CPLANE1

ciliogenesis and planar polarity effector complex subunit 1, the group of Ciliogenesis and planar polarity effector complex subunits

Basic information

Region (hg38): 5:37106228-37249376

Previous symbols: [ "C5orf42" ]

Links

ENSG00000197603NCBI:65250OMIM:614571HGNC:25801Uniprot:Q9H799AlphaFoldGenCCjaxSfariGnomADPubmedClinVar

Phenotypes

GenCC

Source: genCC

  • Joubert syndrome 17 (Definitive), mode of inheritance: AR
  • Joubert syndrome (Supportive), mode of inheritance: AR
  • orofaciodigital syndrome type 6 (Supportive), mode of inheritance: AR
  • Joubert syndrome 17 (Definitive), mode of inheritance: AR
  • Joubert syndrome 17 (Definitive), mode of inheritance: AR
  • Joubert syndrome 17 (Strong), mode of inheritance: AR
  • orofaciodigital syndrome type 6 (Strong), mode of inheritance: AR
  • orofaciodigital syndrome type 6 (Definitive), mode of inheritance: AR
  • Joubert syndrome 17 (Definitive), mode of inheritance: AR

Clinical Genomic Database

Source: CGD

ConditionInheritanceIntervention CategoriesIntervention/Rationale Manifestation CategoriesReferences
Joubert syndrome 17; Orofaciodigital syndrome VIARGeneralGenetic knowledge may be beneficial related to issues such as selection of optimal supportive care, informed medical decision-making, prognostic considerations, and avoidance of unnecessary testingCraniofacial; Genitourinary; Musculoskeletal; Neurologic5816874; 20301500; 22425360; 23169490; 24178751
The condition may involve multi-systemic manifestations, and surveillance and avoidance of certain medications (eg, nephrotoxic agents) may be beneficial

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the CPLANE1 gene.

  • not_provided (1948 variants)
  • Joubert_syndrome_17 (791 variants)
  • Orofaciodigital_syndrome_type_6 (617 variants)
  • not_specified (105 variants)
  • Inborn_genetic_diseases (85 variants)
  • CPLANE1-related_disorder (67 variants)
  • Joubert_syndrome_and_related_disorders (25 variants)
  • Joubert_syndrome (12 variants)
  • Joubert_syndrome_1 (8 variants)
  • See_cases (7 variants)
  • Nephronophthisis (4 variants)
  • Global_developmental_delay (4 variants)
  • Jaundice (3 variants)
  • Craniosynostosis_syndrome (2 variants)
  • Intellectual_disability (2 variants)
  • Encephalocele (2 variants)
  • Polydactyly (2 variants)
  • Median_cleft_lip_and_palate (2 variants)
  • Dysgenesis_of_the_cerebellar_vermis (2 variants)
  • Cleft_lip (1 variants)
  • Typical_Joubert_syndrome_MRI_findings (1 variants)
  • Cleft_palate (1 variants)
  • Astrocytoma (1 variants)
  • Joubert-orofaciodigital_syndrome (1 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the CPLANE1 gene is commonly pathogenic or not. These statistics are base on transcript: NM_001384732.1. 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.

EffectPLPVUSLBBSum
synonymous
2
clinvar
28
clinvar
411
clinvar
13
clinvar
454
missense
8
clinvar
28
clinvar
1017
clinvar
85
clinvar
8
clinvar
1146
nonsense
57
clinvar
39
clinvar
2
clinvar
1
clinvar
99
start loss
1
1
frameshift
81
clinvar
58
clinvar
6
clinvar
145
splice donor/acceptor (+/-2bp)
9
clinvar
48
clinvar
5
clinvar
62
Total 156 175 1058 497 21

Highest pathogenic variant AF is 0.000764446

Loading clinvar variants...

GnomAD

Source: gnomAD

GeneTypeBio TypeTranscript Coding Exons Length
CPLANE1protein_codingprotein_codingENST00000425232 51143201
pLI Probability
LOF Intolerant
pRec Probability
LOF Recessive
Individuals with
no LOFs
Individuals with
Homozygous LOFs
Individuals with
Heterozygous LOFs
Defined p
5.88e-361.0012550102461257470.000979
Z-Score Observed Expected Observed/Expected Mutation Rate Total Possible in Transcript
Missense1.9313071.52e+30.8600.000075020974
Missense in Polyphen308406.020.758595940
Synonymous1.275055430.9310.00002825974
Loss of Function4.92821460.5610.000007082047

LoF frequencies by population

EthnicitySum of pLOFs p
African & African-American0.001630.00161
Ashkenazi Jewish0.0004010.000397
East Asian0.0007080.000707
Finnish0.0005200.000508
European (Non-Finnish)0.001360.00128
Middle Eastern0.0007080.000707
South Asian0.0008210.000784
Other0.001830.00163

dbNSFP

Source: dbNSFP

Function
FUNCTION: Involved in ciliogenesis (PubMed:25877302). Involved in the establishment of cell polarity required for directional cell migration. Proposed to act in association with the CPLANE (ciliogenesis and planar polarity effectors) complex. Involved in recruitment of peripheral IFT-A proteins to basal bodies (By similarity). {ECO:0000250|UniProtKB:Q8CE72, ECO:0000305|PubMed:25877302}.;
Disease
DISEASE: Joubert syndrome 17 (JBTS17) [MIM:614615]: A disorder presenting with cerebellar ataxia, oculomotor apraxia, hypotonia, neonatal breathing abnormalities and psychomotor delay. Neuroradiologically, it is characterized by cerebellar vermian hypoplasia/aplasia, thickened and reoriented superior cerebellar peduncles, and an abnormally large interpeduncular fossa, giving the appearance of a molar tooth on transaxial slices (molar tooth sign). Additional variable features include retinal dystrophy and renal disease. {ECO:0000269|PubMed:22425360, ECO:0000269|PubMed:23012439, ECO:0000269|PubMed:26477546}. Note=The disease is caused by mutations affecting the gene represented in this entry.; DISEASE: Orofaciodigital syndrome 6 (OFD6) [MIM:277170]: A form of orofaciodigital syndrome, a group of heterogeneous disorders characterized by malformations of the oral cavity, face and digits, and associated phenotypic abnormalities that lead to the delineation of various subtypes. OFD6 is characterized by metacarpal abnormalities with central polydactyly, cerebellar abnormalities including the molar tooth sign, tongue hamartomas, additional frenula, and upper lip notch. {ECO:0000269|PubMed:24178751, ECO:0000269|PubMed:25846457, ECO:0000269|PubMed:27081551}. Note=The disease is caused by mutations affecting the gene represented in this entry.;

Intolerance Scores

loftool
rvis_EVS
-0.55
rvis_percentile_EVS
19.94

Haploinsufficiency Scores

pHI
0.110
hipred
N
hipred_score
0.233
ghis
0.544

Mouse Genome Informatics

Gene name
Cplane1
Phenotype
homeostasis/metabolism phenotype; cellular phenotype; craniofacial phenotype; growth/size/body region phenotype; respiratory system phenotype; embryo phenotype; skeleton phenotype; renal/urinary system phenotype; digestive/alimentary phenotype; limbs/digits/tail phenotype; nervous system phenotype (the observable morphological and physiological characteristics of the extensive, intricate network of electochemical structures in the body that is comprised of the brain, spinal cord, nerves, ganglia and parts of the receptor organs that are manifested through development and lifespan); cardiovascular system phenotype (the observable morphological and physiological characteristics of the mammalian heart, blood vessels, or circulatory system that are manifested through development and lifespan); mortality/aging (the observable characteristics related to the ability of a mammalian organism to live and age that are manifested throughout development and life span);

Gene ontology

Biological process
establishment of planar polarity;kidney development;ventricular septum development;heart development;cerebellum development;embryonic digit morphogenesis;roof of mouth development;cilium assembly;coronary vasculature development;protein localization to ciliary transition zone
Cellular component
integral component of membrane;ciliary transition zone
Molecular function