Detection Rates Table
The Detection Rates Table is a compilation of data based on extensive literature review. The detection rates listed reflect the likelihood that Signature Genomic Laboratories' current array CGH technology, the SignatureChip®, will detect a microdeletion or microduplication in patients with phenotypes consistent with each specific clinical condition. These rates are subject to change as additional information is learned about the use of array CGH in clinical diagnostic testing. For most conditions, a negative test result does not exclude a specific clinical diagnosis. The SignatureChip® will not detect sequence alterations or single base pair mutations, or abnormalities in other genes or loci not tested with this technology.
1p36-Xp11.3 |A |B |C |D |E |F |G |H |I |J |K |L |M |N |O |P |R |S |T |U |V |W |X |Subtelomeric |Pericentromeric |Aneuploidy
| Condition | OMIM# | Gene/Locus | Location | Detection rate for deletion/duplication by microarray | Comments | Present on SignatureChip Version | References | |||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| 1 | 2 | 3 | 4 | WG v1 | OS v1 | WG v2 | OS v2 | OS v3 | ||||||||||||
Information based on UCSC Genome Browser, March 2006 Assembly. |
||||||||||||||||||||
| 1p36 Microdeletion *
GeneReviews | 607872 | Multiple | 1p36 | ~99% have a detectable deletion | • | • | • | • | • | • | • | • | • | |||||||
| 1q21.1 Distal microdeletion *
GeneReviews | 612474 | Multiple | 1q21.1 | ~99% have a detectable deletion | Candidate genes ACP6 (611471), GJA5 (121013), and GJA8 (600897). Deletions and duplications have also been described in unaffected individuals. | • | • | • | • | • | ||||||||||
| 1q21.1 Microdeletion with susceptibility for thrombocytopenia-absent radius (TAR)
Resources GeneReviews | 274000 | Multiple | 1q21.1 | ~99% have a detectable deletion | Deletions have also been described in unaffected individuals. | • | • | • | • | • | • | • | • | • |
Klopocki et al. 2007. Am J Hum Genet. 80:232-40. Epub 2006 Dec 21 Medline
| |||||
| 1q41-q42 Microdeletion/Fryns
GeneReviews | 612530 | Multiple | 1q41-q42 | ~99% have a detectable deletion | See also OMIM 229850. | • | • | • | • | • | • | • | • | |||||||
| 1q44 Microdeletion
| Multiple | 1q44 | ~99% have a detectable deletion | Candidate gene AKT3 (611223) | • | • | • | • | • | • | ||||||||||
| 2p15-p16.1 Microdeletion
| 612513 | Multiple | 2p15-p16.1 | ~99% have a detectable deletion | • | • | • | • | • | |||||||||||
| 2p16.3 Microdeletion/Pitt-Hopkins-like 2 *
| 600565 |
NRXN1 | 2p16.3 | Precise detection rate unknown | Deletions have been reported to cause phenotypes in both heterozygotes and compound heterozygotes and have also been described in unaffected individuals. | • | • | • | ||||||||||||
| 2p21 Microdeletion, autosomal recessive
| 606407 | Multiple | 2p21 | ~99% have detectable homozygous deletions | Recessive condition. Phenotypic overlap with Hypotonia-cystinuria syndrome. | • | • | |||||||||||||
| 2q23.1 Microdeletion
|
MBD5 EPC2 | 2q23.1 | ~99% have a detectable deletion | Phenotypic overlap with Mental retardation 1, autosomal dominant (MRD1) (156200). | • | • | • | |||||||||||||
| 2q32.2-q33 Microdeletion
| 119540 | Multiple | 2q33.1 | ~99% have a detectable deletion | Candidate gene SATB2 (119540) | • | • | • | • | • | ||||||||||
| 3q29 Microdeletion
| 609425 | Multiple | 3q29 | ~99% have a detectable deletion | • | • | • | • | • | • | • |
Willatt et al. 2005. Am J Hum Genet 77:154-60. Medline
| ||||||||
| 3q29 Microduplication *
| 611936 | Multiple | 3q29 | ~99% have a detectable duplication | Duplications have also been described in unaffected individuals. | • | • | • | • | • | • | • | ||||||||
| 5p13.2 Microduplication *
| 613174 |
NIPBL | 5p13.2 | ~99% have a detectable duplication | • | • | • | • | • | • | • | • |
Yan et al. 2009. J Med Genet. 46:626-34. Epub 2008 Dec 3 Medline
| |||||||
| 5q35.2-q35.3 Microduplication *
|
NSD1 | 5q35.2-q35.3 | ~99% have a detectable duplication | • | • | • | • | • | • | • | • | • | ||||||||
| 6p25.3 Microdeletion
| 612582 | Multiple | 6p25.3 | ~99% have a detectable deletion | Considerable phenotypic overlap with Craniocerebello-cardiac dysplasia (220210). | • | • | • | • | • | • | • | • | • | ||||||
| 6q24.3 Microdeletion
| 612863 | Multiple | 6q24.3 | ~99% have a detectable deletion | Phenotype may be limited to deletions of the paternally inherited chromosome. | • | • | • |
Nowaczyk et al. 2008. Am J Med Genet. 146:354-60. Medline
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| 6q25.2-q25.3 Microdeletion
| 612863 | Multiple | 6q25.2-q25.3 | ~99% have a detectable deletion | • | • | • |
Nagamani et al. 2009. Eur J Hum Genet. 17:573-81. Epub 2008 Nov 26 Medline
| ||||||||||||
| 7q11.23 Microduplication *
| 609757 | Multiple | 7q11.23 | ~99% have a detectable duplication | • | • | • | • | • | • | • | • | • | |||||||
| 8p23.1 Microdeletion/Congenital diaphragmatic hernia 2 (CDH2)
GeneReviews | 222400 | Multiple | 8p23.1 | ~99% have a detectable deletion | Candidate gene GATA4 (600576). | • | • | • | • | • | • | • | • | |||||||
| 8p23.1 Microduplication *
| Multiple | 8p23.1 | ~99% have a detectable duplication | Candidate gene GATA4 (600576). | • | • | • | • | • | • | • | • |
Barber et al. 2010. Mol Cytogenet. 3:3 Medline
| |||||||
| 8q12 Microduplication *
| Multiple | 8q12.1-q12.3 | ~99% have a detectable duplication | Candidate gene CHD7 (608892). | • | • | • | • | • | • | • | • | • | |||||||
| 9q22.32-q22.33 Microdeletion
| Multiple | 9q22.32-q22.33 | ~99% have a detectable deletion | Candidate genes TGFBR1 (190181) and GABBR2 (607340). | • | • | • | • | • |
Redon et al. 2006. Eur J Hum Genet 14:759-67. Medline
| ||||||||||
| 9q34 Microdeletion/Kleefstra *
| 610253 |
EHMT1 | 9q34.3 | Precise detection rate unknown | Majority of reported deletions are detectable by array CGH. | • | • | • | • | • | • | • | • | • | ||||||
| 10q22.3-q23.31 Microdeletion
| Multiple | 10q22.3-q23.31 | ~99% have a detectable deletion | • | • | • | • | • | ||||||||||||
| 12q14.1-q15 Microdeletion *
| Multiple | 12q14.1-q15 | ~99% have a detectable deletion | Candidate genes LEMD3 (607844), GRIP1 (604597), and HMGA2 (600698). Phenotypic overlap with 12q14.3-related primordial dwarfism/Russell-Silver-like. | • | • | • | • | • | |||||||||||
| 12q14.3-related primordial dwarfism/Russell-Silver-like
|
HMGA2 | 12q14.3 | ~99% have a detectable deletion | Phenotypic overlap with 12q14.1-q15 Microdeletion. | • | • | • | |||||||||||||
| 12q24.21-q24.23 Microduplication *
| Multiple | 12q24.21-q24.23 | ~99% have a detectable duplication | • | • | • | • | • | ||||||||||||
| 14q11.2 Microdeletion
| Multiple | 14q11.2 | ~99% have a detectable deletion | Candidate genes CHD8 (610528) and SUPT16H (605012). | • | • | • | • | • |
Zahir et al. 2007. J Med Genet 44:556-61. Medline
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| 14q12 Microduplication *
| 164874 | Multiple | 14q12 | ~99% have a detectable duplication | Candidate gene FOXG1 (164874). | • | • | • | • | • | ||||||||||
| 14q22-q23 Microdeletion
| Multiple | 14q22-q23 | ~99% have a detectable deletion | • | • | • | • | • |
Nolen et al. 2006. Am J Med Genet 140:1711-18. Medline
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| 14q32.2 Microdeletion causing upd(14)mat phenotype
| Multiple | 14q32.2 | ~99% have a detectable deletion | Candidate genes DLK1 (176290) and RTL1 (611896). Majority have mutations not detectable by array CGH. | • | |||||||||||||||
| 14q32.2 Microdeletion causing upd(14)pat phenotype
| 608149 | Multiple | 14q32.2 | ~99% have a detectable deletion | Candidate genes MEG3 (605636), MEG8 (613648), and RTL1 (611896). Majority have mutations not detectable by array CGH. | • | • | • | ||||||||||||
| 15q11-q13 Microduplication *
Resource GeneReviews | 608636 | Multiple | 15q11-q13 | ~99% of interstitial duplications. Precise detection rate of marker chromosomes depends on size of duplicated region. | Phenotype may be primarily associated with duplications of the maternally inherited chromosome. | • | • | • | • | • | • | • | • | • | ||||||
| 15q13.3 Microdeletion *
GeneReviews | 612001 | Multiple | 15q13.3 | ~99% have a detectable deletion | Candidate gene CHRNA7 (118511) | • | • | • | • | • | ||||||||||
| 15q24.1-q24.2 Microdeletion
| 613406 | Multiple | 15q24.1-q24.2 | ~99% have a detectable deletion | • | • | • | • | • | |||||||||||
| 15q24.1-q24.2 Microduplication *
| 613406 | Multiple | 15q24.1-q24.2 | ~99% have a detectable duplication | Duplications have also been described in an unaffected individuals. | • | • | • | • | • | ||||||||||
| 16p11.2-p12.2 Microdeletion *
| 613604 | Multiple | 16p11.2-p12.2 | ~99% have a detectable deletion | • | • | • | • | • | |||||||||||
| 16p11.2 Microdeletion *
| 611913 | Multiple | 16p11.2 | ~99% have a detectable deletion | Deletions and duplications have also been described in unaffected individuals. | • | • | • | • | • | ||||||||||
| 16p12.1 Microdeletion
| Multiple | 16p12.1 | ~99% have a detectable deletion | Candidate genes CDR2 (117340), EEF2K (606968), UQCRC2 (191329). | • | • | • | • | • |
Girirajan et al. 2010. Nat Genet. 42:203-9. Epub 2010 Feb 14 Medline
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| 16p13.11 Microdeletion *
| Multiple | 16p13.11 | ~99% have a detectable deletion | Deletions and duplications have also been described in unaffected individuals. | • | • | • | • | • | |||||||||||
| 16p13.3 Microdeletion/Severe Rubinstein-Taybi
| 610543 | Multiple | 16p13.3 | ~99% have a detectable deletion | CREBBP (600140) causative for at least a subset of phenotype. Phenotypic overlap with Rubinstein-Taybi (180849). | • | • | • | • | • | • | • | • | • | ||||||
| 16p13.3 Microduplication *
| 613458 |
CREBBP | 16p13.3 | ~99% have a detectable duplication | Duplications have also been described in an unaffected individuals. | • | • | • | • | • | • | • | • | • |
Thienpont et al. 2010. J Med Genet. 47:155-61. Epub 2009 Oct 14 Medline
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| 16q11.2-q12.2 Microdeletion
| Multiple | 16q11.2-q12.2 | ~99% have a detectable deletion | Candidate gene SALL1 (602218) and ZNF423 (604557). Minor phenotypic overlap with Townes-Brocks 1 (107480). | • | • | • | • | • | |||||||||||
| 17p13.1 Microdeletion
| 613776 | Multiple | 17p13.1 | ~99% have a detectable deletion | TP53 (191170) causative for a subset of phenotype. | • | • | • | • | • | ||||||||||
| 17p13.3 Distal microdeletion
|
YWHAE CRK | 17p13.3 | ~99% have a detectable deletion | • | • | • | • | • | ||||||||||||
| 17p13.3 Distal microduplication, not including lissencephaly region (PAFAH1B1) *
| 613215 |
YWHAE CRK | 17p13.3 | ~99% have a detectable duplication | Phenotypic overlap with 17p13.3 Proximal microduplication, including lissencephaly region (PAFAH1B1) (613215). | • | • | • |
Bruno et al. 2010. J Med Genet. 47:299-311 Medline
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| 17p13.3 Proximal microduplication, including lissencephaly region (PAFAH1B1) *
| 613215 |
PAFAH1B1 YWHAE CRK | 17p13.3 | ~99% have a detectable duplication | Phenotypic overlap with 17p13.3 Distal microduplication, not including lissencephaly region (PAFAH1B1) (613215). | • | • | • | • | • | • | |||||||||
| 17q12 Microduplication *
| Multiple | 17q12 | ~99% have a detectable duplication | Candidate genes HNF1B (189907) and LHX1 (601999). Duplications have also been described in unaffected individuals. | • | • | • | • | • | |||||||||||
| 17q21.31 Microdeletion
GeneReviews | 610443 | Multiple | 17q21.31 | ~99% have a detectable deletion | Candidate gene MAPT (157140) | • | • | • | • | • | ||||||||||
| 17q21.31 Microduplication *
| 613533 | Multiple | 17q21.31 | ~99% have a detectable duplication | • | • | • | • | • | |||||||||||
| 17q23.1-q23.2 Microdeletion *
| 613355 | Multiple | 17q23.1-q23.2 | ~99% have a detectable deletion | Candidate genes TBX2 (600747) and TBX4 (601719). | • | • | • | • | • | ||||||||||
| 19q13.11 Microdeletion
| 613026 | Multiple | 19q13.11 | ~99% have a detectable deletion | Candidate genes LSM (610677) and UBA2 (613295). | • | • | • | ||||||||||||
| 22q11.2 Distal microdeletion *
| 611867 | Multiple | 22q11.2 | ~99% have a detectable deletion | • | • | • | • | • | • | ||||||||||
| 22q11.21 Microduplication *
GeneReviews | 608363 | Multiple | 22q11.21 | ~99% have a detectable duplication | Candidate gene TBX1 (602054). Duplications have also been described in unaffected individuals. | • | • | • | • | • | • | • | • | • | ||||||
| 22q13.3 Microdeletion *
GeneReviews | 606232 | Multiple | 22q13.3 | ~99% have a detectable deletion | Candidate gene SHANK3 (606230). | • | • | • | • | • | • | |||||||||
| Xp11.22-p11.23 Microduplication *
| 300801 | Multiple | Xp11.22-p11.23 | ~99% have a detectable duplication | • | • | • | • | • |
Giorda et al. 2009. Am J Hum Genet. 85:394-400. Epub 2009 Aug 27 Medline
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| Xp11.22-linked intellectual disability/Mental retardation 17, X-linked /Mental retardation 31, X-linked *
| 300705 | Multiple | Xp11.22 | Precise detection rate unknown | Candidate gene HSD17B10 (300256) and HUWE1 (300697). Rare mutations in either gene not detectable by array CGH. | • | • | • |
Froyen et al. 2008. Am J Hum Genet 82:432-43. Medline
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| Xp11.3 Microdeletion
| 300578 | Multiple | Xp11.3 | ~99% have a detectable deletion | Candidate genes RP2 (312600) and ZNF674 (300573). | • | • | • | • | • | ||||||||||
| Xp11.4-p21.2 Contiguous gene deletion
| Multiple | Xp11.1-p21.2 | ~99% have a detectable deletion | Multiple genes involved in this condition, including IL1RAPL1 (300206) and OTC (300461). Variable breakpoints contribute to variable phenotypes. | • | • | • | • | • | • | • | • | • | |||||||
| Xq28 Microduplication *
| 300815 | Multiple | Xq28 | ~99% have a detectable duplication | Candidate genes GDI1 (300104) and IKBKG (300248). | • | • | • | • | • | • | • | ||||||||
| Adrenal hypoplasia congenita, X-linked (AHC)
GeneReviews | 300200 |
NR0B1 | Xp21.2 | ~18% have a detectable deletion in isolated AHC; ~99% have a detectable deletion when part of a larger contiguous gene deletion | ~53% have mutations not detectable by array CGH | • | • | • | • | • | • | • | • | • | ||||||
| Adult-onset autosomal dominant leukodystrophy (ADLD) *
(FISH)
| 169500 |
LMNB1 | 5q23.2 | Precise detection rate unknown | Available as FISH test only. Not routinely tested by the SignatureChip® | This test is available as a stand-alone FISH test only. |
Padiath et al. 2006. Nat Genet 38:1114-23. Medline
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| Agammaglobulinemia, X-linked/Bruton agammaglobulinemia, X-linked
GeneReviews | 300755 |
BTK | Xq22.1 | Precise detection rate unknown | ~93% have mutations not detectable by array CGH | • | • | • | • | • | ||||||||||
| Alagille
GeneReviews | 118450 |
JAG1 | 20p12.2 | 3-7% have a detectable deletion | Majority have mutations not detectable by array CGH | • | • | • | • | • | • | • | • | • | ||||||
| Albright hereditary osteodystrophy-like/Brachydactyly with intellectual disability/2q37 Microdeletion
GeneReviews | 600430 |
HDAC4 | 2q37.3 | Precise detection rate unknown | Majority of reported deletions are detectable by array CGH | • | • | • | • | • | • | • | • | • | ||||||
| Alpha thalassemia with intellectual disability (AT-ID)
| 141750 | Multiple | 16p13.3 | ~99% have a detectable deletion | Deletion HBA1 (141800) and HBA2 (141850) responsible for alpha-thalassemia phenotype. Candidate gene for intellectual disability SOX8 (605923). | • | • | • | • | • | • | |||||||||
| Alport plus diffuse leiomyomatosis, X-linked (ATS-DL)
GeneReviews | 301050 |
COL4A5 COL4A6 | Xq22.3 | ~99% have a detectable deletion | Deletions of COL4A5 that also disrupt COL4A6 are responsible for DL phenotype; deletions of COL4A5 that also encompass COL4A6 cause isolated X-linked Alport. | • | • |
Heidet et al. 1995. Hum Mol Genet 4:99-108. Medline
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| Alport, X-linked (ATS)
GeneReviews | 301050 |
COL4A5 | Xq22.3 | ~5.7% have a detectable deletion | • | • | • | |||||||||||||
| Alzheimer disease, early onset with cerebral amyloid angiopathy *
(FISH)
GeneReviews | 104300 |
APP | 21q21.3 | ~8% have a detectable duplication | Available as FISH test only. ~16% have mutations not detectable by FISH. Not routinely tested by the SignatureChip® | This test is available as a stand-alone FISH test only. | ||||||||||||||
| Androgen insensitivity, X-linked
GeneReviews | 300068 |
AR | Xq12 | Deletions uncommon | ~50% have mutations not detectable by array CGH | • | • | • | ||||||||||||
| Angelman
GeneReviews | 105830 |
UBE3A | 15q11.2 | ~70% have a detectable deletion | ~30% have either paternal UPD or mutations not detectable by array CGH | • | • | • | • | • | • | • | • | • | ||||||
| Aniridia II
GeneReviews | 106210 |
PAX6 | 11p13 | Rare deletions unless associated with contiguous gene syndrome | Majority have mutations not detectable by array CGH | • | • | • | • | • | • | • | • | • | ||||||
| ANKRD11 haploinsufficiency/16q24.3 Microdeletion
|
ANKRD11 | 16q24.3 | ~99% have a detectable deletion | • | • | • | • | • | ||||||||||||
| Atrial septal defect (ASD) with atrioventricular conduction defects
Resource | 108900 |
NKX2-5 | 5q35.2 | Deletions uncommon | 10-27% have mutations not detectable by array CGH | • | • | • | • | • | ||||||||||
| Autism with intellectual disability, SHANK2-related
| 613436 |
SHANK2 | 11q13.3 | <1% have a detectable deletion | ~1.4% have mutations not detectable by array CGH | • | • | • | ||||||||||||
| Bannayan-Riley-Ruvalcaba (BRRS)/PTEN hamartoma tumor
Signature Summary on PTEN Hamartoma Tumor Syndrome GeneReviews | 153480 |
PTEN | 10q23.31 | 2-11% have a detectable deletion | ~60% have mutations not detectable by array CGH. Allelic with Cowden (158350) | • | • | • | • | • | ||||||||||
| Basal cell nevus/Gorlin-Goltz
GeneReviews | 109400 |
PTCH1 | 9q22.32 | Deletions uncommon | • | • | • | • | • | • | • | • | • |
Boonen et al. 2005. Am J Med Genet 132:324-28. Medline
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| Beckwith-Wiedemann, IGF2-related *
| 130650 |
IGF2 | 11p15.5 | Duplications uncommon | Majority have paternal isodisomy or mutations not detectable by array CGH | • | • | • | • | • | • | • | • | • | ||||||
| Beckwith-Wiedemann, KCNQ1OT1-related
| 130650 |
KCNQ1OT1 | 11p15.5 | Rare deletions | Majority have paternal isodisomy or mutations not detectable by array CGH | • | • | • | • | • |
Niemitz et al. 2004. Am J Hum Genet 75:844-49. Medline
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| Benign neonatal epilepsy
GeneReviews | 121200 |
KCNQ2 | 20q13.33 | ~3.3% have a detectable deletion | ~37% have mutations not detectable by array CGH | • | • | • | ||||||||||||
| Beta thalassemia
GeneReviews | 141900 |
HBB | 11p15.4 | Precise detection rate unknown; variable depending on ethinicity. | Deletions uncommon and dependent on ethnicity. | • | ||||||||||||||
| Bilateral frontoparietal polymicrogyria, autosomal recessive (BFPP)
GeneReviews | 606854 |
GPR56 | 16q13 | Precise detection rate unknown | Recessive condition. Majority of cases have at least one mutation not detectable by array CGH | • | • | • | • | • |
Piao et al. 2004. Science 303:2033-36. Medline
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| Blepharophimosis, ptosis epicanthus inversus (BPE)
GeneReviews | 110100 |
FOXL2 | 3q22.3 | Precise detection rate unknown | • | • | • | • | • | • |
Crisponi et al. 2001. Nat Genet 27:159-66. Medline
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| Boston-type craniosynostosis/Craniosynostosis type 2 *
Resources | 604757 |
MSX2 | 5q35.2 | Precise detection rate unknown | • | • | • | • | • | |||||||||||
| Branchio-oto-renal (BOR)/Melnick-Fraser
GeneReviews | 113650 |
EYA1 | 8q13.3 | 7-11% have a detectable deletion | ~40% have mutations not detectable by array CGH. | • | • | • | • | • | • | |||||||||
| Campomelic dysplasia (CMPD)
GeneReviews | 114290 |
SOX9 | 17q24.3 | Deletions uncommon | Majority have mutations not detectable by array CGH | • | • | • | • | • | • |
Olney et al. 1999. Am J Med Genet 84:20-24. Medline
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| Cat-eye *
Resource | 115470 | Multiple | 22q11.1 | Precise detection rate unknown | The supernumary marker chromosome is detectable by array CGH | • | • | • | • | • | • | • | • | • | ||||||
| Cerebellar hypoplasia, VLDLR-related, autosomal recessive/Hutterite dysequilibrium, autosomal recessive
GeneReviews | 224050 |
VLDLR | 9p24.2 | Rare deletions in most populations; ~99% have homozygous deletions in Hutterite population | Recessive condition. Rare mutations are not detectable by array CGH. | • | • | • | ||||||||||||
| Cerebral cavernous malformations, type 1 (CCM1)
GeneReviews | 116860 |
KRIT1 | 7q21.2 | Precise detection rate unknown | ~40% have mutations not detectable by array CGH | • | • | • | • | • | ||||||||||
| Cerebral cavernous malformations, type 2 (CCM2)
GeneReviews | 603284 |
CCM2 | 7p13 | ~13% have a detectable deletion | ~38% have mutations not detectable by array CGH | • | • |
Liquori et al. 2007. Am J Hum Genet 80:69-75. Medline
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| Cerebral cavernous malformations, type 3 (CCM3)
GeneReviews | 603285 |
PDCD10 | 3q26.1 | ~1.3% have a detectable deletion | 6-9% have mutations not detectable by array CGH | • | • | • | ||||||||||||
| CHARGE
GeneReviews | 214800 |
CHD7 | 8q12.2 | ~10% have a detectable deletion | Majority have mutations not detectable by array CGH | • | • | • | • | • | • | • | • |
Vissers et al. 2004. Nat Genet 36:955-57. Medline
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| Chondrodysplasia 1, X-linked (CDPX1)
GeneReviews | 302950 |
ARSE | Xp22.33 | ~9-12% have a detectable deletion | ~54-62% have mutations not detectable by array CGH | • | • | • | • | • | • | |||||||||
| Choroideremia, X-linked
GeneReviews | 303100 |
CHM | Xq21.2 | ~3% have a detectable deletion | 57-91% have mutations not detectable by array CGH | • | • | • | ||||||||||||
| Chronic granulomatous disease, X-linked
| 306400 |
CYBB | Xp11.4 | ~5% have a detectable deletion | ~89% have mutations not detectable by array CGH | • | • |
Rae et al. 1998. Am J Hum Genet 62:1320-31. Medline
| ||||||||||||
| Cleidocranial dysplasia (CCD)
GeneReviews | 119600 |
RUNX2 | 6p12.3 | Deletions uncommon | Majority have mutations not detectable by array CGH | • | • | • | • | • | • | |||||||||
| Cohen, autosomal recessive *
GeneReviews | 216550 |
VPS13B | 8q22.2 | ~7.7% have detectable homozygous deletions; ~19.2% have a single detectable deletion | Recessive condition. Majority have at least one mutation not detectable by array CGH. Finnish founder mutation not detectable by array CGH. | • | • | • | ||||||||||||
| Congenital diaphragmatic hernia (CDH)
GeneReviews | 142340 | Multiple | 15q26.1-q26.3 | 1-2% have a detectable deletion | Candidate genes CHD2 (602119) and NR2F2 (107773). | • | • | • | • | • | • | |||||||||
| Congenital hemidysplasia with ichthyosiform erythroderma & limb defects (CHILD)
| 308050 |
NSDHL | Xq28 | Deletions uncommon | Majority have mutations not detectable by array CGH. | • | • | • | • | • | • |
Bornholdt et al. 2005. J Med Genet. 42:e17 Medline
| ||||||||
| Cornelia de Lange/Brachmann-de Lange
GeneReviews | 122470 |
NIPBL | 5p13.2 | Deletions uncommon | ~47% have mutations not detectable by array CGH | • | • | • | • | • | • | • | • | |||||||
| Cowden/PTEN hamartoma tumor
GeneReviews | 158350 |
PTEN | 10q23.31 | ~1% have a detectable deletion | ~80% have mutations not detectable by array CGH. Allelic with Bannayan-Riley-Ruvalcaba (153480). | • | • | • | • | • | ||||||||||
| Craniofrontonasal, X-linked
| 304110 |
EFNB1 | Xq13.1 | Precise detection rate unknown | ~87% have mutations not detectable by array CGH | • | • | • | ||||||||||||
| Cri-du-chat
| 123450 | Multiple | 5p15.2-p15.33 | ~ 99% have a detectable deletion | Candidate genes TERT (187270) and CTNND2 (604275). | • | • | • | • | • | • | • | • | • | ||||||
| Currarino
| 176450 |
MNX1 | 7q36.3 | 2-3% have a detectable deletion | 26-75% have mutations not detectable by array CGH | • | • | • | • | • | • | |||||||||
| Dandy-Walker malformation (DWM)
Resource Resource | 220200 | Multiple | 3q23-q25.1 | Deletions uncommon | Candidate genes ZIC1 (600470) and ZIC4 (608948). | • | • | • | • | • | • |
Grinberg et al. 2004. Nat Genet 36:1053-55. Medline
| ||||||||
| Deafness 22, autosomal recessive
GeneReviews | 607039 |
OTOA | 16p12.2 | Precise detection rate unknown for most ethnicities; ~1% have at least one deletion in Palestinian population | Recessive condition. | • | • | • | • | • |
Shahin et al. 2010. Eur J Hum Genet. 18:407-13. Epub 2009 Nov 4 Medline
| |||||||||
| Diamond-Blackfan anemia 1
GeneReviews | 105650 |
RPS19 | 19q13.2 | ~1.3% have a detectable deletion | ~20% have a mutation not detectable by array CGH | • | ||||||||||||||
| DiGeorge 2
| 601362 | Multiple | 10p14 | <1% have a detectable deletion | • | • | • | • | • | • | • | • | • | |||||||
| DiGeorge/Velocardiofacial (VCF)/22q11.21 Microdeletion
GeneReviews | 188400 |
TBX1 | 22q11.21 | >95% have a detectable deletion | See also OMIM 192430. | • | • | • | • | • | • | • | • | • | ||||||
| Dopa-responsive dystonia (DRD)/Segawa
GeneReviews Resource | 128230 |
GCH1 | 14q22.2-q22.3 | ~8% have a detectable deletion | 50-60% have mutations not detectable by array CGH | • | • |
Zirn et al. 2007. J Neurol Neurosurg Psychiatry 79:183-86. Medline
| ||||||||||||
| Dosage-sensitive sex reversal, X-linked *
GeneReviews | 300018 |
NR0B1 | Xp21.2 | Precise detection rate unknown | • | • | • | • | • | • | • | • | • | |||||||
| Early-onset ataxia with oculomotor apraxia & hypoalbuminemia, autosomal recessive
GeneReviews | 208920 |
APTX | 9p13.3 | Deletions uncommon | Recessive condition. Majority of mutations not detectable by array CGH. | • | • | • | • | • | ||||||||||
| Emery-Dreifuss muscular dystrophy, X-linked (EDMD)
GeneReviews | 181350 |
EMD | Xq28 | Deletions uncommon | Majority of mutations not detectable by array CGH. | • | ||||||||||||||
| EPHA7 haploinsufficiency/6q16.1 Microdeletion
|
EPHA7 | 6q16.1 | Precise detection rate unknown | Majority of reported deletions are detectable by array CGH | • | • | • |
Traylor et al. 2009. Mol Cytogenet. 2:17 Medline
| ||||||||||||
| Epilepsy & intellectual disability restricted to females, X-linked/Juberg-Hellman, X-linked/Dravet-like, X-linked
| 300088 |
PCDH19 | Xq22.1 | ~2.0% have a detectable deletion | ~10% have mutations not detectable by array CGH | • | • | • | ||||||||||||
| Faciogenital dysplasia, X-linked/Aarskog-Scott, X-linked
| 305400 |
FGD1 | Xp11.22 | Deletions uncommon | ~18.3% have mutations not detectable by array CGH | • | • | |||||||||||||
| Familial adenomatous polyposis with intellectual disabilities (FAP-ID)/5q22 Microdeletion
GeneReviews | 175100 |
APC | 5q22.2 | >98% have a detectable deletion | Majority of isolated FAP cases have mutations not detectable by array CGH | • | • | • | • | • | • | |||||||||
| Feingold
GeneReviews | 164280 |
MYCN | 2p24.3 | ~4% have a detectable deletion | ~61% have mutations not detectable by array CGH | • | • | • | • | • | ||||||||||
| FMR1 microdeletion, X-linked
GeneReviews | 300624 |
FMR1 | Xq27.3 | <1% of individuals with Fragile X have a detectable deletion | >99% of individuals with Fragile X have CGG triplet expansions or other mutations not detectable by by array CGH | • | • | • | • | • | ||||||||||
| Focal dermal hypoplasia, X-linked/Goltz, X-linked
GeneReviews | 305600 |
PORCN | Xp11.23 | 5.6-20% have a detectable deletion | 70-72% have mutations not detectable by array CGH | • | • | |||||||||||||
| GLUT1 deficiency
GeneReviews | 606777 |
SLC2A1 | 1p34.2 | ~6.6% have a detectable deletion | ~93.3% have mutations not detectable by array CGH | • | • | • | ||||||||||||
| Glycerol kinase deficiency, X-linked (GKD)
| 300474 |
GK | Xp21.2 | Deletions uncommon | Majority have mutations not detectable by array CGH | • | • | • | • | • | • | • | • | • |
Sargent et al. 2000 J Med Genet 37:434-41. Medline
| |||||
| Greig cephalopolysyndactyly
GeneReviews | 175700 |
GLI3 | 7p14.1 | ~30% have a detectable deletion | • | • | • | • | • | • | • | • | • |
Johnston et al. 2003. Am J Med Genet 123:236-42. Medline
| ||||||
| Growth hormone insensitivity, autosomal recessive/Laron, autosomal recessive
| 262500 |
GHR | 5p12 | Deletions uncommon | Recessive condition. Majority have mutations not detectable by array CGH. | • | • | • | • | • | ||||||||||
| Hemophilia A, X-linked
GeneReviews | 306700 |
F8 | Xq28 | ~2.0% have a detectable deletion | ~93% have mutations not detectable by array CGH | • | • | • | ||||||||||||
| Hemophilia B, X-linked
GeneReviews | 306900 |
F9 | Xq27.1 | ~2.0% have a detectable deletion | ~97% have mutations not detectable by array CGH | • | • | • | ||||||||||||
| Hereditary hemorrhagic telangiectasia, type 2
GeneReviews | 600376 |
ACVRL1 | 12q13.13 | ~1.7% have a detectable deletion | ~40% have mutations not detectable by array CGH | • | • | • | • | • | ||||||||||
| Hereditary paraganglioma-pheochromocytoma, SDHB-related
GeneReviews | 115310 |
SDHB | 1p36.13 | ~4.2% have a detectable deletion | 1.6-5.0% have mutations not detectable by array CGH | • | • | • | • | • | ||||||||||
| Hereditary paraganglioma-pheochromocytoma, SDHD-related
GeneReviews | 168000 |
SDHD | 11q23.1 | Rare deletions | ~5% have mutations not detectable by array CGH | • | • | • | • | • | • | • | • | • | ||||||
| Heterotaxy, X-linked
| 306955 |
ZIC3 | Xq26.3 | Deletions uncommon | ~4% have mutations not detectable by array CGH | • | • | • | • | • | • | • | • | • | ||||||
| Hirschsprung, RET-related
GeneReviews | 142623 |
RET | 10q11.21 | Precise detection rate unknown | Majority of reported deletions are detectable by array CGH | • | • | • | • | • | • | • | • | • | ||||||
| Holoprosencephaly SignatureChip® Detection Rates for Holoprosencephaly | 25-50% of cases with holoprosencephaly (HPE) have abnormal karyotypes, the vast majority of which are detectable by SignatureChip®. 15-20% of HPE cases with normal chromosomes will have sequence mutations in SHH, ZIC2, SIX3, or TGIF. Sequence mutations are not detectable by array CGH. A negative array CGH test result does not exclude the possibility that one or more of these genes may play a role in the subject's phenotype. 4.7% of chromosomally normal and mutation-analysis normal HPE cases have microdeletions in SHH, ZIC2, SIX3 or TGIF (Bendavid et al. 2006. Hum Genet 119:1-8. Medline). The majority of reported microdeletions are detectable by SignatureChip®. | |||||||||||||||||||
| Holoprosencephaly 1
Signature Summary on Holoprosencephaly GeneReviews | 236100 | Multiple | 21q22.3 | ~99% have a detectable deletion | Candidate genes TRAPPC10 (602103) and PWP2 (601475. | • | • | • | • | • | • | • | • | • | ||||||
| Holoprosencephaly 2
Signature Summary on Holoprosencephaly GeneReviews | 157170 |
SIX3 | 2p21 | ~1% have a detectable deletion | ~4% have mutations not detectable by array CGH | • | • | • | • | • | • | • | • | • | ||||||
| Holoprosencephaly 3
Signature Summary on Holoprosencephaly GeneReviews | 142945 |
SHH | 7q36.3 | 1-2% have a detectable deletion | 6-8% have mutations not detectable by array CGH | • | • | • | • | • | • | • | • | • | ||||||
| Holoprosencephaly 4
Signature Summary on Holoprosencephaly GeneReviews | 142946 |
TGIF1 | 18p11.31 | <1% have a detectable deletion | ~1% have mutations not detectable by array CGH | • | • | • | • | • | • | • | • | • | ||||||
| Holoprosencephaly 5
Signature Summary on Holoprosencephaly GeneReviews | 609637 |
ZIC2 | 13q32.3 | <1% have a detectable deletion | ~3% have mutations not detectable by array CGH | • | • | • | • | • | • | • | • | • | ||||||
| Holoprosencephaly 8
Signature Summary on Holoprosencephaly GeneReviews | 609408 | Multiple | 14q13.1-q13.2 | Precise detection rate unknown | Majority of reported deletions are detectable by array CGH | • | • | • | • | • |
Kamnasaran et al. 2005. Genomics 85:608-21. Medline
| |||||||||
| Holt-Oram *
| 142900 |
TBX5 | 12q24.21 | Rare deletions | 30-35% have mutations not detectable by array CGH | • | • | • | • | • | ||||||||||
| Hydrocephalus and nephrogenic diabetes insipidus, X-linked
|
L1CAM AVPR2 | Xq28 | Precise detection rate unknown | Contiguous gene deletion causing X-linked hydrocephalus (307000) and nephrogenic diabetes insipidus (304800) | • | • | • | |||||||||||||
| Hyper-IgE recurrent infection, autosomal recessive
| 243700 |
DOCK8 | 9p24.3 | ~25% have a detectable deletion | Recessive condition. ~75% have mutations not detectable by array CGH. | • | • | • | • | • | • | • | • | • | ||||||
| Hypohidrotic ectodermal dysplasia, X-linked (XHED)
GeneReviews | 305100 |
EDA | Xq13.1 | ~3.8% have a detectable deletion | ~61.5% have mutations not detectable by array CGH | • | • | • |
Vincent et al. 2001. Eur J Hum Genet. 9:355-63 Medline
| |||||||||||
| Hypoparathyroidism, sensorineural deafness, renal disease (HDR)
Resource | 146255 |
GATA3 | 10p14 | ~40% have a detectable deletion | 10-20% have mutations not detectable by array CGH | • | • | • | • | • | • | |||||||||
| Hypospadius 2, X-linked
| 300758 |
MAMLD1 | Xq28 | Precise detection rate unknown | ~9.2% have mutations not detectable by array CGH | • | • | • | • | • | • | |||||||||
| Hypotonia-cystinuria, autosomal recessive
| 606407 |
SLC3A1 PREPL | 2p21 | ~99% have detectable homozygous deletions | Recessive condition. Phenotypic overlap with 2p21 microdeletion syndrome. | • | • |
Jaeken et al. 2006. Am J Hum Genet 78:38-51. Medline
| ||||||||||||
| Idiopathic short stature, X- & Y-linked (ISSX)
GeneReviews | 300582 |
SHOX | Xp22.33 & Yp11.32 | 2-14% have a detectable deletion | Dominant condition. 0.4-12% have mutations not detectable by array CGH. Allelic with Langer mesomelic dysplasia (249700)/Leri-Weill dyschondrosteosis (127300). | • | • | • | • | • | • | • | • | • | ||||||
| Infantile hyperinsulinism with enteropathy & deafness, autosomal recessive
| 606528 |
USH1C ABCC8 | 11p15.1 | Precise detection rate unknown | Recessive condition. Phenotypic overlap with Usher syndrome 1C (276904) and Familial hyperinsulinemic hypoglycemia 1 (256450). | • | • | • | ||||||||||||
| Infantile spasms, CDKL5-related, X-linked/Atypical Rett, CDKL5-related, X-linked
Resource | 300672 |
CDKL5 | Xp22.13 | Deletions uncommon | 5-7% have mutations not detectable by array CGH | • | • | • | • | • | ||||||||||
| Infantile spasms, MAGI2-related
|
MAGI2 | 7q21.11 | Precise detection rate unknown | • | • | • |
Marshall et al. 2008. Am J Hum Genet 83:106-11. Medline
| |||||||||||||
| Intellectual disability with cerebellar hypoplasia & distinctive facial appearance, X-linked/Mental retardation 60, X-linked *
Resources | 300486 |
OPHN1 | Xq12 | Precise detection rate unknown | ~12% of mutations not detectable by array CGH | • | • | • | • | • | ||||||||||
| Intellectual disability with isolated growth hormone deficiency, X-linked *
Resource | 300123 |
SOX3 | Xq27.1 | Precise detection rate unknown | Many reported deletions and duplications are detectable by array CGH | • | • | • | • | • | • | |||||||||
| Intellectual disability with language impairment and autistic features
| 613670 |
FOXP1 | 3p14.1 | Precise detection rate unknown | Majority of reported deletions detectable by array CGH. | • | • | • | • | • | ||||||||||
| Intellectual disability with microcephaly & disproportionate pontine and cerebellar hypoplasia, X-linked
| 300749 |
CASK | Xp11.4 | ~4% have a detectable deletion | ~4% have mutations not detectable by array CGH | • | • | • | • | • | ||||||||||
| Intellectual disability with stereotypical movements, epilepsy, and/or cerebral malformations/5q14.3 Microdeletion
| 613443 |
MEF2C | 5q14.3 | Precise detection rate unknown | Majority have deletions detectable by array CGH. | • | • | • | • | • | ||||||||||
| Jacobsen/11q terminal deletion
Resource | 147791 | Multiple | 11q23-q25 | Precise detection rate unknown | Majority of reported deletions are detectable by array CGH | • | • | • | • | • | • | • | • | • | ||||||
| Joubert 4, autosomal recessive
GeneReviews | 609583 |
NPHP1 | 2q13 | Precise detection rate unknown | Recessive condition. Allelic with Nephronopthisis 1 (256100). | • | • | • | • | • | • | • | • | • |
Parisi et al. 2004. Am J Hum Genet 75:82-91. Medline
| |||||
| Juvenile polyposis (JPS), BMPR1A-related
GeneReviews | 174900 |
BMPR1A | 10q23.2 | 1-7% have a detectable deletion | 11-21% have mutations not detectable by array CGH | • | • | • | • | • | ||||||||||
| Juvenile polyposis (JPS), SMAD4-related
GeneReviews | 174900 |
SMAD4 | 18q21.2 | 4-6% have a detectable deletion | 19-22% have mutations not detectable by array CGH | • | • | • | • | • | ||||||||||
| Kallmann 1, X-linked
GeneReviews | 308700 |
KAL1 | Xp22.31 | 10-12% have a detectable deletion | • | • | • | • | • | • | • | • | • | |||||||
| Langer-Giedion/Trichorhinophalangeal type II
| 150230 |
TRPS1 EXT1 | 8q23.3 8q24.11 | ~75% have a detectable deletion | • | • | • | • | • | • | • | • | • | |||||||
| Langer mesomelic dysplasia, X- & Y-linked (LMD)
| 249700 |
SHOX | Xp22.33 & Yp11.32 | Precise detection rate unknown | Recessive condition. Many reported deletions are detectable by array CGH. Allelic with X-linked idiopathic short stature (300582)/Leri-Weill dyschondrosteosis (127300). | • | • | • | • | • | • | • | • | • | ||||||
| Leri-Weill dyschondrosteosis, X- & Y-linked (LWD)
GeneReviews | 127300 |
SHOX | Xp22.33 & Yp11.32 | 34-41% have detectable deletions | Dominant condition. ~23% have mutations not detectable by array CGH. Allelic with X-linked idiopathic short stature (300582)/Langer mesomelic dysplasia (249700). | • | • | • | • | • | • | • | • | • | ||||||
| Lesch-Nyhan, X-linked (LNS)
GeneReviews | 300322 |
HPRT1 | Xq26.2 | ~3.6% have a detectable deletion | Majority have mutations not detectable by array CGH | • | ||||||||||||||
| Li-Fraumeni 1 (LFS)
GeneReviews | 151623 |
TP53 | 17p13.1 | Deletions uncommon | 71-79% have mutations not detectable by array CGH | • | • | • | • | • | ||||||||||
| Lissencephaly 1
GeneReviews | 607432 |
PAFAH1B1 | 17p13.3 | ~27% have a detectable deletion | ~81% have mutations not detectable by array CGH | • | • | • | • | • | • | • | • | • |
Mei et al. 2008. J Med Genet. 45:355-61. Epub 2008 Feb 19 Medline
| |||||
| Lissencephaly, X-linked
GeneReviews | 300067 |
DCX | Xq22.3 | Precise detection rate unknown | 20-38% have mutations not detectable by array CGH | • | • | • | • | • | • | |||||||||
| Lowe, X-linked
GeneReviews | 309000 |
OCRL | Xq25 | Large deletions uncommon | Majority have mutations not detectable by array CGH | • | • | • | • | • | ||||||||||
| Lymphoproliferative, X-linked (XLP)
GeneReviews | 308240 |
SH2D1A | Xq25 | 4-9% have a detectable deletion | 16-89% have mutations not detectable by array CGH depending on features | • | • | • | • | • | ||||||||||
| Marfan 1 (MFS1)
GeneReviews | 154700 |
FBN1 | 15q21.1 | <1% have a detectable deletion | 60-93% have mutations not detectable by array CGH | • | • | • | • | • | ||||||||||
| McLeod neuroacanthocytosis, X-linked
GeneReviews | 314850 |
XK | Xp21.1 | 5.8-17% have a detectable deletion | ~82% have mutations not detectable by array CGH | • | • | |||||||||||||
| Menkes, X-linked (MNK)
GeneReviews | 309400 |
ATP7A | Xq21.1 | ~1% have a detectable deletion | ~79% have mutations not detectable by array CGH | • | • |
Tümer et al. 2003. Hum Mutat 22:457-64. Medline
| ||||||||||||
| Mental retardation 1, autosomal dominant (MRD1)
| 156200 |
MBD5 | 2q23.1 | Precise detection rate unknown | Phenotypic overlap with 2q23.1 Microdeletion. | • | • | • | • | • | ||||||||||
| Mental retardation 21, X-linked/Mental retardation 34, X-linked
Resource | 300143 |
IL1RAPL1 | Xp21.3 | Precise detection rate unknown | Majority of reported deletions are detectable by array CGH | • | • | • | • | • | • | • | • | • | ||||||
| Mental retardation 5, autosomal dominant
| 612621 |
SYNGAP1 | 6p21.32 | Precise detection rate unknown | 3.2% have mutations not detectable by array | • | ||||||||||||||
| Mental retardation 6, autosomal recessive
| 611092 |
GRIK2 | 6q16.3 | Precise detection rate unknown | Recessive condition. | • | • | • | • | • | • | • |
Motazacker et al. 2007. Am J Hum Genet. 81:792-8. Epub 2007 Aug 31 Medline
| |||||||
| Mental retardation 7, autosomal recessive
| 611093 |
TUSC3 | 8p22 | Precise detection rate unknown | Recessive condition. | • | • | • |
Garshasbi et al. 2008. Am J Hum Genet. 82:1158-64. Epub 2008 May 1 Medline
| |||||||||||
| Mental retardation 9, X-linked/Mental retardation 44, X-linked
Resources | 309549 |
FTSJ1 | Xp11.23 | Precise detection rate unknown | • | • | • | |||||||||||||
| Mental retardation 94, X-linked
| 300699 |
GRIA3 | Xq25 | Precise detection rate unknown | Majority of reported deletions and duplications are detectable by array CGH. | • | • | • | ||||||||||||
| Mesomelic dysplasia Kantaputra type *
| 156232 | Multiple | 2q31.1 | Precise detection rate unknown | Candidate genes HOXD gene cluster. Majority of reported deletions are detectable by array CGH. | • | • | • | • | • | • | • | • | |||||||
| Metachromatic leukodystrophy, autosomal recessive (MLD)/Arylsulfatase A deficiency
GeneReviews | 250100 |
ARSA | 22q13.3 | Deletions uncommon | Recessive condition. Majority have at least one mutation not detectable by array CGH. | • | • | • | • | • | • | |||||||||
| Microphthalmia 3
GeneReviews | 206900 |
SOX2 | 3q26.33 | ~2% have a detectable deletion | ~8% have mutations not detectable by array CGH | • | • | • | • | • |
Bakrania et al. 2007. Br J Ophthalmol. 91:1471-6. Epub 2007 May 23 Medline
| |||||||||
| Microphthalmia 7 with linear skin defects, X-linked
GeneReviews | 309801 |
HCCS | Xp22.2 | Precise detection rate unknown | Majority of reported deletions are detectable by array CGH. Deletions have also been described in unaffected individuals. | • | • | • | • | • | • | • | • | • | ||||||
| Miller-Dieker
GeneReviews | 247200 |
PAFAH1B1 | 17p13.3 | 85-90% have a detectable deletion | • | • | • | • | • | • | • | • | • | |||||||
| Mohr-Tranebjaerg, X-linked/Deafness-dystonia-optic neuropathy, X-linked (DDON)
GeneReviews | 304700 |
TIMM8A | Xq22.1 | Rare deletions unless associated with contiguous gene deletion syndrome | Majority have mutations not detectable by array CGH. Contiguous gene deletion syndrome also involves X-linked agammaglobulinemia (300300). | • | • | • | • | • |
Šedivá et al. 2007. J Clin Immunol 27:640-46. Medline
| |||||||||
| Mowat-Wilson *
GeneReviews | 235730 |
ZEB2 | 2q22.3 | 15-21% have a detectable deletion | 21-28% have mutations not detectable by array CGH | • | • | • | • | • | ||||||||||
| Myoclonus dystonia
GeneReviews Resource | 159900 |
SGCE | 7q21.3 | ~6% have a detectable deletion | 20-28% have mutations not detectable by array CGH | • | • | • | ||||||||||||
| Myotubular myopathy 1, X-linked
GeneReviews | 310400 |
MTM1 | Xq28 | 1-4% have a detectable deletion | 61-99% have mutations not detectable by array CGH | • | • | • | • | • | • | |||||||||
| Nablus mask-like facial
| 608156 | Multiple | 8q22.1 | Precise detection rate unknown | Majority of reported deletions are detectable by array CGH | • | • | • | • | • | ||||||||||
| Nail-patella (NPS)
GeneReviews | 161200 |
LMX1B | 9q33.3 | 1-5% have a detectable deletion | ~85% have mutations not detectable by array CGH | • | • | • | • | • |
Dunston et al. 2004. Genomics 84:565-76. Medline
| |||||||||
| Nephronophthisis 1, autosomal recessive
| 256100 |
NPHP1 | 2q13 | 80% have detectable homozygous deletions | Recessive condition. Allelic with Joubert 4 (609583). | • | • | • | • | • | • | • | • | • |
Saunier et al. 2000. Am J Hum Genet 66:778-89. Medline
| |||||
| Nephropathic cystinosis, autosomal recessive
GeneReviews | 219800 |
CTNS | 17p13.3 | 40-46% have detectable homozygous deletions | Recessive condition. ~35% have at least one mutation not not detectable by array CGH | • | • | • | ||||||||||||
| Neurofibromatosis 1 with intellectual disabilities (NF1-ID) *
GeneReviews | 162200 |
NF1 | 17q11.2 | 5-20% have a detectable deletion | • | • | • | • | • | • | • | • | • | |||||||
| Neurofibromatosis 2 (NF2)
GeneReviews | 101000 |
NF2 | 22q12.2 | 15-21% have a detectable deletion | 34-66% have mutations not detectable by array CGH | • | • | • | • | • | ||||||||||
| Neurosensory deafness, autosomal recessive (DFNB1)
GeneReviews | 220290 |
GJB6 | 13q12.11 | ~0.4% have detectable homozygous deletions; ~7.8% have a single detectable deletion | Recessive condition. Deletions of GJB6 can also cause phenotype in conjunction with mutations in GJB2. | • | • | • | • | • |
del Castillo et al. 2002. N Engl J Med 346:243-49. Medline
| |||||||||
| NFIA haploinsufficiency/1p31.3 Microdeletion
| 613735 |
NFIA | 1p31.3 | Precise detection rate unknown | Majority of reported deletions are detectable by array CGH | • | • | • | • | • | ||||||||||
| Norrie, X-linked *
GeneReviews | 310600 |
NDP | Xp11.3 | ~15% have a detectable deletion | ~85% have mutations not detectable by array CGH | • | • | • | • | • | ||||||||||
| Oculocutaneous albinism 2, autosomal recessive (OCA2) *
GeneReviews | 203200 |
OCA2 | 15q13.1 | Rare homozygous deletions in most ethnicities; ~99% in Navajo population | Recessive condition. 0-91% have at least one mutation not detectable by array CGH depending on ethnicity | • | • | • | ||||||||||||
| Oculofaciocardiodental, X-linked/Microphthalmia 2, X-linked
GeneReviews | 300166 |
BCOR | Xp11.4 | Precise detection rate unknown | OFCD is an X-linked dominant condition. Lenz microphthalmia is an X-linked recessive condition. Majority have mutations not detectable by array CGH. | • | • | • | ||||||||||||
| Okihiro/Duane radial ray (DRRS)
GeneReviews | 607323 |
SALL4 | 20q13.2 | ~6% have a detectable deletion | 63-90% have mutations not detectable by array CGH | • | • | • | • | • | ||||||||||
| Opitz GBBB, X-linked
GeneReviews | 300000 |
MID1 | Xp22.2 | ~2.1% have a detectable deletion | ~19% have mutations not detectable by array CGH | • | • | • | • | • | • | • | • | • |
Ferrentino et al. 2007. Hum Mutat. 28:206-7 Medline
| |||||
| Ornithine transcarbamylase deficiency, X-linked (OTC)
GeneReviews | 311250 |
OTC | Xp11.4 | 3-12% have a detectable deletion | 62-92% have mutations not detectable by array CGH | • | • | • | • | • | ||||||||||
| Osteopathia striata with cranial sclerosis, X-linked
| 300373 |
FAM123B | Xq11.1 | 10-12% have a detectable deletion | Dominant condition. 84-88% have mutations not detectable by array CGH. | • | • | |||||||||||||
| Oto-dental
| 166750 |
FGF3 | 11q13.3 | Precise detection rate unknown | • | • | • | • | • |
Gregory-Evans et al. 2007. Hum Mol Genet 16:2482-93. Medline
| ||||||||||
| Pallister-Killian *
| 601803 | Multiple | 12p | Precise detection rate unknown | Tetrasomy 12p is detectable by SignatureChip® | • | • | • | • | • | • | • | • | • | ||||||
| Parkinsonism with dementia *
(FISH)
GeneReviews | 605543 |
SNCA | 4q22.1 | Precise detection rate unknown | Available as FISH test only. Not routinely tested by the SignatureChip® | This test is available as a stand-alone FISH test only. | ||||||||||||||
| Pelizaeus-Merzbacher, X-linked *
GeneReviews | 312080 |
PLP1 | Xq22.2 | 60-70% have a detectable duplication | ~30% have mutations not detectable by array CGH | • | • | • | • | • | • | • | • | • | ||||||
| Peutz-Jeghers (PJS)
GeneReviews | 175200 |
STK11 | 19p13.3 | 2-9% have a detectable deletion | 87-95% have mutations not detectable by array CGH | • | • | |||||||||||||
| Pitt-Hopkins
| 610954 |
TCF4 | 18q21.1 | ~33% have a detectable deletion | ~16% have mutations not detectable by array CGH | • | • | • | • | • | ||||||||||
| Pitt-Hopkins-like 1, autosomal recessive/Cortical dysplasia-focal epilepsy, autosomal recessive (CDFE)
| 610042 |
CNTNAP2 | 7q35-q36.1 | Precise detection rate unknown | Recessive condition. Majority of deletions detectable by array CGH. Point mutations in Old Order Amish population not detectable. | • | • | • |
Zweier et al. 2009. Am J Hum Genet. 85:655-66. Epub 2009 Nov 5 Medline
| |||||||||||
| Polycystic kidney disease 1 (PKD1)
GeneReviews | 173900 |
PKD1 | 16p13.3 | Rare deletions unless associated with contiguous gene deletion syndrome | Majority have mutations not detectable by array CGH. Contiguous gene deletion syndrome also involves Tuberous sclerosis 2 (191100). | • | • | • | • | • | • | • | • | • | ||||||
| Potocki-Lupski/17p11.2 Microduplication *
| 610883 | Multiple | 17p11.2 | ~99% have a detectable duplication | Candidate gene RAI1 (607642). | • | • | • | • | • | • | • | • | • | ||||||
| Potocki-Shaffer
| 601224 |
EXT2 ALX4 | 11p11.2 | ~99% have a detectable deletion | • | • | • | • | • | • | • | • | • | |||||||
| Prader-Willi (PWS)
GeneReviews | 176270 |
Candidate SNORD116 Cluster (605436) | 15q11.2 | ~70% have a detectable deletion | ~30% have either maternal UPD or mutations not detectable by array CGH | • | • | • | • | • | • | • | • | • | ||||||
| Prader-Willi-like phenotype
| 176270 | Multiple | 6q16.1-q16.3 | Deletions uncommon | Candidate gene SIM1 (603128). | • | • | • | • | • | • | |||||||||
| PTEN Hamartoma Tumor syndrome SignatureChip® Detection Rates for PTEN Hamartoma Tumor Syndrome and Allelic Disorders | PTEN Hamartoma Tumor Syndrome is a syndrome that incorporates several disorders with phenotypic overlap caused by mutations in PTEN, including Bannayan-Riley Ruvalcaba syndrome, Cowden syndrome, Proteus syndrome, and Proteus-like syndrome. While these disorders have specific distinguishing characteristics, they have features in common and recommended management is virtually identical for all. 2-11% of cases of Bannayan-Riley-Ruvalcaba syndrome (BRRS) are caused by deletions of the PTEN gene, the majority of which are detectable by array CGH technology. Approximately 60% have identifiable PTEN point mutations. Subjects with this condition often have autistic features, macrocephaly, hamartomatous intestinal polyps, lipomas and penile freckling. ~1% of Cowden syndrome (CS) are caused by deletions of the PTEN gene, the majority of which are detectable by array CGH technology. Approximately 80% have identifiable PTEN point mutations that are not detectable by array CGH. Subjects with this condition may have cancers of the breast, uterus, thyroid, and urogenital tract as well as macrocephaly, Lhermitte-Duclos disease (macrocephaly, seizures, and intellectual disability associated with dysplastic gangliocytoma of the cerebellum), specific skin lesions (e.g., trichelemmomas, lipomas), hamartomatous polyps, fibrocystic breasts, and urogenital system malformations and tumors. Autistic-like tendencies have also been reported in some patients. No large deletions have been reported in cases of Proteus syndrome or Proteus-like syndrome. However, this disorder has phenotypic overlap with BRRS and CS and is considered part of the PTEN Hamartoma Tumor Syndrome Spectrum. Detection rates for point mutations are not reported consistently, implying a possible second locus for these syndromes. These are disorders of mosaic, progressive overgrowth, including connective tissue nevi, macrocephaly, ovarian and parotid tumors, atypical adipose tissue growth, and vascular malformations. While Macrocephaly/autism syndrome is not considered part of the PTEN Hamartoma Tumor Syndrome, it is allelic to these tumor syndromes and has the overlapping phenotype of both macrocephaly and autistic-like features. Approximately 4% of patients with a head circumference >2 standard deviations above the mean and autism spectrum disorder have point mutations in PTEN, that are not detectable by array CGH. | |||||||||||||||||||
| Renal cysts and diabetes (RCAD)
| 137920 |
HNF1B | 17q12 | ~22% have a detectable deletion | ~45% have mutations not detectable by array CGH | • | • | • | • | • |
Bellanné-Chantelot et al. 2005. Diabetes 54:3126-32. Medline
| |||||||||
| Retinoblastoma with intellectual disability
GeneReviews | 180200 |
RB1 | 13q14.2 | ~80% have a detectable deletion | 3-5% of bilateral and unilateral isolated RB cases have deletions | • | • | • | • | • | • | • | • | • | ||||||
| Rett, congenital variant
| 613454 |
FOXG1 | 14q12 | ~27% have a detectable deletion | ~73% have mutations not detectable by array CGH | • | • | |||||||||||||
| Rieger 1 (RIEG1)/Axenfeld-Rieger
| 180500 |
PITX2 | 4q25 | Precise detection rate unknown | ~40% have mutations not detectable by array CGH | • | • | • | • | • | • | |||||||||
| Rubinstein-Taybi (RTS)
GeneReviews | 180849 |
CREBBP | 16p13.3 | 15% have a detectable deletion | ~36% have mutations not detectable by array CGH. Phenotypic overlap with 16p13.3 Microdeletion/Severe Rubinstein-Taybi (610543). | • | • | • | • | • | • | • | • | • | ||||||
| Saethre-Chotzen
GeneReviews | 101400 |
TWIST1 | 7p21.1 | 11-18% have a detectable deletion | ~25% have mutations not detectable by array CGH | • | • | • | • | • | • | • | • | • | ||||||
| Severe myoclonic epilepsy of infancy (SMEI)/Dravet
GeneReviews | 607208 |
SCN1A | 2q24.3 | ~2% have a detectable deletion | ~33-35% have mutations not detectable by array CGH. | • | • | • | • | • | ||||||||||
| Sex reversal, autosomal dominant 2 (SRA2)
| 154230 | Multiple | 9p24.3 | Precise detection rate unknown | Candidate gene DMRT1 (602424) | • | • | • | • | • | • | |||||||||
| Short stature, pituitary and cerebellar defects, small sella turcica/Pituitary hormone deficiency, combined, 4
| 262700 |
LHX4 | 1q25.2 | Precise detection rate unknown | • | • | • | • | • | |||||||||||
| Siderius type intellectual disability, X-linked
| 300263 |
PHF8 | Xp11.22 | Precise detection rate unknown | Majority have mutations not detectable by array CGH | • | • | |||||||||||||
| Simpson-Golabi-Behmel, X-linked (SGBS)
GeneReviews | 312870 |
GPC3 | Xq26.2 | Precise detection rate unknown | ~70% have mutations not detectable by array CGH | • | • | • | ||||||||||||
| Smith-Magenis (SMS)
GeneReviews | 182290 |
RAI1 | 17p11.2 | 90-99% have a detectable deletion | • | • | • | • | • | • | • | • | • | |||||||
| Sotos
GeneReviews | 117550 |
NSD1 | 5q35.3 | 10-40% have a detectable deletion depending upon ethnicity | 14-90% have mutations not detectable by array CGH depending upon ethnicity | • | • | • | • | • | • | • | • | • | ||||||
| Speech & language disorder 1
Resource | 602081 |
FOXP2 | 7q31.1 | Precise detection rate unknown | ~2% have mutations not detctable by array CGH | • | • | • | • | • | ||||||||||
| Split-hand/foot malformation 1 (SHFM1)/Ectrodactyly
Resource | 183600 |
SHFM1 | 7q21.3 | Precise detection rate unknown | Majority of reported deletions are detectable by array CGH | • | • | • | • | • | • | |||||||||
| Split-hand/foot malformation 3 (SHFM3)/Ectrodactyly *
Resource | 246560 |
FBXW4 | 10q24.32 | Precise detection rate unknown | Majority of reported duplications are detectable by array CGH | • | • | • | • | • | • | • | • | |||||||
| Split-hand/foot malformation 5 (SHFM5)/Ectrodactyly
Resource | 606708 | Multiple | 2q31.1 | Precise detection rate unknown | Candidate genes EVX2 (142991) and HOXD gene cluster | • | • | • | • | • | • | |||||||||
| Steroid sulfatase deficiency, X-linked/Ichthyosis, X-linked
Resources Resources | 308100 |
STS | Xp22.31 | 80-90% have a detectable deletion | 10-20% have mutations not detectable by array CGH | • | • | • | • | • | • | • | • | • | ||||||
| Synpolydactyly/Syndactyly II
Resource | 186000 | HOXD gene cluster | 2q31.1 | Deletions uncommon | Majority have mutations not detectable by array CGH. | • | • | • | • | • | • | • | • | |||||||
| Toe syndactyly, telecanthus, anogenital & renal malformations, X-linked (STAR)
| 300707 |
FAM58A | Xq28 | ~20% have a detectable deletion | ~80% have mutations not detectable by array CGH | • | • | • | • | • | • | • |
Unger et al. 2008. Nat Genet. 40:287-9. Epub 2008 Feb 24 Medline
| |||||||
| Townes-Brocks 1
GeneReviews | 107480 |
SALL1 | 16q12.1 | ~1% have a detectable deletion | Minor phenotypic overlap with 16q11.2-q12.2 Microdeletion. | • | • | • | • | • | ||||||||||
| Trichorhinophalangeal 1
Resource | 190350 |
TRPS1 | 8q23.3 | <20% have a detectable deletion | >80% have mutations not detectable by array CGH | • | • | • | • | • | • | • | • | • | ||||||
| Tuberous sclerosis 1 (TSC1)
GeneReviews | 191100 |
TSC1 | 9q34.13 | Deletions uncommon | 17-26% have mutations not detectable by array CGH | • | • | • | ||||||||||||
| Tuberous sclerosis 2 (TSC2)
GeneReviews | 613254 |
TSC2 | 16p13.3 | 10-30% have a detectable deletion | ~60% have mutations not detectable by array CGH | • | • | • | • | • | • | • | • | • | ||||||
| Ulnar-mammary
Resource | 181450 |
TBX3 | 12q24.21 | Deletions uncommon | Majority have mutations not detectable by array CGH | • | • | • | • | • | ||||||||||
| Usher IIC, autosomal recessive
GeneReviews | 605472 |
GPR98 | 5q14.3 | Deletions uncommon | Recessive condition. Mutations of GPR98 can also cause phenotype in conjunction with mutations in PDZD7. | • | • | • | ||||||||||||
| Van der Woude
GeneReviews | 119300 |
IRF6 | 1q32.2 | 2-3% have a detectable deletion | ~43% have mutations not detectable by array CGH | • | • | • | • | • |
Kondo et al. 2002. Nat Genet. 32:285-9. Epub 2002 Sep 3 Medline
| |||||||||
| von Hippel-Lindau
GeneReviews | 193300 |
VHL | 3p25.3 | ~2.5% have a detectable deletion | 76-88% have mutations not detectable by array CGH | • | • | • | • | • | ||||||||||
| Waardenburg I
GeneReviews | 193500 |
PAX3 | 2q36.1 | 0.7-1.3% have a detectable deletion | ~80% have mutations not detectable by array CGH | • | • | • | • | • | ||||||||||
| Waardenburg IIA
Resource | 193510 |
MITF | 3p14.1 | Precise detection rate unknown | ~22% have mutations not detectable by array CGH | • | • | • | • | • | ||||||||||
| Walker-Warburg, LARGE-related, autosomal recessive/Muscular dystrophy-dystroglycanopathy A1, autosomal recessive
GeneReviews | 236670 |
LARGE | 22q12.3 | Rare deletions | Recessive condition. | • | • | |||||||||||||
| Williams-Beuren (WBS)
GeneReviews | 194050 |
ELN | 7q11.23 | >95% have a detectable deletion | • | • | • | • | • | • | • | • | • | |||||||
| Wilms Tumor 1
GeneReviews | 194070 |
WT1 | 11p13 | Rare deletions unless associated with contiguous gene syndrome | Majority have mutations not detectable by array CGH. Contiguous gene deletion syndrome involves WAGR (194072). | • | • | • | • | • | • | • | • | • |
Royer-Pokora et al. 2004. Am J Med Genet 127:249-57. Medline
| |||||
| Wilms tumor-aniridia-genital anomalies-retardation (WAGR)
GeneReviews | 194072 |
PAX6 WT1 | 11p13 | ~66% have a detectable deletion | • | • | • | • | • | • | • | • | • |
Crolla & van Heyningen 2002. Am J Hum Genet. 71:1138-49. Epub 2002 Oct 17 Medline
| ||||||
| Wolf-Hirschhorn
GeneReviews | 194190 | Multiple | 4p16.3 | >95% have a detectable deletion | Candidate genes LETM1 (604407), FGFR3 (134934), WHSC1 (602952), and WHSC2 (606026). | • | • | • | • | • | • | • | • | • | ||||||
| XX male/SRY dosage abnormalities
Signature Summary on SRY Dosage Abnormalities GeneReviews | 278850 |
SRY | Yp11.31 | ~20% have absent SRY | • | • | • | • | • | |||||||||||
| XY gonadal dysgenesis/SRY dosage abnormalities
Signature Summary on SRY Dosage Abnormalities GeneReviews | 400044 |
SRY | Yp11.31 | Large deletions uncommon | 20-30% have small deletions or mutations not detectable by array CGH | • | • | • | • | • | ||||||||||
| XY sex-reversal, +/- adrenal failure/46,XY sex reversal 3/Adrenocortical insufficiency
GeneReviews | 612965 |
NR5A1 | 9q33.3 | Precise detection rate unknown | ~13% have mutations not detectable by array CGH | • | • | • | • | • | ||||||||||
| All 41 unique subtelomeric regions
| Multiple | 41 sites | 0.5-7% have a detectable deletion | • | • | • | • | • | • | • | • | • | ||||||||
| All 43 unique pericentromeric regions
| Multiple | 43 sites | Detection rate variable depending upon the marker chromosome | • | • | • | • | • | • | • | • | • |
Tsuchiya et al. 2008. Mol Cytogenet. 1:7 Medline
| |||||||
| Aneuploidy
| Multiple | 24 chromosomes | >99% detectable by microarray | • | • | • | • | • | • | • | • | • | ||||||||