RLBP1
retinaldehyde binding protein 1
Basic information
Region (hg38): 15:89209868-89221614
Links
Phenotypes
GenCC
Source:
- 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:
| 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
- not provided (227 variants)
- Retinitis pigmentosa (56 variants)
- Pigmentary retinal dystrophy (55 variants)
- Newfoundland cone-rod dystrophy (54 variants)
- not specified (15 variants)
- Inborn genetic diseases (5 variants)
- Retinitis punctata albescens (5 variants)
- Retinal dystrophy (5 variants)
- RLBP1-Related Disorders (3 variants)
- Retinitis Pigmentosa, Recessive (3 variants)
- Autosomal recessive retinitis pigmentosa (3 variants)
- Bothnia retinal dystrophy (3 variants)
- Progressive sclerosing poliodystrophy (1 variants)
- Newfoundland cone-rod dystrophy;Bothnia retinal dystrophy;Pigmentary retinal dystrophy (1 variants)
- Abnormality of the eye (1 variants)
- Bothnia retinal dystrophy;Pigmentary retinal dystrophy;Newfoundland cone-rod dystrophy (1 variants)
- Retinitis punctata albescens;Retinitis pigmentosa (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.
| Variant type | Pathogenic | Likely pathogenic | VUS | Likely benign | Benign | Sum |
|---|---|---|---|---|---|---|
| synonymous | 1 | 2 | 43 | 4 | 50 | |
| missense | 2 | 5 | 97 | 7 | 1 | 112 |
| nonsense | 4 | 1 | 3 | 8 | ||
| start loss | 0 | |||||
| frameshift | 5 | 1 | 4 | 10 | ||
| inframe indel | 1 | 1 | ||||
| splice variant | 1 | 4 | 12 | 13 | 1 | 31 |
| non coding | 8 | 20 | 11 | 39 | ||
| Total | 14 | 11 | 126 | 83 | 17 |
Highest pathogenic variant AF is 0.0000263
Variants in RLBP1
This is a list of pathogenic ClinVar variants found in the RLBP1 region.
| 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 interpretations 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 | Retinitis pigmentosa • Newfoundland cone-rod dystrophy • Pigmentary retinal dystrophy | Conflicting interpretations 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 (Aug 02, 2022) | |||
| 15-89210308-G-A | Uncertain significance (Aug 23, 2022) | |||
| 15-89210312-C-T | Likely benign (Aug 07, 2022) | |||
| 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 interpretations of pathogenicity (Oct 31, 2022) | ||
| 15-89210315-G-T | Newfoundland cone-rod dystrophy • Retinitis pigmentosa • Pigmentary retinal dystrophy | Conflicting interpretations of pathogenicity (Aug 17, 2021) | ||
| 15-89210322-A-G | Uncertain significance (Sep 24, 2021) | |||
| 15-89210332-C-G | Uncertain significance (Aug 27, 2021) | |||
| 15-89210338-C-A | Uncertain significance (Mar 12, 2022) | |||
| 15-89210346-C-T | Uncertain significance (Aug 31, 2021) | |||
| 15-89210347-C-T | Uncertain significance (Aug 27, 2021) | |||
| 15-89210354-C-T | Likely benign (Nov 28, 2018) |
GnomAD
Source:
| 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:
- 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