Gene | Proband (gender) | Type | Location (hg19) | Ref | Alt | GenBank No | Functional effect | Nucleotide change | AA. alteration | gnomAD allele frequency | pLI | Phenotypes in OMIM (Inheritance) | ACMG |
---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Autosomal genes (n = 8) | |||||||||||||
 ANO5# | 14,640.p1 (M) | Chet | chr11:22,242,756 | G | A | NM_213599 | SP/Syn | c.294G > A | SP/p.A98A | 0.0007 | 0 | Gnathodiaphyseal dysplasia (AD); Miyoshi muscular dystrophy 3 (AR); Muscular dystrophy, limb-girdle, autosomal recessive 12 (AR) | VUS |
chr11: 22,294,441 | C | G | NM_213599 | Mis | c.2141C > G | p.T714S | 0.0009 | P | |||||
 ATAD3A* | 14,517.p1 (M) | Chet | chr1:1,469,361 | G | A | NM_001170535 | Mis | c.1670G > A | p.R557H | 0.0002 | 0 | Harel-Yoon syndrome (AD, AR); Pontocerebellar hypoplasia, hypotonia, and respiratory insufficiency syndrome, neonatal lethal (AR) | VUS |
chr1:1,469,380 | G | - | NM_001170535 | FS | c.1689delG | p.Q563Hfs*9 | 0 | P | |||||
 ATG7 | 13,998.p1 (M) | Chet | chr3:11,389,351 | G | T | NM_006395 | SP/Mis | c.1126G > T | SP/p.G376C | 5.58E-05 | 0 |  | VUS |
chr3:11,404,365 | G | A | NM_006395 | Mis | c.1762G > A | p.V588M | 0.0001 |  | VUS | ||||
 HIPK3 | 13,076.p1 (M) | Homo | chr11:33,374,639 | T | C | NM_001048200 | SP/Mis | c.3110 T > C | SP/p.V1037A | 0.0008 | 0.28 |  | VUS |
I NTS4 | 14,051.p1 (M) | Chet | chr11:77,635,920 | G | A | NM_033547 | SG | c.1390C > T | p.R464X | 1.23E-05 | 0 |  | VUS |
chr11:77,649,828 | G | A | NM_033547 | Mis | c.1034C > T | p.S345L | 0.0004 |  | VUS | ||||
 LLGL1 | 14,404.p1 (M) | Homo | chr17:18,138,154 | G | A | NM_004140 | SP/Mis | c.907G > A | SP/p.G303S | 0.0009 | 0 |  | VUS |
 RFT1* | 11,176.p1 (M) | Chet | chr3:53,133,472 | T | C | NM_052859 | Mis | c.1133A > G | p.Y378C | 0.0005 | 0 | Congenital disorder of glycosylation (AR) | VUS |
chr3:53,126,384 | C | – | NM_052859 | SP | c.1458 + 1G > - | SP | 4.53E-06 | P | |||||
 VPS13B* | 12,651.p1 (M) | Chet | chr8:100,829,780 | G | A | NM_017890 | Mis | c.8185G > A | p.G2729R | 7.98E-06 | 0 | Cohen syndrome (AR) | LP |
chr8:100,396,500 | G | A | NM_017890 | SG | c.2889G > A | p.W963X | 0 | P | |||||
X-linked genes (n = 13) | |||||||||||||
 AFF2* | 14,096.p1 (M) | Hem | chrX:148,068,931 | - | C | NM_001170628 | FS | c.2582dupC | p.I863Hfs*6 | 0 | 1 | Mental retardation, X-linked, FRAXE type (XLR) | P |
 APOO | 14,187.p1 (M) | Hem | chrX:23,886,804 | G | A | NM_024122 | SP/Syn | c.294C > T | SP/p.D98D | 0 | 0.6 |  | VUS |
 CCDC22* | 12,325.p1 (M) | Hem | chrX:49,105,278 | A | C | NM_014008 | SP/Mis | c.1432A > C | SP/p.M478L | 0 | 1 | Ritscher-Schinzel syndrome 2 (XLR) | LP |
11,720.p1 (M) | chrX:49,105,359 | C | T | NM_014008 | Mis | c.1513C > T | p.R505W | 6.18E-05 | LP | ||||
 CUL4B* | 14,363.p1 (M) | Hem | chrX:119,708,407 | A | G | NM_003588 | SP/Syn | c.66 T > C | SP/p.G22G | 0 | 1 | Mental retardation, syndromic 15 (XLR) | LP |
 CYBB# | 14,070.p1 (M) | Hem | chrX:37,664,420 | A | G | NM_000397 | SP/Mis | c.1313A > G | SP/p.K438R | 4.39E-05 | 1 | Chronic granulomatous disease, X linked (XLR); Immunodeficiency 34, mycobacteriosis (XLR) | LP |
 GRIPAP1 | 14,524.p1 (M) | Hem | chrX:48,837,828 | C | T | NM_020137 | SP/Syn | c.1830G > A | SP/p.A610A | 0.0001 | 1 |  | VUS |
 HDAC8* | 13,136.p1 (M) | Hem | chrX:71,694,562 | G | - | NM_001166419 | FS | c.755delC | p.P252Qfs | 7.35E-05 | 0.98 | Cornelia de Lange syndrome 5 (XLD) | LP |
 IL13RA1 | 11,167.p1 (M) | Hem | chrX:117,881,009 | T | G | NM_001560 | Mis | c.321 T > G | p.S107R | 0 | 0.96 |  | VUS |
11,488.p1 (M) | chrX:117,895,252 | C | T | NM_001560 | SP/Syn | c.828C > T | SP/p.Y276Y | 2.48E-05 |  | VUS | |||
 MED12* | 11,217.p1 (M) | Hem | chrX:70,343,445 | G | A | NM_005120 | SP/Mis | c.1619G > A | SP/p.R540H | 1.33E-05 | 1 | Lujan-Fryns syndrome (XLR), Ohdo syndrome(XLR), Opitz-Kaveggia syndrome (XLR) | VUS |
12,626.p1 (M) | chrX:70,352,298 | A | G | NM_005120 | Mis | c.4325A > G | p.H1442R | 0 | LP | ||||
 RBMX* | 13,063.p1 (M) | Hem | chrX:135,957,417 | C | T | NM_002139 | SP/Mis | c.782G > A | SP/p.S261N | 0 | 0.83 | Mental retardation, X-linked, syndromic 11, Shashi type (XLR) | LP |
 SLC38A5 | 14,423.p1 (M) | Hem | chrX:48,325,258 | C | T | NM_033518 | SP/Mis | c.247G > A | SP/p.A83T | 0 | 0.98 |  | VUS |
 UBE2A* | 12,440.p1 (M) | Hem | chrX:118,716,638 | A | T | NM_003336 | SP/Mis | c.329A > T | SP/p.Q110L | 0 | 0.82 | Mental retardation, X-linked syndromic, Nascimento-type (XLR) | LP |
 USP9X* | 13,929.p1 (M) | Hem | chrX:40,982,891 | A | G | NM_001039590 | Mis | c.10A > G | p.T4A | 1.52E-05 | 1 | Mental retardation, X-linked 99(XLR); Mental retardation, X-linked 99, syndromic, female-restricted (XLD) | LP |
11,358.p1 (M) | chrX:40,996,058 | G | A | NM_001039590 | SP/Mis | c.437G > A | SP/p.R146K | 0 | LP | ||||
12,628.p1 (M) | chrX:41,012,318 | G | C | NM_001039590 | Mis | c.1881G > C | p.M627I | 1.39E-05 | LP |