Use of Whole-Exome Sequencing to Determine the Genetic Basis of Multiple Mitochondrial Respiratory Chain Complex Deficiency

Supplementary Online Content

Taylor RW, Pyle A, Griffin H, et al. Use of whole-exome sequencing to determine the genetic basis of multiple mitochondrial respiratory chain complex deficiency. JAMA. doi:10.1001/jama.2014.7184

eTable 1. Genetic Summary eTable 2. Clinical Presentation, Laboratory Investigations, and Exome Sequencing Result for 53 Patients With Multiple Respiratory Chain Complex Defects eTable 3. Exome Coverage and Depth Statistics eReferences

This supplementary material is provided by the authors to give readers additional information about their work.

GO- In- ID Gene Chr Position Ref. Var. Mutation Transcript Lieber ESP6500 1000G dbSNP term House P1, P2, P3, Hom. c.1349G>C RMND1 6 151726371 C G NM_017909.3 Y Y 0.002 - - - P4, P5 p.*450Serext*32 c.713A>G P6 RMND1 6 151748614 T C NM_017909.3 Y Y - - - - p.Asn238Ser c.829_830+2delGAGT P6 RMND1 6 151751289 TACTC T NM_017909.3 Y Y - 0.0004 - rs144972972 p.Glu277Glyfs*20 c.2882C>T P7 AARS2 6 44268360 G A NM_020745.3 Y Y - - - - p.Ala961Val P7, P8, P9, c.1774C>T AARS2 6 44272249 G A NM_020745.3 Y Y - 0.0002 - rs138119149 P11 p.Arg592Trp c.1774C>T P10 AARS2 6 44272249 G A NM_020745.3 Y Y - 0.0002 - rs138119149 p.Arg592Trp c.647_648insG P10 AARS2 6 44278832 G GC NM_020745.3 Y Y - - - - p.Cys218Leufs*6 c.631_631delG P12 MTO1 6 74183182 AG A NM_012123.3 Y Y - - - - p.Gly211Aspfs*3 c.1402G>A P12 MTO1 6 74191784 G A NM_012123.3 Y Y - 0.0003 - rs143747297 p.Ala468Thr Hom. c.1232C>T P13, P14 MTO1 6 74190500 C T NM_012123.3 Y Y 0.002 - - - p.Thr411Ile c.122T>G P15 MTO1 6 74171699 T G NM_012123.3 Y Y - - - - p.Val41Gly c.767A>G P15 MTO1 6 74183319 A G NM_012123.3 Y Y - - - - p.His256Arg c.1402G>A P15 MTO1 6 74191784 G A NM_012123.3 Y Y - 0.0003 - rs143747297 p.Ala468Thr Hom. c.193A>G P16 EARS2 16 23563572 T C NM_001083614.1 Y Y - - - - p.Lys65Glu c.322C>T P17 EARS2 16 23546353 C T NM_001083614.1 Y Y - - - - p.Arg108Trp c.814G>A P17 EARS2 16 23555998 G A NM_001083614.1 Y Y - 0.0003 - - p.Ala272Thr

© 2014 American Medical Association. All rights reserved. Downloaded From: https://jamanetwork.com/ on 09/24/2021 GO- In- ID Gene Chr Position Ref. Var. Mutation Transcript Lieber ESP6500 1000G dbSNP term House c.452C>T P18 MTFMT 15 65295576 G A NM_139242.3 Y Y - 0.0001 - rs200286768 p.Pro151Leu c.994C>T P18 MTFMT 15 65316100 G A NM_139242.3 Y Y - - - - p.Arg332* c.1100_1101delTT P19 MTFMT 15 65295468 GAA G NM_139242.3 Y Y - 0.0001 - - p.Phe367Serfs*22 c.626C>T P19 MTFMT 15 65313871 G A NM_139242.3 Y Y - 0.0008 - rs201431517 p.Arg181Serfs*5 c.292C>T P20 MGME1 20 17956347 C T NM_052865.2 Y Y 0.002 0.0032 0.0027 rs143417446 p.Arg98Trp c.554C>T P20 MGME1 20 17968871 C T NM_052865.2 Y Y 0.006 0.0105 0.0100 rs76599088 p.Thr185Ile Hom. c.96_99dupATCC P21 C12ORF65 12 123738316 T TATCC NM_152269 Y Y - - - - p.Pro34Ilefs*25 Hom. c.137G>A P22 YARS2 12 32908672 C T NM_001040436.2 Y Y - - - - p.Gly46Asp Hom. c. 342C>A P23 PUS1 12 132416842 C A NM_025215.5 Y Y - - - - p.Cys114* Hom. c.287A>G P24 TRMU 22 46739197 A G NM_018006.4 Y Y - - - - p.Asn96Ser Hom. c.1A>G P25 TK2 16 66583964 T C NM_004614.3 Y Y - - - - p.Met1Val Hom. c.418G>A P26 SCO2 22 50962423 C T NM_001169111.1 Y Y - 0.0002 - rs74315511 p.Glu140Lys c.1478C>T P27 ELAC2 17 12899902 C T NM_018127.6 Y Y 0.045 0.0288 0.0200 rs5030739 p.Pro493Leu c.1621G>A P27 ELAC2 17 12901771 G A NM_018127.6 Y Y - - - - p.Ala541Thr Hom. c.3G>T P28 ETHE1 19 44031327 C A NM_014297.3 Y Y - - - rs119103249 p.Met1Ile c.1045G>A P29 VARS2 6 30886663 G A NM_001167734.1 Y Y - - - - p.Ala349Thr c.1787C>A P29 VARS2 6 30889753 C A NM_001167734.1 Y Y - - - - p.Ala596Asp

© 2014 American Medical Association. All rights reserved. Downloaded From: https://jamanetwork.com/ on 09/24/2021 GO- In- ID Gene Chr Position Ref. Var. Mutation Transcript Lieber ESP6500 1000G dbSNP term House Hom. c.397_400delTTCT P30 FLAD1 1 154960604 CTTCT C NM_025207.4 N N - - - - p.Phe134Cysfs8 Hom. c.2065C>T P31 GARS 7 30672024 C T NM_002047.2 Y Y - - - - p.Arg689Cys c.550G>A P32 PTCD1 7 99030945 C T NM_015545.3 Y Y - - - - p.Gly184Arg c.337C>T P32 PTCD1 7 99032478 G A NM_015545.3 Y Y - - 0.0005 rs201306967 p.Arg113Trp c.388C>T P32 PTCD1 7 99032529 G A NM_015545.3 Y Y 0.002 0.0038 0.0005 rs35556439 p.Arg130* Hom. c.1333G>A P33 SLC25A12 2 172644389 C T NM_003705.4 Y Y - 0.0004 - rs142912356 p.Ala445Thr Hom. P33 METAP1D 2 172930482 T A NM_199227.1 Y Y - - - - c.497+2T>A c.1157A>C P34 ACSM5 16 20442346 A C NM_017888.2 Y Y 0.006 0.0055 0.0046 rs148243446 p.Lys386Thr c.1273C>A P34 ACSM5 16 20442608 C A NM_017888.2 Y Y 0.009 - - rs79364355 p.Pro425Thr Hom. c.206T>C P35 PERP 6 138428272 A G NM_022121.4 N Y - - - - p.Met69Thr c.1052A>C P35 MEF2A 15 100252738 A C NM_005587.2 N Y 0.007 - - rs201861701 p.Gln351Pro c.1055A>C P35 MEF2A 15 100252741 A C NM_005587.2 N Y 0.004 - - rs199811207 p.Gln352Pro c.68A>G P35 ACSM5 16 20422874 A G NM_017888.2 Y Y 0.007 0.0028 0.0018 rs144606521 p.His23Arg c.73A>C P35 ACSM5 16 20422879 A C NM_017888.2 Y Y 0.007 0.0025 - rs148462851 p.Lys25Gln Hom. c.1276C>T P36 HKDC1 10 71008190 C T NM_025130.3 N Y 0.002 0.0052 0.0018 rs148832840 p.Arg426Cys Hom. c.20C>T P36 ETFA 15 76603710 G A NM_000126.3 Y Y 0.002 - - - p.Pro7Leu Hom. c.2393C>T P36 IREB2 15 78786319 C T NM_004136.2 Y Y - 0.0005 - rs147288797 p.Thr798Ile

© 2014 American Medical Association. All rights reserved. Downloaded From: https://jamanetwork.com/ on 09/24/2021 GO- In- ID Gene Chr Position Ref. Var. Mutation Transcript Lieber ESP6500 1000G dbSNP term House Hom. c.241C>T P36 SMCR7 17 18166493 C T NM_139162.3 N Y - - - - p.Gln81* c.1876C>T P37 PC 11 66619351 C T NM_000920.3 Y Y - - - rs113994145 p.Arg626Trp c.1892G>A P37 PC 11 66619367 G A NM_000920.3 Y Y - - - - p.Arg631Gln Hom. c.230C>T P38 TPO 2 1440117 C T NM_000547.5 Y Y - 0.0002 - - p.Ala77Val c.9979G>A P39 HERC2 15 28419619 C T NM_004667.5 N Y 0.058 - 0.0600 rs141441362 p.Val3327Met c.6448C>G P39 HERC2 15 28459329 G C NM_004667.5 N Y - - - - p.Leu2150Val Hom. c.1648A>C P40 MAGI1 3 65376943 T G NM_015520.1 N N 0.002 0.0019 0.0014 rs61740330 p.Thr550Pro Hom. c.322G>C P40 TAF9 5 68647992 C G NM_032013.3 N N - 0.0003 0.0005 rs190151255 p.Glu108Gln Hom. c.505C>T P40 TPX2 20 30359382 C T NM_012112.4 N N - - - - p.Pro169Ser Hom. c.184G>A P40 NDRG3 20 35309281 C T NM_001015891 N N - - - - p.Gly62Ser c.368T>C P41 FAAH2 X 57337118 T C NM_174912.3 N N - - - - p.Phe123Ser (X-linked) c.493C>T P41 SLC25A43 X 118540640 C T NM_145305.2 Y Y - 0.0002 - rs138285581 p.Arg165* (X-linked) c.1738G>T P42 ARHGEF5 7 144061500 G T NM_005435.3 N N 0.015 - 0.0400 rs201664716 p.Gly580Cys c.4066A>G P42 ARHGEF5 7 144070303 A G NM_005435.3 N N - 0.0001 - - p.Asn1356Asp c.55G>C P42 DLAT 11 111896251 G C NM_001931.4 Y Y 0.004 0.0081 0.0046 rs61757217 p.Glu19Gln c.626A>G P42 DLAT 11 111899635 A G NM_001931.4 Y Y 0.007 0.0490 0.0300 rs11553595 p.Gln209Arg c.34G>A P42 SDHD 11 111957665 G A NM_003002.3 Y Y 0.007 0.0079 0.0100 rs28937576 p.Gly12Ser

© 2014 American Medical Association. All rights reserved. Downloaded From: https://jamanetwork.com/ on 09/24/2021 GO- In- ID Gene Chr Position Ref. Var. Mutation Transcript Lieber ESP6500 1000G dbSNP term House c.269T>C P42 SDHD 11 111965600 T C NM_003002.3 Y Y - - - rs201726097 p.Leu90Ser c.232G>A P42 POLRMT 19 630130 C T NM_005035.3 Y Y 0.006 0.0023 0.0018 rs140649984 p.Val78Met c.112C>T P42 POLRMT 19 632915 G A NM_005035.3 Y Y 0.093 0.0840 0.1400 rs12610885 p.Pro38Ser c.4132A>G P43 LRPPRC 2 44115792 T C NM_133259.3 Y Y - 0.0005 - rs149693840 p.Ser1378Gly c.1210C>T P43 HTRA2 2 74759840 C T NM_013247.4 Y Y - - - - p.Arg404Trp c.1810G>C P43 ALDH1L1 3 125831693 C G NM_001270364.1 Y Y - - - - p.Glu604Gln c.239G>A P43 SLC25A4 4 186066045 G A NM_001151.3 Y Y - - - - p.Arg80His c.23C>T P43 BCKDHB 6 80816433 C T NM_183050.2 Y Y - - - - p.Ala8Val c.1003G>A P43 ACSM2A 16 20487000 G A NM_001010845.2 Y Y 0.002 0.0001 - rs4643305 p.Val335Ile c.242G>A P43 TYMP 22 50967740 C T NM_001113755.2 Y Y 0.002 0.0013 0.0009 rs143789597 p.Arg81Gln c.1003C>A P44 PPL 16 4945687 G T NM_002705.4 N Y 0.074 0.0555 0.0500 rs35340520 p.Leu335Met c.263A>G P44 PPL 16 4953941 T C NM_002705.4 N Y - - - - p.Asp88Gly c.425A>G P44 SLC5A10 17 18874359 A G NM_152351.4 N Y - - - - p.Glu142Gly c.1670T>C P44 SLC5A10 17 18923704 T C NM_152351.4 N Y - - - - p.Leu557Pro c.4240A>G P45 FNDC1 6 159660797 A G NM_032532.2 N Y 0.006 - - - p.Thr1414Ala c.4358C>A P45 FNDC1 6 159660915 C A NM_032532.2 N Y - 0.0013 - rs200218522 p.Thr1453Asn c.2657T>C P45 FASN 17 80046120 A G NM_004104.4 Y Y 0.002 - - - p.Phe886Ser

© 2014 American Medical Association. All rights reserved. Downloaded From: https://jamanetwork.com/ on 09/24/2021 GO- In- ID Gene Chr Position Ref. Var. Mutation Transcript Lieber ESP6500 1000G dbSNP term House c.1850C>T P45 FASN 17 80048271 G A NM_004104.4 Y Y - 0.0011 0.0014 rs45444391 p.Pro617Leu c.316A>G P46 PDPR 16 70164334 A G NM_017990.3 Y Y 0.299 - 0.3300 rs10852462 p.Ile106Val c.958A>G P46 PDPR 16 70178343 A G NM_017990.3 Y Y - - - - p.Thr320Ala c.79G>C P46 LONP1 19 5693616 C T NM_004793.3 Y Y 0.009 0.0121 0.0100 rs35804229 p.Ala27Pro c.2485G>A P46 LONP1 19 5720065 C G NM_004793.3 Y Y 0.002 - - - p.Ala829Thr Hom. c.671A>G P47 MIPEP 13 24444267 T C NM_005932.3 Y Y - 0.0048 0.0041 rs74724219 p.Asn224Ser Hom. c.1162C>T P47 STARD13 13 33703628 G A NM_178006.3 N Y - - - - p.His388Tyr

ID = patient number; Chr = chromosome number; Position = position according to UCSC, hg19 human genome reference sequence; Ref. = reference allele; Var. = variant allele; Transcript = transcript code according to NCBI, “Gene” indicates whether the gene is predicted to encode a protein localized to mitochondria. Lieber – Y = gene predicted to encode a mitochondrial protein;1 GO-terms – Y = gene predicted to be mitochondrial based on Gene Ontology (http://www.geneontology.org/); MAF = minor allele frequency; for “In House” the MAF is based on 293 in-house exomes from patients who do not have multiple respiratory chain complex defects; for “ESP6500” the MAF is derived from 6500 exomes (NHLBI Exome Sequencing Project: http://evs.gs.washington.edu/EVS/); for 1000g the MAF is derived from the1000 genomes project, April 2012 (http://www.1000genomes.org/); dbSNP = single nucleotide polymorphism identifier from the on-line data base dbSNP137.

eTable 2. Clinical Presentation, Laboratory Investigations, and Exome Sequencing Result for 53 Patients With Multiple Respiratory Chain Complex Defects

A) Presumptive

Functional and biochemical Patient Information Clinical Presentation Genetic Analysis analysis

Onset/ Country ID/ Family Death(†) Additional of Mu C H L Histochemistry CI CIII CIV Gene Variant A U Sex History Current presentation Origin age

Deafness, British 6m/ 1/M C + - - - dysplastic COX mosaic RMND1 Hom. c.1349G>C: p.*450Serext*32 1 2 Pakistani 4y ↓↓ ↓↓ ↓↓ kidneys & LA

Deafness, British 3m/ Global COX 2/M* C + + - - anaemia N RMND1 Hom. c.1349G>C: p.*450Serext*32 1 2 Pakistani 1y† defect ↓↓ ↓↓ & LA Deafness, British 18m/ renal 3/F C + + + - COX mosaic RMND1 Hom. c.1349G>C: p.*450Serext*32 - - Pakistani 5y dysplasia & ↓↓ ↓↓ ↓↓ LA Deafness & British 6m/ COX mosaic, 4/F* C + - + - renal tubular RMND1 Hom. c.1349G>C: p.*450Serext*32 1 2 Pakistani 10y† lipid ↓↓ ↓↓ ↓↓ acidosis

British <1m/ Deafness & 5/F C + - - - COX mosaic RMND1 Hom. c.1349G>C: p.*450Serext*32 1 2 Pakistani 18m LA ↓↓ ↓↓ ↓↓

Seizures, 18m/ deafness & c.713A>G:p.Asn238Ser 6/M British N + - - - COX mosaic N RMND1 1 2 5y† renal tubular ↓↓ ↓↓ c.829_830+2delGAGT:p.Glu277Glyfs*2 acidosis

birth/ c.1774C>T: p.Arg592Trp 7/M* British N + + + - LA COX mosaic AARS2 1 2 6w† ↓↓ ↓ ↓↓ c.2882C>T: p.Ala961Val

Downloaded From: https://jamanetwork.com/ on 09/24/2021 Functional and biochemical Patient Information Clinical Presentation Genetic Analysis analysis

Onset/ ID/ Country of Family Death(†) Additional Mu C H L Histochemistry CI CIII CIV Gene Variant A U Sex Origin History Current presentation age

birth/ Global COX c.1616A>G: p.Tyr539Cys 8/M German N + + + - LA ↓↓ ↓ ↓↓ AARS2 - - 1m† defect c.1774C>T: p.Arg592Trp

* 3w/ SDH+/COX- 9/F German C + - + - LA ↓↓ ↓ ↓↓ AARS2 Hom. c.1774C>T: p.Arg592Trp - - 2m† mosaic

birth/ c.647_648insG: p.Cys218Leufs*6 10/F British N - - + - Congenital LA COX mosaic ↓↓ ↓ ↓↓ AARS2 - - 3m† c.1774C>T: p.Arg592Trp

6m/ 11/F British N - - + - - COX mosaic ↓↓ N ↓↓ AARS2 Hom. c.1774C>T: p.Arg592Trp - - 11m†

* birth/ Global COX c.631_631delG: p.Gly211Aspfs*3 12/F Croatian 1S + + + - LA ↓↓ N ↓↓ MTO1 - - 1m defect c.1282G>A: p.Ala428Thr

* British birth/ 13/M C + - + - - COX mosaic ↓↓ N ↓↓ MTO1 Hom. c.1232C>T: p.Thr411Ile - - Pakistani 1y†

Coagulopathy, * British 1y/ Global COX 14/M C + + + + renal failure & ↓↓ N ↓↓ MTO1 Hom. c.1232C>T: p.Thr411Ile - - Pakistani 3y† defect LA

c.122T>G: p.Val41Gly <1y/ 15/M British N + - - - LA COX mosaic ↓↓ N ↓↓ MTO1 c.767A>G: p.His256Arg - - 2y c.1282G>A: p.Ala428Thr

© 2014 American Medical Association. All rights reserved. Downloaded From: https://jamanetwork.com/ on 09/24/2021 Functional and biochemical Patient Information Clinical Presentation Genetic Analysis analysis

Onset/ ID/ Country of Family Death(†) Additional Mu C H L Histochemistry CI CIII CIV Gene Variant A U Sex Origin History Current presentation age

* birth/ 16/M Turkish N + - - + - COX mosaic ↓↓ N ↓↓ EARS2 Hom. c.193A>G: p.Lys65Glu 1 4 3m†

FTT, fatty * 2m/ liver, LA, c.322C>T: p.Arg108Trp 17/M British N + + - + COX mosaic ↓↓ N ↓ EARS2 1 2 6m† leukoenceph c.814G>A: p.Ala272Thr & b f

* 3y/ SDH+/COX- c.452C>T: p.Pro151Leu 18/F German 1S + - - - LA ↓↓ N ↓↓ MTFMT 2 1 16y mosaic c.994C>T: p.Arg332*

birth/ mild sensory c.626C>T: p.Ser209Leu 19/F British N + + + - COX mosaic ↓↓ N ↓↓ MTFMT - - 20y neuropathy c.1100_1101delTT: p.Phe367Serfs*22

2y/ mtDNA COX mosaic; c.532C>T: p.Arg178Trp 20/M British N - - + - ↓↓ N ↓↓ MGME1 1 2 2.5y† depletion lipid c.794C>T: p.Thr265Ile

LA, OA & 2.5y/ Hom. c.96_99dupATCC: 21/F Irish 1S + + - - mtDNA Myopathy ↓↓ ↓↓ ↓↓ C12orf65 2 2 13 p.Pro34Ilefs*25 depletion Exercise * 14y/ intolerance, Global COX 22/M Lebanese C + - - - ↓↓ N. ↓↓ YARS2 Hom. c.137G>A: p.Gly46Asp - - 37y† sideroblastic defect anaemia & LA growth 4y/ 23/F Turkish C + + - - retardation & COX mosaic ↓↓ N ↓↓ PUS1 Hom. c. 426C>A: p.Cys142* 1 2 17y mild anaemia

Onset/ ID/ Country of Family Death(†) Additional Mu C H L Histochemistry CI CIII CIV Gene Variant A U Sex Origin History Current presentation age

British birth/ 24/M C + + + - LA COX mosaic ↓↓ N ↓↓ TRMU Hom. c.287A>G: p.Asn96Ser - - Pakistani 1m†

LA, weakness++, birth/ 25/F British C + + - - lissencephaly COX mosaic ↓↓ ↓↓ ↓↓ TK2 Hom. c.1A>G: p.Met1Val - - <1m† & mtDNA depletion FTT & 7m/ 26/F Polish N + + - - elevated CSF COX mosaic ↓↓ N ↓↓ SCO2 Hom. c.418G>A: p.Glu140Lys 1 2 18m† lactate

* birth/ SDH+/COX- c.1478C>T: p.Pro493Leu 27/F German N + - + - LA ↓↓ N ↓↓ ELAC2 - - 3w† mosaic c.1621G>A: p.Ala541Thr

* 4y/ Variable fibre 28/M Turkish 1S + + - - LA ↓↓ N ↓↓ ETHE1 Hom. c.3G>T: p.Met1Ile 2 3 7y size

Abbreviations: + : present; - : absent; M: male, F: female; *: included in reference,2 C: consanguinity, N: no family history, 1S or 2S: number of other affected sibs, Clinical Presentation, Mu: muscle, C: central nervous system, H: heart, L: liver, mt prolif: mitochondrial proliferation, N: no data, CC: corpus callosum; LA: lactic acidosis, PEO: progressive external ophthalmoparesis, OA: optic atrophy, AN: axonal neuropathy, FTT: failure to thrive, leukoenceph: leukoencephalopathy, CSF: cerebrospinal fluid, CK: creatine kinase, RRF: ragged red fibers, COX: cytochrome c oxidase; SDH: succinate dehydrogenase, underlined genes (C): known disease genes, but clinical presentation is not compatible with this gene defect, H and L: respiratory chain measurement was performed in H heart and L liver. Hom: homozygous. ↓↓: severe biochemical defect, ↓: mild biochemical defect, segregation analysis, where A: number of affecteds screened (including the index patient), U: number of unaffecteds (including sibs and parents). A = number of affected individuals genotyped within the family, U = number of unaffected individuals genotyped in the family. Where indicated, all of the variants segregated appropriately with the phenotype. Biochemical data has been reported previously for some cases (* in Table 1) before a genetic diagnosis was possible.2-4 (A) Presumptive pathogenic variants = homozygous or compound heterozygous mutations in genes previously shown to cause multiple respiratory chain complex deficiencies.

Functional and biochemical Patient Information Clinical Presentation Genetic Analysis analysis Onset/ Country ID/ Family Death(†) Additional of Mu C H L Histochemistry CI CIII CIV Gene Variant A U Sex History Current presentation Origin age

PEO, ptosis <1/ c.1135G>A: p.Ala379Thr 29/M British N + + - - & COX mosaic ↓↓ N ↓↓ VARS2 2 7 10y c.1877C>A: p.Ala626Asp ataxia

Lipid, * 4m/ Respiratory Hom. c.397_400 delTTCT: 30/M Turkish C + - - - global COX ↓↓ N ↓↓ FLAD1 1 2 8m† insufficiency p.Phe134Cysfs*8 defect

* C birth/ Global COX Hom. c.2065C>T: 31/F Turkish + - + - - ↓↓ N ↓↓ GARS 1 2 2S 1m† defect p.Arg689Cys

c.337C>T: p.Arg113Trp * 4m/ Global COX H H H c.388C>T: p.Arg130* 32/F British N - - + - - ↓↓ ↓ ↓↓ PTCD1 - - 8m† defect c.550G>A: p.Gly184Arg

Abbreviations: + : present; - : absent; M: male, F: female; *: included in reference,2 C: consanguinity, N: no family history, 1S or 2S: number of other affected sibs, Clinical Presentation, Mu: muscle, C: central nervous system, H: heart, L: liver, mt prolif: mitochondrial proliferation, N: no data, CC: corpus callosum; LA: lactic acidosis, PEO: progressive external ophthalmoparesis, OA: optic atrophy, AN: axonal neuropathy, FTT: failure to thrive, leukoenceph: leukoencephalopathy, CSF: cerebrospinal fluid, CK: creatine kinase, RRF: ragged red fibers, COX: cytochrome c oxidase; SDH: succinate dehydrogenase, underlined genes (C): known disease genes, but clinical presentation is not compatible with this gene defect, H and L: respiratory chain measurement was performed in H heart and L liver. Hom: homozygous. ↓↓: severe biochemical defect, ↓: mild biochemical defect, segregation analysis, where A: number of affecteds screened (including the index patient), U: number of unaffecteds (including sibs and parents). A = number of affected individuals genotyped within the family, U = number of unaffected individuals genotyped in the family. Where indicated, all of the variants segregated appropriately with the phenotype. Biochemical data has been reported previously for some cases (* in Table 1) before a genetic diagnosis was possible.2-4 (B) Possible pathogenic variants = homozygous or compound heterozygous mutations in novel genes which may cause a mitochondrial translation defect based on their predicted function and similarity to known disease genes.

Hom. c.1333G>A: * 2y/ SLC25A12 33/F Turkish C + + - - - N ↓↓ N ↓↓ p.Ala445Thr - - 6y METAP1D Hom. c.497+2T>A

17y/ Global c.1157A>C: p.Lys386Thr 34/M British N - + - - OA & AN ↓↓ N ↓↓ ACSM5 1 2 20y COX defect c.1273C>A: p.Pro425Thr

PERP Hom. c.206T>C: p.Met69Thr MEF2A c.1262A>C: p.Gln421Pro 7y/ PEO, CK↑ RRF, COX 35/F Georgian C + + - - ↓↓ N ↓↓ c.1265A>C: p.Gln422Pro - - 10y (400) mosaic ACSM5 c.68A>G: p.His23Arg c.73A>C:p.Lys25Gln Hom. c.1276C>T: HKDC1 p.Arg426Cys 10y/ ETFA 36/M German C + - - - CK↑ (760) COX mosaic ↓↓ N ↓↓ Hom. c.20C>T: p.Pro7Leu 1 3 14y IREB2 Hom. c.2393C>T: p.Thr798Ile SMCR7 Hom. c.241C>T: p.Gln81* Seizures & <1m/ COX normal & c.1876C>T: p.Arg626Trp 37/F British N + + - - congenital ↓ N ↓ PC - - 5m lipid storage c.1892G>A: p.Arg631Gln LA

LA & 4y/ 38/M Turkish C + + - + growth COX mosaic ↓↓ N ↓↓ TPO Hom. c.443C>T: p.Ala148Val - - 6y retardation Central c.6448C>G: p.Leu2150Val <1y/ hypotonia, mild COX HERC2 39/M British N + + - - ↓ N ↓ c.9979G>A: p.Val3327Met - - 5y ptosis defect

& deafness MAGI1 Hom. c.2290A>C: p.Thr764Pro * 2w/ NDRG3 Hom. c.469G>A: p.Gly157Ser 40/M Turkish C + - - - LA COX mosaic ↓↓ N ↓↓ - - 3w† TPX2 Hom. c.505C>T: p.Pro169Ser TAF9 Hom. c.406G>C: p.Glu136Gln

Onset/ Country ID/ Family Death(†) Additional of Mu C H L Histochemistry CI CIII CIV Gene Variant A U Sex History Current presentation Origin age c.493C>T: p.Arg165* (X- * birth/ SLC25A43 linked) 41/M Croatian N + + + - CK↑ COX mosaic ↓↓ N ↓↓ - - 9m† FAAH2 c.368T>C: p.Phe123Ser (X- linked) c.55G>C: p.Glu19Gln DLAT c.626A>G: p.Gln209Arg

c.34G>A: p.Gly12Ser SDHD 6y/ COX mosaic, c.386T>C: p.Leu129Ser 42/M Hungarian N + - - - CK↑ ↓↓ ↓↓ ↓↓ 1 3 14y RRF & lipid c.112C>T:p.Pro38Ser POLRMT c.232G>A:p.Val78Met

c.1738G>T:p.Gly580Cys ARHGEF5 c.4066A>G:p.Asn1356Asp TYMP c.242G>A: p.Arg81Gln ACSM2A c.1003G>A: p.Val335Ile congenital birth/ LRPPRC c.4132A>G: p.Ser1378Gly 43/F British N + - - - LA & mtDNA COX mosaic ↓↓ ↓↓ ↓↓ - - <1m† HTRA2 c.1210C>T: p.Arg404Trp depletion ALDH1L1 c.2143G>C:p.Glu715Gln BCKDHB c.23C>T:p.Ala8Val c.263A>G: p.Asp88Gly PPL * 18m/ COX normal L L c.1003C>A: p.Leu335Met 44/M Turkish 1S + - - + - ↓↓ ↓ N 2 4 2y SDH + c.674A>G: p.Glu225Gly SLC5A10 c.1799T>C: p.Leu600Pro Immune defect, c.1850C>T: p.Pro617Leu Healthy deafness, FASN 1m/ c.2657T>C: p.Phe886Ser 45/F German dizygotic + + - + seizures, COX mosaic ↓↓ N ↓↓ 1 3 6m† c.4429A>G: p.Thr1477Ala twin renal failure, FNDC1 c.4547C>A: p.Thr1516Asn mtDNA depletion c.616A>G: p.Ile206Val PDPR 6y/ PEO, LA, COX mosaic c.1774A>G: p.Thr592Ala 46/M German N + - - - ↓↓ N ↓↓ 1 2 21y CK↑ (800) & RRF c.79G>C: p.Ala27Pro LONP1 c.2485G>A: p.Ala829Thr

Onset/ Country ID/ Family Death(†) Additional of Mu C H L Histochemistry CI CIII CIV Gene Variant A U Sex History Current presentation Origin age Hom. c.671A>G: 2m/ Alpers’ MIPEP p.Asn224Ser 47/M Egyptian C + + - + COX mosaic ↓ N ↓ - - 2y† phenotype STARD13 Hom. c.1186C>T: p.His396Tyr

Abbreviations: + : present; - : absent; M: male, F: female; *: included in references,2 C: consanguinity, N: no family history, 1S or 2S: number of other affected sibs, Clinical Presentation, Mu: muscle, C: central nervous system, H: heart, L: liver, mt prolif: mitochondrial proliferation, N: no data, CC: corpus callosum; LA: lactic acidosis, PEO: progressive external ophthalmoparesis, OA: optic atrophy, AN: axonal neuropathy, FTT: failure to thrive, leukoenceph: leukoencephalopathy, CSF: cerebrospinal fluid, CK: creatine kinase, RRF: ragged red fibers, COX: cytochrome c oxidase; SDH: succinate dehydrogenase, underlined genes (C): known disease genes, but clinical presentation is not compatible with this gene defect, H and L: respiratory chain measurement was performed in H heart and L liver. Hom: homozygous. ↓↓: severe biochemical defect, ↓: mild biochemical defect, segregation analysis, where A: number of affecteds screened (including the index patient), U: number of unaffecteds (including sibs and parents). A = number of affected individuals genotyped within the family, U = number of unaffected individuals genotyped in the family. Where indicated, all of the variants segregated appropriately with the phenotype. Biochemical data has been reported previously for some cases (* in Table 1) before a genetic diagnosis was possible.2-4 (C) Variants of unknown significance = homozygous or compound heterozygous mutations in novel or known disease genes not known to be associated with mitochondrial pathology.

Patient Information Clinical Presentation Functional and biochemical analysis Genetic Analysis

Onset/ Country ID/ Family Death(†) Additional of Mu C H L Histochemistry CI CIII CIV Gene Variant A U Sex History Current presentation Origin age 4m/ COX normal & 48/M Turkish C + + + + - ↓ ↓ ↓ - - - - 1y RRF

* 1y/ COX normal & 49/F German N + + - - LA ↓↓ ↓ N - - - - 3y Lipid storage

* British birth/ Global 50/F C - - + - - ↓↓ ↓↓ ↓↓ - - - - Pakistani 4d† COX defect

British adult- Respiratory 51/F C + - - - COX mosaic ↓↓ N ↓↓ - - - - Pakistani onset failure

2y/ COX normal & 52/M German N + + - + LA N ↓ ↓ - - - - 5y† RRF

birth/ 53/F German N + + - - LA N ↓↓ N ↓↓ - - - - 4y

Abbreviations: + : present; - : absent; M: male, F: female; *: included in references,2 C: consanguinity, N: no family history, 1S or 2S: number of other affected sibs, Clinical Presentation, Mu: muscle, C: central nervous system, H: heart, L: liver, mt prolif: mitochondrial proliferation, N: no data, CC: corpus callosum; LA: lactic acidosis, PEO: progressive external ophthalmoparesis, OA: optic atrophy, AN: axonal neuropathy, FTT: failure to thrive, leukoenceph: leukoencephalopathy, CSF: cerebrospinal fluid, CK: creatine kinase, RRF: ragged red fibers, COX: cytochrome c oxidase; SDH: succinate dehydrogenase, underlined genes (C): known disease genes, but clinical presentation is not compatible with this gene defect, H and L: respiratory chain measurement was performed in H heart and L liver. Hom: homozygous. ↓↓: severe biochemical defect, ↓: mild biochemical defect, segregation analysis, where A: number of affecteds screened (including the index patient), U: number of unaffecteds (including sibs and parents). A = number of affected individuals genotyped within the family, U = number of unaffected individuals genotyped in the family. Where indicated, all of the variants segregated appropriately with the phenotype. Biochemical data has been reported previously for some cases (* in Table 1) before a genetic diagnosis was possible.2-4 (D) Unresolved = patients where a single plausible genetic cause could not be identified. Biochemical defects were classified as mild if the respiratory chain complex activities were below the reference range for the Newcastle-upon-Tyne or Munich laboratories, but greater than 30% of the lower limit of normal. Biochemical defects were classified as severe if the respiratory chain complex activities were less than 30% of the lower limit of normal.

Number Mean Number % Number indels Number % CCDS Number % CCDS Number % CCDS per CCDS CCDS SNVs on on Min Max CCDS bases bases CCDS bases bases CCDS bases bases ID CCDS bases bases Target Target Depth Depth covered 10- covered covered 5- covered covered 1- covered base covered covered (62Mb +/- (62Mb fold 10-fold fold 5-fold fold 1-fold depth 20-fold 20-fold 500bp) +/- 500bp) P1 89.1 0 7,657 29,070,378 91.0 30,030,051 94.0 30,434,912 95.3 30,939,161 96.9 77,742 9,148 P2 93.8 0 7,969 29,241,284 91.6 30,078,673 94.2 30,449,514 95.3 30,937,148 96.9 77,816 9,128 P3 71.7 0 4,132 28,217,346 88.4 29,940,460 93.8 30,544,217 95.6 31,036,438 97.2 70,622 7,930 P4 86.1 0 5,953 27,998,329 87.7 28,898,127 90.5 29,399,070 92.1 30,078,079 94.2 63,942 7,808 P5 70.2 0 4,385 29,125,999 91.2 30,471,090 95.4 30,894,366 96.7 31,272,292 97.9 71,611 7,091 P6 86.9 0 6,086 29,659,313 92.9 30,655,895 96.0 31,004,828 97.1 31,397,757 98.3 70,056 7,832 P7 58.5 0 3,572 27,385,324 85.8 29,670,256 92.9 30,406,313 95.2 30,950,396 96.9 66,902 7,516 P8 71.2 0 4,136 28,141,867 88.1 29,487,108 92.3 30,047,510 94.1 30,708,148 96.2 74,969 8,697 P9 113.6 0 6,309 29,913,861 93.7 30,603,143 95.8 30,926,825 96.8 31,320,311 98.1 83,021 10,503 P10 66.3 0 2,135 26,973,201 84.5 28,902,112 90.5 29,715,190 93.0 30,563,992 95.7 70,818 8,806 P11 77.8 0 5,667 28,566,955 89.5 29,772,720 93.2 30,265,514 94.8 30,846,850 96.6 73,642 8,709 P12 106.2 0 7,975 29,898,171 93.6 30,586,992 95.8 30,914,537 96.8 31,314,926 98.1 81,147 9,906 P13 79.0 0 4,428 28,046,314 87.8 28,942,805 90.6 29,415,876 92.1 30,103,284 94.3 65,538 7,585 P14 55.9 0 3,962 27,118,221 84.9 29,697,990 93.0 30,484,534 95.5 31,015,555 97.1 67,145 7,355 P15 83.9 0 6,182 29,438,627 92.2 30,641,813 96.0 31,027,039 97.2 31,393,690 98.3 66,588 7,434 P16 75.4 0 5,469 27,750,330 86.9 28,760,761 90.1 29,296,461 91.7 30,037,783 94.1 63,983 7,501 P17 113.0 0 7,972 29,553,746 92.5 30,188,786 94.5 30,510,822 95.5 30,982,223 97.0 81,156 9,686 P18 80.3 0 4,845 29,156,970 91.3 30,371,454 95.1 30,857,408 96.6 31,323,021 98.1 76,714 9,061 P19 93.2 0 4,943 28,988,388 90.8 29,880,709 93.6 30,298,883 94.9 30,848,366 96.6 78,891 9,238 P20 91.8 0 5,158 28,676,044 89.8 29,652,006 92.9 30,119,485 94.3 30,724,371 96.2 77,854 9,360 P21 92.3 0 4,411 28,786,804 90.1 29,792,797 93.3 30,258,784 94.8 30,835,670 96.6 76,127 9,143 P22 92.5 0 7,500 29,170,222 91.3 30,050,251 94.1 30,439,653 95.3 31,008,645 97.1 85,341 9,571 P23 47.3 0 1,586 27,580,599 86.4 30,014,941 94.0 30,698,125 96.1 31,211,171 97.7 69,811 6,695 P24 85.1 0 5,958 29,533,091 92.5 30,653,321 96.0 31,036,129 97.2 31,395,135 98.3 68,052 7,856 P25 81.6 0 5,704 29,476,669 92.3 30,609,303 95.8 30,990,413 97.0 31,365,665 98.2 67,191 7,529 P26 77.0 0 5,811 29,288,735 91.7 30,545,199 95.6 30,946,419 96.9 31,344,331 98.2 67,344 7,503 P27 70.3 0 4,109 28,072,800 87.9 29,409,552 92.1 29,977,924 93.9 30,652,965 96.0 73,711 8,449 P28 67.3 0 3,650 26,423,589 82.7 28,695,981 89.9 29,873,523 93.5 31,157,732 97.6 43,884 2,112 P29 99.6 0 5,268 29,370,072 92.0 30,129,349 94.3 30,486,877 95.5 30,985,115 97.0 81,507 9,491 P30 73.9 0 5,731 27,812,857 87.1 28,811,348 90.2 29,331,920 91.8 30,043,924 94.1 64,576 7,543

© 2014 American Medical Association. All rights reserved. Downloaded From: https://jamanetwork.com/ on 09/24/2021 Number Mean Number % Number indels Number % CCDS Number % CCDS Number % CCDS per CCDS CCDS SNVs on on Min Max CCDS bases bases CCDS bases bases CCDS bases bases ID CCDS bases bases Target Target Depth Depth covered 10- covered covered 5- covered covered 1- covered base covered covered (62Mb +/- (62Mb fold 10-fold fold 5-fold fold 1-fold depth 20-fold 20-fold 500bp) +/- 500bp) P31 74.2 0 6,626 27,795,104 87.0 28,816,989 90.2 29,351,320 91.9 30,055,801 94.1 64,611 7,567 P32 97.6 0 6,567 28,952,214 90.7 29,841,074 93.4 30,283,461 94.8 30,846,635 96.6 78,376 9,333 P33 77.1 0 4,125 28,466,141 89.1 29,613,392 92.7 30,104,717 94.3 30,728,798 96.2 77,018 8,990 P34 76.8 0 4,419 26,432,456 82.8 28,537,231 89.4 29,764,688 93.2 31,166,318 97.6 45,635 2,377 P35 83.2 0 4,601 28,891,872 90.5 29,836,541 93.4 30,262,714 94.8 30,809,802 96.5 76,741 8,885 P36 71.7 0 934 27,141,057 85.0 29,615,838 92.7 30,509,000 95.5 31,110,273 97.4 54,627 3,521 P37 104.4 0 7,952 29,083,664 91.1 29,876,834 93.6 30,270,927 94.8 30,822,816 96.5 79,233 9,516 P38 77.8 0 4,370 28,727,897 90.0 29,840,397 93.4 30,301,041 94.9 30,855,556 96.6 77,244 9,177 P39 95.5 0 7,522 28,942,965 90.6 29,846,853 93.5 30,272,392 94.8 30,837,122 96.6 77,364 9,244 P40 63.8 0 3,306 25,561,963 80.0 27,924,631 87.4 29,218,645 91.5 30,765,792 96.3 44,969 2,325 P41 82.8 0 6,569 29,009,777 90.8 30,001,641 93.9 30,415,817 95.2 30,961,212 97.0 79,133 8,691 P42 70.3 0 6,217 28,696,173 89.9 30,453,037 95.4 30,941,533 96.9 31,366,552 98.2 67,306 7,309 P43 74.9 0 5,652 28,752,645 90.0 30,155,482 94.4 30,624,255 95.9 31,034,365 97.2 70,853 8,028 P44 43.0 0 2,005 19,429,411 60.8 22,987,815 72.0 25,203,575 78.9 27,927,323 87.5 37,529 1,882 P45 58.5 0 4,652 28,385,278 88.9 30,262,625 94.8 30,810,007 96.5 31,262,394 97.9 71,577 6,890 P46 75.1 0 5,133 29,347,723 91.9 30,600,433 95.8 30,996,750 97.1 31,356,126 98.2 73,973 7,388 P47 63.6 0 4,923 28,478,840 89.2 30,381,254 95.1 30,904,142 96.8 31,314,997 98.1 76,546 7,349 P48 86.2 0 5,476 28,808,851 90.2 29,747,257 93.1 30,159,492 94.4 30,736,594 96.2 75,391 8,164 P49 82.1 0 4,625 28,937,523 90.6 29,945,075 93.8 30,383,646 95.1 30,919,063 96.8 78,093 10,378 P50 77.6 0 5,306 27,838,155 87.2 28,780,881 90.1 29,292,637 91.7 30,019,556 94.0 64,503 7,642 P51 65.9 0 809 26,716,740 83.7 29,402,090 92.1 30,414,635 95.2 31,066,162 97.3 54,277 3,809 P52 80.8 0 5,715 28,686,483 89.8 29,770,553 93.2 30,233,491 94.7 30,808,141 96.5 76,801 8,931 P53 72.7 0 2,862 28,323,188 88.7 29,559,159 92.6 30,083,690 94.2 30,719,694 96.2 75,588 8,841 Coverage calculated for Consensus Coding Sequence (CCDS) bases (31,935,069 bp). Variants ‘on-target’ to Illumina Truseq 62Mb targets +/-500bp. SNV = single nucleotide variant.

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