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

Gene ID: 92211, updated on 14-Nov-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: HPA RNA-seq normal tissues 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?
  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
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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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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

    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

  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

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