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Table 2 Detailed information on 49 variants in the 45 patients identified by reanalysis

From: Diagnostic performance of automated, streamlined, daily updated exome analysis in patients with neurodevelopmental delay

ID Sex Gene Zygosity HGVS c Class Molecular diagnosis OMIM Inheritance Allele origin Dx Note
43 F TFE3 Het NM_006521.6: c.560C > T P Intellectual developmental disorder, X-linked, syndromic, with pigmentary mosaicism and coarse facies 301066 XL Unknown Yes New disease
59 M SPEN Het NM_015001.3: c.5806C > T P Radio-Tartaglia syndrome 619312 AD Assumed de novo Yes New disease
62 M ADH5 Het NM_000671.4:c.966del P AMED syndrome, digenic 619151 AR Unknown Yes New disease
86 F GABRG2 Het NM_198903.2:c.316G > A P Epileptic encephalopathy, early infantile, 74 618396 AD Assumed de novo Yes New disease
90 F MSL3 Het NM_078629.3:c.1226_1229del P Basilicata-Akhtar syndrome 301032 XL Assumed de novo Yes New disease
92 F TFE3 Het NM_006521.5: c.559A > G LP Intellectual developmental disorder, X-linked, syndromic, with pigmentary mosaicism and coarse facies 301066 XL Assumed de novo Yes New disease
99 M MAPK8 IP3 Het NM_001318852.1: c.1735C > T P Neurodevelopmental disorder with or without variable brain abnormalities 618443 AD Assumed de novo Yes New disease
138 F LTBP1 Het NM_206943.2:c.1342C > T LP Cutis laxa, autosomal recessive, type IIE 619451 AR Unknown Yes New disease
   LTBP1 Het NM_206943.2: c.4793_4794del LP     Unknown   
206 M PTPN23 Het NM_015466.3: c.345del LP Neurodevelopmental disorder and structural brain anomalies with or without seizures and spasticity 618890 AR Unknown Yes New disease
   PTPN23 Het NM_015466.3:c.4052A > G VUS   618890 AR Unknown   
275 F TFE3 Het NM_006521.5: c.569A > G LP Intellectual developmental disorder, X-linked, syndromic, with pigmentary mosaicism and coarse facies 301066 XL Unknown Yes New disease
345 M DLG4 Het NM_001365.4:c.1608-2A > G LP Intellectual developmental disorder 62 618793 AD Unknown Yes New disease
399 F MAP1 B Het NM_005909.4:c.6715del LP Periventricular nodular heterotopia 9 618918 AD Unknown Yes New disease
434 M EMC10 Het NM_206538.3:c.343C > T LP Neurodevelopmental disorder with dysmorphic facies and variable seizures 619264 AR Unknown Yes New disease
   EMC10 Het NM_206538.3:c.70C > T LP   619264 AR Unknown   
517 M ZNF292 Het NM_015021.3:c.6015dup LP Intellectual developmental disorder, autosomal dominant 64 619188 AD Unknown Yes New disease
532 M ZMYM2 Het NM_001190964.4:c.3472C > T LP Neurodevelopmental-craniofacial syndrome with variable renal and cardiac abnormalities 619522 AD Unknown Yes New disease
536 F PHF21A Het NM_001101802.1:c.1171A > T P Intellectual developmental disorder with behavioral abnormalities and craniofacial dysmorphism with or without seizures 618725 AD Assumed de novo Yes New disease
548 F ALKBH8 Hom NM_001301010.1:c.1430_1438del LP Intellectual developmental disorder, autosomal recessive 71 618504 AR Trans phase Yes New disease
570 M TET3 Het NM_001287491.1:c.2161_2183dup P Beck-Fahrner syndrome 618798 AD/AR Assumed de novo Yes New disease
604 M SETD1B Het NM_015048.1:c.5508dup LP INTELLECTUAL DEVELOPMENTAL DISORDER WITH SEIZURES AND LANGUAGE DELAY; IDDSELD 619000 AD Unknown Yes New disease
656 F SATB1 Het NM_001195470.2:c.1574A > G LP Kohlschutter-Tonz syndrome-like 619229 AD Assumed de novo Yes New disease
709 F RALA Het NM_005402.3:c.404_429dup LP Hiatt-Neu-Cooper neurodevelopmental syndrome 619311 AD Unknown Yes New disease
752 M KCNMA1 Het NM_001271519.1:c.2423C > T LP Liang-Wang syndrome 618729 AD Unknown Yes New disease
776 F NCDN Het NM_001014839.1:c.990dup LP Neurodevelopmental disorder with infantile epileptic spasms 619373 AD/AR Unknown Yes New disease
792 M GRIA2 Het NM_001083619.1:c.1957_1958insT LP Neurodevelopmental disorder with language impairment and behavioral abnormalities 618917 AD Unknown Yes New disease
1051 F SETD1A Het NM_014712.2:c.4582-2_4582-1del LP Neurodevelopmental disorder with speech impairment and dysmorphic facies 619056 AD Unknown Yes New disease
1053 F ZNF292 Het NM_015021.3:c.3862dup LP Intellectual developmental disorder, autosomal dominant 63 619188 AD Unknown Yes New disease
116 M KCNT2 Het NM_198503.3:c.2501_2507del LP Developmental and epileptic encephalopathy 57 617771 AD Unknown Yes Variant update
196 F HUEW1 Het NM_031407.6:c.12404A > C LP Mental retardation, X-linked syndromic, Turner type 309590 XL Assumed de novo Yes Variant update
286 M KMT2D Het NM_003482.3:c.10744C > T P Kabuki syndrome 1 147920 AD Unknown Yes Variant update
379 M HK1 Het NM_001322365.1:c.901G > A LP Neurodevelopmental disorder with visual defects and brain anomalies 618547 AD Unknown Yes Variant update
354 F ACTB Het NM_001101.3:c.124G > A LP Baraitser-Winter syndrome 1 243310 AD Assumed de novo Yes Clinical update
411 F TRPM3 Het NM_001007471.2:c.2968G > A P TRPM3-related intellectual disabilities with epilepsy PMID
31278393
AD Unknown Not yet Candidate gene
1052 M TMPRSS9 Het NM_182973.2:c.1094C > A LP TMPRSS9-related autism spectrum disorder PMID
31943016
AR Unknown Not yet Candidate gene
120 F CHRM1 Het NM_000738.2:c.1274 T > C LP CHRM1-related neurodevelopmental disorder PMID
34212451
AD Unknown Not yet Candidate gene
105 F ATAD3A Het NM_018188.3:c.1879C > T VUS Pontocerebellar hypoplasia, hypotonia, and respiratory insufficiency syndrome, neonatal lethal 618810 AR Unknown Not yet New disease
   ATAD3A Het NM_018188.3:c.1586G > A VUS   618810 AR Unknown   New disease
39 M CUL3 Het NM_003590.5:c.383G > A VUS Neurodevelopmental disorder with or without autism or seizures 619239 AD Unknown Not yet New disease
703 F POLR2A Het NM_000937.4:c.1832A > T VUS Neurodevelopmental disorder with hypotonia and variable intellectual and behavioral abnormalities 618603 AD Unknown Not yet New disease
860 F USP9X Het NM_001039590.3:c.4796 T > C VUS Mental retardation, X-linked 99, syndromic, female-restricted 300968 XD Unknown Not yet Variant update
885 F KDM1A Het NM_001009999.2:c.1901C > T VUS Cleft palate, psychomotor retardation, and distinctive facial features 616728 AD Unknown Not yet Variant update
25 M CHD7 Het NM_017780.3:c.2499-11 T > A VUS CHARGE syndrome 214800 AD Unknown Not yet Variant update
67 M FGFR1 Het NM_001174067.1:c.1099G > A VUS Osteoglophonic dysplasia 166250 AD Unknown Not yet Variant update
514 F EBF3 Het NM_001005463.3:c.373G > A VUS Hypotonia, ataxia, and delayed development syndrome 617330 AD Unknown Not yet Variant update
902 F SPTBN1 Het NM_003128.2:c.5708G > A VUS Developmental delay, impaired speech, and behavioral abnormalities 619475 AD Unknown Not yet Variant update
979 F SPTBN1 Het NM_003128.3:c.2471 T > C VUS Developmental delay, impaired speech, and behavioral abnormalities 619475 AD Unknown Not yet Variant update
990 M NSF Het NM_006178.4:c.1359G > A VUS Developmental and epileptic encephalopathy 96 619340 AD Unknown Not yet Variant update
  1. P, pathogenic; LP, Likley pathogenic; VUS, uncertain significance of variant; AD, autosomal dominant; AR, autosomal recessive; XL, X-linked; heterozygous, Het; homozygous, Hom; Dx, diagnosis; Bold: novel variant