Table S1: Other Variants in Subjects 1 and 2

Table S1: Other variants in Subjects 1 and 2

Variants of unknown clinical significance in disease genes related to Subject 1's clinical phenotype Gene Variant Transcript Inheritance Disorders associated Inheritance SIFT PolyPhen-2 Mutation Alleles in Alleles Alleles in with gene [OMIMa patterns of Taster NHLBI reported in the 1000 number] associated Exome ExAC Browser Genomes disorders Variant Server (ESP5400) MYH6 c.4780C>T, NM_002471.3 Paternal Atrial septal defect Autosomal Damaging Probably Disease None Nono 1 Het p.R1594W 3 [OMIM:614089]; dominant Damaging Causing Cardiomyopathy, dilated, 1EE [OMIM:613252]; Cardiomyopathy, familial hypertrophic, 14 [OMIM:613251] B3GAT3 c.500G>C, NM_012200.3 Not Multiple joint Autosomal Damaging Probably Disease None None None p.W167S Determined dislocations, short recessive Damaging Causing stature, craniofacial dysmorphism, and congenital heart defects [OMIM:245600]

Pathogenic variants in known disease genes related to Subject 2's clinical phenotype Gene Variant Transcript Inheritance Disorders associated Inheritance SIFT PolyPhen-2 Mutation Alleles in Alleles Alleles in with gene [OMIMa patterns of Taster NHLBI reported in the 1000 number] associated Exome ExAC Browser Genomes disorders Variant Server (ESP5400) POMT1 c.1864C>T, NM_007171.3 Maternal Muscular Autosomal N/A N/A Disease None None None p.R622X dystrophy- recessive causing dystroglycanopathy with mental retardation [OMIM:613155] [OMIM:236670] [OMIM:609308]

Variants of unknown clinical significance in disease genes related to Subject 2's clinical phenotype Gene Variant Transcript Inheritance Disorders Inheritance SIFT PolyPhen Mutation Alleles in Alleles Alleles in associated with patterns of -2 Taster NHLBI reported in 1000 gene [OMIMa associated Exome the ExAC Genomes number] disorders Variant Browser Server (ESP5400) TTN c.25722_25724del, NM_133378.4 Paternal Cardiomyopathy; Autosomal N/A N/A Disease None Total 6 None p.E8575del Myopathy; dominant, causing Hets/84676: Muscular autosomal Africans dystrophy; recessive 3/7352; Latino 2/7190; [OMIM:603689], European (non- [OMIM:613765], Finnish) [OMIM:604145], 1/45348 [OMIM:600334], [OMIM:608807], [OMIM:611705] SYNE2 c.14792A>G, NM_182914.2 Maternal Emery-Dreifuss Autosomal Tolerated Benign Polymorphism Total Total 90 None p.K4931R muscular dominant 12/10746: Hets/121002: dystrophy 5, 11/7009 European Non- autosomal European Finnish American; 79/66536; dominant 1 /3737 other 1/906; [OMIM:612999] African Latino American 4/11524; African 3/10394; South Asian 3/16452 COL6A2 c.2960C>T, NM_001849.3 Maternal Bethlem Autosomal Tolerated Probably Polymorphism Total Total 7 3 Het p.T987M myopathy dominant, Damaging 1/10753: hets/115550: [OMIM:158810]; autosomal 1/7017 South Asian Myosclerosis, recessive European 2/16118; American African congenital 1/9532; Latino [OMIM:255600]; 1/11204; Ullrich congenital European (non- muscular Finnish) dystrophy 3/63516 [OMIM:254090] NEB c.16983C>G, NM_004543.4 Not Nemaline Autosomal Tolerated Benign Disease Total 42/ None None p.D5661E Determined myopathy 2, recessive causing 10148: autosomal 36/6768 recessive European American; [OMIM:256030] 6/3380 Arican American a OMIM = Online Mendelian Inheritance in Man (http://www.ncbi.nlm.nih.gov/omim) Table S2. Confirmation of Subject 3’s Xq13.1 deletion. Interval amplified (hg19) Primer Name Primer Sequence Product Amplified size (bp) from Subject 3?a 5' hNONO Min-Max 3-2F 5’-CCAGCATTCTGTGTACCCATC-3’ chrX:70,475,674-70,475,826 153 Yes 5' hNONO Min-Max 3-2R 5’-AGAGCAGCCAAGGATTCAAG-3’ 5’ hNONO Min-Max 4F 5’-ACATCTGGTTCCATGGAAGGT-3’ chrX:70,479,568-70,479,672 106 No 5’ hNONOMIn-Max4R 5’-CCAACTGTGGCCACTCTTG-3’ 5’ hNONO Min-Max 1F 5’-AGAGTGGCCACAGTTGGTAAG-3’ chrX:70,479,657-70,479,812 156 No 5’ hNONO Min-Max 1R 5’-CTGTAACAAGGCTGAAGTATATGATAA-3’ 5’hNONO Min-Max 5F 5-TCACAACAGGCAAACTCACA-3’ chrX:70,481,520-70,481,626 106 No 5’hNONO Min-Max 5R 5’-TGGGGTTCTACAGAGTCCCT-3’ 5’ hNONO Min-Max 2F 5’-TTTCTGAATTCAAGGATTTCCA-3’ chrX:70,481,573-70,481,677 105 No 5’ hNONO Min-Max 2R 5’-TCTGCAGTGTAATGCTTCTTCA-3’ 5’ hNONO Min-Max NC F 5’-AGGCTTCATGGTGTGCTTCT-3’ chrX:70,483,717-70,483,866 150 No 5’ hNONO Min-Max NC R 5’-ACATTGGGACCCACAAAATC-3’ 3’ hNONO Min-Max NC F 5’-GGCAGTGGAAATAATTCTCAGAT-3’ chrX:70,511,897-70,512,049 153 No 3’ hNONO Min-Max NC R 5’-TCCAAAGGGCATACTTTAGCTC-3’ 3’ hNONO Min-Max End 2F 5’-AGACGTGGGATGACGATTATGA-3’ chrX:70,515,703-70,515,821 119 Yes 3’ hNONO Min-Max End 2R 5’-GGCACAAATCAACTTTTCAGAACT-3’ 3’ hNONO Min-Max End PC F 5’-AGAAGAAGCCTGGTGGGGTA-3’ chrX:70,516,351-70,516,645 285 Yes 3’ hNONO Min-Max End PC R 5’-CTGCCAGTGAACATGTGCAG-3’ a = In all cases where no product was amplified using DNA from Subject 3, a product of predicted size was amplified using DNA from a female control sample.

Table S3. Genes screened for deleterious sequence changes in Subject 3.

Gene Disease ACTA1 Myopathy, actin, congenital, with cores [OMIM: 161800]; Myopathy, congenital, with fiber-type disproportion 1 [OMIM: 255310] ACVR1 Fibrodysplasia ossificans progressiva [OMIM: 135100] ADCK3 Coenzyme Q10 deficiency, primary, 4 [OMIM: 612016] AMPD1 Myopathy due to myoadenylate deaminase deficiency [OMIM: 615511] AMPD3 Adenosine monophosphate deaminase deficiency ANO5 Gnathodiaphyseal dysplasia [OMIM: 166260]; Miyoshi muscular dystrophy 3 [OMIM: 613319]; Muscular dystrophy, limb-girdle, type 2L [OMIM: 611307] BAG3 Cardiomyopathy, dilated, 1HH [OMIM: 613881]; Myopathy, myofibrillar, 6 [OMIM: 612954] BIN1 Myopathy, centronuclear, autosomal recessive [OMIM: 255200] CAPN3 Muscular dystrophy, limb-girdle, type 2A [OMIM: 253600] CAV3 Cardiomyopathy, familial hypertrophic [OMIM: 192600]; Creatine phosphokinase, elevated serum [OMIM: 123320]; Long QT syndrome 9 [OMIM: 611818]; Muscular dystrophy, limb- girdle, type IC [OMIM: 607801]; Myopathy, distal, Tateyama type [OMIM: 614321]; Rippling muscle disease [OMIM: 606072] CCDC78 Myopathy, centronuclear, 4 [OMIM: 614807] CFL2 Nemaline myopathy 7, autosomal recessive [OMIM: 610687] CNTN1 Myopathy, lethal congenital COQ2 Coenzyme Q10 deficiency, primary, 1 [OMIM: 607426] COQ6 Coenzyme Q10 deficiency, primary, 6 [OMIM: 614650] COQ9 Coenzyme Q10 deficiency, primary, 5 [OMIM: 614654] CRYAB Cardiomyopathy, dilated, 1II [OMIM: 615184]; Cataract 16, multiple types [OMIM: 613763]; Myopathy, myofibrillar, 2 [OMIM: 608810]; Myopathy, myofibrillar, fatal infantile hypertrophy, alpha-B crystallin-related [OMIM: 613869] DAG1 Muscular dystrophy-dystroglycanopathy (congenital with brain and eye anomalies), type A, 9 [OMIM: 616538]; Muscular dystrophy-dystroglycanopathy (limb-girdle), type C, 9 [OMIM: 613818] DES Cardiomyopathy, dilated, 1I [OMIM: 604765]; Myopathy, myofibrillar, 1 [OMIM: 601419]; Scapuloperoneal syndrome, neurogenic, Kaeser type [OMIM: 181400] DMD Becker muscular dystrophy [OMIM: 300376]; Cardiomyopathy, dilated, 3B [OMIM: 302045]; Duchenne muscular dystrophy [OMIM: 310200] DNAJB6 Muscular dystrophy, limb-girdle, type 1E [OMIM: 603511] DNM2 Charcot-Marie-Tooth disease, axonal, type 2M [OMIM: 606482]; Lethal congenital contracture syndrome 5 [OMIM: 615368]; Myopathy, centronuclear [OMIM: 160150] DPM3 Congenital disorder of glycosylation, type Io [OMIM: 612937] DYSF Miyoshi muscular dystrophy 1 [OMIM: 254130]; Muscular dystrophy, limb-girdle, type 2B [OMIM: 253601]; Myopathy, distal, with anterior tibial onset [OMIM: 606768] EMD Emery-Dreifuss muscular dystrophy 1, X-linked [OMIM: 310300] FHL1 Emery-Dreifuss muscular dystrophy 6, X-linked [OMIM: 300696]; Reducing body myopathy, X-linked 1a, severe, infantile or early childhood onset [OMIM: 300717]; Reducing body myopathy, X-linked 1b, with late childhood or adult onset [OMIM: 300718]; Scapuloperoneal myopathy, X-linked dominant [OMIM: 300695] FKRP Muscular dystrophy-dystroglycanopathy (congenital with brain and eye anomalies), type A, 5 [OMIM: 613153]; Muscular dystrophy-dystroglycanopathy (congenital with or without mental retardation), type B, 5 [OMIM: 606612]; Muscular dystrophy-dystroglycanopathy (limb-girdle), type C, 5 [OMIM: 607155] FKTN Cardiomyopathy, dilated, 1X [OMIM: 611615]; Muscular dystrophy-dystroglycanopathy (congenital with brain and eye anomalies), type A, 4 [OMIM: 253800]; Muscular dystrophy- dystroglycanopathy (congenital without mental retardation), type B, 4 [OMIM: 613152]; Muscular dystrophy-dystroglycanopathy (limb-girdle), type C, 4 [OMIM: 611588] FLNC Myopathy, distal, 4 [OMIM: 614065]; Myopathy, myofibrillar, 5 [OMIM: 609524] GATM Cerebral creatine deficiency syndrome 3 [OMIM: 612718] GMPPB Muscular dystrophy-dystroglycanopathy (congenital with brain and eye anomalies), type A, 14 [OMIM: 615350]; Muscular dystrophy-dystroglycanopathy (congenital with mental retardation), type B, 14 [OMIM: 615351]; Muscular dystrophy-dystroglycanopathy (limb- girdle), type C, 14 [OMIM: 615352] GNE Inclusion body myopathy, autosomal recessive [OMIM: 600737]; Nonaka myopathy [OMIM: 605820]; Sialuria [OMIM: 269921] ISCU Myopathy with lactic acidosis, hereditary [OMIM: 255125] ISPD Muscular dystrophy-dystroglycanopathy (congenital with brain and eye anomalies), type A, 7 [OMIM: 614643]; Muscular dystrophy-dystroglycanopathy (limb-girdle), type C, 7 [OMIM: 616052] KBTBD13 Nemaline myopathy 6, autosomal dominant [OMIM: 609273] KLHL40 Nemaline myopathy 8, autosomal recessive [OMIM: 615348] KLHL9 Myopathy, distal, early-onset LAMP2 Danon disease [OMIM: 300257] LDB3 Cardiomyopathy, hypertrophic, 24 [OMIM: 601493]; Myopathy, myofibrillar, 4 [OMIM: 609452] LMNA Cardiomyopathy, dilated, 1A [OMIM: 115200]; Charcot-Marie-Tooth disease, type 2B1 [OMIM: 605588]; Emery-Dreifuss muscular dystrophy 2, AD [OMIM: 181350]; Emery- Dreifuss muscular dystrophy 3, AR [OMIM: 616516]; Heart-hand syndrome, Slovenian type [OMIM: 610140]; Hutchinson-Gilford progeria [OMIM: 176670]; Lipodystrophy, familial partial, 2 [OMIM: 151660]; Malouf syndrome [OMIM: 212112]; Mandibuloacral dysplasia [OMIM: 248370]; Muscular dystrophy, congenital [OMIM: 613205]; Muscular dystrophy, limb-girdle, type 1B [OMIM: 159001]; Restrictive dermopathy, lethal [OMIM: 275210] MEGF10 Myopathy, areflexia, respiratory distress, and dysphagia, early-onset [OMIM: 614399] MTM1 Myotubular myopathy, X-linked [OMIM: 310400] MTMR14 Myopathy, centronuclear MYBPC3 Cardiomyopathy, dilated, 1MM [OMIM: 615396]; Cardiomyopathy, hypertrophic, 4 [OMIM: 115197] MYF6 Myopathy, centronuclear, 3 [OMIM: 614408] MYH2 Proximal myopathy and ophthalmoplegia [OMIM: 605637] MYH7 Cardiomyopathy, dilated, 1S [OMIM: 613426]; Cardiomyopathy, hypertrophic, 1 [OMIM: 192600]; Liang distal myopathy [OMIM: 160500]; Myopathy, myosin storage, autosomal dominant [OMIM: 608358]; Myopathy, myosin storage, autosomal recessive [OMIM: 255160]; Scapuloperoneal syndrome, myopathic type [OMIM: 181430] MYOT Muscular dystrophy, limb-girdle, type 1A [OMIM: 159000]; Myopathy, myofibrillar, 3 [OMIM: 609200]; Myopathy, spheroid body [OMIM: 182920] NEB Nemaline myopathy 2, autosomal recessive [OMIM: 256030] PABPN1 Oculopharyngeal muscular dystrophy [OMIM: 164300] PDSS1 Coenzyme Q10 deficiency, primary, 2 [OMIM: 614651] PDSS2 Coenzyme Q10 deficiency, primary, 3 [OMIM: 614652] PLEC Epidermolysis bullosa simplex with muscular dystrophy [OMIM: 226670]; Epidermolysis bullosa simplex with pyloric atresia [OMIM: 612138]; Epidermolysis bullosa simplex, Ogna type [OMIM: 131950]; Muscular dystrophy, limb-girdle, type 2Q [OMIM: 613723] POMGNT1 Muscular dystrophy-dystroglycanopathy (congenital with brain and eye anomalies), type A, 3 [OMIM: 253280]; Muscular dystrophy-dystroglycanopathy (congenital with mental retardation), type B, 3 [OMIM: 613151]; Muscular dystrophy-dystroglycanopathy (limb- girdle), type C, 3 [OMIM: 613157] POMT1 Muscular dystrophy-dystroglycanopathy (congenital with brain and eye anomalies), type A, 1 [OMIM: 236670]; Muscular dystrophy-dystroglycanopathy (congenital with mental retardation), type B, 1 [OMIM: 613155]; Muscular dystrophy-dystroglycanopathy (limb- girdle), type C, 1 [OMIM: 609308] POMT2 Muscular dystrophy-dystroglycanopathy (congenital with brain and eye anomalies), type A, 2 [OMIM: 613150]; Muscular dystrophy-dystroglycanopathy (congenital with mental retardation), type B, 2 [OMIM: 613156]; Muscular dystrophy-dystroglycanopathy (limb- girdle), type C, 2 [OMIM: 613158] PTPLA Centronuclear myopathy PTRF Lipodystrophy, congenital generalized, type 4 [OMIM: 613327] RYR1 Central core disease [OMIM: 117000]; King-Denborough syndrome [OMIM: 145600]; Minicore myopathy with external ophthalmoplegia [OMIM: 255320] RYR2 Arrhythmogenic right ventricular dysplasia 2 [OMIM: 600996]; Ventricular tachycardia, catecholaminergic polymorphic, 1 [OMIM: 604772] SEPN1 Muscular dystrophy, rigid spine, 1 [OMIM: 602771]; Myopathy, congenital, with fiber-type disproportion [OMIM: 255310] SGCA Muscular dystrophy, limb-girdle, type 2D [OMIM: 608099] SGCB Muscular dystrophy, limb-girdle, type 2E [OMIM: 604286] SGCD Cardiomyopathy, dilated, 1L [OMIM: 606685]; Muscular dystrophy, limb-girdle, type 2F [OMIM: 601287] SGCE Dystonia-11, myoclonic [OMIM: 159900] SGCG Muscular dystrophy, limb-girdle, type 2C [OMIM: 253700] SMCHD1 Fascioscapulohumeral muscular dystrophy 2, digenic [OMIM: 158901] STAC3 Native American myopathy [OMIM: 255995] STIM1 Immunodeficiency 10 [OMIM: 612783]; Myopathy, tubular aggregate, 1 160565; Stormorken syndrome [OMIM: 185070] SYNE1 Emery-Dreifuss muscular dystrophy 4, autosomal dominant [OMIM: 612998]; Spinocerebellar ataxia, autosomal recessive 8 [OMIM: 610743] SYNE2 Emery-Dreifuss muscular dystrophy 5, autosomal dominant [OMIM: 612999] TCAP Cardiomyopathy, hypertrophic, 25 [OMIM: 607487]; Muscular dystrophy, limb-girdle, type 2G [OMIM: 601954] TIA1 Welander distal myopathy [OMIM: 604454] TMEM43 Arrhythmogenic right ventricular dysplasia 5 [OMIM: 604400]; Emery-Dreifuss muscular dystrophy 7, AD [OMIM: 614302] TNNT1 Nemaline myopathy 5, Amish type [OMIM: 605355] TNPO3 Muscular dystrophy, limb-girdle, type 1F [OMIM: 608423] TPM2 Arthrogryposis multiplex congenita, distal, type 1 [OMIM: 108120]; Arthrogryposis, distal, type 2B [OMIM: 601680]; CAP myopathy 2 [OMIM: 609285] TPM3 CAP myopathy 1 [OMIM: 609284]; Myopathy, congenital, with fiber-type disproportion [OMIM: 255310] TRAPPC11 Muscular dystrophy, limb-girdle, type 2S [OMIM: 615356] TRIM32 Muscular dystrophy, limb-girdle, type 2H [OMIM: 254110] TTN Cardiomyopathy, dilated, 1G [OMIM: 604145]; Cardiomyopathy, familial hypertrophic, 9 [OMIM: 613765]; Muscular dystrophy, limb-girdle, type 2J [OMIM: 608807]; Myopathy, early-onset, with fatal cardiomyopathy [OMIM: 611705]; Myopathy, proximal, with early respiratory muscle involvement [OMIM: 603689]; Tibial muscular dystrophy, tardive [OMIM: 600334] VCP Amyotrophic lateral sclerosis 14, with or without frontotemporal dementia [OMIM: 613954]; Inclusion body myopathy with early-onset Paget disease and frontotemporal dementia 1 [OMIM: 167320]

OMIM = Online Mendelian Inheritance in Man (http://www.ncbi.nlm.nih.gov/omim)

Figure S1: Photos of Subjects 1-3. A-D) Photos of Subject 1 taken at A) 3.5 years, B) 7 years, C) 8 years, and D) 9 years of age. E) Photo of Subject 2 taken at 5 years of age. F-G) Photos of Subject 3 taken prior to cardiac transplantation when he was between 6 to 8 months of age.

Figure S2: Cardiac evaluation of Subject 3. A) Cardiac 4-chamber view of the left ventricle reveled a non-compact

(NC, red line) to compact (C, green line) ratio >2 consistent with a diagnosis of LVNC. B) After transplantation, the heart was serially section revealing a left ventricle with markedly increased trabeculations (*) filling the lumen near the apex.

Figure S3: NONO is ubiquitously expressed in the mouse heart at P21. A-C) 6 µm sections of P21 mouse heart.

NONO expression was detected using an anti-NONO antibody directed at amino acids 7-21 of human NONO (rabbit polyclonal antibody N8789, Sigma-Aldrich). Sections were counter stained with methyl green. A) NONO is expressed in the nuclei of cells in both the atrium (Atr) and the ventricle (Ven). B) NONO is expressed in the nuclei of cells in the epicardium (Epi), the ventricular wall myocardium (Myo V) and the arteries (A) and veins (V) within the myocardium. C)

NONO is expressed in the nuclei of cells in the myocardium of the ventricular septum (Myo S) and in the endocardium

(End).