Retinitis Pigmentosa (includes RPGR ORF15) Panel

Summary and Pricing

Test Method

Exome Sequencing with CNV Detection
Test Code Test Copy Genes Gene CPT Codes Copy CPT Codes
2699 ABCA4 81408,81479 Order Options and Pricing
ABHD12 81479,81479
ADGRA3 81479,81479
AIPL1 81479,81479
ARL2BP 81479,81479
ARL6 81479,81479
BEST1 81406,81479
C1QTNF5 81479,81479
CA4 81479,81479
CACNA1F 81479,81479
CDHR1 81479,81479
CEP290 81408,81479
CERKL 81479,81479
CFAP418 81479,81479
CHM 81479,81479
CLN3 81479,81479
CLRN1 81404,81479
CNGA1 81479,81479
CNGB1 81479,81479
CRB1 81406,81479
CRX 81404,81479
DHDDS 81479,81479
EMC1 81479,81479
EYS 81479,81479
FAM161A 81479,81479
FLVCR1 81479,81479
FSCN2 81479,81479
GUCA1B 81479,81479
GUCY2D 81479,81479
IDH3B 81479,81479
IMPDH1 81479,81479
IMPG2 81479,81479
INPP5E 81479,81479
KIAA1549 81479,81479
KLHL7 81479,81479
LCA5 81479,81479
LRAT 81479,81479
MAK 81479,81479
MERTK 81479,81479
MFRP 81479,81479
NEUROD1 81479,81479
NR2E3 81479,81479
NRL 81479,81479
OFD1 81479,81479
PCARE 81479,81479
PDE6A 81479,81479
PDE6B 81479,81479
PDE6G 81479,81479
PITPNM3 81479,81479
PLA2G5 81479,81479
PRCD 81479,81479
PRKCG 81406,81479
PROM1 81479,81479
PRPF3 81479,81479
PRPF31 81479,81479
PRPF6 81479,81479
PRPF8 81479,81479
PRPH2 81404,81479
RBP3 81479,81479
RD3 81479,81479
RDH12 81479,81479
RGR 81479,81479
RHO 81404,81479
RLBP1 81479,81479
ROM1 81479,81479
RP1 81404,81479
RP2 81479,81479
RPE65 81406,81479
RPGR 81479,81479
RPGRIP1 81479,81479
SAG 81479,81479
SEMA4A 81479,81479
SLC7A14 81479,81479
SNRNP200 81479,81479
SPATA7 81479,81479
TOPORS 81479,81479
TTC8 81479,81479
TULP1 81479,81479
USH2A 81408,81479
ZNF513 81479,81479
Test Code Test Copy Genes Panel CPT Code Gene CPT Codes Copy CPT Code Base Price
2699Genes x (80)81434 81404, 81406, 81408, 81479 $1270 Order Options and Pricing

Pricing Comments

CPT code 81434 can be used if analysis includes ABCA4, CNGA1, CRB1, EYS, PDE6A, PDE6B, PRPF31, PRPH2, RDH12, RHO, RP1, RP2, RPE65, RPGR, and USH2A. We are happy to accommodate requests for testing single genes in this panel or a subset of these genes. The price will remain the list price. If desired, free reflex testing to remaining genes on panel is available. Alternatively, a single gene or subset of genes can also be ordered via our PGxome Custom Panel tool.

An additional 25% charge will be applied to STAT orders. STAT orders are prioritized throughout the testing process.

For Reflex to PGxome pricing click here.

Turnaround Time

18 days on average for standard orders or 14 days on average for STAT orders.

Once a specimen has started the testing process in our lab, the most accurate prediction of TAT will be displayed in the myPrevent portal as an Estimated Report Date (ERD) range. We calculate the ERD for each specimen as testing progresses; therefore the ERD range may differ from our published average TAT. View more about turnaround times here.

Targeted Testing

For ordering sequencing of targeted known variants, go to our Targeted Variants page.

EMAIL CONTACTS

Genetic Counselors

Geneticist

Clinical Features and Genetics

Clinical Features

Retinitis pigmentosa (RP) represents a group of hereditary retinal dystrophies with a worldwide prevalence of ~1 in 4000 (Booij 2005). RP is clinically characterized by retinal pigment deposits visible on fundus examination, nyctalopia (night blindness), followed by progressive degeneration of the photoreceptors, which eventually leads to blindness (van Soest et al. 1999).

Genetics

Nonsyndromic and syndromic RP is remarkably heterogeneous both clinically and genetically and exhibits autosomal dominant (AD, 15%-25% of the cases), autosomal recessive (AR, 5%-20% of the cases) or X-linked (XL, 5%-15% of the cases) inheritance (Fahim et al. 2013). Unknown, simplex cases (single occurrence in a family) account for 40%-50%of cases and rarely digenic inheritance has been reported (Fahim et al. 2013). To date, over 80 genes have been linked to RP (RetNet; Daiger et al. 2007; Daiger et al. 2013; Audo et al. 2012; Neveling et al. 2012; Fu et al. 2013; Zhao et al. 2015; http://www.omim.org/; Human Gene Mutation Database), but likely more RP genes remain to be discovered (Daiger et al. 2010; Daiger et al. 2013; Perez-Carro et al. 2016).

The most common genes involved in AD RP are RHO (26-28% of RP cases), PRPF31/RP11 (5-8%), PRPH2/RDS (4-8%), RP1 (6%), IMPDH1 (1-3%), KLHL7 (0.5-1.5%), NR2E3 (0.5-1.5%), PRPF3/RP18 (1%), PRPF8/RP13 (3%), CRX (1%) and TOPORS (1%) (Fahim et al. 2013; Daiger et al. 2010; Sullivan et al. 2013).

The most common genes involved in AR RP are USH2A (10-15%), ABCA4 (2-5%), PDE6A (2-5%), PDE6B (2-5%), RPE65 (2-5%), and CNGA1 (1-2%). BEST1, PCARE (C2ORF71), C8ORF37, CLRN1, CNGB1, DHDDS, FAM161A, IDH3B, IMPG2, LRAT, MAK, MERTK, NRL, PDE6G, PRCD, PROM1, RBP3, RGR, RHO, RLBP1, RP1, SAG, SPATA7, TTC8, CERKL, TULP1, ZNF513, and ARL6 each account for less than 1% of RP cases (Fahim et al. 2013).It has been reported that it is now possible to detect disease-causing variants in about 56% of patients with adRP, 30% of patients with recessive RP, and nearly 90% of patients with X-linked RP, which indicates that the there are several or many more RP genes that have yet to be discovered (Daiger et al. 2010).See individual gene test descriptions for more information on molecular biology of gene products.

Clinical Sensitivity - Sequencing with CNV PGxome

It is now possible to detect disease-causing pathogenic variants in about 56% of patients with AD RP, 30% of patients with recessive RP, and nearly 90% of patients with X-linked RP (Daiger et al. 2010).

Genomic rearrangements in PRPF31 (causative for AD RP) are now known to account for 2.5% of AD RP (Sullivan et al. 2006). Deletions and rearrangements are also found in ABCA4, which is causative for AR RP (Yatsenko et al. 2003). In addition, copy number variants have been reported in ABHD12, ARL6, BEST1, CACNA1F, CEP290, CHM, CRB1, CRX, EYS, GUCY2D, IMPG2, MERTK, NR2E3, PDE6B, PRPF31, PRPH2, RDH12, RHO, RLBP1, RP2, RPE65, RPGR, RPGRIP1, SAG, SPATA7, TULP1 and USH2A (Human Gene Mutation Database).

Testing Strategy

This test is performed using Next-Gen sequencing with additional Sanger sequencing as necessary.

This panel typically provides 99.5% coverage of all coding exons of the genes plus 10 bases of flanking noncoding DNA in all available transcripts along with other non-coding regions in which pathogenic variants have been identified at PreventionGenetics or reported elsewhere. We define coverage as ≥20X NGS reads or Sanger sequencing.

Please note that analysis of the RPGR Exon 15 (ORF15) repetitive region is especially difficult; we utilize special chemistry for this region.

Since this test is performed using exome capture probes, a reflex to any of our exome based tests is available (PGxome, PGxome Custom Panels).

Indications for Test

All patients with symptoms suggestive of Retinitis pigmentosa are candidates.

Diseases

Name Inheritance OMIM ID
Aland Island Eye Disease XL 300600
Bothnia Retinal Dystrophy AR 607475
Cerebellar Atrophy, Vsual Impairment, and Psychomotor Retardation AR 616875
Choroideremia XL 303100
Cone-Rod Dystrophy 13 AR 608194
Cone-Rod Dystrophy 15 AR 613660
Cone-rod dystrophy 16 AR 614500
Cone-Rod Dystrophy 2 AD 120970
Cone-Rod Dystrophy 5 AR 600977
Cone-Rod Dystrophy 6 AR 601777
Cone-Rod Dystrophy X-Linked 3 XL 300476
Fleck Retina, Familial Benign AR 228980
Joubert Syndrome 5 AR 610188
Late-Onset Retinal Degeneration AD 605670
Leber Congenital Amaurosis 1 AD 204000
Leber Congenital Amaurosis 10 AR 611755
Leber Congenital Amaurosis 12 AR 610612
Leber Congenital Amaurosis 13 AR 612712
Leber Congenital Amaurosis 14 AR 613341
Leber Congenital Amaurosis 3 AR 604232
Leber Congenital Amaurosis 4 AR 604393
Leber Congenital Amaurosis 5 AD 604537
Leber Congenital Amaurosis 6 AR 613826
Leber Congenital Amaurosis 7 AR 613829
Microphthalmia, Isolated 5 AR 611040
MORM Syndrome AR 610156
Newfoundland Rod-Cone Dystrophy AD 607476
Night Blindness, Congenital Stationary, Type 2A XL 300071
Pigmentary Retinal Dystrophy AD 136880
Polyneuropathy, Hearing Loss, Ataxia, Retinitis Pigmentosa, And Cataract AR 612674
Posterior Column Ataxia With Retinitis Pigmentosa AR 609033
Retinitis Pigmentosa AD,AR 268000
Retinitis Pigmentosa 1 AD 180100
Retinitis Pigmentosa 10 AD 180105
Retinitis Pigmentosa 11 AD 600138
Retinitis Pigmentosa 12 AR 600105
Retinitis Pigmentosa 13 AD 600059
Retinitis Pigmentosa 14 AR 600132
Retinitis Pigmentosa 15 XL 300029
Retinitis Pigmentosa 17 AD 600852
Retinitis Pigmentosa 18 AD 601414
Retinitis Pigmentosa 19 AR 601718
Retinitis Pigmentosa 2 XL 312600
Retinitis Pigmentosa 20 AR 613794
Retinitis Pigmentosa 23 XL 300424
Retinitis Pigmentosa 25 AR 602772
Retinitis Pigmentosa 26 AR 608380
Retinitis Pigmentosa 27 AD 613750
Retinitis Pigmentosa 28 AR 606068
Retinitis Pigmentosa 30 AD 607921
Retinitis Pigmentosa 31 AD 609923
Retinitis Pigmentosa 33 AD 610359
Retinitis Pigmentosa 35 AR, AD 610282
Retinitis Pigmentosa 36 AR 610599
Retinitis Pigmentosa 37 AR, AD 611131
Retinitis Pigmentosa 38 AR 613862
Retinitis Pigmentosa 39 AR 613809
Retinitis Pigmentosa 4 AR, AD 613731
Retinitis Pigmentosa 40 AR 613801
Retinitis Pigmentosa 41 AR 612095
Retinitis Pigmentosa 42 AR 612943
Retinitis Pigmentosa 43 AR 613810
Retinitis Pigmentosa 44 AD,AR 613769
Retinitis Pigmentosa 45 AR 613767
Retinitis Pigmentosa 46 AR 612572
Retinitis Pigmentosa 47 AR 613758
Retinitis Pigmentosa 48 AD 613827
Retinitis Pigmentosa 49 AR 613756
Retinitis Pigmentosa 50 AR, AD 613194
Retinitis Pigmentosa 51 AR 613464
Retinitis Pigmentosa 54 AR 613428
Retinitis Pigmentosa 55 AR 613575
Retinitis Pigmentosa 56 AR 613581
Retinitis Pigmentosa 57 AR 613582
Retinitis Pigmentosa 58 AD 613617
Retinitis Pigmentosa 59 AR 613861
Retinitis Pigmentosa 60 AD 613983
Retinitis Pigmentosa 61 AR 614180
Retinitis Pigmentosa 62 AR 614181
Retinitis Pigmentosa 66 AR 615233
Retinitis Pigmentosa 68 AR 615725
Retinitis Pigmentosa 7 AR, AD 608133
Retinitis Pigmentosa with or without Situs Inversus AR 615434
Retinitis Pigmentosa, X-Linked, And Sinorespiratory Infections, With Or Without Deafness XL 300455
Senior-Loken Syndrome 6 AR 610189

Related Test

Name
PGxome®

Citations

  • Audo I. et al. 2012. Orphanet Journal of Rare Diseases. 7: 8. PubMed ID: 22277662
  • Booij J.C. et al. 2005. Journal of Medical Genetics. 42: e67. PubMed ID: 16272259
  • Daiger S.P. et al. 2007. Archives of Ophthalmology. 125: 151-8. PubMed ID: 17296890
  • Daiger S.P. et al. 2010. Advances in Experimental Medicine and Biology. 664: 325-31. PubMed ID: 20238032
  • Daiger S.P. et al. 2013. Clinical genetics. 84: 132-41. PubMed ID: 23701314
  • Fahim A.T. et al. 2013. Retinitis Pigmentosa Overview. In: Pagon RA, Adam MP, Bird TD, Dolan CR, Fong C-T, Smith RJ, and Stephens K, editors. GeneReviews(®), Seattle (WA): University of Washington, Seattle. PubMed ID: 20301590
  • Fu Q. et al. 2013. Investigative Ophthalmology & Visual Science. 54: 4158-66. PubMed ID: 23661369
  • http://www.omim.org/
  • Human Gene Mutation Database (Bio-base).
  • Neveling K. et al. 2012. Human Mutation. 33: 963-72. PubMed ID: 22334370
  • Perez-Carro R. et al. 2016. Scientific Reports. 6: 19531.  PubMed ID: 26806561
  • Sullivan L.S. et al. 2006. Investigative Ophthalmology & Visual Science. 47: 4579-88. PubMed ID: 17003455
  • Sullivan L.S. et al. 2013. Investigative ophthalmology & visual science. 54: 6255-61. PubMed ID: 23950152
  • van Soest S. et al. 1999. Survey of Ophthalmology. 43: 321-34. PubMed ID: 10025514
  • Yatsenko A.N. et al. 2003. Human Mutation. 21:636-44. PubMed ID: 12754711
  • Zhao L. et al. 2015. Human Genetics. 134: 217-30.  PubMed ID: 25472526

Ordering/Specimens

Ordering Options

We offer several options when ordering sequencing tests. For more information on these options, see our Ordering Instructions page. To view available options, click on the Order Options button within the test description.

myPrevent - Online Ordering

  • The test can be added to your online orders in the Summary and Pricing section.
  • Once the test has been added log in to myPrevent to fill out an online requisition form.

Requisition Form

  • A completed requisition form must accompany all specimens.
  • Billing information along with specimen and shipping instructions are within the requisition form.
  • All testing must be ordered by a qualified healthcare provider.

For Requisition Forms, visit our Forms page


Specimen Types

Specimen Requirements and Shipping Details

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ORDER OPTIONS

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2) Select Additional Test Options

STAT and Prenatal Test Options are not available with Patient Plus.

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