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    CDHR1 cadherin related family member 1 [ Homo sapiens (human) ]

    Gene ID: 92211, updated on 10-Dec-2024

    Summary

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    Official Symbol
    CDHR1provided by HGNC
    Official Full Name
    cadherin related family member 1provided by HGNC
    Primary source
    HGNC:HGNC:14550
    See related
    Ensembl:ENSG00000148600 MIM:609502; AllianceGenome:HGNC:14550
    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
    RP65; PRCAD; CORD15; PCDH21
    Summary
    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]
    Expression
    Biased expression in skin (RPKM 98.8), colon (RPKM 10.9) and 1 other tissue See more
    Orthologs
    mouse all
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    Genomic context

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    See CDHR1 in Genome Data Viewer
    Location:
    10q23.1
    Exon count:
    19
    Annotation release Status Assembly Chr Location
    RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 10 NC_000010.11 (84194537..84219621)
    RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 10 NC_060934.1 (85073058..85098147)
    RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 10 NC_000010.10 (85954293..85979377)

    Chromosome 10 - NC_000010.11Genomic Context describing neighboring genes Neighboring gene ATAC-STARR-seq lymphoblastoid active region 3674 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr10:85931151-85931652 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 3676 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 3677 Neighboring gene competing endogenous lncRNA 2 for microRNA let-7b Neighboring gene H3K4me1 hESC enhancer GRCh37_chr10:85936583-85937084 Neighboring gene G protein-coupled receptor 15 ligand Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr10:85939583-85940403 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 2550 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 2551 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr10:85963048-85963548 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr10:85963549-85964049 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr10:85974015-85974538 Neighboring gene leucine rich repeat, Ig-like and transmembrane domains 2 Neighboring gene leucine rich repeat, Ig-like and transmembrane domains 1

    Genomic regions, transcripts, and products

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    Go to nucleotide: Graphics FASTA GenBank

    Expression

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    • Project title: Tissue-specific circular RNA induction during human fetal development
    • Description: 35 human fetal samples from 6 tissues (3 - 7 replicates per tissue) collected between 10 and 20 weeks gestational time were sequenced using Illumina TruSeq Stranded Total RNA
    • BioProject: PRJNA270632
    • Publication: PMID 26076956
    • Analysis date: Mon Apr 2 22:54:59 2018

    Bibliography

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    Related articles in PubMed

    1. Clinical Phenotypes of CDHR1-Associated Retinal Dystrophies. Malechka VV, et al. Genes (Basel), 2022 May 22. PMID 35627310, Free PMC Article
    2. Deep phenotyping of the Cdhr1(-/-) mouse validates its use in pre-clinical studies for human CDHR1-associated retinal degeneration. Yusuf IH, et al. Exp Eye Res, 2021 Jul. PMID 33964272
    3. Protocadherin-21 (PCDH21), a candidate gene for human retinal dystrophies. Bolz H, et al. Mol Vis, 2005 Nov 3. PMID 16288196
    4. A clinical study of patients with novel CDHR1 genotypes associated with late-onset macular dystrophy. Ba-Abbad R, et al. Eye (Lond), 2021 May. PMID 32681094, Free PMC Article
    5. Identification of a novel homozygous nonsense mutation in the CDHR1 gene in a Chinese family with autosomal recessive retinitis pigmentosa. Gan L, et al. Clin Chim Acta, 2020 Aug. PMID 32277948

    See all (30) citations in PubMed

    GeneRIFs: Gene References Into Functions

    What's a GeneRIF?
    1. Clinical Phenotypes of CDHR1-Associated Retinal Dystrophies.
      Title: Clinical Phenotypes of CDHR1-Associated Retinal Dystrophies.
    2. A rare case of RGR/CDHR1 haplotype identified in Bulgarian patient with cone-rod dystrophy.
      Title: A rare case of RGR/CDHR1 haplotype identified in Bulgarian patient with cone-rod dystrophy.
    3. Deep phenotyping of the Cdhr1(-/-) mouse validates its use in pre-clinical studies for human CDHR1-associated retinal degeneration.
      Title: Deep phenotyping of the Cdhr1(-/-) mouse validates its use in pre-clinical studies for human CDHR1-associated retinal degeneration.
    4. A clinical study of patients with novel CDHR1 genotypes associated with late-onset macular dystrophy.
      Title: A clinical study of patients with novel CDHR1 genotypes associated with late-onset macular dystrophy.
    5. Identification of a novel homozygous nonsense mutation in the CDHR1 gene in a Chinese family with autosomal recessive retinitis pigmentosa.
      Title: Identification of a novel homozygous nonsense mutation in the CDHR1 gene in a Chinese family with autosomal recessive retinitis pigmentosa.
    6. Patients with biallelic c.783G>A CDHR1 mutations demonstrate a retinal phenotype consistent with autosomal recessive central areolar choroidal dystrophy (CACD).
      Title: A Specific Macula-Predominant Retinal Phenotype Is Associated With the CDHR1 Variant c.783G>A, a Silent Mutation Leading to In-Frame Exon Skipping.
    7. our study is the first to indicate that the novel homozygous variant c.T1641A (p.Y547*) in the CHDR1 gene might be the disease-causing mutation for retinal dystrophy in our patient, extending its mutation spectrums.
      Title: A novel, homozygous nonsense variant of the CDHR1 gene in a Chinese family causes autosomal recessive retinal dystrophy by NGS-based genetic diagnosis.
    8. Mutations in CDHR1 are a rare cause of retinal dystrophy. This study further expands the mutational spectrum of this gene and the associated clinical presentation.
      Title: CDHR1 mutations in retinal dystrophies.
    9. CDHR1-related retinal dystrophy should be considered in adult patients with a retinal dystrophy who present with symptoms of cone-and-rod dysfunction and macular atrophy on ophthalmoscopic examination.
      Title: Clinical characteristics of recessive retinal degeneration due to mutations in the CDHR1 gene and a review of the literature.
    10. the recessive retinal disorder previously reported to be due to homozygous mutation in RGR is, at least in part, due to variants in CDHR1 and that the true consequences of RGR knock-out on human retinal structure and function are yet to be determined.
      Title: Reevaluation of the Retinal Dystrophy Due to Recessive Alleles of RGR With the Discovery of a Cis-Acting Mutation in CDHR1.
    Submit: New GeneRIF Correction See all GeneRIFs (18)

    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
    Cone-rod dystrophy 15
    MedGen: C3150912 OMIM: 613660 GeneReviews: Not available
    		Compare labs

    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

    Homology

    Clone Names

    • KIAA1775, DKFZp434A132

    Gene Ontology Provided by GOA

    Function Evidence Code Pubs
    enables calcium ion binding IEA
    Inferred from Electronic Annotation
    more info
    		  
    Process Evidence Code Pubs
    involved_in cell adhesion IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    involved_in homophilic cell adhesion via plasma membrane adhesion molecules IEA
    Inferred from Electronic Annotation
    more info
    		  
    involved_in photoreceptor cell maintenance IMP
    Inferred from Mutant Phenotype
    more info
    		 PubMed 
    involved_in photoreceptor cell morphogenesis IMP
    Inferred from Mutant Phenotype
    more info
    		 PubMed 
    involved_in photoreceptor cell outer segment organization IMP
    Inferred from Mutant Phenotype
    more info
    		 PubMed 
    Component Evidence Code Pubs
    located_in photoreceptor outer segment membrane IEA
    Inferred from Electronic Annotation
    more info
    		  
    is_active_in plasma membrane IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  

    General protein information

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    Preferred Names
    cadherin-related family member 1
    Names
    MT-protocadherin
    photoreceptor cadherin
    protocadherin-21

    NCBI Reference Sequences (RefSeq)

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    NEW Try the new Transcript table

    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

    1. NG_028034.1 RefSeqGene

      Range
      4882..29039
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. NM_001171971.3 → NP_001165442.1  cadherin-related family member 1 isoform 2 precursor

      See identical proteins and their annotated locations for NP_001165442.1

      Status: REVIEWED

      Description
      Transcript Variant: This variant (2) differs in the 3' coding region and 3' UTR, compared to variant 1. The resulting isoform (2) has a distinct C-terminus and is shorter than isoform 1.
      Source sequence(s)
      AB593154, AC022389, BC038799
      Consensus CDS
      CCDS53548.1
      UniProtKB/Swiss-Prot
      Q96JP9
      UniProtKB/TrEMBL
      F1T0L2
      Related
      ENSP00000331063.3, ENST00000332904.7
      Conserved Domains (1) summary
      cd11304
      Location:139 → 241
      Cadherin_repeat; Cadherin tandem repeat domain

    2. NM_033100.4 → NP_149091.1  cadherin-related family member 1 isoform 1 precursor

      See identical proteins and their annotated locations for NP_149091.1

      Status: REVIEWED

      Description
      Transcript Variant: This variant (1) represents the longer transcript and encodes the longer isoform (1).
      Source sequence(s)
      AA576346, AB593154, AB593155, AC022389, BM674749
      Consensus CDS
      CCDS7372.1
      UniProtKB/Swiss-Prot
      Q69YZ8, Q8IXY5, Q96JP9
      UniProtKB/TrEMBL
      F1T0L2
      Related
      ENSP00000485478.1, ENST00000623527.4
      Conserved Domains (1) summary
      cd11304
      Location:139 → 241
      Cadherin_repeat; Cadherin tandem repeat domain

    RefSeqs of Annotated Genomes: GCF_000001405.40-RS_2024_08

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

    Reference GRCh38.p14 Primary Assembly

    Genomic

    1. NC_000010.11 Reference GRCh38.p14 Primary Assembly

      Range
      84194537..84219621
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_011540338.2 → XP_011538640.1  cadherin-related family member 1 isoform X2

      Conserved Domains (1) summary
      cd11304
      Location:197 → 299
      Cadherin_repeat; Cadherin tandem repeat domain

    2. XM_011540337.2 → XP_011538639.1  cadherin-related family member 1 isoform X1

      Conserved Domains (1) summary
      cd11304
      Location:197 → 299
      Cadherin_repeat; Cadherin tandem repeat domain

    3. XM_011540340.4 → XP_011538642.1  cadherin-related family member 1 isoform X4

      Conserved Domains (1) summary
      cd11304
      Location:197 → 299
      Cadherin_repeat; Cadherin tandem repeat domain

    4. XM_047425997.1 → XP_047281953.1  cadherin-related family member 1 isoform X5

      UniProtKB/TrEMBL
      B3KWC7
      Related
      ENSP00000361189.4, ENST00000372117.6

    5. XM_011540339.2 → XP_011538641.1  cadherin-related family member 1 isoform X3

      Conserved Domains (1) summary
      cd11304
      Location:328 → 423
      Cadherin_repeat; Cadherin tandem repeat domain

    Alternate T2T-CHM13v2.0

    Genomic

    1. NC_060934.1 Alternate T2T-CHM13v2.0

      Range
      85073058..85098147
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_054367145.1 → XP_054223120.1  cadherin-related family member 1 isoform X1

    2. XM_054367146.1 → XP_054223121.1  cadherin-related family member 1 isoform X2

    3. XM_054367148.1 → XP_054223123.1  cadherin-related family member 1 isoform X4

    4. XM_054367149.1 → XP_054223124.1  cadherin-related family member 1 isoform X5

      UniProtKB/TrEMBL
      B3KWC7

    5. XM_054367147.1 → XP_054223122.1  cadherin-related family member 1 isoform X3

    Nucleotide Protein
    Heading Accession and Version
    Protein Accession Links
    GenPept Link UniProtKB Link
    Q96JP9.2 GenPept UniProtKB/Swiss-Prot:Q96JP9

    Gene LinkOut

    The following LinkOut resources are supplied by external providers. These providers are responsible for maintaining the links.

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