
5
clinvar
2
clinvar
2
clinvar
9
start loss
1
clinvar
1
frameshift
6
clinvar
1
clinvar
7
inframe indel
1
clinvar
2
clinvar
3
splice donor/acceptor (+/-2bp)
4
clinvar
1
clinvar
5
splice region
1
8
12
21
non coding
14
clinvar
25
clinvar
13
clinvar
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)887533
15-89209905-G-A Pigmentary retinal dystrophy • Retinitis pigmentosa • Newfoundland cone-rod dystrophy Benign/Likely benign (Jan 12, 2018)317224
15-89209929-C-T Retinitis pigmentosa • Newfoundland cone-rod dystrophy • Pigmentary retinal dystrophy Conflicting classifications of pathogenicity (Jan 12, 2018)317225
15-89209951-A-G Newfoundland cone-rod dystrophy • Retinitis pigmentosa • Pigmentary retinal dystrophy Uncertain significance (Jan 13, 2018)317226
15-89209963-G-A Retinitis pigmentosa • Newfoundland cone-rod dystrophy • Pigmentary retinal dystrophy Benign (Apr 13, 2018)317227
15-89209984-A-T Newfoundland cone-rod dystrophy • Pigmentary retinal dystrophy • Retinitis pigmentosa Uncertain significance (Jan 12, 2018)886398
15-89209989-C-T Pigmentary retinal dystrophy • Newfoundland cone-rod dystrophy • Retinitis pigmentosa Benign (May 14, 2021)317228
15-89210029-C-T Retinitis pigmentosa • Pigmentary retinal dystrophy • Newfoundland cone-rod dystrophy Uncertain significance (Jan 13, 2018)886399
15-89210043-T-G Pigmentary retinal dystrophy • Retinitis pigmentosa • Newfoundland cone-rod dystrophy Benign/Likely benign (May 25, 2021)317229
15-89210068-T-G Pigmentary retinal dystrophy • Retinitis pigmentosa • Newfoundland cone-rod dystrophy Conflicting classifications of pathogenicity (Jan 12, 2018)887403
15-89210073-C-T Pigmentary retinal dystrophy • Newfoundland cone-rod dystrophy • Retinitis pigmentosa Uncertain significance (Jan 12, 2018)887404
15-89210118-A-C Newfoundland cone-rod dystrophy • Retinitis pigmentosa • Pigmentary retinal dystrophy Benign (May 14, 2021)317230
15-89210150-C-T Retinitis pigmentosa • Newfoundland cone-rod dystrophy • Pigmentary retinal dystrophy Uncertain significance (Jan 13, 2018)884446
15-89210303-A-T Likely benign (Jan 25, 2024)739180
15-89210308-G-A Uncertain significance (Aug 23, 2022)2110403
15-89210312-C-T Likely benign (Dec 06, 2023)2022636
15-89210314-G-A not specified Uncertain significance (Oct 13, 2022)850206
15-89210315-G-C Pigmentary retinal dystrophy • Newfoundland cone-rod dystrophy • Retinitis pigmentosa Conflicting classifications of pathogenicity (Feb 01, 2024)317231
15-89210315-G-T Newfoundland cone-rod dystrophy • Retinitis pigmentosa • Pigmentary retinal dystrophy Conflicting classifications of pathogenicity (Oct 25, 2023)884447
15-89210318-G-T Likely benign (May 13, 2023)2879391
15-89210322-A-G Uncertain significance (Sep 24, 2021)1417729
15-89210330-C-T Likely benign (Mar 08, 2023)2874588
15-89210332-C-G Uncertain significance (Feb 25, 2020)1000296
15-89210333-A-G Likely benign (Dec 24, 2023)2705218
15-89210338-C-A Uncertain significance (Mar 12, 2022)1046288

GnomAD

Source: gnomAD

GeneTypeBio TypeTranscript Coding Exons Length
RLBP1protein_codingprotein_codingENST00000268125 711883
pLI Probability
LOF Intolerant
pRec Probability
LOF Recessive
Individuals with
no LOFs
Individuals with
Homozygous LOFs
Individuals with
Heterozygous LOFs
Defined p
0.00001130.8261257010471257480.000187
Z-Score Observed Expected Observed/Expected Mutation Rate Total Possible in Transcript
Missense-0.3081951831.060.00001212081
Missense in Polyphen7978.1341.0111821
Synonymous0.3267073.60.9520.00000487596
Loss of Function1.331015.70.6378.55e-7171

LoF frequencies by population

EthnicitySum of pLOFs p
African & African-American0.0001650.000152
Ashkenazi Jewish0.000.00
East Asian0.001410.00141
Finnish0.00004620.0000462
European (Non-Finnish)0.00009700.0000967
Middle Eastern0.001410.00141
South Asian0.0001310.000131
Other0.0003270.000326

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

AllRecessiveDominant
MendelianMediumMediumMedium
Primary ImmunodeficiencyMediumMediumMedium
CancerMediumMediumMedium

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