Gene | AR disease trait | Genomic region cytogenetic interval | NAHR deletion prevalence in adults | NAHR deletion Impact to Recessive Disease (NIRD) | Top 3 allele contribution to diseasea (NAHRdelCNV in bold) | Fraction of NAHRdelCNV allele frequency | Aggregate carrier allele frequency |
---|---|---|---|---|---|---|---|
NPHP1 | Nephronophthisis 1, juvenile, MIM# 256100 | 2q13 NPHP1 | 5.811x10-3 | 7.7 | 98, 3, 2 | 85 | 6.82x10-3 |
ADRA2B | Autosomal recessive mental retardation (from DECIPHER) | 2q11.2 | 7.36x10-5 | 4.1 | 95, 10, 10 | 90 | 8.18x10-5 |
ALDOA | Glycogen storage disease XII, MIM# 611881 | 16p11.2 proximal | 5.076x10-4 | 4.1 | 95, 10, 10 | 90 | 5.64x10-4 |
CEP19 | Morbid obesity and spermatogenic failure, MIM# 615703 | 3q29 | 2.136x10-5 | 4.1 | 95, 10, 10 | 90 | 2.37x10-5 |
CORO1A | Immunodeficiency 8, MIM# 615401 | 16p11.2 proximal | 5.076x10-4 | 4.1 | 95, 10, 10 | 90 | 5.64x10-4 |
COX5A | Mitochondrial complex IV deficiency, nuclear type 20, MIM# 619064 | 15q24 BPA-BPC | 2.374x10-6 | 4.1 | 95, 10, 10 | 90 | 2.64x10-6 |
EDC3 | Mental retardation, autosomal recessive 50, MIM# 616460 | 15q24 BPA-BPC | 2.374x10-6 | 4.1 | 95, 10, 10 | 90 | 2.64x10-6 |
LAT | Immunodeficiency 52, MIM# 617514 | 16p11.2 distal | 1.377x10-4 | 4.1 | 95, 10, 10 | 90 | 1.53x10-4 |
MIEF2 | Combined oxidative phosphorylation deficiency 49, MIM# 619024 | Smith Magenis Syndrome | 5.333x10-5 | 4.1 | 95, 10, 10 | 90 | 5.93x10-5 |
SLC18A3 | Myasthenic syndrome, congenital, 21, presynaptic, MIM# 617239 | 10q11.21q11.23 | 1.353x10-4 | 4.1 | 95, 10, 10 | 90 | 1.50x10-4 |
PMP22 | Dejerine-Sottas disease, MIM# 145900 | 17p12 HNPP | 3.148x10-4 | 4.2 | 94, 11, 9 | 89 | 3.54x10-4 |
OTUD7A | Neurodevelopmental disorder (this study) | 15q13.3 BP4-BP5 | 9.97x10-5 | 5.4 | 93, 10, 9 | 74 | 1.35x10-4 |
GRAP | Deafness, autosomal recessive 114, MIM# 618456 | Smith Magenis Syndrome | 5.333x10-5 | 4.6 | 91, 41, 7 | 84 | 6.38x10-5 |
RBM8A | Thrombocytopenia-absent radius syndrome, MIM# 274000 | 1q21.1 TAR | 1.78x10-4 | 9.8 | 90, 1, 1 | 90 | 1.98x10-4 |
PRODH | Hyperprolinemia, type I, MIM# 239500 | 22q11.2 LCRA-D | 1.417x10-4 | 5 | 85, 39, 28 | 75 | 1.90x10-4 |
UQCRC2 | Mitochondrial complex III deficiency, nuclear type 5, MIM# 615160 | 16p12.1 | 5.84x10-4 | 5 | 85, 50, 7 | 75 | 7.83x10-4 |
NDE1 | Lissencephaly 4 (with microcephaly), MIM# 614019 | 16p13.11 | 3.11x10-4 | 5.1 | 84, 54, 15 | 72 | 4.30x10-4 |
PEX11B | Peroxisome biogenesis disorder 14B, MIM# 614920 | 1q21 TAR | 1.78x10-4 | 4.7 | 83, 21, 18 | 72 | 2.48x10-4 |
PRRT2 | Autosomal recessive mental retardation (from DECIPHER) | 16p11.2 proximal | 5.076x10-4 | 5.2 | 79, 60, 8 | 65 | 7.77x10-4 |
TUFM | Combined oxidative phosphorylation deficiency 4, MIM# 610678 | 16p11.2 distal | 1.377x10-4 | 3.9 | 79, 10, 10 | 65 | 2.13x10-4 |
COX10 | Mitochondrial complex IV deficiency, nuclear type 3, MIM# 619046 | 17p12 HNPP | 3.148x10-4 | 5.1 | 77, 48, 25 | 62 | 5.05x10-4 |
POLR3GL | Endosteal Hyperostosis and Oligodontia (from DECIPHER) | 1q21 TAR | 1.78Ex10-4 | 4.1 | 74, 20, 13 | 59 | 3.00x10-4 |
SCARF2 | Van den Ende-Gupta syndrome, MIM# 600920 | 22q11.2 LCRA-D | 1.417x10-4 | 3.8 | 73, 38, 8 | 58 | 2.45x10-4 |
B9D1 | Joubert syndrome 27, MIM# 617120 | Smith Magenis Syndrome | 5.333x10-5 | 5.3 | 72, 74, 12 | 56 | 9.47x10-5 |
MYH11 | Megacystis-microcolon-intestinal hypoperistalsis syndrome (from DECIPHER) | 16p13.11 | 3.11x10-4 | 5 | 72, 24, 7 | 57 | 5.48x10-4 |
NCAPH | Microcephaly 23, primary, autosomal recessive, MIM# 617985 | 2q11.2 | 7.36x10-5 | 2.9 | 71, 27, 27 | 55 | 1.33x10-4 |
ANAPC1 | Rothmund-Thomson syndrome, type 1, MIM# 618625 | 2q13 | 1.258x10-4 | 3.8 | 66, 13, 11 | 50 | 2.54x10-4 |
CD19 | Immunodeficiency, common variable, 3, MIM# 613493 | 16p11.2 distal | 1.377x10-4 | 4 | 65, 38, 28 | 48 | 2.86x10-4 |
HJV | Hemochromatosis, type 2A, MIM# 602390 | 1q21 TAR | 1.78x10-4 | 5.2 | 62, 83, 5 | 45 | 3.97x104 |
PIGW | Glycosylphosphatidylinositol biosynthesis defect 11, MIM# 616025 | 17q12 | 6.886x10-4 | 5.2 | 61, 64, 35 | 44 | 1.56x10-4 |
IGLL1 | Agammaglobulinemia 2, MIM# 613500 | 22q11.2 LCRD-H | 1.187x10-5 | 5.2 | 61, 51, 51 | 43 | 2.79x10-5 |
ATPAF2 | Mitochondrial complex V (ATP synthase) deficiency, nuclear type 1, MIM# 604273 | Smith Magenis Syndrome | 5.333x10-5 | 4.1 | 58, 78, 12 | 41 | 1.29x10-4 |
CNNM4 | Jalili syndrome, MIM# 217080 | 2q11.2 | 7.36x10-5 | 3.2 | 57, 16, 9 | 40 | 1.84x10-4 |
RBP3 | Retinitis pigmentosa 66, MIM# 615233 | 10q11.21q11.23 | 1.353x10-4 | 4.1 | 58, 30, 9 | 40 | 3.42x10-4 |
SLC25A1 | Myasthenic syndrome, congenital, 23, presynaptic, MIM# 618197 | 22q11.2 LCRA-D | 1.417x10-4 | 4.2 | 56, 40, 16 | 38 | 3.69x10-4 |
FDFT1 | Squalene synthase deficiency, MIM# 618156 | 8p23.1 | 9.495x10-6 | 5.1 | 55, 53, 53 | 38 | 2.52x10-5 |
GP1BB | Giant platelet disorder, isolated, MIM# 231200 | 22q11.2 LCRA-D | 1.417x10-4 | 4.6 | 86, 55, 5 | 38 | 3.75x10-4 |
SGCG | Muscular dystrophy, limb-girdle, autosomal recessive 5, MIM# 253700 | 13q12.12 | 2.018x10-4 | 4.7 | 53, 25, 16 | 36 | 5.62x10-4 |
CHAT | Myasthenic syndrome, congenital, 6, presynaptic, MIM# 254210 | 10q11.21q11.23 | 1.353x10-4 | 4.1 | 52, 25, 7 | 35 | 3.92x10-4 |
SNAP29 | Cerebral dysgenesis, neuropathy, ichthyosis, and palmoplantar keratoderma syndrome, MIM# 609528 | 22q11.2 LCRA-D | 1.417x10-4 | 4.3 | 50, 46, 29 | 33 | 4.23x10-4 |
CDC45 | Meier-Gorlin syndrome 7, MIM# 617063 | 22q11.2_LCRA-D | 1.417x10-4 | 4.2 | 49, 31, 20 | 33 | 4.34x10-4 |
TBX6 | Spondylocostal dysostosis 5, MIM# 122600 | 16p11.2 proximal | 5.076x10-4 | 5.6 | 47, 20, 5 | 47 | 1.08x10-3 |
NSMCE3 | Lung disease, immunodeficiency, and chromosome breakage syndrome, MIM# 617241 | 15q11q13 BP3-BP4 | 3.798x10-5 | 4.8 | 91, 46, 4 | 29 | 1.29x10-4 |
NRROS | Seizures, early-onset, with neurodegeneration and brain calcification, MIM# 618875 | 3q29 | 2.136x10-5 | 4.8 | 93, 44, 2 | 29 | 7.48x10-5 |
TFRC | Immunodeficiency 46, MIM# 616740 | 3q29 | 2.136x10-5 | 1.6 | 39, 42, 29 | 24 | 8.94x10-5 |
PCYT1A | Spondylometaphyseal dysplasia with cone-rod dystrophy, MIM# 608940 | 3q29 | 2.136x10-5 | 1.8 | 37, 39, 17 | 22 | 9.49x10-5 |
SACS | Spastic ataxia, Charlevoix-Saguenay type, MIM# 270550 | 13q12.12 | 2.018x10-4 | 4.4 | 36, 14, 13 | 22 | 9.09x10-4 |
OTOA | Deafness, autosomal recessive 22, MIM# 607039 | 16p12.1 | 5.84x10-4 | 4.4 | 80, 35, 5 | 21 | 2.78x10-3 |
LMAN2L | Mental retardation, autosomal recessive, 52, MIM# 616887 | 2q11.2 | 7.36x10-5 | 3.4 | 32, 32, 26 | 19 | 3.89x10-4 |
MIPEP | Combined oxidative phosphorylation deficiency 31, MIM# 617228 | 13q12.12 | 2.018x10-4 | 3.9 | 32, 15, 14 | 19 | 1.05x10-3 |
TXNRD2 | Glucocorticoid deficiency 5, MIM# 617825 | 22q11.2 LCRA-D | 1.417x10-4 | 3.4 | 49, 37, 31 | 18 | 7.86x10-4 |
ATP2A1 | Brody myopathy, MIM# 601003 | 16p11.2 distal | 1.377x10-4 | 4.1 | 73, 30, 7 | 18 | 7.79x10-4 |
PI4KA | Polymicrogyria, perisylvian, with cerebellar hypoplasia and arthrogryposis, MIM# 616531 | 22q11.2 LCRA-D | 1.417x10-4 | 4.3 | 28, 16, 14 | 16 | 8.68x10-4 |
DYNLT2B | Short-rib thoracic dysplasia 17 with or without polydactyly, MIM# 617405 | 3q29 | 2.136x10-5 | 1.1 | 60, 44, 27 | 16 | 1.36x10-4 |
TANGO2 | Metabolic encephalomyopathic crises, recurrent, with rhabdomyolysis, cardiac arrhythmias, and neurodegeneration, MIM# 616878 | 22q11.2 LCRA-D | 1.417x10-4 | 2.6 | 80, 23, 23 | 13 | 1.11x10-3 |
ZNHIT3 | PEHO syndrome, MIM# 260565 | 17q12 | 6.886x10-5 | 3.7 | 96, 22, 2 | 13 | 5.47x10-4 |
ERCC6 | Cockayne syndrome, type B, MIM# 133540 | 10q11.21q11.23 | 1.353x10-4 | 3.5 | 21, 15, 14 | 12 | 1.17x10-3 |
FAN1 | Interstitial nephritis, karyomegalic, MIM# 614817 | 15q13.3 BP4-BP5 | 9.97x10-5 | 3.0 | 23, 21, 20 | 11 | 8.94x10-4 |
ALDH3A2 | Sjogren-Larsson syndrome, MIM# 270200 | Smith Magenis Syndrome | 5.333x10-5 | 2.7 | 41, 24, 20 | 11 | 4.71x10-4 |