Supplemental Table 3. Variants identified in NEPTUNE cohort using Relaxed Filter. Coordinates refer to GChg37 build. Reference and alternate alleles are provided. Variants resulting in non-synonymous variant changes are listed with amino acid change. ** denotes splice-site change as variant effect. Presence in 2012 version of Human Gene Mutation Database (HGMD) is listed. Frequency of particular variants are listed.

Gene / Coordinates / RefSeq / Reference / Alternate / AA Change / HGMD / Frequency
ACTN4 / 39196735 / rs149027682 / C / T / P179L / No / 2
ACTN4 / 39208702 / rs201128110 / G / A / A427T / No / 1
ACTN4 / 39214805 / . / C / G / I567M / No / 1
ACTN4 / 39220006 / rs113969422 / C / A / D890E / No / 4
CD2AP / 47471102 / . / A / G / K31E / No / 1
CD2AP / 47563608 / rs138727736 / A / G / T374A / Yes / 3
CD2AP / 47567096 / . / T / C / L445P / No / 1
CD2AP / 47576971 / . / C / T / S582F / No / 1
CD2AP / 47580229 / . / G / A / R612Q / No / 1
CFH / 196658696 / rs145650378 / C / A / H371N / No / 1
CFH / 196659307 / . / C / A / A425E / No / 1
CFH / 196682946 / rs371053403 / C / T / A473V / No / 1
CFH / 196695923 / rs201961184 / C / T / L697F / No / 1
CFH / 196709816 / rs149474608 / G / T / Q950H / Yes / 2
CFH / 196709833 / rs145975787 / C / T / T956M / Yes / 1
COQ2 / 84188876 / rs567729948 / C / T / G322R / No / 1
COQ6 / 74417037 / . / T / G / M1R / No / 1
COQ6 / 74417117 / . / T / C / S28P / No / 1
COQ6 / 74422201 / rs148540645 / C / T / R116W / No / 1
COQ6 / 74422545 / rs45496292 / A / G / D132G / No / 2
COQ6 / 74427982 / . / C / G / P333R / No / 1
COQ6 / 74427993 / rs139010315 / A / G / R337G / No / 1
COQ6 / 74428063 / rs367817034 / G / A / R360Q / No / 1
CUBN / 16867008 / rs148626202 / C / T / R3613H / No / 1
CUBN / 16870912 / rs1801232 / G / T / N3552K / No / 27
CUBN / 16871041 / . / T / C / ** / No / 1
CUBN / 16877170 / . / G / A / A3402V / No / 1
CUBN / 16878312 / . / T / C / M3368V / No / 1
CUBN / 16882520 / rs570241713 / T / A / T3281S / No / 1
CUBN / 16882952 / rs142446396 / G / A / T3253M / No / 1
CUBN / 16911749 / rs117035284 / C / T / G3114S / No / 3
CUBN / 16911754 / rs150985118 / A / G / F3112S / No / 1
CUBN / 16916403 / rs117400821 / G / A / T3069I / No / 4
CUBN / 16919034 / rs115888073 / C / T / V2990I / No / 2
CUBN / 16919034 / rs115888073 / C / T / V2990I / No / 1
CUBN / 16930427 / rs117620008 / A / G / F2965S / No / 1
CUBN / 16949651 / . / G / C / P2521A / No / 1
CUBN / 16955978 / rs117128556 / A / T / D2455E / No / 3
CUBN / 16957918 / rs141819241 / G / A / S2371F / No / 1
CUBN / 16960683 / rs140806389 / T / A / Y2313F / No / 2
CUBN / 16962110 / rs140862613 / C / G / D2225H / No / 1
CUBN / 16962122 / rs143291127 / C / T / V2221I / No / 1
CUBN / 16967324 / rs374765382 / C / T / D2188N / No / 2
CUBN / 16967417 / rs144360241 / T / C / N2157D / No / 1
CUBN / 16970285 / rs146995189 / G / C / Q2048E / No / 1
CUBN / 16970304 / rs75386064 / T / C / ** / No / 1
CUBN / 16975259 / rs150924438 / G / A / T1984M / No / 1
CUBN / 16979660 / rs141489700 / C / G / G1953R / No / 1
CUBN / 16981015 / rs76789390 / T / C / I1894V / No / 3
CUBN / 16982151 / rs143944436 / G / A / R1810* / No / 2
CUBN / 16990479 / rs191787640 / G / A / S1736L / No / 1
CUBN / 16994284 / . / G / A / Q1654* / No / 1
CUBN / 16996473 / rs529907907 / G / C / I1590M / No / 1
CUBN / 16996541 / rs533512333 / C / T / D1568N / No / 1
CUBN / 17032419 / . / T / C / R1422G / No / 1
CUBN / 17083061 / rs149749419 / G / A / H1330Y / No / 1
CUBN / 17087032 / rs145881708 / G / C / P1216A / No / 1
CUBN / 17088067 / rs141164907 / A / G / L1119S / No / 2
CUBN / 17110616 / . / C / A / A927S / No / 1
CUBN / 17110639 / rs148869805 / T / C / H919R / No / 4
CUBN / 17110642 / . / T / C / N918S / No / 1
CUBN / 17110739 / rs138545198 / C / T / E886K / No / 2
CUBN / 17110763 / rs563114115 / T / C / S878G / No / 1
CUBN / 17113589 / . / A / C / L821V / No / 1
CUBN / 17126314 / rs77886913 / C / T / V753M / No / 1
CUBN / 17126389 / rs147752521 / A / G / F728L / No / 2
CUBN / 17142088 / rs147449194 / C / T / D561N / No / 2
CUBN / 17151662 / rs138044409 / T / C / D363G / No / 1
CUBN / 17152923 / rs202153130 / G / A / P337L / Yes / 1
CUBN / 17152972 / rs143829410 / G / A / P321S / No / 1
CUBN / 17153023 / rs78201384 / C / T / E304K / No / 9
CUBN / 17171244 / rs149358798 / C / T / R43Q / No / 1
CUBN / 17171762 / rs11254385 / C / A / M1I / No / 1
INF2 / 105173653 / rs146529868 / C / T / P350L / No / 2
INF2 / 105174186 / rs181694819 / C / T / P528S / No / 5
INF2 / 105174205 / . / T / C / M534T / No / 1
INF2 / 105174225 / . / C / G / Q541E / No / 1
INF2 / 105174244 / rs376451593 / G / A / G547D / No / 1
INF2 / 105174268 / . / G / A / R555Q / No / 1
INF2 / 105176471 / rs533208785 / G / A / A729T / No / 1
INF2 / 105178005 / rs79327775 / C / T / R820W / No / 2
INF2 / 105178036 / rs377340315 / G / T / G830V / No / 1
INF2 / 105179916 / rs368569489 / A / G / M1005V / No / 1
INF2 / 105180602 / rs368995122 / G / A / G1035S / No / 1
INF2 / 105180633 / rs200369827 / G / A / R1045Q / No / 1
INF2 / 105180743 / rs143540449 / G / T / A1082S / No / 2
INF2 / 105180798 / . / C / T / A1100V / No / 1
INF2 / 105180903 / rs3803311 / C / T / T1135M / No / 2
INF2 / 105181089 / rs372714774 / C / T / A1197V / No / 1
ITGA3 / 48148852 / rs61730088 / C / T / A310V / No / 3
ITGA3 / 48149517 / . / T / C / I376T / No / 1
ITGA3 / 48151849 / rs61730081 / G / A / V474M / No / 3
ITGA3 / 48154403 / rs143134783 / C / T / S663L / No / 1
ITGA3 / 48156449 / rs146671278 / A / G / M804V / No / 1
ITGA3 / 48156557 / rs2301626 / G / A / G840S / No / 1
ITGA3 / 48165148 / rs146126922 / C / G / P987R / No / 2
LAMB2 / 49159683 / rs373872524 / C / A / S1565I / No / 1
LAMB2 / 49160316 / . / C / T / R1465Q / No / 1
LAMB2 / 49160340 / rs148818522 / C / T / R1457Q / No / 1
LAMB2 / 49160640 / rs150064487 / G / T / H1383Q / No / 1
LAMB2 / 49160671 / rs112933248 / T / C / D1373G / No / 1
LAMB2 / 49161464 / rs374189761 / C / T / R1165H / No / 1
LAMB2 / 49161531 / . / A / G / C1143R / No / 1
LAMB2 / 49161830 / rs79677861 / C / T / E1109K / No / 1
LAMB2 / 49161903 / . / C / A / W1084C / No / 1
LAMB2 / 49162269 / rs529614319 / T / C / I992V / No / 1
LAMB2 / 49162454 / rs372148651 / G / A / R957W / No / 1
LAMB2 / 49162716 / rs375392013 / C / T / R897H / No / 1
LAMB2 / 49162885 / . / T / G / S841R / No / 1
LAMB2 / 49165951 / . / A / G / L653P / No / 2
LAMB2 / 49165996 / . / A / C / L638W / No / 1
LAMB2 / 49167113 / rs144230655 / C / T / S481N / No / 1
LAMB2 / 49167666 / rs538490757 / C / T / R408H / No / 1
LAMB2 / 49168821 / rs144133177 / G / A / R235W / No / 1
LAMB2 / 49169117 / . / C / T / D167N / No / 1
LAMB2 / 49170064 / rs144765752 / G / C / P37A / No / 3
LAMB2 / 49170096 / . / A / C / V26G / No / 1
MYO1E / 59430501 / rs147579391 / G / T / P1049H / No / 1
MYO1E / 59453385 / rs569391805 / G / A / A891V / No / 1
MYO1E / 59455356 / rs147596471 / G / C / T876R / No / 2
MYO1E / 59464189 / rs201495758 / C / T / R796Q / No / 1
MYO1E / 59470642 / rs368888160 / C / T / D667N / No / 1
MYO1E / 59497622 / rs140447165 / G / C / I531M / No / 2
MYO1E / 59502783 / rs190122242 / T / G / E431A / No / 1
MYO1E / 59506876 / rs142638347 / A / G / I384T / No / 1
MYO1E / 59506892 / rs150983259 / G / C / H379D / No / 1
MYO1E / 59519746 / rs141565214 / T / C / D185G / No / 1
NEIL1 / 75641392 / rs184655220 / C / G / A49G / No / 4
NEIL1 / 75641449 / rs187873972 / C / A / P68H / No / 2
NEIL1 / 75641494 / rs5745906 / G / A / G83D / Yes / 1
NEIL1 / 75646094 / rs140982397 / G / A / G245R / No / 1
NEIL1 / 75646106 / rs185157815 / G / A / G249R / No / 1
NEIL1 / 75647018 / rs147989844 / C / G / P321A / No / 1
NEIL1 / 75647024 / rs142433613 / A / G / R323G / No / 2
NEIL1 / 75647073 / rs79039072 / G / A / R339Q / No / 2
NPHS1 / 36321820 / rs115489112 / G / A / H1174Y / No / 1
NPHS1 / 36326643 / rs370387270 / C / T / E1044K / No / 1
NPHS1 / 36330201 / rs367986918 / C / T / S1016N / Yes / 1
NPHS1 / 36330456 / rs114849139 / C / G / V957L / Yes / 1
NPHS1 / 36332686 / rs138173172 / C / A / A916S / Yes / 3
NPHS1 / 36336317 / . / G / A / A628V / No / 1
NPHS1 / 36336398 / rs114615449 / C / G / G601A / No / 1
NPHS1 / 36336401 / rs566516658 / T / C / K600R / No / 1
NPHS1 / 36336927 / rs368913905 / G / A / T537M / Yes / 1
NPHS1 / 36339044 / rs28939695 / C / T / E447K / Yes / 1
NPHS1 / 36339287 / rs372069596 / C / T / G395S / No / 1
NPHS1 / 36340040 / . / G / C / P284A / No / 1
NPHS1 / 36340175 / rs115308424 / C / T / R268Q / No / 2
NPHS1 / 36341311 / rs145125791 / T / A / N188I / Yes / 3
NPHS1 / 36341905 / rs368602816 / A / T / S162T / No / 1
NPHS1 / 36342505 / rs140626538 / A / G / V43A / No / 2
NPHS1 / 36342518 / rs375670819 / C / T / E39K / No / 1
NPHS2 / 179521760 / . / G / A / A284V / Yes / 1
NPHS2 / 179526214 / rs61747728 / C / T / R229Q / Yes / 16
PDSS2 / 107566787 / rs35555197 / C / T / V223I / No / 1
PDSS2 / 107655457 / rs200386735 / T / C / S126G / No / 1
PDSS2 / 107780479 / rs3734676 / C / G / R4P / No / 7
PDSS2 / 107780483 / rs3734675 / A / G / F3L / No / 7
PLCE1 / 95790868 / rs538129490 / C / T / A22V / No / 1
PLCE1 / 95790942 / . / A / C / S47R / No / 1
PLCE1 / 95791492 / rs376748611 / A / G / Y230C / No / 1
PLCE1 / 95791680 / rs192084195 / G / T / A293S / No / 1
PLCE1 / 95791983 / . / C / T / R394C / No / 1
PLCE1 / 95892037 / rs199689540 / T / C / V438A / No / 1
PLCE1 / 95892124 / rs192219615 / C / T / T467I / No / 1
PLCE1 / 95930939 / rs61751493 / C / T / R499C / No / 1
PLCE1 / 95930948 / rs200875238 / G / A / G502S / No / 1
PLCE1 / 95931179 / rs368809484 / A / G / I579V / No / 1
PLCE1 / 95931181 / . / C / G / I579M / No / 1
PLCE1 / 95987132 / . / T / A / Y627N / No / 1
PLCE1 / 95993830 / . / A / C / M659L / No / 1
PLCE1 / 96005710 / rs78217273 / A / G / I810V / No / 1
PLCE1 / 96006010 / rs61751497 / G / A / V910I / No / 4
PLCE1 / 96018567 / rs200141684 / A / G / S1189G / No / 1
PLCE1 / 96018597 / rs199781223 / G / A / G1199S / No / 1
PLCE1 / 96066247 / rs374201007 / G / A / V1896I / No / 3
PLCE1 / 96081767 / . / C / G / T2151R / No / 2
PLCE1 / 96084122 / rs111929795 / A / G / K2173R / No / 1
PTPRO / 15475691 / rs139015332 / G / T / A11S / No / 1
PTPRO / 15654574 / rs117540301 / A / G / I228V / No / 3
PTPRO / 15656958 / . / G / C / E408Q / No / 1
PTPRO / 15669811 / . / A / G / Y567C / No / 1
PTPRO / 15677829 / rs150159022 / C / T / T658M / No / 1
PTPRO / 15731845 / rs372031406 / G / A / R963Q / No / 1
PTPRO / 15733737 / . / T / G / M1035R / No / 1
SCARB2 / 77084448 / rs141250135 / A / G / M443T / No / 1
SCARB2 / 77084505 / . / C / T / R424Q / No / 1
SCARB2 / 77087432 / rs147142116 / T / C / M404V / No / 1
SCARB2 / 77089607 / rs144147706 / G / A / A379V / No / 1
SCARB2 / 77100837 / rs147159813 / C / T / V149M / No / 2
SCARB2 / 77102148 / rs143558324 / G / C / P128A / No / 2
SCARB2 / 77134617 / rs368906199 / C / T / R27Q / No / 1
SCARB2 / 77134693 / . / C / T / G2S / No / 1
SMARCAL1 / 217279768 / rs11555797 / G / A / R114H / No / 7
SMARCAL1 / 217279867 / . / A / G / H147R / No / 1
SMARCAL1 / 217285025 / . / A / C / K289T / No / 1
SMARCAL1 / 217285160 / rs138575228 / G / A / R334Q / No / 1
SMARCAL1 / 217293442 / rs2066520 / A / T / D424V / No / 1
SMARCAL1 / 217297533 / rs142164846 / G / A / R476Q / Yes / 1
SMARCAL1 / 217315664 / rs2066526 / C / A / D649E / No / 1
SMARCAL1 / 217347476 / rs190386780 / A / C / K881Q / No / 1
TRPC6 / 101325773 / rs61890853 / G / T / F848L / No / 1
TRPC6 / 101341946 / . / T / C / K793E / No / 1
WT1 / 32456713 / . / C / T / G60E / No / 1
WT1 / 32456725 / . / C / T / R56Q / No / 1
WT1 / 32456762 / . / C / T / G44S / No / 1