CDHR1

cadherin related family member 1, the group of Cadherin related

Basic information

Region (hg38): 10:84194537-84219621

Previous symbols: [ "PCDH21" ]

Links

ENSG00000148600

∙ NCBI:92211 ∙ OMIM:609502 ∙ HGNC:14550 ∙ Uniprot:Q96JP9 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

Phenotypes

GenCC

Source: genCC

retinitis pigmentosa (Supportive), mode of inheritance: AD
cone-rod dystrophy (Supportive), mode of inheritance: AD
cone-rod dystrophy 15 (Definitive), mode of inheritance: AR
cone-rod dystrophy 15 (Strong), mode of inheritance: AR
cone-rod dystrophy 15 (Definitive), mode of inheritance: AR

Clinical Genomic Database

Source: CGD

Condition	Inheritance	Intervention Categories	Intervention/Rationale	Manifestation Categories	References
Cone-rod dystrophy 15; Retinitis pigmentosa 65	AR	General	Genetic knowledge may be beneficial related to issues such as selection of optimal supportive care, informed medical decision-making, prognostic considerations, and avoidance of unnecessary testing	Ophthalmologic	20805371

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the CDHR1 gene.

not_provided (763 variants)
Inborn_genetic_diseases (122 variants)
Cone-rod_dystrophy_15 (104 variants)
Retinal_dystrophy (50 variants)
CDHR1-related_disorder (29 variants)
not_specified (15 variants)
Cone-Rod_Dystrophy,_Recessive (13 variants)
Retinitis_pigmentosa (11 variants)
Retinitis_pigmentosa_65 (6 variants)
Cone-rod_dystrophy (4 variants)
Macular_dystrophy,_retinal,_5 (4 variants)
Optic_atrophy (2 variants)
Leber_congenital_amaurosis (1 variants)
Cone-rod_dystrophy_12 (1 variants)
maculopathy (1 variants)
Cone_dystrophy (1 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the CDHR1 gene is commonly pathogenic or not. These statistics are base on transcript: NM_000033100.4. Only rare variants are included in the table.

In the table, we include only reliable ClinVar variants with their consequences to MANE Select, Mane Plus Clinical transcripts, or transcripts with TSL equals 1. Click the count to view the source variants.

Warning: slight differences between displayed counts and the number of variants in ClinVar may occur, primarily due to (1) the application of a different transcript and/or consequence by our variant effect predictor or (2) differences in clinical significance: we classify Benign/Likely benign variants as Likely benign and Pathogenic/Likely pathogenic variants as Likely pathogenic.

Effect	PathogenicP	Likely pathogenicLP	VUSVUS	Likely benignLB	BenignB	Sum
synonymous		1 clinvar	6 clinvar	164 clinvar	1 clinvar	172
missense		7 clinvar	370 clinvar	48 clinvar	2 clinvar	427
nonsense	16 clinvar	4 clinvar	3 clinvar			23
start loss	1	1				2
frameshift	30 clinvar	12 clinvar	4 clinvar			46
splice donor/acceptor (+/-2bp)	11 clinvar	16 clinvar	1 clinvar			28
Total	58	41	384	212	3

Highest pathogenic variant AF is 0.00236715

Loading clinvar variants...

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
CDHR1	protein_coding	protein_coding	ENST00000372117	17	24968

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
2.84e-21	0.00199	125652	0	96	125748	0.000382

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	-0.697	534	491	1.09	0.0000305	5605
Missense in Polyphen		165	155.58	1.0606		1777
Synonymous	-0.229	210	206	1.02	0.0000145	1769
Loss of Function	0.126	32	32.8	0.976	0.00000160	392

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.00118	0.00117
Ashkenazi Jewish	0.00	0.00
East Asian	0.000109	0.000109
Finnish	0.0000924	0.0000924
European (Non-Finnish)	0.000318	0.000316
Middle Eastern	0.000109	0.000109
South Asian	0.000687	0.000686
Other	0.000815	0.000815

dbNSFP

Source: dbNSFP

Function: FUNCTION: Potential calcium-dependent cell-adhesion protein. May be required for the structural integrity of the outer segment (OS) of photoreceptor cells (By similarity). {ECO:0000250}.;
Disease: DISEASE: 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.;

Recessive Scores

pRec: 0.144

Intolerance Scores

loftool: 0.893
rvis_EVS: 0.01
rvis_percentile_EVS: 54.18

Haploinsufficiency Scores

pHI: 0.443
hipred: N
hipred_score: 0.342
ghis: 0.494

Essentials

essential_gene_CRISPR: N
essential_gene_CRISPR2: N
essential_gene_gene_trap: N
gene_indispensability_pred: E
gene_indispensability_score: 0.539

Gene Damage Prediction

	All	Recessive	Dominant
Mendelian	Medium	Medium	Medium
Primary Immunodeficiency	Medium	Medium	Medium
Cancer	Medium	Medium	Medium

Mouse Genome Informatics

Gene name: Cdhr1
Phenotype: vision/eye phenotype; normal phenotype;

Gene ontology

Biological process: cell adhesion;homophilic cell adhesion via plasma membrane adhesion molecules;photoreceptor cell morphogenesis;photoreceptor cell outer segment organization;photoreceptor cell maintenance
Cellular component: cellular_component;integral component of plasma membrane;photoreceptor outer segment membrane
Molecular function: molecular_function;calcium ion binding