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

Summary

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

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_000010.11 Genomic Context describing neighboring genes

Genomic regions, transcripts, and products

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Genomic Sequence:

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Expression

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See details

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?

Clinical Phenotypes of CDHR1-Associated Retinal Dystrophies.
Title: Clinical Phenotypes of CDHR1-Associated Retinal Dystrophies.
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.
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.
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.
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.
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.
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.
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.
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.
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

RH15739 (e-PCR)
- UniSTS:62211

G42184 (e-PCR)
- UniSTS:105102

Gene Ontology Provided by GOA

Function	Evidence Code	Pubs
enables calcium ion binding	IEA Inferred from Electronic Annotation more info
enables molecular_function	ND No biological Data available 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
is_active_in cellular_component	ND No biological Data available more info
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

NG_028034.1 RefSeqGene

Range

4882..29039

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GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

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
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

NC_000010.11 Reference GRCh38.p14 Primary Assembly

Range

84194537..84219621

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GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

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

Related

ENSP00000361189.4, ENST00000372117.6
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