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Table 4 Functional classification of 10 genes sharing putative pathogenic variants in at least two trios

From: Whole exome sequencing in three families segregating a pediatric case of sarcoidosis

Trios Gene Chr. Position Variant QUAL Depth Annotation Reference SIFT Polyphen Alamut EXaC
Autophagy and Intracellular Trafficking
 T1 + T2 (homoz) Sec16A 9 139368953 SNP 28,526
23,786
602
430
c.3115C > T
p.Arg1039Cys
(NM_014866.1)
rs3812594 0.14 0.689 * Class3
Unknown
Exon skip?
0.21
 T1 + T3 (homoz) AP5B1 11 65,547,333 SNP 15,898
27,369
187
219
c.631C > T
p.Leu211Phe
(NM_138368.4)
rs12146493 0 * 0.999 * Class 3
Exon skip
0.29
 T1 + T2 (c/het) RREB1 6 7231843
7246998
7230680
7247344
SNP (T1p)
SNP (T1 m)
SNP (T2p)
SNP (T2 m)
2748
6191
33,331
14,853
226
202
371
173
c.3511G > A
p.Asp1171Asn
(NM_001003698.3)
c.4150G > A
p.Gly1384Arg
(NM_001003698.3)
c.2348G > T
p.Gly783Val
(NM_001003698.3)
c.4496C > A
p.Ser1499Tyr
(NM_001003698.3)
rs9379084
rs2281833
rs9502564
rs35742417
0 *
0.12
0.06
0.01 *
0.999 *
0
0.156
0.025
Class3
Unknown
Exon skip?
nd
nd
Class3
Unknown
Exon skip?
0.11
0.27
0.44
0.14
G-Proteins Regulation
 T1 (homoz) OBSCN 1 228505204 SNP 11,933 256 c.16472G > A
p.Arg5491His
(NM_001271223.2)
rs4653942 0 * 0.91 * Class3
Unknown
0.26
 T3 (homoz)    228494790 SNP 39,725 479 c.14986G > A
p.Gly4996Arg
(NM_001271223.2)
rs435776 0.01 * 0.939 * Class 3
Unknown
0.41
 T2 (de novo) CTNND2 5 10981914 SNP 299 111 c.3388G > A
p.Ala1130Thr
(NM_001332.3)
nd nd nd nd nd
 T2 + T3 (c/het) DNAH11 7 21893993 SNP (T2p) 46,459 445 c.11122G > T
p.Val3708Leu
(NM_001277115.1
rs4722064 0.02 * 0.611 * Class 3
Unknown
0.43
21584693 SNP (T2 m) 1610 159 c.421G > T
p.Asp141Tyr
(NM_001277115.1)
rs72655969 0 * 0.601 * Class 3
Unknown
0.012
21,628,242 SNP (T3p) 20,259 553 c.1961C > G
p.Ser654Cys
(NM_001277115.1)
rs62441683 0.67 0.02 Class 3
Unknown
0.13
21678643 SNP (T3 m) 19,593 850 c.4904A > G
p.Asp1635Gly
(NM_001277115.1)
rs17144835 0 * 0.783 * Class 3
Unknown
Exon skip?
0.045
T-Cell Activation and Immune Synapse
 T1 + T3 (c/het) IDO2 8 39862881 SNP (T1p) 14,321 289 c.742C > T
p.Arg248Trp
(NM_194294.2)
rs10109853 0 * 1 * Class 3
Unknown
0.48
39873053 SNP (T1 m) 7771 184 c.1195G > A
p.Ala399Thr
(NM_194294.2)
rs72632016 0.57 0.024 Class 3
Unknown
0.06
39872935 SNP (T3p) 21,240 451 c.1077 T > A
p.Tyr359*
(NM_194294.2)
rs4503083 STOP * STOP * Truncating
Polymorphism
0.226
39862893 SNP (T3 m) 3510 154 c.754 T > A
p.Ser252Thr
(NM_194294.2)
rs35212142 0.02 * 0.444 * Class 3
Unknown
0.02
 T1 (de novo) IGSF3 1 117122285 In frame INS 14,580 191 c.3122_3123insGGA
p.Asp1040_1041insGlu
(NM_001542.3)
rs114915440 IF INS IF INS In frame
polymorphism
0.25
Mitosis and Immune Synapse
 T1 (de novo) SPICE1 3 113172543 SNP 3572 291 c.1912 T > G
p.Ser638Ala
(NM_144718.3)
nd nd nd Unknown nd
 T1 (homoz) KNL1 (CASC5) 15 40916237 SNP 57,541 697 c.3853A > G
p.Lys1285Glu
(NM_170589.4)
rs17747633 0.05 * 0.058 Class 3
Unknown
Exon skip?
0.32
 T2 (homoz)    40915190 SNP 183,916 368 c.2806A > G
p.Arg936Gly
(NM170589.4)
rs8040502 1 0 Class 3
Unknown
0.24
 T3 (homoz)    40914177 SNP 66,997 297 c.1793 T > C
p.Met598Thr
(NM170589.4)
rs11858113 0.01 * 0.006 Class3
Unkown
0.39
  1. Abbreviations: nd not defined, Chr. chromosome, SNP single nucleotide polymorphism, QUAL. a quality parameter measuring the probability p that the observation of the variant is due to chance (for ex: QUAL = n, p = 1/n). INS insertion, DEL deletion, DUP duplication, NM NCBI reference sequence of mRNA, ExAC minor allele frequency as defined in Exome aggregation consortium, SIFT and POLYPHEN scores are indicated in italic bold characters and an asterisk when considered as pathogenic in silico