PMC Ciliopathies Panel

Associated Conditions
- Alström syndrome
- Autosomal dominant polycystic kidney disease (ADPKD)
- Autosomal recessive polycystic kidney disease (ARPKD)
- Bardet-Biedl syndrome
- Cystic fibrosis
- DREAM-PL syndrome (dysmorphic facies, renal agenesis, ambiguous genitalia, microcephaly, polydactyly, and lissencephaly)
- Ellis-van Creveld syndrome
- Endocrine-cerebro-osteodysplasia syndrome
- Joubert syndrome and related disorders, including Meckel-Gruber syndrome and hydrolethalus syndrome
- Nephronophthisis
- Oral-facial-digital syndrome (OFD)
- Polycystic liver disease (PCLD)
- Primary ciliary dyskinesia
- Senior-Loken syndrome
- Short-rib dysplasias
- Smith-Lemli-Opitz syndrome (SLOS)
- STAR syndrome
- Stromme syndrome
- Heterotaxy, visceral, 4, autosomal
- Retinitis pigmentosa, Joubert syndrome
- Joubert syndrome 30
- Spinocerebellar ataxia
- Bardet-Biedl syndrome 18
- Retinal dystrophy with or without macular staphyloma (RDMS), Spondylometaphyseal dysplasia, axial (SMDAX)
- Orofaciodigital syndrome XIV
- Orofaciodigital syndrome VI, Joubert syndrome 17
- COACH syndrome, Joubert syndrome, Meckel syndrome
- Ciliary dyskinesia -Lethal Ciliopathy
- Short-rib thoracic dysplasia 13 with or without polydactyly
- Morbid obesity and spermatogenic failure, Bardet-Biedl syndrome
- Bardet-Biedl syndrome, Leber congenital amaurosis, Joubert syndrome, Senior-Loken syndrome, Meckel syndrome
- Multinucleated neurons, anhydramnios, renal dysplasia, cerebellar hypoplasia and hydranencephaly (MARCH)
- Obesity, severe, and type II diabetes
- Focal segmental glomerulosclerosis, Ventriculomegaly with cystic kidney disease
- Jeune asphyxiating thoracic dystrophy, Joubert syndrome
- Deafness, Nephronophthisis, Sclerosing cholangitis, neonatal
- Orofaciodigital syndrome V
- Smith-Lemli-Opitz syndrome
- Short -rib thoracic dysplasia with or without polydactyly type 1, Short -rib thoracic dysplasia with or without polydactyly type 3, Jeune asphyxiating thoracic dystrophy, SRPS type 2 (Majewski)
- Short-rib thoracic dysplasia 15 with polydactyly
- Weyers acrofacial dysostosis, Ellis-van Creveld syndrome
- Ellis-van Creveld syndrome, Weyers acrodental dysostosis
- Interstitial nephritis, karyomegalic
- Culler-Jones syndrome
- Acrocallosal syndrome, Pallister-Hall syndrome, Grieg cephalopolysndactyly syndrome, Postaxial polydactyly type A, Preaxial polydactyly type 3, Preaxial polydactyly type 4
- Hydrolethalus syndrome
- Endocrine-cerebroosteodysplasia, Epilepsy, juvenile myoclonic
- Sensenbrenner syndrome, Cranioectodermal dysplasia (Levin-Sensenbrenner) type 1, Cranioectodermal dysplasia (Levin-Sensenbrenner) type 2
- Retinitis pigmentosa, Short -rib thoracic dysplasia with or without polydactyly, Asphyxiating thoracic dysplasia (ATD; Jeune)
- Bardet Biedl syndrome 19
- Cranioectodermal dysplasia 3
- Short-rib thoracic dysplasia 16 with or without polydactyly
- Bardet Biedl syndrome 20
- Short rib thoracic dysplasia with polydactyly, Cone-Rod dystrophy, autosomal recessive
- Joubert syndrome, Mental retardation, truncal obesity, retinal dystrophy, and micropenis (MORM syndrome)
- Joubert syndrome 26
- Short rib thoracic dysplasia with polydactyly, Joubert syndrome
- Orofaciodigital syndrome XV
- Meckel syndrome 12
- Acrocallosal syndrome, Hydrolethalus syndrome, Al-Gazali-Bakalinova syndrome, Joubert syndrome
- Left-right axis malformations
- Bardet-Biedl syndrome 17
- Nephronophthisis 20
- Bardet-Biedl syndrome, McKusick-Kaufman syndrome
- Bardet-Biedl syndrome, Meckel syndrome
- Short -rib thoracic dysplasia with or without polydactyly, SRPS type 2 (Majewski)
- Nephronophthisis, Renal-hepatic-pancreatic dysplasia
- Heterotaxy, visceral
- Nephronophthisis, Joubert syndrome, Senior-Loken syndrome
- Nephronophthisis, Renal-hepatic-pancreatic dysplasia, Meckel syndrome
- Nephronophthisis, Senior-Loken syndrome
- Simpson-Golabi-Behmel syndrome, Retinitis pigmentosa, Orofaciodigital syndrome, Joubert syndrome
- Joubert syndrome 22
- Polycystic kidney disease 1
- Polycystic kidney disease 2
- Polycystic kidney disease
- Congenital disorder of glycosylation
- Laurence-Moon syndrome, Boucher-Neuhauser syndrome, Spastic paraplegia 39
- Cone-rod dystrophy 20
- COACH syndrome, Joubert syndrome, Meckel syndrome, Retinal degeneration in ciliopathy, modifier
- Retinal dystrophy, Retinitis pigmentosa
- Senior-Loken syndrome, Retinal dystrophy
- Bardet-Biedl syndrome, Senior-Loken syndrome
- Medulloblastoma, Basal cell nevus syndrome
- Short-rib thoracic dysplasia 17 with or without polydactyly, Jeune Asphyxiating Thoracic Dystrophy
- Orofaciodigital syndrome (Mohr-Majewski syndrome), Joubert syndrome
- Nephronophthisis, COACH syndrome, Joubert syndrome, Meckel syndrome
- Senior-Loken syndrome 9
- Bardet-Biedl syndrome, Muscular dystrophy, limb-girdle
- Short-rib thoracic dysplasia, Nephronophthisis, Asphyxiating thoracic dysplasia (ATD; Jeune)
- Intellectual disability, X-linked 99, Intellectual disability, X-linked 99, syndromic, female restricted
- Meckel-Gruber syndrome, modifier, Bardet-Biedl syndrome, Congenital heart defects, hamartomas of tongue, and polysyndactyly
- Retinitis pigmentosa, Nephronophthisis, Short -rib thoracic dysplasia with or without polydactyly, Senior-Loken syndrome, Cranioectodermal dysplasia (Levin-Sensenbrenner) type 1, Cranioectodermal dysplasia (Levin-Sensenbrenner) type 2, Asphyxiating thoracic dysplasia (ATD; Jeune)
- Cranioectodermal dysplasia (Levin-Sensenbrenner) type 1, Cranioectodermal dysplasia (Levin-Sensenbrenner) type 2, Short rib-polydactyly syndrome type 5
- Short-rib thoracic dysplasia 8 with or without polydactyly
- Nephronophthisis-like nephropathy 1
- Heterotaxy, visceral, VACTERL association, Congenital heart defects, nonsyndromic
- Nephronophthisis, Joubert syndrome

Methodology

Targeted Exome/ Slice Exome (Next Generation Sequencing including Copy Number Variation)

Coverage

120x

Assay Information
- PIBF1: Sequencing analysis for exons 16 includes only cds +/- 10 bp.
- CEP290: Analysis includes the intronic variant NM_025114.3:c.2991+1655A >G.
- NOTCH2: Deletion/duplication and sequencing analysis is not offered for exons 1-4.
- RPGR: To detect X-linked retinitis pigmentosa sequence variants in exon 15 of NM_001034853.2| RPGR (ORF15) must also be analyzed.
- LRRCC1: Deletion/duplication analysis is not offered for exon 3. Sequencing analysis for exons 3 includes only cds +/- 10 bp.
- ARMC4: Deletion/duplication and sequencing analysis is not offered for exon 9.
- CRB2: Deletion/duplication analysis is not offered for exons 5-6.
- ARMC9: Deletion/duplication analysis is not offered for exons 1-2| 5-6.
- PKHD1: Deletion/duplication analysis is not offered for exon 13.
- BBS9: Deletion/duplication analysis is not offered for exon 4.
- CFTR: Analysis includes the intronic variants: NM_000492.3:c.3718-2477C >T (also known as 3849+10kbC >T)| c.1210-34TG13T5 (also known as T5TG13)| c.1210-34TG12T5 (also known as T5TG12)| c.1210-34TG11T5 (also known as T5TG11)| and c.1679+1634A >G. Sequencing analysis for exons 7 includes only cds +/- 10 bp.
- SEC63: Sequencing analysis for exons 4| 13 includes only cds +/- 0 bp.

Ordering information

Turnaround Time: 10 business days

Preferred Speciment: Saliva Kits (available upon request)

Alternate Specimens: Nail clippings or 3-mL whole blood in purple top EDTA tube

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Limitations

All sequencing technologies have limitations. A negative result from this analysis does not rule out a possible genetic diagnosis as some variants may not be detected by this test. This test is not designed to detect low level mosaicism, structural rearrangements, indels >40bp, deep intronic variants of unknown clinical significance, or large cytogenetic CNVs. Certain inherent qualities of the human genome, for example repetitive regions/homopolymers, GC rich, pseudogenes, and rare polymorphisms, pose significant technical challenges such as sequence misalignment that may potentially impact the accuracy of the results. False negative results may also occur in the setting of allogeneic bone marrow, stem cell transplantation, active or chronic hematologic conditions, recent blood transfusions, suboptimal DNA quality or PCR trace contamination. Other potential sources of error include sample mix-ups and clerical issues.

References
- 1. Richards S et al. Genetics in medicine. Standards and guidelines for the interpretation of sequence variants: a joint consensus recommendation of the American College of Medical Genetics and Genomics and the Association for Molecular Pathology. 2015 May;17(5):405-24 (PMID: 25741868)
- 2. GnomAD (gnomAD)
- 3. CSPEC (ClinGen variant classification rules registry) Criteria Specification Registry
- 4. Normal copy number variation in healthy individuals database of genomic variants: http://dgv.tcag.ca/dgv/app/home
- 5. Riggs, E.R., Andersen, E.F., Cherry, A.M. et al. Technical standards for the interpretation and reporting of constitutional copy-number variants: a joint consensus recommendation of the American College of Medical Genetics and Genomics (ACMG) and the Clinical Genome Resource (ClinGen). Genet Med 22, 245–257 (2020). https://doi.org/10.1038/s41436-019-0686-8
- 6. Landrum MJ, Lee JM, Riley GR, Jang W, Rubinstein WS, Church DM, Maglott DR. ClinVar: public archive of relationships among sequence variation and human phenotype. Nucleic Acids Res. 2014 Jan 1;42(1):D980-5. doi: 10.1093/nar/gkt1113. PubMed PMID: 24234437.
- 7. Online Mendelian Inheritance in Man, OMIM®. McKusick-Nathans Institute of Genetic Medicine, Johns Hopkins University (Baltimore, MD), Copyright® 1966-2012. World Wide Web URL: http://omim.org.
- 8. http://tinyurl.com/ACMGv4 (ACMG/ Clingen draft Interpretation SOP); clingen_variant-curation_sopv1.pdf

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Test Description

Associated Conditions

Methodology

Coverage

Assay Information

Ordering information

Limitations

References

Tagged Genes