Table 2.
the studied patients and their responsible genes and variants in our study
| patient no | Family No. | Gene | Variant Coordinates hg38 | NM# | Nucleotide change | AA change | Novel/reported | Reference |
|---|---|---|---|---|---|---|---|---|
| 1 | 1 | PLA2G6 | Chr22:g38115658 | NM_003560.4 | c.1903 C > T | p.Arg635Ter | Reported | PMIDs:32,357,911, 29,482,223, 16,783,378, 30,340,910, 25,164,370, 22,934,738 |
| 2 | 2 | PLA2G6 | Chr22:g38140111 | NM_003560.4 | c.668 C > T | p.Pro223Leu | Reported | PMID: 29,454,663 |
| 3 | 3 | PLA2G6 | Chr22:g38113581 | NM_003560.4 | c.2108T > A | p.Val703Glu | Novel | - |
| 4 | 4 | PLA2G6 | Chr22:g38140111 | NM_003560.4 | c.668 C > T | p.Pro223Leu | Reported | PMID: 29,454,663 |
| 5 | 5 | PLA2G6 | Chr22:g38132946 | NM_003560.4 | c.962T > C | p.Leu321Pro | Novel | - |
| PLA2G6 | Chr22:g38132869 | c.1039G > A | p.Gly347Arg | Reported | PMIDs:31,496,990, 27,196,560, 26,196,026, 16,783,378, | |||
| 6 | 6 | PLA2G6 | Chr22:g38115589 | NM_003560.4 | c.1972 A > G | p.Asn658Asp | Novel | - |
| 7 | 7 | PLA2G6 | Chr22:g38135012 | NM_003560.4 | c.865_869dup | p.Leu291AlafsTer16 | Novel | - |
| 8 | 8 | PLA2G6 | Chr22:g38140106 | NM_003560.4 | c.673 C > T | p.His225Tyr | Reported | PMID: 24,130,795 |
| 9 | 9 | PLA2G6 | Chr22:g38120879 | NM_003560.4 | c.1622 A > C | p.Tyr541Ser | Novel | - |
| 10 | 10 | PLA2G6 | Chr22:g38112212 | NM_003560.4 | c.2370T > G | p.Tyr790Ter | Reported | PMIDs:30,868,093, 20,886,109, 32,357,911, 29,913,018, 30,293,248, 20,495,927 |
| 11 | 11 | PLA2G6 | Chr22:g38115589 | NM_003560.4 | c.1972 A > G | p.Asn658Asp | Novel | - |
| 12 | 12 | PLA2G6 | Chr22:g38112559 | NM_003560.4 | c.2221 C > T | p.Arg741Trp | Reported | PMIDs: 27,196,560, 20,886,109, 31,516,627, 30,713,958 |
| 13 | 13 | PLA2G6 | Chr22:g38123259 | NM_003560.4 | c.1428-1G > A | Reported | PMID:35,083,005 | |
| 14 | 14 | PLA2G6 | Chr22:g38115612 | NM_003560.4 | c.1949T > C | p.Phe650Ser | Reported | PMID:35,083,005 |
| 15 | 15 | PLA2G6 | Chr22:g38120889 | NM_003560.4 | c.1612 C > A | p.Arg538Ser | Reported | PMID:30,363,890 |
| 16 | 16 | PLA2G6 | Chr22:g38132923 | NM_003560.4 | c.985 C > T | p.Arg329Cys | Reported | PMID:27,196,560 |
| 17 | 17 | PLA2G6 | Chr22:g38126370 | NM_003560.4 | c.1427 + 1G > C | Novel | - | |
| 18 | 18 | PLA2G6 | Chr22:g38115546 | NM_003560.4 | c.2015 A > T | p.Asn672Ile | Novel | - |
| 19 | 19 | PLA2G6 | Chr22:g38132923 | NM_003560.4 | c.985 C > T | p.Arg329Cys | Reported | PMID:27,196,560 |
| 20 | 20 | CWF19L1 | Chr10:g100253470 | NM_018294.6 | c.574T > C | p.Tyr192His | Novel | - |
| 21 | 21 | SNX14 | Chr6:g85543737 | NM_153816.6 | c.1132 C > T | p.Arg378Ter | Reported | PMID:33,193,593, 25,848,753 |
| 22 | 22 | THG1L | Chr5:g157734595 | NM_017872.5 | c.388G > A | p.Ala130Thr | Novel | - |
| 23 | 23 | VPS13D | Chr1:g12333243 | NM_015378.4 | c.8305G > C | p.Glu2769Gln | Novel | - |
| 24 | 24 | RUBCN | Chr3:g197693780 | NM_014687.4 | c.1721 C > G | p.Ser574Ter | Novel | - |
| 25 | 25 | GRID2 | Chr4:g 93,224,683 | NM_001510.4 | c.1033 C > T | p.Arg345Ter | Novel | - |
| 26 | 26 | MME | Chr3:g155180448 | NM_001354642.1 | c.2242 C > T | p.Arg748Trp | Novel | - |
| 27 | 27 | FAT2 | Chr5:g151505702 | NM_001447.3 | c.12913G > T | p.Ala4305Ser | Novel | - |
| 28 | 28 | ATM | Chr11:g108321299 | NM_000051.4 | c.6453-2 A > G | Novel | - | |
| 29 | 29 | ATM | Chr11:g108315863 | NM_000051.4 | c.6047 A > G | p.Asp2016Gly | Reported | PMID:9,887,333, 11,826,030, 24,825,865, 11,826,026, 11,826,029 |
| 30 | 30 | ATM | Chr11:g108279526 | NM_000051.4 | c.3320T > G | p.Leu1107Ter | Novel | - |
| 31 | 31 | ATM | Chr11:g108244954 | NM_000051.4 | c.829G > T | p.Glu277Ter | Reported | PMID:32,962,506, 32,091,409 |
| 32 | 32 | ATM | Chr11:g108316015 | NM_000051.4 | c.6100 C > T | p.Arg2034Ter | Reported | PMID:11,505,391, 29,731,985 |
| 33 | 33 | ATM | Chr11:g108316015 | NM_000051.4 | c.6100 C > T | p.Arg2034Ter | Reported | PMID:11,505,391, 29,731,985 |
| 34 | 34 | ATM | Chr11:g108335008 | NM_000051.4 | c.8050 C > T | p.Gln2684Ter | Novel | - |
| 35 | 35 | ATM | Chr11:g108365138 | NM_000051.4 | c.6100 C > T | p.Tyr2969Ter | Reported | PMID:11,505,391, 29,731,985 |
| ATM | Chr11:g108227691 | NM_000051.4 | c.67 C > T | p.Arg23Ter | Reported | PMID:26,506,520 | ||
| 36 | 36 | ATM | Chr11:g108307928 | NM_000051.4 | c.5712dup | p.Ser1905IlefsTer25 | Reported | PMID:18,321,536 |
| 37,38 | 37 | ATM | Chr11:g108317432 | NM_000051.4 | c.6259delG | p.Glu2087LysfsTer9 | Reported | PMID:32,095,276 |
| 39 | 38 | ATM | Chr11:g108244954 | NM_000051.4 | c.829G > T | p.Glu277Ter | Reported | PMID:32,962,506, 32,091,409 |
| 40 | 39 | ATM | Chr11:g108315863 | NM_000051.4 | c.6047 A > G | p.Asp2016Gly | Reported | PMID:9,887,333, 11,826,030, 24,825,865, 11,826,026, 11,826,029 |
| 41 | 40 | ATM | Chr11:g108284374 | NM_000051.4 | c.3895del | p.Ala1299ProfsTer50 | Novel | - |
| 42 | 41 | ATM | Chr11:g108330234 | NM_000051.4 | c.7328G > A | p.Arg2443Gln | Reported | PMID:31,740,029, 31,754,145, 26,630,574, 27,175,599 |
| 43 | 42 | SACS | Chr13:g23333063 | NM_014363.6 | c.10,813 A > T | p.Lys3605Ter | Reported | PMID: 35,731,353 |
| 44 | 43 | SACS | Chr13:g23334010 | NM_014363.6 | c.9866 C > G | p.Ser3289Ter | Reported | PMID: 35,731,353 |
| 45 | 44 | SACS | Chr13:g23335744 | NM_014363.6 | c.8132 C > A | p.Ser2711Ter | Reported | PMID: 35,731,353 |
| 46 | 45 | SACS | Chr13:g23341436 | NM_014363.6 | c.2439_2440delAT | p.Val815GlyfsTer4 | Reported | PMID: 35,731,353 |
| 47 | 46 | SACS | Chr13:g23340595 | NM_014363.6 | c.3281dupA | p.Asn1094LysfsTer18 | Reported | PMID: 35,731,353 |
| 48 | 47 | SACS | Chr13:g23340449 | NM_014363.6 | c.3427 C > T | p.Gln1143Ter | Reported | PMID: 35,731,353 |
| 49 | 48 | SACS | Chr13:g23335160 | NM_014363.6 | c.8716 C > T | p.Arg2906Ter | Reported | PMID: 35,731,353 |
| 50 | 49 | SACS | Chr13:g23336372 | NM_014363.6 | c.7504 C > T | p.Arg2502Ter | Reported | PMID: 35,731,353 |
| 51 | 50 | SACS | Chr13:g23340183 | NM_014363.6 | c.3695_3697del | p.Val1232del | Reported | PMID: 35,731,353 |
| 52 | 51 | SACS | Chr13:g23332097 | NM_014363.6 | c.11779G > C | p.Ala3927Pro | Reported | PMID: 35,731,353 |
| 53 | 52 | SACS | Chr13:g23332097 | NM_014363.6 | c.11779G > C | p.Ala3927Pro | Reported | PMID: 35,731,353 |
| 54 | 53 | SACS | Chr13:g.23,907,390 | NM_014363.6 | c.10,625 A > G | p.Asp3542Gly | Novel | |
| Chr13:g.23,905,173 | NM_014363.6 | c.12831_12841dupTCCTCTTTTCT | p.Ser4281PhefsTer31 | Novel | ||||
| 55 | 54 | APTX | Chr9:g32974539 | ENST00000379817.7 | c.793 A > T | p.Ser265Cys | Novel | - |
| 56,57 | 55 | APTX | Chr9:g32984821 | ENST00000379817.7 | c.582del | p.Lys194AsnfsTer20 | Novel | - |
| 58 | 56 | APTX | Chr9:g32984667 | ENST00000379817.7 | c.734G > A | p.Arg245His | Novel | - |
| 59 | 57 | APTX | Chr9:g32984842 | ENST00000379817.7 | c.559 C > T | p.Gln187Ter | Reported | PMID:29,356,829 |
| 60 | 58 | APTX | Chr9:g32987650 | NM_001195248.2 | c.376delA | p.Arg126GlyfsTer26 | Novel | - |
| 61 | 59 | COQ8A | Chr1:g226983633 | NM_020247.5 | c.1162G > A | p.Gly388Ser | Novel | - |
| 62 | 60 | COQ8A | Chr1:g226982107 | NM_020247.5 | c.811 C > T | p.Arg271Cys | Reported | PMID:24,218,524, 30,637,285, 32,337,771, 24,164,873, 29,255,295, 29,915,382 |
| 63 | 61 | COQ8A | Chr1:g227169811 | NM_020247.5 | c.814G > T | p.Gly272Cys | Reported | PMID:35,275,351 |
| 64,65 | 62 | TTPA | Chr8:g63061291 | NM_000370.3 | c.798del | p.Glu267LysfsTer27 | Novel | - |
| 66 | 63 | NPC2 | Chr14:g74484506 | NM_001375440.1 | c.272 A > T | p.Asp91Val | Novel | - |
| 67 | 64 | NPC2 | Chr14:74484506 | NM_006432.5 | c.272 A > T | p.Asp91Val | Novel | - |
| 68 | 65 | MFSD8 | Chr4:g127965071 | NM_152778.3 | c.62 + 1G > A | Novel | - | |
| 69 | 66 | MFSD8 | Chr4:g127930787 | NM_001371596.1 | c.894T > G | p.Tyr298Ter | Reported | PMID:17,564,970 |
| 70,71 | 67 | MFSD8 | Chr4:g127943750 | NM_001371596.1 | c.439 + 2T > C | - | Novel | - |
| 72 | 68 | TPP1 | Chr11:g6615170 | NM_000391.4 | c.1425 + 1G > T | Novel | -submitted | |
| 73 | 69 | CLN3 | Chr16:g28477598 | NM_001286110.2 | c.1073_1074insAGAGAAATGAATGAGCCTACAGATGATAGGATGTGGTGTT | p.Cys359GlufsTer3 | Novel | - |
| 74 | 70 | CLN6 | Chr15:g68211685 | NM_017882.3 | c.476 C > T | p.Pro159Leu | Reported | PMID:30,285,654, 19,201,763 |
| 75 | 71 | CLN5 | Chr13:g76992159 | ENST00000377453.9 | c.61 C > T | p.Arg21Trp | Reported | PMID:22,727,047, PMID:21,990,111 |
| 77 | 72 | POLG | Chr15:g89318535 | ENST00000268124.11 | c.3482 + 6 C > T | Novel | - | |
| 78 | 73 | BRAT1 | Chr7:g2544941 | ENST00000340611.9 | c.398 A > G | p.His133Arg | Novel | - |
| 79 | 74 | MT-ATP6 | ChrM:8993 | ENST00000361899.2 | c.467T > G | p.Leu156Arg | Reported | PMID: 1,539,598 |
| 80 | 75 | DARS2 | Chr1:g173857548 | NM_018122.5 | c.1781G > A | p.Gly594Glu | Novel | - |
| 81,82 | 76 | NARS2 | Chr11:g78559588 | NM_024678.6 | c.545T > A | p.Ile182Lys | Reported | PMID:34,374,940 |
| 83 | 77 | TMEM237 | Chr2:g201632053 | NM_001044385.3 | c.550dup | p.Ser184LysfsTer8 | Novel | - |
| 84 | 78 | AHI1 | Chr6:g135463145 | NM_001134831.2 | c.910dup | p.Thr304AsnfsTer6 | Reported | PMID:26,541,515 |
| 85 | 79 | CEP120 | Chr5:123377502 | NM_001375405.1 | c.2230 C > T | p.Arg744Cys | Novel | - |
| 86 | 80 | ATCAY | Chr19(hg38):g3913774 | NM_033064.5 | c.883_884del | p.Lys295AspfsTer52 | Reported | [27] |
| 87 | 81 | GAN | Chr16:g81363869 | NM_022041.4 | c.1162delC | p.Leu388Ter | Reported | [28] |
| 88,89 | 82 | GAN | Chr16:g81354492 | NM_022041.4 | c.370T > A | p.Phe124Ile | Reported | [28] |
| 90 | 83 | SAMD9 | Chr7:g93101540 | NM_001193307.1 | c.4558G > T | p.Glu1520Ter | Novel | - |
| 91 | 84 | HEXA | Chr15:g72345461 | NM_000520.6 | c.1511G > A | p.Arg504His | Reported | PMID:16,088,929, 31,367,523, 29,482,223 |
| 92 | 85 | KIF1C | Chr17:g5020864 | NM_006612.6 | c.1996G > T | p.Glu666Ter | Novel | - |
| 93 | 86 | RNASET2 | Chr6:g166938996 | NM_003730.6 | c.345G > A | p.Trp115Ter | Novel | - |
| 94 | 87 | FIG4 | Chr6:g109776937 | NM_014845.6 | c.1766 A > G | p.Asp589Gly | Novel | - |
| 95,96 | 88 | SIL1 | Chr5:g138951290 | NM_022464.5 | c.910 C > T | p.Gln304Ter | Novel | - |
| 97 | 89 | ADD3 | Chr10:g110122249 | NM_016824.5 | c.1100G > A | p.Gly367Asp | Reported | PMID:23,836,506, 28,492,530, 30,369,941, 28,042,670, 27,391,121 |
| 98 | 90 | WDR81 | Chr17:g1726544 | NM_001163809.2 | c.1585 C > G | p.Arg529Gly | Novel | - |
| 99 | 91 | ERLIN2 | Chr8:37744568 | NM_007175.8 | c.299-3 C > T | - | Novel | - |
| 100 | 92 | ELP2 | Chr18:36159780 | NM_018255.4 | c.1580G > A | p.Ser527Asn | Novel | - |
Five patients were homozygous for Anemia Fancony expansion