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Aliases for CDHR1 Gene

Aliases for CDHR1 Gene

  • Cadherin Related Family Member 1 2 3 5
  • Cadherin-Related Family Member 1 2 3
  • Photoreceptor Cadherin 3 4
  • Protocadherin-21 3 4
  • PCDH21 3 4
  • PRCAD 3 4
  • MT-Protocadherin 3
  • Protocadherin 21 2
  • KIAA1775 4
  • CORD15 3
  • PrCAD 4
  • RP65 3

External Ids for CDHR1 Gene

Previous HGNC Symbols for CDHR1 Gene

  • PCDH21

Previous GeneCards Identifiers for CDHR1 Gene

  • GC10P085954
  • GC10P079799

Summaries for CDHR1 Gene

Entrez Gene Summary for CDHR1 Gene

  • This gene belongs to the cadherin superfamily of calcium-dependent cell adhesion molecules. The encoded protein is a photoreceptor-specific cadherin that plays a role in outer segment disc morphogenesis. Mutations in this gene are associated with inherited retinal dystrophies. Alternatively spliced transcript variants encoding different isoforms have been identified. [provided by RefSeq, Jul 2013]

GeneCards Summary for CDHR1 Gene

CDHR1 (Cadherin Related Family Member 1) is a Protein Coding gene. Diseases associated with CDHR1 include Cone-Rod Dystrophy 15 and Fundus Dystrophy. Gene Ontology (GO) annotations related to this gene include calcium ion binding. An important paralog of this gene is CDHR2.

UniProtKB/Swiss-Prot for CDHR1 Gene

  • Potential calcium-dependent cell-adhesion protein. May be required for the structural integrity of the outer segment (OS) of photoreceptor cells (By similarity).

Additional gene information for CDHR1 Gene

No data available for CIViC summary , Tocris Summary , Gene Wiki entry , PharmGKB "VIP" Summary , fRNAdb sequence ontologies and piRNA Summary for CDHR1 Gene

Genomics for CDHR1 Gene

GeneHancer (GH) Regulatory Elements for CDHR1 Gene

Promoters and enhancers for CDHR1 Gene
GeneHancer (GH) Identifier GH Type GH
Score
GH Sources Gene Association Score Total Score TSS distance (kb) Number of Genes Away Size (kb) Transcription Factor
Binding Sites
Gene Targets
GH10J084194 Promoter/Enhancer 1.3 EPDnew ENCODE dbSUPER 662.9 -0.1 -105 0.2 MXI1 KLF1 PKNOX1 SP3 L3MBTL2 SP2 ZNF398 PATZ1 VEZF1 ZNF341 CDHR1 GC10P084182
GH10J084195 Promoter/Enhancer 1.1 EPDnew dbSUPER 650.7 +0.0 11 0.1 MXI1 PKNOX1 L3MBTL2 ZNF398 VEZF1 ZNF341 KLF8 CREM EZH2 CDHR1 GC10P084182 PIR57101
GH10J084137 Promoter/Enhancer 2.1 EPDnew Ensembl ENCODE 10.5 -55.2 -55234 4.2 FEZF1 DMAP1 YY1 E2F8 ZNF143 SP3 NFYC SSRP1 ZNF610 NBN GHITM ENSG00000271933 RPS3AP5 CDHR1 C10orf99 GC10M084047
GH10J084176 Enhancer 1.5 FANTOM5 Ensembl ENCODE dbSUPER 10.7 -16.6 -16592 4 HDAC1 HDGF PKNOX1 YBX1 BMI1 ZNF280A ZNF207 ATF7 FOS IKZF2 LRIT2 CDHR1 CCSER2 C10orf99 GC10P084182
GH10J084186 Enhancer 0.7 dbSUPER 21.4 -7.2 -7180 2 HDGF HDAC1 ZSCAN4 ZNF266 ZNF175 GLI4 CDC5L ZNF239 SRF SOX6 ENSG00000271933 RPS3AP5 CDHR1 LRIT2 GHITM GC10P084182
- Elite GeneHancer and/or Elite GeneHancer-gene association Download GeneHancer data from 2017 publication | Request up-to-date GeneHancer data (full dataset)

GeneHancers around CDHR1 on UCSC Golden Path with GeneCards custom track

Genomic Locations for CDHR1 Gene

Genomic Locations for CDHR1 Gene
chr10:84,194,635-84,219,621
(GRCh38/hg38)
Size:
24,987 bases
Orientation:
Plus strand
chr10:85,954,410-85,979,377
(GRCh37/hg19)
Size:
24,968 bases
Orientation:
Plus strand

Genomic View for CDHR1 Gene

Genes around CDHR1 on UCSC Golden Path with GeneCards custom track

Cytogenetic band:
CDHR1 Gene in genomic location: bands according to Ensembl, locations according to GeneLoc (and/or Entrez Gene and/or Ensembl if different)
Genomic Location for CDHR1 Gene
GeneLoc Logo Genomic Neighborhood Exon StructureGene Density

RefSeq DNA sequence for CDHR1 Gene

Proteins for CDHR1 Gene

  • Protein details for CDHR1 Gene (UniProtKB/Swiss-Prot)

    Protein Symbol:
    Q96JP9-CDHR1_HUMAN
    Recommended name:
    Cadherin-related family member 1
    Protein Accession:
    Q96JP9
    Secondary Accessions:
    • Q69YZ8
    • Q8IXY5

    Protein attributes for CDHR1 Gene

    Size:
    859 amino acids
    Molecular mass:
    93595 Da
    Quaternary structure:
    • Interacts with PROM1.

    Alternative splice isoforms for CDHR1 Gene

    UniProtKB/Swiss-Prot:

neXtProt entry for CDHR1 Gene

Post-translational modifications for CDHR1 Gene

  • Undergoes proteolytic cleavage; produces a soluble 95 kDa N-terminal fragment and a 25 kDa cell-associated C-terminal fragment.
  • Glycosylation at posLast=296296, posLast=8989, and posLast=5858
  • Modification sites at PhosphoSitePlus

No data available for DME Specific Peptides for CDHR1 Gene

Domains & Families for CDHR1 Gene

Gene Families for CDHR1 Gene

HGNC:
Human Protein Atlas (HPA):
  • Disease related genes
  • Predicted intracellular proteins
  • Predicted membrane proteins
  • Predicted secreted proteins

Protein Domains for CDHR1 Gene

Blocks:
InterPro:
ProtoNet:

Suggested Antigen Peptide Sequences for CDHR1 Gene

Graphical View of Domain Structure for InterPro Entry

genes like me logo Genes that share domains with CDHR1: view

No data available for UniProtKB/Swiss-Prot for CDHR1 Gene

Function for CDHR1 Gene

Molecular function for CDHR1 Gene

UniProtKB/Swiss-Prot Function:
Potential calcium-dependent cell-adhesion protein. May be required for the structural integrity of the outer segment (OS) of photoreceptor cells (By similarity).

Gene Ontology (GO) - Molecular Function for CDHR1 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0003674 molecular_function ND --
GO:0005509 calcium ion binding IEA --
genes like me logo Genes that share ontologies with CDHR1: view
genes like me logo Genes that share phenotypes with CDHR1: view

Human Phenotype Ontology for CDHR1 Gene

HPO Id HPO Name Alternative Ids Definition Synonyms

Animal Models for CDHR1 Gene

MGI Knock Outs for CDHR1:

Animal Model Products

CRISPR Products

Inhibitory RNA Products

  • Search GeneCopoeia for shRNA, lentivirus and/or AAV clone products for CDHR1

Clone Products

No data available for Enzyme Numbers (IUBMB) , Phenotypes From GWAS Catalog , Transcription Factor Targets and HOMER Transcription for CDHR1 Gene

Localization for CDHR1 Gene

Subcellular locations from UniProtKB/Swiss-Prot for CDHR1 Gene

Cell membrane; Single-pass membrane protein. Note=Localized at the junction between the inner and outer segments of rod and cone photoreceptors cells. Confined to the base of the OS. Localized on the edges of nascent evaginating disks on the side of the OS opposite the connecting cilium. Expressed at postnatal day 2 at the apical tip of the rod photoreceptor cells, the site of the developing OS. Colocalized with rhodopsin between postnatal days 2 and 9 at the base of the growing OS region (By similarity). {ECO:0000250}.

Subcellular locations from

COMPARTMENTS
Extracellular space Cytosol Plasma membrane Cytoskeleton Lysosome Endosome Peroxisome ER Golgi Apparatus Nucleus Mitochondrion 0 1 2 3 4 5 Confidence
COMPARTMENTS Subcellular localization image for CDHR1 gene
Compartment Confidence
plasma membrane 4
extracellular 1
mitochondrion 1
peroxisome 1
cytosol 1

Gene Ontology (GO) - Cellular Components for CDHR1 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0005575 cellular_component ND --
GO:0005886 plasma membrane IEA --
GO:0005887 integral component of plasma membrane IEA --
GO:0016020 membrane IEA --
GO:0016021 integral component of membrane IEA --
genes like me logo Genes that share ontologies with CDHR1: view

No data available for Subcellular locations from the Human Protein Atlas (HPA) for CDHR1 Gene

Pathways & Interactions for CDHR1 Gene

SuperPathways for CDHR1 Gene

No Data Available

Gene Ontology (GO) - Biological Process for CDHR1 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0007155 cell adhesion IEA --
GO:0007156 homophilic cell adhesion via plasma membrane adhesion molecules IEA --
GO:0008594 photoreceptor cell morphogenesis IMP 23044944
GO:0009987 cellular process IEA --
GO:0035845 photoreceptor cell outer segment organization IMP 23044944
genes like me logo Genes that share ontologies with CDHR1: view

No data available for Pathways by source and SIGNOR curated interactions for CDHR1 Gene

Drugs & Compounds for CDHR1 Gene

(1) Drugs for CDHR1 Gene - From: HMDB

Name Status Disease Links Group Role Mechanism of Action Clinical Trials
calcium Approved Nutra 0
genes like me logo Genes that share compounds with CDHR1: view

Transcripts for CDHR1 Gene

Unigene Clusters for CDHR1 Gene

Cadherin-related family member 1:
Representative Sequences:

CRISPR Products

Inhibitory RNA Products

  • Search GeneCopoeia for shRNA, lentivirus and/or AAV clone products for CDHR1

Clone Products

Alternative Splicing Database (ASD) splice patterns (SP) for CDHR1 Gene

ExUns: 1a · 1b · 1c ^ 2 ^ 3 ^ 4 ^ 5 ^ 6 ^ 7 ^ 8 ^ 9 ^ 10 ^ 11a · 11b ^ 12 ^ 13 ^ 14 ^ 15 ^ 16a · 16b ^ 17a · 17b · 17c ^ 18
SP1: - - - -
SP2: -
SP3: - -
SP4: - - -
SP5:

Relevant External Links for CDHR1 Gene

GeneLoc Exon Structure for
CDHR1
ECgene alternative splicing isoforms for
CDHR1

Expression for CDHR1 Gene

mRNA expression in normal human tissues from GTEx, Illumina, BioGPS, and CGAP SAGE for CDHR1 Gene

mRNA expression in embryonic tissues and stem cells from LifeMap Discovery

mRNA differential expression in normal tissues according to GTEx for CDHR1 Gene

This gene is overexpressed in Skin - Not Sun Exposed (Suprapubic) (x16.1), Skin - Sun Exposed (Lower leg) (x14.6), and Colon - Transverse (x4.9).

Protein differential expression in normal tissues from HIPED for CDHR1 Gene

This gene is overexpressed in Vitreous humor (35.0), Lung (22.6), and Platelet (7.0).

Integrated Proteomics: protein expression in normal tissues and cell lines from ProteomicsDB and MOPED for CDHR1 Gene



Protein tissue co-expression partners for CDHR1 Gene

NURSA nuclear receptor signaling pathways regulating expression of CDHR1 Gene:

CDHR1

SOURCE GeneReport for Unigene cluster for CDHR1 Gene:

Hs.137556

Evidence on tissue expression from TISSUES for CDHR1 Gene

  • Nervous system(4.5)
  • Eye(3.7)
  • Skin(2.2)

Phenotype-based relationships between genes and organs from Gene ORGANizer for CDHR1 Gene

Germ Layers:
  • ectoderm
  • endoderm
  • mesoderm
Systems:
  • cardiovascular
  • endocrine
  • immune
  • integumentary
  • nervous
  • reproductive
  • respiratory
  • skeletal muscle
  • skeleton
Regions:
Head and neck:
  • brain
  • cerebellum
  • cranial nerve
  • ear
  • eye
  • eyelid
  • face
  • head
  • lacrimal apparatus
  • middle ear
  • nose
  • outer ear
  • pituitary gland
  • skull
Thorax:
  • breast
Pelvis:
  • ovary
  • penis
  • prostate
  • testicle
  • uterus
  • vagina
  • vulva
General:
  • blood
  • blood vessel
  • hair
  • peripheral nervous system
  • red blood cell
  • skin
genes like me logo Genes that share expression patterns with CDHR1: view

No data available for mRNA Expression by UniProt/SwissProt for CDHR1 Gene

Orthologs for CDHR1 Gene

This gene was present in the common ancestor of animals.

Orthologs for CDHR1 Gene

Organism Taxonomy Gene Similarity Type Details
chimpanzee
(Pan troglodytes)
Mammalia CDHR1 34 33
  • 99.34 (n)
OneToOne
cow
(Bos Taurus)
Mammalia CDHR1 34 33
  • 86.42 (n)
OneToOne
rat
(Rattus norvegicus)
Mammalia Cdhr1 33
  • 84.48 (n)
mouse
(Mus musculus)
Mammalia Cdhr1 16 34 33
  • 84.43 (n)
dog
(Canis familiaris)
Mammalia CDHR1 34 33
  • 83.17 (n)
OneToOne
oppossum
(Monodelphis domestica)
Mammalia CDHR1 34
  • 73 (a)
OneToOne
platypus
(Ornithorhynchus anatinus)
Mammalia CDHR1 34
  • 57 (a)
OneToOne
chicken
(Gallus gallus)
Aves CDHR1 34 33
  • 70.4 (n)
OneToOne
lizard
(Anolis carolinensis)
Reptilia CDHR1 34
  • 68 (a)
OneToOne
tropical clawed frog
(Silurana tropicalis)
Amphibia cdhr1 33
  • 64 (n)
zebrafish
(Danio rerio)
Actinopterygii cdhr1a 34 33
  • 62.45 (n)
OneToMany
CDHR1 (2 of 2) 34
  • 57 (a)
OneToMany
Dr.11065 33
fruit fly
(Drosophila melanogaster)
Insecta Cad86C 34
  • 11 (a)
OneToMany
sea squirt
(Ciona savignyi)
Ascidiacea -- 34
  • 33 (a)
OneToOne
Species where no ortholog for CDHR1 was found in the sources mined by GeneCards:
  • A. gosspyii yeast (Ashbya gossypii)
  • Actinobacteria (Mycobacterium tuberculosis)
  • African clawed frog (Xenopus laevis)
  • African malaria mosquito (Anopheles gambiae)
  • Alicante grape (Vitis vinifera)
  • alpha proteobacteria (Wolbachia pipientis)
  • amoeba (Dictyostelium discoideum)
  • Archea (Pyrococcus horikoshii)
  • baker's yeast (Saccharomyces cerevisiae)
  • barley (Hordeum vulgare)
  • beta proteobacteria (Neisseria meningitidis)
  • bread mold (Neurospora crassa)
  • Chromalveolata (Phytophthora infestans)
  • common water flea (Daphnia pulex)
  • corn (Zea mays)
  • E. coli (Escherichia coli)
  • filamentous fungi (Aspergillus nidulans)
  • Firmicute bacteria (Streptococcus pneumoniae)
  • fission yeast (Schizosaccharomyces pombe)
  • green algae (Chlamydomonas reinhardtii)
  • honey bee (Apis mellifera)
  • K. lactis yeast (Kluyveromyces lactis)
  • loblloly pine (Pinus taeda)
  • malaria parasite (Plasmodium falciparum)
  • medicago trunc (Medicago Truncatula)
  • moss (Physcomitrella patens)
  • orangutan (Pongo pygmaeus)
  • pig (Sus scrofa)
  • rainbow trout (Oncorhynchus mykiss)
  • rice (Oryza sativa)
  • rice blast fungus (Magnaporthe grisea)
  • schistosome parasite (Schistosoma mansoni)
  • sea anemone (Nematostella vectensis)
  • sea urchin (Strongylocentrotus purpuratus)
  • sorghum (Sorghum bicolor)
  • soybean (Glycine max)
  • stem rust fungus (Puccinia graminis)
  • sugarcane (Saccharum officinarum)
  • thale cress (Arabidopsis thaliana)
  • tomato (Lycopersicon esculentum)
  • toxoplasmosis (Toxoplasma gondii)
  • Trichoplax (Trichoplax adhaerens)
  • wheat (Triticum aestivum)
  • worm (Caenorhabditis elegans)

Evolution for CDHR1 Gene

ENSEMBL:
Gene Tree for CDHR1 (if available)
TreeFam:
Gene Tree for CDHR1 (if available)
Aminode:
Evolutionary constrained regions (ECRs) for CDHR1: view image

Paralogs for CDHR1 Gene

Paralogs for CDHR1 Gene

genes like me logo Genes that share paralogs with CDHR1: view

Variants for CDHR1 Gene

Sequence variations from dbSNP and Humsavar for CDHR1 Gene

SNP ID Clin Chr 10 pos Variation AA Info Type
rs1006439324 uncertain-significance, Cone-Rod Dystrophy, Recessive 84,215,703(+) A/C 3_prime_UTR_variant, genic_downstream_transcript_variant, intron_variant
rs1016541624 uncertain-significance, Cone-Rod Dystrophy, Recessive 84,215,881(+) C/T 3_prime_UTR_variant, genic_downstream_transcript_variant, intron_variant
rs1043070925 uncertain-significance, Cone-Rod Dystrophy, Recessive 84,216,917(+) G/A/C 3_prime_UTR_variant, genic_downstream_transcript_variant, intron_variant
rs1055056242 uncertain-significance, Cone-Rod Dystrophy, Recessive 84,215,795(+) G/A 3_prime_UTR_variant, genic_downstream_transcript_variant, intron_variant
rs1059341 benign, Cone-Rod Dystrophy, Recessive 84,217,209(+) A/C/T 3_prime_UTR_variant, genic_downstream_transcript_variant, intron_variant

Structural Variations from Database of Genomic Variants (DGV) for CDHR1 Gene

Variant ID Type Subtype PubMed ID
nsv1046749 CNV gain 25217958
nsv1141879 OTHER inversion 24896259
nsv551745 CNV gain 21841781
nsv551753 CNV loss 21841781

Variation tolerance for CDHR1 Gene

Residual Variation Intolerance Score: 95.6% of all genes are more intolerant (likely to be disease-causing)
Gene Damage Index Score: 5.37; 70.94% of all genes are more intolerant (likely to be disease-causing)

Additional Variant Information for CDHR1 Gene

Human Gene Mutation Database (HGMD)
CDHR1
SNPedia medical, phenotypic, and genealogical associations of SNPs for
CDHR1

SNP Genotyping and Copy Number Assay Products

No data available for Polymorphic Variants from UniProtKB/Swiss-Prot for CDHR1 Gene

Disorders for CDHR1 Gene

MalaCards: The human disease database

(6) MalaCards diseases for CDHR1 Gene - From: HGMD, OMIM, ClinVar, GTR, Orphanet, Swiss-Prot, DISEASES, and GeneCards

Disorder Aliases PubMed IDs
cone-rod dystrophy 15
  • cord15
fundus dystrophy
  • retinal dystrophy
retinitis pigmentosa
  • retinitis pigmentosa 1
prolonged electroretinal response suppression
  • perrs
usher syndrome, type id
  • ush1d
- elite association - COSMIC cancer census association via MalaCards
Search CDHR1 in MalaCards View complete list of genes associated with diseases

UniProtKB/Swiss-Prot

CDHR1_HUMAN
  • Cone-rod dystrophy 15 (CORD15) [MIM:613660]: An inherited retinal dystrophy characterized by retinal pigment deposits visible on fundus examination, predominantly in the macular region, and initial loss of cone photoreceptors followed by rod degeneration. This leads to decreased visual acuity and sensitivity in the central visual field, followed by loss of peripheral vision. Severe loss of vision occurs earlier than in retinitis pigmentosa, due to cone photoreceptors degenerating at a higher rate than rod photoreceptors. {ECO:0000269 PubMed:20805371, ECO:0000269 PubMed:26350383}. Note=The disease is caused by mutations affecting the gene represented in this entry.

Additional Disease Information for CDHR1

Genetic Association Database
(GAD)
Human Genome Epidemiology Navigator
(HuGE)
ATLAS of Genetics and Cytogenetics in Oncology and Haematology
genes like me logo Genes that share disorders with CDHR1: view

No data available for Genatlas for CDHR1 Gene

Publications for CDHR1 Gene

  1. Mutant prominin 1 found in patients with macular degeneration disrupts photoreceptor disk morphogenesis in mice. (PMID: 18654668) Yang Z … Zhang K (The Journal of clinical investigation 2008) 3 4 22 58
  2. Protocadherin-21 (PCDH21), a candidate gene for human retinal dystrophies. (PMID: 16288196) Bolz H … Gal A (Molecular vision 2005) 3 4 22 58
  3. Identification of three novel non-classical cadherin genes through comprehensive analysis of large cDNAs. (PMID: 11597768) Nakajima D … Ohara O (Brain research. Molecular brain research 2001) 2 3 4 58
  4. Identification of two novel mutations in CDHR1 in consanguineous Spanish families with autosomal recessive retinal dystrophy. (PMID: 26350383) Nikopoulos K … Ayuso C (Scientific reports 2015) 3 4 58
  5. Mutations in PCDH21 cause autosomal recessive cone-rod dystrophy. (PMID: 20805371) Ostergaard E … Rosenberg T (Journal of medical genetics 2010) 3 4 58

Products for CDHR1 Gene

Sources for CDHR1 Gene

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