CRB1
protein-codingcrumbs cell polarity complex component 1, the group of Crumbs complex
Gene summary
This gene encodes a protein which is similar to the Drosophila crumbs protein and localizes to the inner segment of mammalian photoreceptors. In Drosophila crumbs localizes to the stalk of the fly photoreceptor and may be a component of the molecular scaffold that controls proper development of polarity in the eye. Mutations in this gene are associated with a severe form of retinitis pigmentosa, RP12, and with Leber congenital amaurosis. Alternate splicing results in multiple transcript variants, some protein coding and some non-protein coding.[provided by RefSeq, Apr 2012]
- RP12
MANE transcript
Inheritance
ClinVar variants
Top phenotype
gnomAD constraint
Max pathogenic AF
Genomic locus
External References & Databases
Transcript & Mutation Effects
hg38 • Region Span ~210.3 kbGenCC Phenotypes & Disease Associations
Curated gene-disease validity assertions and inheritance patterns
Inheritance Pattern: AR
Disease ID:MONDO:0013453
Submitter: G2P
Inheritance Pattern: AR
Disease ID:MONDO:0010818
Submitter: G2P
Inheritance Pattern: AD
Disease ID:MONDO:0008246
Submitter: G2P
Inheritance Pattern: Unknown
Disease ID:MONDO:0008246
Submitter: Natera
Inheritance Pattern: AR
Disease ID:MONDO:0013453
Submitter: Natera
Inheritance Pattern: AD
Disease ID:MONDO:0008246
Submitter: ClinGen
The *CRB1* gene was first reported in relation to ocular disease in 1999, in affected members from a family with autosomal recessive inheritance who were diagnosed with retinitis pigmentosa 12 (PMID: 10373321). The spectrum of disease with autosomal recessive inheritance subsequently expanded to include cases diagnosed as Leber congenital amaurosis 8 or Coats-like exudative vasculopathy (PMID: 11389483). Cases with autosomal dominant inheritance also emerged in 2005 with the publication of a family with members diagnosed with pigmented paravenous retinochoroidal atrophy (McKay et al., PMID: 15623792). Family members with pigmented paravenous retinochoroidal atrophy exhibited variable expressivity of clinical features including paravenous chorioretinal atrophy, bone spicule pigmentation, optic disc drusen, loss of visual acuity after age 30 years, and/or decreased rod electroretinogram amplitudes. Per criteria outlined by the ClinGen Lumping & Splitting Working Group, the pigmented paravenous retinochoroidal atrophy cases were distinguishable from autosomal recessive cases by their mode of inheritance, the scarcity of additional affected families following the initial report, and the absence of evidence of affected status among heterozygous carriers from the autosomal recessive pedigrees. Therefore, cases caused by inherited *CRB1* variants have been split into two separate disease entities, with the present curation focusing on autosomal dominant cases. Two suspected disease-causing variants were scored as part of this curation (both missense), which have been reported in two total families (PMID: 15623792, PMID: 40623937). The variants both show high frequencies among control individuals in the gnomAD database, and functional characterization of their potential mechanism of pathogenicity has not been performed. At least one reported family had multiple affected individuals who were heterozygous for the suspected disease-causing variant, but they were not sufficient in number to contribute to the scoring of the gene-disease relationship through segregation evidence (PMID: 15623792). This gene-disease association is supported by evidence that *CRB1* is highly specifically expressed in the human retina and to a lesser extent in the retinal pigment epithelium, the optic nerve, and the brain (PMID: 30239781). CRB1 protein localizes to the subapical cell surfaces of rod, cone, and Müller glial cells in order to maintain adherens junctions, regulate apical-basal polarity, and modulate apical membrane size in collaboration with the cadherin-catenin complex (PMID: 760678,7 PMID: 28424578, PMID: 32817065). Animal models of biallelic *CRB1* loss-of-function show ocular or photoreceptor dysfunction, but their relevance to autosomal dominant human disease is unclear (PMID: 28306104, PMID: 39965731, PMID: 32817065, PMID: 12915475). In summary, *CRB1* has a Disputed association with autosomal dominant pigmented paravenous retinochoroidal atrophy. This assertion has been found in at least 2 publications but has very limited segregation and proband evidence accumulated over the past 20 years since the initial report, as well as questions about the potential for the variants to be disease-causing. This classification was approved by the ClinGen Retina Gene Curation Expert Panel on July 2nd, 2026 (SOP Version 12).
Inheritance Pattern: AR
Disease ID:MONDO:0020242
Submitter: G2P
Inheritance Pattern: AR
Disease ID:MONDO:0010818
Submitter: Labcorp Genetics (formerly Invitae)
Inheritance Pattern: AR
Disease ID:MONDO:0013453
Submitter: Labcorp Genetics (formerly Invitae)
Inheritance Pattern: AD
Disease ID:MONDO:0008246
Submitter: Orphanet
Inheritance Pattern: AR
Disease ID:MONDO:0019118
Submitter: ClinGen
The *CRB1* gene was first reported in relation to ocular disease in 1999, in affected members from a family with autosomal recessive inheritance who were diagnosed with retinitis pigmentosa 12 (den Hollander et al., PMID: 10373321). The spectrum of disease subsequently expanded to include cases diagnosed as Leber congenital amaurosis 8 or RP with Coats-like exudative vasculopathy (PMID: 11389483), or isolated macular disease (PMID: 29391521). Affected individuals generally exhibit retinal features including night blindness, progressive loss of visual acuity, peripheral visual field constriction, photophobia, pigmentary retinopathy with para-arteriolar preservation, central thinning of the outer nuclear layer, hypermetropia, drusen, vascular sheathing, and/or cystoid macular edema. A family was subsequently identified with pigmented paravenous chorioretinal atrophy showing autosomal dominant inheritance (PMID: 15623792). Per criteria outlined by the ClinGen Lumping & Splitting Working Group, the cases diagnosed with retinitis pigmentosa 12 or Leber congenital amaurosis 8 shared a recessive mode of inheritance and biallelic loss-of-function mechanism, with overlapping phenotypes that were consistent with a single spectrum of disease. The autosomal dominant cases were distinguishable by their mode of inheritance, the scarcity of additional affected families following the initial report, and the absence of evidence of affected status among heterozygous carriers from the autosomal recessive pedigrees. Therefore, cases caused by inherited *CRB1* variants have been split into two separate disease entities, with the present curation focusing on autosomal recessive cases referred to as *CRB1*-related retinopathy. Fifteen suspected disease-causing variants were scored as part of this curation (seven missense, one in-frame deletion, three frameshift, three nonsense, and one predicted to disrupt splicing). These variants have been collectively reported in ten probands in three publications (PMID: 10373321, PMID: 11231775, PMID: 22065545). The variant types indicate that the mechanism of pathogenicity is biallelic loss-of-function. At least one reported family had a large number of affected individuals who were homozygous for the suspected disease-causing variant, contributing to the scoring of the gene-disease relationship through segregation evidence. This gene-disease association is also supported by evidence that *CRB1* is highly specifically expressed in the human retina and to a lesser extent in the retinal pigment epithelium, the optic nerve, and the brain (PMID: 30239781). CRB1 protein localizes to the subapical cell surfaces of rod, cone, and Müller glial cells in order to maintain adherens junctions, regulate apical-basal polarity, and modulate apical membrane size in collaboration with the cadherin-catenin complex (PMID: 760678,7 PMID: 28424578, PMID: 32817065). Mutations in the *Drosophila* ortholog *crumbs* result in embryonic lethality associated with morphological abnormalities, cell death of epithelial tissues, and overactivation of autophagy in the eye leading to neurodegeneration (PMID: 28306104, PMID: 39965731). *Crb1* loss-of-function in zebrafish results in retinal dystrophy with enhanced rod sensitivity to damage by white light and loss of cone sensitivity to bright white light (PMID: 32817065). Homozygous *Crb1* loss-of-function in mice causes congenitally short photoreceptor inner and outer segments, as well as retinal folds associated with retinal spotting and regions of photoreceptor degeneration (PMID: 12915475). In summary, CRB1 has a Definitive association with *CRB1*-related retinopathy. This has been repeatedly demonstrated in both research and diagnostic settings, and has been upheld over time without the emergence of contradictory evidence. This classification was approved by the ClinGen Retina Gene Curation Expert Panel on March 5th, 2026 (SOP Version 12).
Inheritance Pattern: AR
Disease ID:MONDO:0013453
Submitter: Laboratory for Molecular Medicine
This gene-disease relationship has undergone rapid assessment. Classifications are based on preliminary review of gene-disease validity during analysis of genomic sequencing results.
Inheritance Pattern: AD
Disease ID:MONDO:0005514
Submitter: Orphanet
Inheritance Pattern: AD
Disease ID:MONDO:0019200
Submitter: Orphanet
Inheritance Pattern: AD
Disease ID:MONDO:0018998
Submitter: Orphanet
Clinical Genomic Database (CGD)
Manifestation: Ophthalmologic
Intervention: General
Rationale: 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
ClinVar Associated Diseases & Phenotypes
Reported disease conditions connected to CRB1 variants in ClinVar
ClinVar Variants & Pathogenicity by Type
Statistics based on transcript NM_201253.3. Only rare variants are included.
We include only reliable ClinVar variants with their consequences to MANE Select, MANE Plus Clinical transcripts, or transcripts with TSL equal to 1. Click a count to filter the variants table below.
Slight differences between displayed counts and ClinVar may occur due to a different transcript/consequence chosen by our variant effect predictor, or because we classify Benign/Likely benign as Likely benign and Pathogenic/Likely pathogenic as Likely pathogenic.
| Effect | PathogenicP | Likely pathogenicLP | VUS | Likely benignLB | BenignB | Sum |
|---|---|---|---|---|---|---|
| synonymous | 1 | 23 | 603 | 627 | ||
| missense | 29 | 227 | 726 | 44 | 1 | 1027 |
| nonsense | 74 | 67 | 141 | |||
| start loss | 2 | 2 | ||||
| frameshift | 111 | 97 | 5 | 1 | 214 | |
| splice donor/acceptor (+/-2bp) | 22 | 33 | 1 | 56 | ||
| Total | 236 | 427 | 755 | 648 | 1 | 2067 |
Highest pathogenic variant AF is 0.0012272622
Transcript Catalog
Annotated transcript isoforms across RefSeq and Ensembl databases
| Transcript ID | Source | Protein ID | Coding Exons | MANE Status |
|---|---|---|---|---|
| RefSeq | NP_957705.1 | 12 | MANE Select | |
| Ensembl | ENSP00000356370.3 | 12 | MANE Select | |
| RefSeq | NP_001180569.1 | 10 | Standard | |
| RefSeq | NP_001244894.1 | 12 | Standard |
Gene Ontology (GO) Annotations & Pathways
Biological processes, molecular functions, cellular components and pathways
Pathways ConsensusPathDB
- Hippo signaling pathway - Homo sapiens (human)
Biological Process
- plasma membrane organization
- heterophilic cell-cell adhesion via plasma membrane cell adhesion molecules
- establishment or maintenance of cell polarity
- cell-cell signaling
- eye photoreceptor cell development
Molecular Function
- calcium ion binding
- protein binding
Cellular Component
- photoreceptor inner segment
- extracellular region
- plasma membrane
- microvillus
- cell-cell adherens junction
gnomAD Constraint
Source:
- Gene type
- protein_coding
- Transcript type
- protein_coding
- Transcript
- ENST00000367400
- Coding exons
- 12
- Length
- 276994
- Individuals with no LoFs
- 125643
- Homozygous LoFs
- 0
- Heterozygous LoFs
- 105
- Defined
- 125748
- p
- 0.000418
| Z-Score | Observed | Expected | Observed/Expected | Mutation Rate | Total Possible | |
|---|---|---|---|---|---|---|
| Missense | -1.28 | 822 | 725 | 1.13 | 0.0000363 | 9340 |
| Missense (PolyPhen) | 258 | 249.03 | 1.036 | 3278 | ||
| Synonymous | -0.791 | 294 | 277 | 1.06 | 0.0000154 | 2632 |
| Loss of Function | 2.57 | 33 | 53.2 | 0.620 | 0.00000254 | 718 |
Population LoF Frequency
| Population | CAF | p-value | Status |
|---|---|---|---|
| African | 0.00037 | 0.00037 | rare |
| Latino/Admixed American | 0.00035 | 0.00035 | rare |
| Ashkenazi Jewish | 0.000099 | 0.000099 | rare |
| East Asian | 0.00087 | 0.00087 | rare |
| Finnish | 0.000092 | 0.000092 | rare |
| European (Non-Finnish) | 0.00050 | 0.00050 | rare |
| South Asian | 0.00023 | 0.00023 | rare |
| Other | 0.00065 | 0.00065 | rare |
dbNSFP Gene Annotations
Source:
- Function
- FUNCTION: Plays a role in photoreceptor morphogenesis in the retina. May maintain cell polarization and adhesion.;
- Disease
- DISEASE: Note=CRB1 mutations have been found in various retinal dystrophies, chronic and disabling disorders of visual function. They predominantly involve the posterior portion of the ocular fundus, due to degeneration in the sensory layer of the retina, retinal pigment epithelium, Bruch membrane, choroid, or a combination of these tissues. Onset of inherited retinal dystrophies is painless, bilateral and typically progressive. Most people experience gradual peripheral vision loss or tunnel vision, and difficulties with poor illumination and night vision. Central vision is usually unaffected, so the person may still be able to read. However, it can also deteriorate to cause total blindness. Examples of retinal dystrophies are retinitis pigmentosa, Leber congenital amaurosis, cone-rod dystrophy among others. {ECO:0000269|PubMed:20683928, ECO:0000269|PubMed:22065545, ECO:0000269|PubMed:28819299}.; DISEASE: Retinitis pigmentosa 12 (RP12) [MIM:600105]: 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. RP12 is an autosomal recessive, severe form often manifesting in early childhood. Patients experiment progressive visual field loss with severe visual impairment before the age of twenty. Some patients have a preserved paraarteriolar retinal pigment epithelium (PPRPE) and hypermetropia. {ECO:0000269|PubMed:10508521, ECO:0000269|PubMed:11389483, ECO:0000269|PubMed:11559858, ECO:0000269|PubMed:12573663, ECO:0000269|PubMed:12843338, ECO:0000269|PubMed:15459956, ECO:0000269|PubMed:19140180, ECO:0000269|PubMed:19956407, ECO:0000269|PubMed:20591486, ECO:0000269|PubMed:20956273, ECO:0000269|PubMed:21987686, ECO:0000269|PubMed:22065545, ECO:0000269|PubMed:22128245, ECO:0000269|PubMed:22334370, ECO:0000269|PubMed:28819299}. Note=The disease is caused by mutations affecting the gene represented in this entry.; DISEASE: Leber congenital amaurosis 8 (LCA8) [MIM:613835]: A severe dystrophy of the retina, typically becoming evident in the first years of life. Visual function is usually poor and often accompanied by nystagmus, sluggish or near-absent pupillary responses, photophobia, high hyperopia and keratoconus. {ECO:0000269|PubMed:11231775, ECO:0000269|PubMed:11389483, ECO:0000269|PubMed:12567265, ECO:0000269|PubMed:12573663, ECO:0000269|PubMed:12700176, ECO:0000269|PubMed:12843338, ECO:0000269|PubMed:15024725, ECO:0000269|PubMed:15459956, ECO:0000269|PubMed:15691574, ECO:0000269|PubMed:16205573, ECO:0000269|PubMed:16936081, ECO:0000269|PubMed:17128490, ECO:0000269|PubMed:17438615, ECO:0000269|PubMed:17724218, ECO:0000269|PubMed:18055821, ECO:0000269|PubMed:18682808, ECO:0000269|PubMed:20108431, ECO:0000269|PubMed:20956273, ECO:0000269|PubMed:21602930, ECO:0000269|PubMed:28819299}. Note=The disease is caused by mutations affecting the gene represented in this entry.; DISEASE: Pigmented paravenous chorioretinal atrophy (PPCRA) [MIM:172870]: Unusual retinal degeneration characterized by accumulation of pigmentation along retinal veins. PPCRA is dominantly inherited, but exhibited variable expressivity. Males are more likely to exhibit a severe phenotype, whereas females may remain virtually asymptomatic even in later years. The PPCRA phenotype is associated with a mutation in CRB1 gene which is likely to affect the structure of the CRB1 protein. {ECO:0000269|PubMed:15623792}. Note=The disease is caused by mutations affecting the gene represented in this entry.;
Recessive Scores
- pRec
- 0.195
Intolerance Scores
- LoFtool
- 0.0401
- RVIS EVS
- -2.56
- RVIS percentile EVS
- 0.84
Essentials
- Essential (CRISPR)
- N
- Essential (CRISPR2)
- N
- Essential (gene trap)
- N
- Indispensability pred.
- E
- Indispensability score
- 0.633
Gene Damage Prediction
| All | Recessive | Dominant | |
|---|---|---|---|
| Mendelian | Medium | Medium | Medium |
| Primary Immunodeficiency | Medium | Medium | Medium |
| Cancer | Medium | Medium | Medium |