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Table 1 Summary of the negative clinical WES cases and genetic findings. For a full list of cases including negative and previously published, please refer to Additional file 5: Table S4. The symbol “a” indicates a novel gene (no assigned OMIM phenotype) for condition to be reported elsewhere

From: Analysis of transcript-deleterious variants in Mendelian disorders: implications for RNA-based diagnostics

ID Phenotype Gene Mutation HGVS nomenclature Zygosity Type of mutation Class of transcript-deleterious variants Notes
17DG0527 Global developmental delay, hypotonia, epilepsy, postnatal microcephaly, strabismus and choreoathetosis a   Homozygous Frameshift indel   Novel gene for this condition
15DG1507 Epilepsy and global developmental delay a   Homozygous Transcript-deleterious variant c Novel gene for this condition
18DG0320 Multiple congenital anomalies a   Homozygous Missense   Novel gene for this condition
18DG0989 Neonatal adrenoleukodystrphy a   Homozygous Missense   Novel gene for this condition
19DG0509 Undefined epileptic encephalopathy a   Homozygous Nonsense   Novel gene for this condition
18DG0669 Microcephaly, atrial septal defect, ventricular septal defect a   Homozygous Transcript-deleterious variant a Novel gene for this condition
17DG0738 Chronic interstitial kidney disease with small kidneys a   Homozygous Nonsense   Novel gene for this condition
19DG0230 Griscelli syndrome a   Homozygous Missense   Unpublished
17DG0872 Hydrocephalus, agenesis of corpus callosum, macrocephaly a   Homozygous Transcript-deleterious variant b Novel gene for this condition
17DG1071 Cholestasis, progressive familial intrahepatic 3 ABCB4 NM_000443.3:c.286+335A>G:p.(Val96Glyfs*11) Homozygous Transcript-deleterious variant c Unpublished
16DG0145 Intellectual disability ADAT3 NM_138422.1:c.382G>A:p. (Val128Met) Homozygous Missense   Unpublished
16DG1223 Oligohydramios, short long bones and echogenic kidneys ANKS3 NM_133450:c.352G>A:p.(Ala118Thr) Homozygous Missense   PMID:27417436
18DG0295 Joubert syndrome ARL3 NM_004311.3:c.445C>T:p.(Arg149Cys) Homozygous Missense   PMID: 30269812
15DG2104 Joubert Syndrome ARMC9 NM_025139.3:c.51+5G>T:p.?, r.1_51del Homozygous Transcript-deleterious variant c PMID: 27431290
15DG2485 Asparagine synthetase deficiency ASNS NM_133436.2:c.28A>C:p.(Ser10Arg) Homozygous Missense   PMID:30214071
15DG0357 Bardet-Biedl syndrome BBS1 NM_024649.4:r. [1232_3423del] Homozygous Large deletion   PMID: 27894351
16DG1620 Osteopetrosis CLCN7 NM_001287.5:c.739-18G>A;(p.Met250Argfs*6) Homozygous Transcript-deleterious variant c PMID: 29620724
19DG1262 Multiple congenital anomalies COG6 NM_020751.2:c.695-8T>G Homozygous Transcript-deleterious variant c Unpublished
PSMMC0118 Short stature on growth hormone replacement, subclinical hypothyroidism, grade 1 hydronephrosis (Lt), delayed bone age, IVF pregnancy, first of a twin, delayed development CREBRF NM_001168393.2:c.475delT;p.(Ser159Hisfs*57) Heterozygous Frameshift indel   PMID: 31130284
17DG0967 Cholestasis with high GGT and renal failure DCDC2 NM_001195610.1:c.223_293del:p.(Arg75Leufs*16) Homozygous Frameshift indel   Unpublished
17DG0996 Cholestasis DCDC2 NM_001195610.1:c.223_293del:p.(Arg75Leufs*16) Homozygous Frameshift indel   Unpublished
13DG2237 Warsaw breakage syndrome DDX11 NM_004399.2: c.2426T>G:p. (Val809Gly) Homozygous Missense   PMID: 30214071
17DG0022 Chronic unexplained diarrhea DGAT1 NM_012079.5:c.836T>C:p.(Leu279Pro) Homozygous Missense   Unpublished
16DG0357 Acromesomelia DIP2C NM_014974.2:c.3283C>T:p.(Arg1095Trp) Homozygous Missense   PMID:29620724
17DG0756 Congenital disorder of glycosylation FUT8 NM_178155.2:c.943C>T:p.(Arg315*) Homozygous Nonsense   PMID: 30237576
16DG0733 Severe progressive microcephaly, global developmental delay and epilepsy GPR56 NM_005682.5:c.1503C>A;p.(Tyr501*) Homozygous Nonsense   PMID: 27431290
PSMMC0115 Unexplained macrocephaly, epilepsy, short stature and developmental delay KCND1 NM_004979.6:c.1883G>A:p.(Arg628Lys) Hemizygous Missense   Unpublished
15DG2234 Microcephaly, cerebral white matter abnormality and intellectual disability KCTD3 NM_016121.3 c.1036_1073del:p.(P346Tfs*4) Homozygous Transcript-deleterious variant d Unpublished
13DG2107 Psychomotor retardation and seizures KCTD3 NM_016121.3 c.1036_1073del:p.(P346Tfs*4) Homozygous Transcript-deleterious variant d PMID:25558065
17DG0404 High GGT neonatal cholestasis/sclerosing cholangitis KIF12 NM_138424.1:c.610G>A:p.(Val204Met) Homozygous Missense   PMID: 30250217
18DG0966 Methylmalonic aciduria and homocystinuria LMBRD1 NM_018368.4:c.1156C>T:p.(Arg386*) Homozygous Nonsense   Unpublished
16DG0559 Joubert syndrome LRRC34 NM_001172779:c.199A>T:p.(Lys67*) Homozygous Nonsense   In press
17DG0731 Disseminated tuberculosis, hypogammaglobulinemia, nearly all T and B cells are naive MAP3K14/NIK NM_003954.3:c.916delT: p.(Cys306Valfs*2) Homozygous Frameshift indel   doi.org/10.1016/j.jaci.2018.11.003
15DG2492 Short stature, global developmental delay, dysmorphism, congenital heart disease , PUJ obstruction and partial agenesis of corpus callosum MFSD11 NM_001242532.1:c.143G>C:p.(Gly48Ala) Homozygous Missense   PMID: 28940097
16DG0621 Severe neurodevelopmental disorder MICU2 NM_152726.3:c.42G>A:p.(Trp14*) Homozygous Nonsense   PMID: 29053821
17DG1094 Megacystis MYH11 NM_022844.2:c.1033+1G>A Homozygous Transcript-deleterious variant a PMID: 30237576
12DG2078 Klippel-Feil syndrome and myopathy MYO18B NM_032608.5:c.6905C A:p.(Ser2302*) Homozygous Nonsense   PMID:25748484
18DG0176 Microcephaly, developmental delay, visual impairment, hyponatremia, failure to thrive, choreoathetoid movement, seizures NUP214 NM_005085:c.461:p.(Asp154Gly) Homozygous Missense   PMID:30758658
16DG1424 Diarrhea, failure to thrive, intestinal failure and TPN dependence PERCC1 Deletion of regulatory element (chr16:1480850_1483950del) Homozygous Transcript-deleterious variant f Unpublished
18DG0670 Erythrokeratoderma PERP NM_022121.4:c.466G>A:p.(Gly156Arg) Homozygous Missense   PMID: 31898316
16DG1048 Peroxisome biogenesis disorder 12A (Zellweger) PEX19 NM_001193644.1:c.161C>T:p. (Ser54Leu) Homozygous Missense   PMID: 30561787
13DG0810 Congenital Microcephaly PPFIBP1 NM_001198915.1:c.960_961del:p.(Glu320Aspfs*3 Homozygous Frameshift indel   PMID: 30214071
16DG0201 Short stature, brachydactyly, intellectual disability and seizures PRMT7 NM_019023.2:c. 190C>T:P. (Gln64*) Homozygous Nonsense   PMID: 28940097
15DG2427 Syndromic cataract RIC1 NM_020829.3: c.3794G>C:p.(Arg1265Pro) Homozygous Transcript-deleterious variant b PMID: 27878435
13DG1181 Primary microcephaly RTTN NM_173630.3:c.5746-20A>G:p.1917_1942del Homozygous Transcript-deleterious variant c PMID: 30214071
17DG1005 Bardet-Biedl syndrome SCLT1 NM_144643.2:c.290+2T>C:p.(Lys79Valfs*4) Homozygous Transcript-deleterious variant a PMID: 30237576
16DG0760 Epilepsy, generalized, with febrile seizures plus, type 1 SCN1B NM_001037.3:c.355T>G:p.(Tyr119Asp) Homozygous Missense   PMID: 28218389
PSMMC0210 Hypotonia, global developmental delay, cardiac disease, leukodystophy SCN3A NM_001081676.1:c.1485T>G:p.(Ser495Arg) Heterozygous Missense   Unpublished
18DG0278 Congenital insensitivity to pain SCN9A NM_002977.3:c.2311-14T>G Homozygous Transcript-deleterious variant c Unpublished
14DG0045 Renal failure, morbid obesity, intellectual disability, retinitis pigmentosa (sibling of 14DG0047, see Table S5) SDCCAG8 NM_006642.2:c.741-152G>A, p.Arg247Serfs*23; NM_006642.2: r.740_741ins741-202_741-1 Homozygous Transcript-deleterious variant c In press
16DG0276 Tricho-Hepato-Enteric Syndrome SKIV2L NM_006929.5:c.3561_3581del; p.(Ser1189_Leu1195del) Homozygous Non-frameshift indel   Unpublished
16DG0815 Tricho-Hepato-Enteric Syndrome SKIV2L NM_006929.5:c.3561_3581del; p.(Ser1189_Leu1195del) Homozygous Non-frameshift indel   Unpublished
17DG0977 Tricho-Hepato-Enteric Syndrome SKIV2L NM_006929.4:c.3561_3581del,p.(Ser1189_Leu1195del) Homozygous Non-frameshift indel   Unpublished
18DG0594 Pseudovaginal perineoscrotal hypospadias SRD5A2 NM_000348:c.682G>A:p.(Ala228Thr) Homozygous Missense   Unpublished
17DG0821 Congenital adrenal hyperplasia (CAH) STAR NM_000349.2:c.201_202del:p.(Tyr68Glnfs*2) Homozygous Frameshift indel   Unpublished
18DG0512 Osteogenesis imperfecta, type XIV TMEM38B NM_018112.2:c.455_542del;p.(Gly152Alafs*5) Homozygous Frameshift indel   Unpublished
16DG0114 Muscular dystrophy-dystroglycanopathy TMEM5 NM_014254.3:c.686A>G:p.(Tyr229Cys) Homozygous Missense   Unpublished
16DG1117 Leukodystrophy TRAK1 NM_001042646: c.287-2A>G Homozygous Transcript-deleterious variant a PMID:28940097
16DG0659 Muscular dystrophy, limb-girdle, autosomal recessive 18 TRAPPC11 NM_021942.6:c.464C>T:p.(Ser155Leu) Homozygous Missense   Unpublished
16DG1614 Global developmental delay and epilepsy UFC1 NM_016406.3:c.317C>T:p. (Thr106Ile) Homozygous Missense   PMID: 29868776
16DG0018 Osteogenesis imperfecta WNT3A NM_033131.3:c.254G>A:p.(Arg85Gln) Homozygous Missense   PMID: 29620724
14DG0613 Primary microcephaly YARS NM_003680.3:c.789C>A:p.(Phe263Leu) Homozygous Missense   PMID: 28383543/30214071
15DG2661 Dysmorphism ZFAT NM_020863.3:c.1199G>A:p.(Arg400Gln) Homozygous Missense   PMID: 28640246/28940097