Supplementary Data
Fig S1 MED25 gene and protein structure. A. MED25 gene’s evolutionary conservation, as presented by
Evolutionary Conserved Regions (ECR) browser. Gene conservation is shown by pairwise alignments between
human and 4 other representative species (from bottom: rhesus, mouse, rat and zebrafish). Sequence conservation
of coding exons (blue) and introns (orange) as well as transposons and repeats (green) can be visualized. Layer
height presents the percentage identity of sequence pairwise alignment. Pink lines above the region represent ECR
conserved regions. The location of MED25 (Y39C) mutation in the first exon is shown via blue arrow. B.
Comparative demonstration of the MED25 Pfam, SUPERFAMILY domains and LRSLL motif in human, rhesus,
mouse, rat and zebrafish (from the bottom). Most of the domains are conserved in all 5 organisms.
Table S1: MED25 Oligonucleotides
Sequence Name
Product
Sequence
Number
5' d FAM- pdCAAGpdCApdCpdUApdCpdCpdUGpdCpdUpdC-
MED25 c. 116 A>G_P1
SS316498-01
MED25 c. 116 A>G_P2
SS316387-01
MED25 c. 116 A>G_F
SS316328-09
5' d GCCAACCTGGGACCCTACTT 3'
MED25 c. 116 A>G_R
SS316328-10
5' d GTCGGAGTCAGGCAAGAAAC 3'
BHQ-1 plus 3'
5' d CAL Flour Gold 540AAGpdCApdCpdUGpdCpdCpdUGpdCpdUpdC -BHQ-1 plus 3'
List S1: genes that are located within the homozygotic area of chr19: 450000000550000000 (399 genes, hg19):
ACPT, AKT1S1, ALDH16A1, AP2A1, AP2S1, APOC1, APOC1P1, APOC2, APOC4, APOE, ASPDH, ATF5,
BAX, BBC3, BCAM, BCAT2, BCL2L12, BCL3, BIRC8, BLOC1S3, BSPH1, C19orf41, C19orf48, C19orf63,
C19orf73, C19orf75, C19orf76, C5AR1, CA11, CABP5, CACNG6, CACNG7, CACNG8, CALM3, CARD8,
CBLC, CCDC114, CCDC155, CCDC61, CCDC8, CCDC9, CD33, CD37, CD3EAP, CDC42EP5, CEACAM16,
CEACAM18, CEACAM19, CEACAM20, CGB, CGB1, CGB2, CGB5, CGB7, CGB8, CKM, CLDND2,
CLEC11A, CLPTM1, CNOT3, CPT1C, CRX, CTU1, CYTH2, DACT3, DBP, DHDH, DHX34,
DKFZp434J0226, DKKL1, DMPK, DMWD, DPRX, EHD2, ELSPBP1, EML2, EMP3, ERCC1, ERCC2, ETFB,
EXOC3L2, FAM71E1, FAM83E, FBXO46, FCGRT, FGF21, FKRP, FLJ26850, FLJ40125, FLJ41856, FLT3LG,
FOSB, FOXA3, FPR1, FPR2, FPR3, FTL, FUT1, FUT2, FUZ, GEMIN7, GIPR, GLTSCR1, GLTSCR2, GNG8,
GPR32, GPR4, GPR77, GRIN2D, GRLF1, GRWD1, GYS1, HAS1, HIF3A, HRC, HSD17B14, IGFL1, IGFL2,
IGFL3, IGFL4, IGLON5, IL4I1, IRF2BP1, IRF3, IZUMO1, JOSD2, KCNA7, KCNC3, KCNJ14, KDELR1,
KLC3, KLK1, KLK10, KLK11, KLK12, KLK13, KLK14, KLK15, KLK2, KLK3, KLK4, KLK5, KLK6, KLK7,
KLK8, KLK9, KLKP1, KPTN, LAIR1, LENG1, LENG8, LENG9, LHB, LIG1, LILRA3, LILRA4, LILRA5,
LILRA6, LILRB2, LILRB3, LILRB5, LIM2, LIN7B, LMTK3, LOC147804, LOC284379, LRRC4B, MAMSTR,
MARK4, MBOAT7, MED25, MEIS3, MIR125A, MIR150, MIR371, MIR372, MIR373, MIR498, MIR512-2,
MIR516A1, MIR516A2, MIR516B1, MIR516B2, MIR517A, MIR517B, MIR517C, MIR518A1, MIR518A2,
MIR518B, MIR518C, MIR518D, MIR518E, MIR518F, MIR519A1, MIR519A2, MIR519B, MIR519C,
1
MIR519D, MIR519E, MIR520A, MIR520B, MIR520C, MIR520D, MIR520E, MIR520F, MIR520G, MIR520H,
MIR521-1, MIR521-2, MIR522, MIR523, MIR524, MIR525, MIR526A1, MIR526A2, MIR526B, MIR527,
MIR642, MIR643, MIR769, MIR99B, MIRLET7E, MYADM, MYBPC2, MYH14, MYPOP, NANOS2, NAPA,
NAPSA, NAPSB, NCRNA00085, NDUFA3, NKG7, NKPD1, NLRP12, NOSIP, NOVA2, NPAS1, NR1H2,
NTF4, NTN5, NUCB1, NUP62, NUP62_ATF5, OLT-2, OPA3, OSCAR, PGLYRP1, PIH1D1, PLA2G4C,
PLEKHA4, PNKP, PNMAL1, PNMAL2, POLD1, PPFIA3, PPP1R13L, PPP1R15A, PPP2R1A, PPP5C, PRKCG,
PRKD2, PRMT1, PRPF31, PRR12, PRR24, PRRG2, PTGIR, PTH2, PTOV1, PVR, PVRL2, QPCTL, RASIP1,
RCN3, RELB, RPL18, RPS11, RPS9, RRAS, RSHL1, RTN2, RUVBL2, SAE1, SCAF1, SEC1, SEPW1, SFRS16,
SHANK1, SIGLEC10, SIGLEC11, SIGLEC12, SIGLEC14, SIGLEC16, SIGLEC5, SIGLEC6, SIGLEC7,
SIGLEC8, SIGLEC9, SIGLECP3, SIX5, SLC17A7, SLC1A5, SLC6A16, SLC8A2, SNAR-C3, SNAR-C4,
SNAR-D, SNAR-E, SNAR-F, SNAR-G1, SNAR-G2, SNORD23, SNORD32A, SNORD33, SNORD34,
SNORD35A, SNORD35B, SNORD88A, SNORD88B, SNORD88C, SNRNP70, SNRPD2, SPACA4, SPHK2,
SPIB, STRN4, SULT2A1, SULT2B1, SYMPK, SYNGR4, SYT3, TBC1D17, TEAD2, TFPT, TMC4, TMEM143,
TMEM160, TOMM40, TPRX1, TRAPPC6A, TRPM4, TSEN34, TSKS, TTYH1, TULP2, VASP, VN1R2,
VN1R4, VRK3, VSIG10L, VSTM1, ZC3H4, ZNF114, ZNF137, ZNF160, ZNF175, ZNF180, ZNF28, ZNF296,
ZNF320, ZNF321, ZNF331, ZNF347, ZNF350, ZNF415, ZNF432, ZNF468, ZNF473, ZNF480, ZNF525,
ZNF528, ZNF534, ZNF541, ZNF577, ZNF578, ZNF600, ZNF610, ZNF611, ZNF613, ZNF614, ZNF615,
ZNF616, ZNF649, ZNF665, ZNF677, ZNF701, ZNF702P, ZNF761, ZNF765, ZNF766, ZNF808, ZNF813,
ZNF816A, ZNF83, ZNF836, ZNF841, ZNF845, ZNF880.
*The homozygotic genomic area (chr19: 450000000-550000000) in the families contains 2600 targeted regions
(787Kbp sequenced in total) in 399 genes (based on the coordinates of Trusec enrichment kit). The average
coverage of regions per sample was >100x.
2
Table S2. List of candidate variants that are located within the homozygotic area of chr19: 450000000-550000000 (399 genes, hg19):
Gene
Position (hg19)
REF
ALT
Protein change
rs#
Family
Segregation
Allele count, Homozygote
count in ExAC database1
NPAS1
chr19:47544375
C
T
p.(Arg212Cys)
.
doesn’t follow
3,0
DHDH
chr19:49442849
TGGGGGGG
TGGGGGGGG
p.(Ala173Glyfs)
rs3830420
not checked
25794, 3607
TRPM4
chr19:49686146
G
A
p.(Trp171*)
rs71352737
not checked
151,2
MED25
chr19:50321714
A
G
p.(Tyr39Cys)
.
Follows
0,0
MYH14
chr19:50735262
G
A
p.(Arg342Gln)
.
Follows
11,0
SIGLEC8
chr19:51961605
C
G
p.(Gly13Arg)
rs142744819
not checked
21,1
SIGLEC12
chr19:52000150
C
T
p.(Arg528Lys)
rs114249698
not checked
14,0
ZNF880
chr19:52887145
TAAAAA
TAAAA
p.(Asn106Ilefs)
rs34470614
not checked
17984 ,3620
ZNF525
chr19:53884101
T
C
p.(Ile54Thr)
.
doesn’t follow
1,0
LOC284379
chr19:54103610
G
A
p.(Thr131Ile)
.
doesn’t follow
Gene Not Available
LILRB3
chr19:54726237
C
G
p.(Glu90Gln)
rs138323850
not checked
608,98
LILRA6
chr19:54742965
G
A
p.(Ala420Val)
rs148424804
not checked
15,0
Remarks
also listed as pseudo
also listed as pseudo
leukocyte immunoglobulin-like
receptor, homozygote LoF
count in the gene=1
Table S2: The 12 variants that were found in the homozygotic region in the family. The top five candidates were examined for disease segregation in the family (see more information
in the main text). The ExAC database spans 60,706 unrelated individuals sequenced as part of various disease-specific and population genetic studies and therefore is highly useful
to estimate the abundance of alleles in the population.
1
Exome Aggregation Consortium (ExAC), Cambridge, MA (URL: http://exac.broadinstitute.org) [date (February, 2015) accessed].
3