CRB1 crumbs cell polarity complex component 1 [Homo sapiens (human)] - Gene

Summary

Official Symbol: CRB1provided by HGNC
Official Full Name: crumbs cell polarity complex component 1provided by HGNC
Primary source: HGNC:HGNC:2343
See related: Ensembl:ENSG00000134376 MIM:604210; AllianceGenome:HGNC:2343
Gene type: protein coding
RefSeq status: REVIEWED
Organism: Homo sapiens
Lineage: Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Primates; Haplorrhini; Catarrhini; Hominidae; Homo
Also known as: LCA8; RP12; CRB1-A; CRB1-B; CRB1-C
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]
Expression: Biased expression in brain (RPKM 4.0) and testis (RPKM 1.3) See more
Orthologs: mouse all
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Genomic context

Location:: 1q31.3

Exon count:: 17

Annotation release	Status	Assembly	Chr	Location
RS_2023_10	current	GRCh38.p14 (GCF_000001405.40)	1	NC_000001.11 (197201504..197478455)
RS_2023_10	current	T2T-CHM13v2.0 (GCF_009914755.1)	1	NC_060925.1 (196463303..196740260)
105.20220307	previous assembly	GRCh37.p13 (GCF_000001405.25)	1	NC_000001.10 (197170634..197447585)

Chromosome 1 - NC_000001.11 Genomic Context describing neighboring genes

Genomic regions, transcripts, and products

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Go to reference sequence details

Genomic Sequence:

Go to nucleotide: Graphics FASTA GenBank

Expression

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See details

Project title: HPA RNA-seq normal tissues
Description: RNA-seq was performed of tissue samples from 95 human individuals representing 27 different tissues in order to determine tissue-specificity of all protein-coding genes
BioProject: PRJEB4337
Publication: PMID 24309898
Analysis date: Wed Apr 4 07:08:55 2018

Bibliography

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GeneRIFs: Gene References Into Functions

What's a GeneRIF?

Quality of life in patients with CRB1-associated retinal dystrophies: A longitudinal study.
Title: Quality of life in patients with CRB1-associated retinal dystrophies: A longitudinal study.
Genotype-phenotype associations in CRB1 bi-allelic patients: a novel mutation, a systematic review and meta-analysis.
Title: Genotype-phenotype associations in CRB1 bi-allelic patients: a novel mutation, a systematic review and meta-analysis.
Human CRB1 and CRB2 form homo- and heteromeric protein complexes in the retina.
Title: Human CRB1 and CRB2 form homo- and heteromeric protein complexes in the retina.
A novel pathogenic CRB1 variant presenting as Leber Congenital Amaurosis 8 and evaluation of gene editing feasibility.
Title: A novel pathogenic CRB1 variant presenting as Leber Congenital Amaurosis 8 and evaluation of gene editing feasibility.
Foveal Hypoplasia in CRB1-Related Retinopathies.
Title: Foveal Hypoplasia in CRB1-Related Retinopathies.
CRB1 is required for recycling by RAB11A+ vesicles in human retinal organoids.
Title: CRB1 is required for recycling by RAB11A+ vesicles in human retinal organoids.
CRB1-Associated Retinal Dystrophies: Genetics, Clinical Characteristics, and Natural History.
Title: CRB1-Associated Retinal Dystrophies: Genetics, Clinical Characteristics, and Natural History.
A novel nonsense variant (c.1499C>G) in CRB1 caused Leber congenital amaurosis-8 in a Chinese family and a literature review.
Title: A novel nonsense variant (c.1499C>G) in CRB1 caused Leber congenital amaurosis-8 in a Chinese family and a literature review.
CRB1-associated retinal dystrophies in a Belgian cohort: genetic characteristics and long-term clinical follow-up.
Title: CRB1-associated retinal dystrophies in a Belgian cohort: genetic characteristics and long-term clinical follow-up.
In Silico Analysis of Pathogenic CRB1 Single Nucleotide Variants and Their Amenability to Base Editing as a Potential Lead for Therapeutic Intervention.
Title: In Silico Analysis of Pathogenic CRB1 Single Nucleotide Variants and Their Amenability to Base Editing as a Potential Lead for Therapeutic Intervention.

Submit: New GeneRIF Correction See all GeneRIFs (77)

Phenotypes

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Find tests for this gene in the NIH Genetic Testing Registry (GTR)

Review eQTL and phenotype association data in this region using PheGenI

Associated conditions

Description	Tests
Leber congenital amaurosis 8 MedGen: C3151202 OMIM: 613835 GeneReviews: Leber Congenital Amaurosis / Early-Onset Severe Retinal Dystrophy Overview	Compare labs
Pigmented paravenous retinochoroidal atrophy MedGen: C1868310 OMIM: 172870 GeneReviews: Not available	Compare labs
Retinitis pigmentosa 12 MedGen: C1838647 OMIM: 600105 GeneReviews: Nonsyndromic Retinitis Pigmentosa Overview	Compare labs

EBI GWAS Catalog

Description
Lupus nephritis susceptibility Loci in women with systemic lupus erythematosus. EBI GWAS Catalog EBI GWAS CatalogPubMed
Variants of DENND1B associated with asthma in children. EBI GWAS Catalog EBI GWAS CatalogPubMed

Variation

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See variants in ClinVar

See studies and variants in dbVar

See Variation Viewer (GRCh37.p13)

See Variation Viewer (GRCh38)

Interactions

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Products	Interactant	Other Gene	Complex	Source	Pubs	Description

General gene information

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Markers

G65609 (e-PCR)
- UniSTS:225545

AFM329vc1 (e-PCR)
- UniSTS:43560

SHGC-83435 (e-PCR)
- UniSTS:101932

SHGC-76093 (e-PCR)
- UniSTS:52527

RH121207 (e-PCR)
- UniSTS:138317

RH123645 (e-PCR)
- UniSTS:136066

SHGC-148695 (e-PCR)
- UniSTS:176560

AL034109 (e-PCR)
- UniSTS:93873

RH103147 (e-PCR)
- UniSTS:97481

STS-N59646 (e-PCR)
- UniSTS:83150

RH91397 (e-PCR)
- UniSTS:88549

AB072758 (e-PCR)
- UniSTS:479742

Gene Ontology Provided by GOA

Function	Evidence Code	Pubs
enables calcium ion binding	IEA Inferred from Electronic Annotation more info
enables protein binding	IPI Inferred from Physical Interaction more info	PubMed

Process	Evidence Code	Pubs
involved_in blood vessel remodeling	IEA Inferred from Electronic Annotation more info
involved_in cell-cell signaling	TAS Traceable Author Statement more info	PubMed
involved_in cellular response to light stimulus	IEA Inferred from Electronic Annotation more info
involved_in detection of light stimulus involved in visual perception	IEA Inferred from Electronic Annotation more info
involved_in establishment of bipolar cell polarity involved in cell morphogenesis	IEA Inferred from Electronic Annotation more info
involved_in establishment or maintenance of cell polarity	TAS Traceable Author Statement more info	PubMed
involved_in establishment or maintenance of epithelial cell apical/basal polarity	IBA Inferred from Biological aspect of Ancestor more info
involved_in establishment or maintenance of epithelial cell apical/basal polarity	NAS Non-traceable Author Statement more info	PubMed
involved_in eye photoreceptor cell development	IEA Inferred from Electronic Annotation more info
involved_in gene expression	IEA Inferred from Electronic Annotation more info
involved_in glial cell differentiation	IEA Inferred from Electronic Annotation more info
involved_in heterophilic cell-cell adhesion via plasma membrane cell adhesion molecules	IBA Inferred from Biological aspect of Ancestor more info
involved_in photoreceptor cell maintenance	IEA Inferred from Electronic Annotation more info
involved_in photoreceptor cell outer segment organization	IEA Inferred from Electronic Annotation more info
involved_in plasma membrane organization	IEA Inferred from Electronic Annotation more info
involved_in post-embryonic retina morphogenesis in camera-type eye	IEA Inferred from Electronic Annotation more info
involved_in protein localization	IEA Inferred from Electronic Annotation more info
involved_in retina layer formation	IEA Inferred from Electronic Annotation more info

Component	Evidence Code	Pubs
located_in adherens junction	IDA Inferred from Direct Assay more info	PubMed
located_in apical junction complex	NAS Non-traceable Author Statement more info	PubMed
located_in apical plasma membrane	NAS Non-traceable Author Statement more info	PubMed
located_in extracellular region	IEA Inferred from Electronic Annotation more info
located_in glial cell projection	IEA Inferred from Electronic Annotation more info
located_in microvillus	IEA Inferred from Electronic Annotation more info
located_in photoreceptor inner segment	IEA Inferred from Electronic Annotation more info
located_in photoreceptor outer segment	IEA Inferred from Electronic Annotation more info
is_active_in plasma membrane	IBA Inferred from Biological aspect of Ancestor more info
part_of protein-containing complex	IBA Inferred from Biological aspect of Ancestor more info
part_of protein-containing complex	IDA Inferred from Direct Assay more info	PubMed
part_of subapical complex	IEA Inferred from Electronic Annotation more info

General protein information

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Preferred Names: protein crumbs homolog 1

Names: crumbs 1, cell polarity complex component; crumbs family member 1, photoreceptor morphogenesis associated

NCBI Reference Sequences (RefSeq)

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RefSeqs maintained independently of Annotated Genomes

These reference sequences exist independently of genome builds. Explain

These reference sequences are curated independently of the genome annotation cycle, so their versions may not match the RefSeq versions in the current genome build. Identify version mismatches by comparing the version of the RefSeq in this section to the one reported in Genomic regions, transcripts, and products above.

Genomic

NG_008483.3 RefSeqGene

Range

71750..281953

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GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

NM_001193640.2 → NP_001180569.1 protein crumbs homolog 1 isoform 2 precursor

See identical proteins and their annotated locations for NP_001180569.1

Status: REVIEWED

Description

Transcript Variant: This variant (2) lacks two in-frame exons compared to variant 1. The resulting isoform (2) has the same N- and C-termini but is shorter compared to isoform 1.

Source sequence(s)

AL136322, AL139136, AL513325

Consensus CDS

CCDS53454.1

UniProtKB/TrEMBL

A8K118

Related

ENSP00000356369.2, ENST00000367399.6

Conserved Domains (3) summary

smart00179
Location:285 → 326

EGF_CA; Calcium-binding EGF-like domain

cd00054
Location:148 → 183

EGF_CA; Calcium-binding EGF-like domain, present in a large number of membrane-bound and extracellular (mostly animal) proteins. Many of these proteins require calcium for their biological function and calcium-binding sites have been found to be located at the ...

pfam02210
Location:402 → 537

Laminin_G_2; Laminin G domain
NM_001257965.2 → NP_001244894.1 protein crumbs homolog 1 isoform 3

Status: REVIEWED

Description

Transcript Variant: This variant (3) contains three noncoding exons in place of the first exon and contains an alternate in-frame exon compared to variant 1. The resulting isoform (3) is shorter at the N- terminus and contains an alternate internal segment compared to isoform 1.

Source sequence(s)

AL136322, AL139136, AL356315, AL513325

Consensus CDS

CCDS58053.1

UniProtKB/TrEMBL

B7Z826, F5H0L2

Related

ENSP00000438786.1, ENST00000535699.5

Conserved Domains (3) summary

smart00179
Location:328 → 369

EGF_CA; Calcium-binding EGF-like domain

cd00054
Location:79 → 114

EGF_CA; Calcium-binding EGF-like domain, present in a large number of membrane-bound and extracellular (mostly animal) proteins. Many of these proteins require calcium for their biological function and calcium-binding sites have been found to be located at the ...

pfam02210
Location:445 → 580

Laminin_G_2; Laminin G domain
NM_001257966.2 → NP_001244895.1 protein crumbs homolog 1 isoform 4 precursor

See identical proteins and their annotated locations for NP_001244895.1

Status: REVIEWED

Description

Transcript Variant: This variant (4) lacks an alternate in-frame segment of two coding exons and most of a third compared to variant 1. The resulting isoform (4) has the same N- and C-termini but lacks an alternate internal segment compared to isoform 1.

Source sequence(s)

AL136322, AL139136, AL513325

Consensus CDS

CCDS58052.1

UniProtKB/TrEMBL

A0A7D6VMU1

Related

ENSP00000438091.1, ENST00000538660.5

Conserved Domains (3) summary

smart00179
Location:397 → 438

EGF_CA; Calcium-binding EGF-like domain

cd00054
Location:148 → 183

EGF_CA; Calcium-binding EGF-like domain, present in a large number of membrane-bound and extracellular (mostly animal) proteins. Many of these proteins require calcium for their biological function and calcium-binding sites have been found to be located at the ...

pfam02210
Location:514 → 649

Laminin_G_2; Laminin G domain
NM_201253.3 → NP_957705.1 protein crumbs homolog 1 isoform 1 precursor

See identical proteins and their annotated locations for NP_957705.1

Status: REVIEWED

Description

Transcript Variant: This variant (1) encodes the longest isoform (1).

Source sequence(s)

AL136322, AL139136, AL513325

Consensus CDS

CCDS1390.1

UniProtKB/Swiss-Prot

A2A308, B7Z5T2, B9EG71, P82279, Q5K3A6, Q5TC28, Q5VUT1, Q6N027, Q8WWY0, Q8WWY1

UniProtKB/TrEMBL

A0A7D6VM04, A8K118

Related

ENSP00000356370.3, ENST00000367400.8

Conserved Domains (3) summary

smart00179
Location:397 → 438

EGF_CA; Calcium-binding EGF-like domain

cd00054
Location:148 → 183

EGF_CA; Calcium-binding EGF-like domain, present in a large number of membrane-bound and extracellular (mostly animal) proteins. Many of these proteins require calcium for their biological function and calcium-binding sites have been found to be located at the ...

pfam02210
Location:514 → 649

Laminin_G_2; Laminin G domain

RNA

NR_047563.2 RNA Sequence

Status: REVIEWED

Description

Transcript Variant: This variant (5) lacks an alternate internal segment of a coding exon compared to variant 1, that causes a frameshift. The resulting transcript is a candidate for nonsense-mediated mRNA decay (NMD) and is thought to be non-protein coding.

Source sequence(s)

AL136322, AL139136, AL513325
NR_047564.2 RNA Sequence

Status: REVIEWED

Description

Transcript Variant: This variant (6) uses an alternate splice junction at the 3' end of a coding exon compared to variant 1, that causes a frameshift. The resulting transcript is a candidate for nonsense-mediated mRNA decay (NMD) and is thought to be non-protein coding.

Source sequence(s)

AL136322, AL139136, AL513325

Related

ENST00000484075.5

RefSeqs of Annotated Genomes: GCF_000001405.40-RS_2023_10

The following sections contain reference sequences that belong to a specific genome build. Explain

Reference GRCh38.p14 Primary Assembly

Genomic

NC_000001.11 Reference GRCh38.p14 Primary Assembly

Range

197201504..197478455

Download

GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

XM_047416573.1 → XP_047272529.1 protein crumbs homolog 1 isoform X2
XM_017000852.2 → XP_016856341.1 protein crumbs homolog 1 isoform X7

UniProtKB/TrEMBL

A8K118
XM_011509367.2 → XP_011507669.1 protein crumbs homolog 1 isoform X3

UniProtKB/TrEMBL

A8K118

Conserved Domains (3) summary

smart00179
Location:397 → 438

EGF_CA; Calcium-binding EGF-like domain

cd00054
Location:148 → 183

EGF_CA; Calcium-binding EGF-like domain, present in a large number of membrane-bound and extracellular (mostly animal) proteins. Many of these proteins require calcium for their biological function and calcium-binding sites have been found to be located at the ...

pfam02210
Location:514 → 649

Laminin_G_2; Laminin G domain
XM_047416574.1 → XP_047272530.1 protein crumbs homolog 1 isoform X4
XM_011509365.3 → XP_011507667.1 protein crumbs homolog 1 isoform X1

UniProtKB/TrEMBL

A8K118

Related

ENSP00000491102.1, ENST00000638467.1

Conserved Domains (3) summary

smart00179
Location:397 → 438

EGF_CA; Calcium-binding EGF-like domain

cd00054
Location:148 → 183

EGF_CA; Calcium-binding EGF-like domain, present in a large number of membrane-bound and extracellular (mostly animal) proteins. Many of these proteins require calcium for their biological function and calcium-binding sites have been found to be located at the ...

pfam02210
Location:514 → 649

Laminin_G_2; Laminin G domain
XM_047416572.1 → XP_047272528.1 protein crumbs homolog 1 isoform X2
XM_047416575.1 → XP_047272531.1 protein crumbs homolog 1 isoform X5

Related

ENSP00000505267.1, ENST00000681519.1
XM_011509369.3 → XP_011507671.1 protein crumbs homolog 1 isoform X6

See identical proteins and their annotated locations for XP_011507671.1

UniProtKB/TrEMBL

B7Z824

Conserved Domains (2) summary

cd00054
Location:627 → 656

EGF_CA; Calcium-binding EGF-like domain, present in a large number of membrane-bound and extracellular (mostly animal) proteins. Many of these proteins require calcium for their biological function and calcium-binding sites have been found to be located at the ...

pfam02210
Location:461 → 586

Laminin_G_2; Laminin G domain

Alternate T2T-CHM13v2.0

Genomic

NC_060925.1 Alternate T2T-CHM13v2.0

Range

196463303..196740260

Download

GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

XM_054335671.1 → XP_054191646.1 protein crumbs homolog 1 isoform X2
XM_054335676.1 → XP_054191651.1 protein crumbs homolog 1 isoform X7
XM_054335672.1 → XP_054191647.1 protein crumbs homolog 1 isoform X3
XM_054335673.1 → XP_054191648.1 protein crumbs homolog 1 isoform X4
XM_054335669.1 → XP_054191644.1 protein crumbs homolog 1 isoform X1
XM_054335670.1 → XP_054191645.1 protein crumbs homolog 1 isoform X2
XM_054335674.1 → XP_054191649.1 protein crumbs homolog 1 isoform X5
XM_054335675.1 → XP_054191650.1 protein crumbs homolog 1 isoform X6

UniProtKB/TrEMBL

B7Z824

Suppressed Reference Sequence(s)

The following Reference Sequences have been suppressed. Explain

NM_012076.2: Suppressed sequence

Description

NM_012076.2: This RefSeq was permanently suppressed because it is a nonsense-mediated mRNA decay (NMD) candidate.