Table S1 – Detailed list of 98 X-linked syndromes with MR and multiple congenital anomalies (31 of these are mapped and 38 have a cloned gene). Entries are listed in alphabetical order but those that have an OMIM number are indicated first, followed by those that have appeared only in PubMed publications. All entries indicated in red are allelic to the most common or first described condition, i.e. due to mutations in the same gene (e.g. Martinez, Juberg-Marsidi, Chudley-Lowry are due to mutations in the ATRX/XNP gene, just like the alpha-thalassemia mental retardation syndrome). If a condition was not mapped by linkage analysis but through a cytogenetic abnormality (translocation, microdeletion, duplication), this fact has been indicated in the notes column. OMIM /Ref. Name Locus Gene 1 #305400 Aarskog-Scott Xp11.2 FGD1 *300546 2 *300546 %300262 MRX Abidi 3 %300218 4 %304050 Ahmad /MRXS7 Aicardi 5 6 7 8 304200 %300261 300431 #301040 Akesson Armfield Atkin-Flaitz ATR-X #301040 #309580 Martinez Juberg-Marsidi #309580 #309580 #309580 Chudley-Lowry SmithFinemanMyers CarpenterWaziri Holmes-Gang [1,2] MRX #309580 Xq12q21 Xp11.3q22 Xp22 Description short stature, hypertelorism, downslanting palpebral fissures, anteverted nostrils, shawl scrotum, joint hyperlaxity nonspecific MR Short stature, small head, sloping forehead, hearing loss Obesity, hypogonadism, tapered fingers dominant, lethal Abnormal facies (prominent premaxilla, upturned nasal tip, sparse lateral eyebrows), in males; t(X;3) in agenesis of corpus callosum, chorioretinopathy, microphthalmia, seizures two cases Cutis verticis gyrata, thyroid aplasia Macrocephaly, glaucoma, cleft palate, seizures, short stature, small hands and feet Macrocephaly, “coarse” face, short stature, obesity, macroorchidism Xq28 Xq13.3 Notes ATRX (XNP) *300032 Microcephaly, “coarse” face, genital and skeletal anomalies, -thalassemia and HbH inclusions in some Spastic diplegia, microcephaly and short stature Short stature, deafness, flat nasal bridge, ocular abnormalities, rudimentary scrotum with cryptorchidism Short stature, obesity, small genitalia Short stature, peculiar face, microcephaly, seizures Short stature, prominent lips, bushy eyebrows, depressed nasal bridge with wide nose tip, spaced teeth, brachydactyly Microcephaly, epicanthal folds, short nose with anteverted nostrils, short upper lip, equinovarus deformity nonspecific MR 9 #301900 10 301950 11 %300612 12 #300354 #300639 BorjesonForssmanLehmann Branchial arch BrooksWisniewskiBrown Cabezas Xq26.2 Xq24 13 *300524 14 308830 15 %309620 Cantu' Christian 16 *300243 Christianson Xq26.3 17 #303600 Coffin-Lowry Xp22.1  18 #300590 20 %305450 MRX Cornelia de Lange, Xlinked Dyskeratosis congenita HoyeraalHreidarsson FG (FGS1) %309520 21 %300321 Lujan FGS2 22 %300406 23 %300422 FGS3 FGS4 Xp22 Xp11.3Xp11.4 24 %300581 FGS5 Xq22.3 #300240 Obesity, hypogonadism, round face, narrow palpebral fissures, epilepsy Short stature, downslanting eyelids, low set ears, webbed neck, highly arched palate Peculiar face, growth retardation, optic atrophy, spastic diplegia, atrophic hydrocephalus Wei / MR X-linked hypotonic facies 2 Cantagrel Xq13.2 19 #305000 PHF6 *300414 CUL4B *300304 Short stature, prominent lower lip, obesity, hypogonadism, muscle wasting, tremor Short stature, large mouth with prominent lips, short thumbs, restlessness, seizures KIAA2022 *300524 inv(X)(p22.3q13. 2), familial Xq27q28 Xp11.22 Xq28 Xq13.1 Xq28 SLC9A6 *300231 RSK2 (RPS6KA3) *300075 nonspecific MR (MRX19) Facial dysmorphism (less typical), growth deficits with feeding problems, small hands, epilepsy, enlarged ventricles SMC1A / SMC1L1 *300040 DKC1 *300126 Reticulate skin pigmentation, nail dystrophy, mucosal leukoplakia, progressive bone marrow failure Growth retardation, microcephaly, cerebellar hypoplasia, aplastic anemia & immunodeficiency Macrocephaly, agenesis of corpus callosum, gastrointestinal anomalies, deafness MED12 *300188 (FLNA +300017) ? see ref.  Short stature, microcephaly, short philtrum, short nose with thick tip, profound MR, spastic tetraparesis Macrocephaly, dwarfism, keratosis follicularis Skeletal dysplasia (short stature, ridging of the metopic suture, fusion of cervical vertebrae, thoracic hemivertebrae, scoliosis, sacral hypoplasia, and short middle phalanges), abducens (VI) nerve palsy Angelman-like phenotype, profound MR, mutism despite normal hearing, craniofacial dysmorphism, grand-mal epilepsy, ophthalmoplegia, cerebellar atrophy “Coarse” face, drumstick phalanges, skeletal anomalies inv(X)(q12q28), familial (CASK *300172) ? see ref.  duplication that includes PRPS1 Marfanoid habitus, triangular face, narrow palate, hypernasal voice Prominent forehead, hypotonia, failure to thrive, constipation, and anteriorly placed anus 25 #300676 %309520  26 #300659 27 #300624 #300623 28 %305600 [7,8] 29 #300472 30 %302000 31 300064 32 307010 33 #307030 34 %307700 35 +309900 36 #308300 37 #300534 38 *300471 39 *300319 [9,10] 40 #309000 (FGS6) MRXS14 Lujan MRX (FGS7) Macrocephaly XLMR Fragile X Xq24 Xq21.1 UPF3B *300298 FMR1 *309550 Fragile X-associated Tremor Ataxia Syndrome Goltz / Focal Xp11.23 PORCN *300651 Dermal hypoplasia Graham (IGBP1 *300139) ? Hereditary Xq27.3bullous q28 dysfunction Hyde-Forster Hydrocephalus with cerebellar agenesis GK *300474 HyperXp21.2 glycerolemia HypoparaXq26thyroidism, q27 X-linked IDS Hunter disease Xq28 +309900 IKBKG / Incontinentia Xq28 NEMO pigmenti / IP2 *300248 JARID1CXp11.22 JARID1C / SMCX related XLMR *314690 Jones Xq22.1 Lowe OculoCerebro Renal Xq25 marfanoid habitus nonspecific MR Macrocephaly, large prominent ears, pointed chin BRWD3 *300553 Xq27.3 Jun either FG phenotype or Lujan phenotype (marfanoid habitus) NXF5 *300319 OCRL1 *300535 triplet expansion (>200 CGG) triplet expansion (50-200 CGG) dominant, lethal in males Macrocephaly, long face, long ears, macroorchidism 2 brothers with a promoter variant? Short stature, agenesis of corpus callosum, coloboma of the iris and retina, low set ears, sensorineural deafness, micrognatia, high forehead, pectus excavatum and scoliosis in 2 brothers (+choanal atresia & PDA/VSD in one) Short stature, microcephaly, alopecia, bullous dystrophy, hypogenitalism, early lethality 2 brothers Craniofacial anomalies with plagiocephaly, flattened occiput Hydrocephalus, cerebellar agenesis, absence of Magendie and Luschka’s foramina Glyceroluria, poor growth, esotropia, osteoporosis Enzyme deficiency Late-onset tremor, gait unsteadiness, dementia, brain atrophy Focal dermal hypoplasia, short missing digits, polysyndactyly, microphthalmia neonatal tetany, parathyroid agenesis, seizures - survivors may have cataracts, short stature and mental retardation Enzyme deficiency dominant, lethal in males “Coarse” face, dysostosis multiplex, dwarfism, hepatosplenomegaly, heart involvement Incontinentia pigmenti, incomplete dentition, retinal abnormalities Short stature, slowly progressive spastic paraplegia, maxillary hypoplasia, facial hypotonia and dysmorphism inv(X)(p21.1q22. 1) + missense Enzyme deficiency Cubitus valgus, mild microcephaly, short philtrum, deep-set eyes, downslanting palpebral fissures, multiple nevi, seizures short stature, downslanted palpebral fissures, large everted ears Hydrophthalmia, cataract, vitamin D-resistant rickets 41 +300646 Marfanoid 42 %300519 Martin-Probst 43 %309800 MCOPS1 / Lenz MCOPS2 / ANOP2 / OculoFacio CardioDental MCOPS4 / ANOP1 44 #300166 45 %301590 46 #309801 47 %300148 48 #309400 #304150 49 %309605 50 #300123 %312000 51 #302350 52 *312180 53 #300000 54 #311200 #300209 55 #311300 MCOPS7 / MIDAS MEHMO Xq25q26.1 (Xq11q21) Xq27q28 Xp11.4 ZDHHC9 +300646 ATR-X excluded Telecanthus, hypertelorism, broad mouth, low set ears, mild-severe MR, microcephaly, short stature, pancytopenia Microphthalmia, thumb and skeletal anomalies, urogenital and cardiovascular anomalies Microphthalmia, cataracts, radiculomegaly and septal heart defects Overlaps MCOPS1/Lenz %309800 dominant, lethal in males Anophthalmos, ankyloblepharon, orbital underdevelopment BCOR *300485 (Xq27q28) Xp22.2 Hypotonia, marfanoid habitus, pronounced language handicap HCCS *300056 Xp22.13p21.1 ATP7A Menkes Xq21.1 *300011 Occipital horn syndrome / Cutis laxa, X-linked MilesXp11.2Carpenter q23 /MRXS4 SOX3 MRGH Xq27.1 *313430 PanhypoSOX3 pituitarism duplication *313430 Nance-Horan Xp22.13 NHS *300457 UBE2A Nascimento Xq24 *312180 MID1 Opitz G/BBB Xp22.2 *300552 OFD1 Oro-FacioXp22.2 *300170 Digital 1 SimpsonGolabi-Behmel, type 2 FLNA Oto-PalatoXq28 *300017 Digital 1 Microphthalmia, dermal aplasia, sclerocornea Epilepsy, hypogonadism and hypogenitalism, microcephaly, obesity Enzyme deficiency Growth retardation, peculiar hair, focal cerebral & cerebellar degeneration occipital bone exostoses, long face and philtrum, arched palate, long neck, narrow chest and shoulders, bladder diverticula Microcephalus, asymmetric face, hypogonadism, joint hypermobility, 10 digital arches 11 ala in-frame Isolated GH deficiency, short stature, small sella turcica insertion Duplication Combined deficiency of pituitary hormones (SOX3) and 7 ala in-frame insertion Cataract, microcornea, cone-shaped incisors, supernumerary teeth generalized hirsutism, synophris, upslanted palpebral fissures, large mouth, short stature, obesity, severe speech impairment, seizures Hypertelorism, midline abnormalities, heart defects, hypospadias dominant, lethal in males Midline clefting of face, tongue nodules, syndactyly early demise, macrocephaly, hypertelorism, short broad nose, large mouth, prominent philtrum, cleft palate, redundant skin, hypoplastic nails, broad thumbs, short fingers, gastrointestinal and genitourinary anomalies (including polycystic kidneys). Short stature, hearing loss, cleft palate, characteristic face, broad thumbs & halluces, syndactyly #304120 #305620 #309350 #300049 #300048 56 311450 57 %304340 58 %309610 59 300404 60 #309500 dominant, lethal in males Epilepsy, periventricular nodular heterotopia, mild hypoplasia of corpus callosum and/or cerebellum in females; syndactyly and severe MR in few sporadic affected males Chronic idiopathic intestinal pseudoobstruction (CIIP), seizures Characteristic face, clefting, subluxed elbow, camptodactily Dandy-Walker anomaly, ataxia, seizures, iron accumulation in basal ganglia, spasticity, hydrocephalus, hypotonia, long “coarse” face Peculiar face, dental anomalies, sacral dimple, joint dysplasia, epilepsy 2 maternal half brothers PQBP1 +300463 Brain anomalies, growth retardation, ectodermal dysplasia, skeletal malformations, Hirschsprung disease, ear deformity and deafness, eye hypoplasia, cleft palate, cryptorchidism, and kidney dysplasia/hypoplasia Microcephaly, short stature #309500 +300463 Golabi-Ito-Hall Congenital heart defect, cleft palate, short stature, facial anomalies (anal atresia, iris coloboma, situs inversus) Short stature, triangular face, epicanthic folds, microcephaly, brittle hair  Porteous Short stature, high-pitched voice, high forehead, receding hairline #309500 Fichera #309500 300258 308200 314320 312840 MRX Roifman Rud Say-Meyer Schimke Microcephaly, prognathism, malocclusion, spastic diplegia, cerebellar vermis hypoplasia (?), skewed X-inactivation in females nonspecific MRX (MRX55) spondyloepiphyseal dysplasia, growth retardation, immune deficiency, retinal dystrophy Ichthyosis, epilepsy, nystagmus, hypogonadism Trigonocephaly, short stature Early onset choreoathetosis with later spasticity, postnatal microcephaly and growth failure, external ophthalmoplegia, variable deafness Coarse facial features, puffy eyelids, obesity, large ears and large testes 65 %300238 66 #300263 Xp11.23 lethal skeletal dysplasia, cleft palate, microcephaly, downward-slanting palpebral fissures, small thorax, and bowed limbs with absent fibulae marked frontal hyperostosis, underdeveloped mandible, cryptorchidism, subluxated radial heads and metaphyseal dysplasia Prominent supraorbital ridge, cleft palate, micrognathia, malaligned teeth Renpenning /MRXS8 SutherlandHaan /MRXS3 Hamel #309500 61 62 63 64 Oto-PalatoDigital 2 Frontometaphy seal dysplasia MelnickNeedles syndrome Bilateral Periventricular Nodular Heterotopia Chronic idiopathic intestinal pseudoobstruction Pallister W syndrome Pettigrew Xq26/MRXS5 q27.1 Prieto /MRXS2 Xp21.1p11.3 Reish Shashi Xq26/MRXS11 q27 Siderius-Hamel Xp11.22 Microcephaly, short stature, small testes, spastic diplegia PHF8 *300560 Cleft lip and palate, broad nasal tip, large hands 67 #312870 68 #309583 69 300232 70 #300434 SimpsonGolabi-Behmel SnyderRobinson Spondyloepimetaphyseal dysplasia Stocco dos Santos Xq26.2 Xp22.11 Xp11.22 (p11.3q21.1) Tranebjaerg I Turner [12,13] #300630 73 #314390 Fried MRX VACTERL with Xp22.2 hydrocephalus Van den Bosch Vitale Xq24 76 %309545 Xp22.2 78 %300421 Wilson /MRXS12 Wilson-Turner /MRXS6 Wittwer (Xp11Xq27) Xp21.1q22 (Xp22) 79  Carpenter Xq23q24 80  81  Cerebralcerebellarcoloboma syndrome Chassaing 82  Chudley 83  Cilliers 84  85  86  Hall Hockey Homfray 77 %309585 Macrocephaly, long thin face, high narrow/cleft palate, asthenic body build, scoliosis short stature, brachydactyly, seizures, small corpus callosum 71 309480 72 #300630 74 %314500 75 *300360 Macrosomia, “coarse” face, polydactyly, extra nipples, heart defects GPC3 *300037 SMS *300105 KIAA1202 / SHROOM4 *300579 Short stature, bilateral hip luxation, hypertelorism, seizures, cortical atrophy Epilepsy, psoriasis Severe hypotonia, short stature, high forehead, prominent ears, small pointed chin AP1S2 *300629 Hydrocephalus, spastic diplegia, calcification of basal ganglia nonspecific MR (MRX59) Vertebral, anal, tracheo-esophageal, renal and radial defects, hydrocephalus FANCB *300515 may include Vasquez (97)? dominant, lethal in males dominant, lethal in males Xq21.2q23 Xq25q26 Choroideremia, acrokeratosis verruciformis, anhydrosis, skeletal deformities Short stature, brachydactyly, narrow downslanted palpebral fissures, large bulbous nose, macrostomia Aphasia, growth failure, brachycephaly, large mouth with thick lips, seizures, frequent infections Obesity, gynecomastia, tapering fingers, emotional lability Square face, high broad forehead, frontal bossing, hypertelorism, downslanting palpebral fissures, anteverted nares Congenital hip dislocation, microcephaly, hypertelorism and dysmorphic facial features, short neck and sternum early demise, dysmorphisms, hypotonia, retinal colobomas, hydrocephalus, cerebellar vermis hypoplasia, seizures (X-linked Joubert syndrome ?) lethal chondrodysplasia, platyspondily, brachydactily, hydrocephaly and microphthalmia; female carriers with mild MR and short stature Prognathism, synophrys, hirsutism, seizures, abnormal gait and weakness, hypogammaglobulinemia hypergonadotrophic hypogonadism, small testes, short stature, microcephaly Cleft lip/palate, facial dysmorphism, inguinal hernia, digital defects Precocious puberty, progressive IQ deterioration (mild to moderate) Coarse facial features, epilepsy, progressive joint contractures 87  Johnson 88  Oosterwijk 89  90 [25,26] 91  Seemanova Shrimpton /MRXS9 Stevenson 92  Stevenson 93  94  95 [31,32] Stoll Tariverdian Turner  Xq12q21 (Xp11.4q24) van Esch 97  Vasquez 98  Young-Hughes A/synphalangism of hands and feet, hearing loss, verrucosis and hypertrichosis, immunodeficiency Microcephaly, microphthalmia, congenital cataract, peculiar face, microgenitalism Microcephaly, variably short stature Xq12q21.31 Xq12q21.2 Hypotonia, areflexia, tapered fingers, arches increased, genu valgum dominant, lethal in males Xp11.22 MRX 96  Macrocephaly, macroorchidism, midface hypoplasia, triangular face Xp22.1p21.3 HUWE1 missense mutation either missense or duplication not ARX or IL1RAPL1 may be BFLS? See %309585 microcephaly, short stature, hypotelorism, small ears, short philtrum, small mandible, small hands and feet, and mild cognitive impairment Short stature, prominent forehead, hypertelorism, broad nasal tip, anteverted nares Acromegaly, CNS anomalies, macroorchidism Macrocephaly and heterozygote expression, previously linked to Xp21.2-q13 nonspecific MR (including MRX17 and MRX31: in both cases there was a microduplication involving the HUWE1 and the HADH2 genes) Short stature, microcephaly, hypogonadism Hypogonadism, gynecomastia, short stature, obesity Short stature, obesity, hypogonadism References for Table S1:  Guerrini R, Shanahan JL, Carrozzo R, Bonanni P, Higgs DR, Gibbons RJ (2000) A nonsense mutation of the ATRX gene causing mild mental retardation and epilepsy. 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