Table 2.
Nucleotide variants found in the IDS gene
| Nucleotide change number | Nucleotide; protein change found | Type of nucleotide change | Exons of IDS gene | HGMD accession | Allele frequency (%) in presented cohort | Comments |
|---|---|---|---|---|---|---|
| 1 | c.103G>C; p.Asp35His | Missense | 1 | None | 0.88 |
Novel (NC_000023.11:g.149505035C>G) ClinVar accession SCV001450592 |
| 2 | c.136G>T; p.Asp46Tyr | Missense | 2 | None | 0.44 |
Novel (NC_000023.11:g.149504261C>A) ClinVar accession SCV001450595 one another described in the same codon |
| 3 | c.136G>A; p.Asp46Asn | Missense | 2 | None | 0.44 |
Novel (NC_000023.11:g.149504261C>T) ClinVar accession SCV001450596 one another described in the same codon |
| 4 | c.160T>G; p.Tyr54Asp | Missense | 2 | CM981010 | 0.44 | |
| 5 | c.187A>G; p.Asn63Asp | Missense | 2 | CM960853 | 1.3 | |
| 6 | c.236C>A; p.Ala79Glu | Missense | 2 | CM981012 | 0.88 | |
| 7 | c.253G>A; p.Ala85Thr | Missense | 3 | CM960855 | 2.2 | |
| 8 | c.253G>T; p.Ala85Ser | Missense | 3 | CM981013 | 0.44 | |
| 9 | c.257C>T; p.Pro86Leu | Missense | 3 | CM950659 | 1.3 | |
| 10 | c.257C>G; p.Pro86Arg | Missense | 3 | CM930414 | 0.44 | |
| 11 | c.263G>A; p.Arg88His | Missense | 3 | CM960857 | 2.65 | |
| 12 | c.262C>T; p.Arg88Cys | Missense | 3 | CM950661 | 1.76 | |
| 13 | c.263G>T; p.Arg88Leu | Missense | 3 | CM981014 | 0.44 | |
| 14 | c.263G>C; p.Arg88Pro | Missense | 3 | CM970749 | 0.44 | |
| 15 | c.283A>T; p.Arg95Trp | Missense | 3 | None | 0.44 |
Novel (NC_000023.11:g.149503447T>A) ClinVar accession SCV001450598 three other described in the same codon |
| 16 | c.305T>G; p.Leu102Arg | Missense | 3 | CM981017 | 0.88 | |
| 17 | c.307T>G; p.Tyr103Asp | Missense | 3 | None | 0.44 |
Novel (NC_000023.11:g.149503423A>C) ClinVar accession SCV001450601 two other described in the same codon |
| 18 | c.325T>C; p.Trp109Arg | Missense | 3 | CM128183 | 0.88 | |
| 19 | c.359C>G; p.Pro120Arg | Missense | 3 | CM930417 | 0.44 | |
| 20 | c.395C>G; p.Ser132Trp | Missense | 3 | CM950663 | 0.88 | |
| 21 | c.403A>G; p.Lys135Glu | Missense | 3 | None | 0.44 |
Novel (NC_000023.11:g.149503327T>C) ClinVar accession SCV001450599 two other described in the same codon |
| 22 | c.476A>C; p.His159Pro | Missense | 4 | CM981026 | 0.44 | |
| 23 | c.512G>A; p.Cys171Tyr | Missense | 5 | None | 0.44 |
Novel (NC_000023.11:g.149498303C>T) ClinVar accession SCV001450602 one another described in the same codon |
| 24 | c.545T>C; p.Leu182Pro | Missense | 5 | CM981027 | 0.44 | |
| 25 | c.551G>T; p.Cys184Phe | Missense | 5 | CM960862 | 0.44 | |
| 26 | c.587T>C; p.Leu196Ser | Missense | 5 | CM981029 | 0.88 | |
| 27 | c.590C>T; p.Pro197Leu | Missense | 5 | None | 1.76 |
Novel (NC_000023.11:g.149498225G>A) ClinVar accession SCV001450603 |
| 28 | c.593A>G; p.Asp198Gly | Missense | 5 | CM981030 | 0.44 | |
| 29 | c.671G>A; p.Gly224Glu | Missense | 5 | CM981031 | 0.44 | |
| 30 | c.697A>G; p.Arg233Gly | Missense | 5 | CM146285 | 1.3 | |
| 31 | c.776T>C; p.Leu259Pro | Missense | 6 | CM030889 | 0.44 | |
| 32 | c.795C>A; p.Asn265Lys | Missense | 6 | CM128190 | 0.88 | |
| 33 | c.795C>G; p.Asn265Lys | Missense | 6 | CM141180 | 0.44 | |
| 34 | c.998C>T; p.Ser333Leu | Missense | 7 | CM920367 | 3.09 | |
| 35 | c.1004A>G; p.His335Arg | Missense | 7 | CM981045 | 0.44 | |
| 36 | c.1006G>C; p.Gly336Arg | Missense | 8 | CM970753 | 0.44 | |
| 37 | c.1019G>A; p.Gly340Asp | Missense | 8 | CM981048 | 1.3 | |
| 38 | c.1028G>A; p.Gly343Glu | Missense | 8 | None | 0.44 |
Novel (NC_000023.11:g.149487077C>T) ClinVar accession SCV001450616 |
| 39 | c.1035G>C, p.Trp345Cys | Missense | 8 | CM950668 | 0.44 | |
| 40 | c.1034G>C; p.Trp345Ser | Missense | 8 | None | 0.44 |
Novel (NC_000023.11:g.149487071C>G) ClinVar accession SCV001450617 four other described in the same codon |
| 41 | p.1037C>T; p.Ala346Val | Missense | 8 | CM950669 | 1.3 | |
| 42 | c.1204G>A; p.Glu402Lys | Missense | 9 | CM167391 | 0.88 | |
| 43 | c.1295G>A; p.Cys432Tyr | Missense | 9 | CM981052 | 0.88 | |
| 44 | c.1402C>T; p.Arg468Trp | Missense | 9 | CM920369 | 2.2 | |
| 45 | c.1403G>A; p.Arg468Gln | Missense | 9 | CM930422 | 4.4 | |
| 46 |
c.1411G>C; p.Asp471His c.1418C>T; p.Pro473Leu |
Missense | 9 | None | 0.44 |
Novel Novel (NC_000023.11:g.[149482988C>G;149482981G>A]) ClinVar accession SCV001450627 |
| 47 | c.1432G>T; p.Asp478Tyr | Missense | 9 | CM981054 | 0.44 | |
| 48 | c.1432G>A; p.Asp478Asn | Missense | 9 | BM1234454 | 0.44 | |
| 49 | c.1454T>G; p.Ileu485Arg | Missense | 9 | CM940967 | 0.88 | |
| 50 | c.1565T>C; p.Leu522Pro | Missense | 9 | HM971766 | 0.44 | |
| 51 | c.196C>T; p.Gln66Term | Nonsense | 2 | CM068304 | 0.44 | |
| 52 | c.361C>T; p.Gln121Term | Nonsense | 3 | CM128174 | 0.44 | |
| 53 | c.514C>T; p.Arg172Term | Nonsense | 5 | CM920366 | 2.65 | |
| 54 | c.598C>T p.Gln200Term | Nonsense | 6 | CM146284 | 0.88 | |
| 55 | c.800G>A; p.Trp267Term | Nonsense | 6 | CM050243 | 0.44 | |
| 56 | c.814C>T; p.Gln272Term | Nonsense | 6 | None | 0.44 |
Novel (NC_000023.11:g.149496411G>A) ClinVar accession SCV001450612 |
| 57 | c.829C>T; p.Gln277Term | Nonsense | 6 | None | 0.44 |
Novel (NC_000023.11:g.149496396G>A) ClinVar accession SCV001450613 |
| 58 | c.998C>A; p.Ser333Term | Nonsense | 7 | None | 0.88 |
Novel (NC_000023.11:g.149490322G>T) ClinVar accession SCV001450615 two other described in the same codon |
| 59 | c.1010G>A; p.Trp337Term | Nonsense | 8 | CM128194 | 0.88 | |
| 60 | c.1234G>T; p.Gly412Term | Nonsense | 9 | None | 0.44 |
Novel (NC_000023.11:g.149483165C>A) ClinVar accession SCV001450623 |
| 61 | c.1288G>T; p.Glu430Term | Nonsense | 9 | CM146287 | 0.44 | |
| 62 | c.1327C>T; p.Arg443Term | Nonsense | 9 | CM920368 | 1.3 | |
| 63 | c.1340T>A; p.Leu447Term | Nonsense | 9 | None | 0.44 |
Novel (NC_000023.11:g.149483059A>T) ClinVar accession SCV001450625 |
| 64 | c.1375G>T; p.Glu459Term | Nonsense | 9 | CM1719915 | 0.44 | |
| 65 | c.1445T>G; p.Leu482Term | Nonsense | 9 | CM981058 | 0.44 | |
| 66 | c.1608T>A; p.Tyr536Term | Nonsense | 9 | CM141189 | 0.44 | |
| 67 | IVS1 as A-G -2; c.104-2A>G | Splicing substitutions | CS982224 | 0.44 | ||
| 68 | IVS2 ds G-C +1; c.240+1G>C | Splicing substitutions | CS050391 | 0.44 | ||
| 69 | IVS2 ds G-T +1; c.240+1G>T | Splicing substitutions | CS982227 | 0.44 | ||
| 70 | IVS2 as C-G -9; c.241-9C>G | Splicing substitutions | None | 0.88 |
Novel (NC_000023.11:g.149503498G>C) ClinVar accession SCV001450634 |
|
| 71 | IVS4 ds G-A +1; c.507+1G>A | Splicing substitutions | CS982228 | 0.88 | ||
| 72 | IVS6 ds G-A +1; c.879+1G>A | Splicing substitutions | CS982229 | 0.44 | ||
| 73 | IVS6 as A-G -2; c.880-2A>G | Splicing substitutions | CS930833 | 0.44 | ||
| 74 | IVS7 ds T-G +2 c.1006+2T>G | Splicing substitutions | None | 0.44 |
Novel (NC_000023.11:g.149490312A>C) ClinVar accession SCV001450635 |
|
| 75 | IVS7 as G-A -1; c.1007-1G>A | Splicing substitutions | CS120471 | 0.44 | ||
| 76 | IVS8 as C-A -15; c.1181-15C>A | Splicing substitutions | CS013824 | 0.44 | ||
| 77 | IVS8 ds C-T -59; c.1122C>T | Splicing substitutions | CS963080 | 5.75 | ||
| 78 | c.118_120delCTT; p.Leu40del | Small deletion | 2 | None | 0.44 |
Novel (NC_000023.11:g.149504277_149504279delAAG) ClinVar accession SCV001450593 |
| 79 | c.121_123delCTC p.Leu41del | Small deletion | 2 | CD941707 | 0.44 | |
| 80 | c.133delG; p.Asp45Metfs | Small deletion | 2 | None | 0.44 |
Novel (NC_000023.11:g.149504264delC) ClinVar accession SCV001450594 |
| 81 | c.248delT; p.Val83Glyfs | Small deletion | 3 | None | 0.44 |
Novel (NC_000023.11:g.149503482delA) ClinVar accession SCV001450597 |
| 82 | c.305delT; p.Leu102Argfs | Small deletion | 3 | None | 0.44 |
Novel (NC_000023.11:g.149503425delA) ClinVar accession SCV001450600 |
| 83 | c.404_405delAA; p.Lys135Serfs | Small deletion | 3 | None | 0.44 |
Described ClinVar accession VCV000499561.1 |
| 84 | c.410_411delTT p.Phe137Serfs | Small deletion | 3 | CD012530 | 0.44 | |
| 85 | c.596_599delAACA; p.Lys199Argfs | Small deletion | 5 | CD941708 | 2.21 | |
| 86 | c.613delG; p.Ala205Profs | Small deletion | 5 | None | 0.44 |
Novel (NC_000023.11:g.149498202delC) ClinVar accession SCV001450604 |
| 87 | c.625_627del TTG; p.Leu209del | Small deletion | 5 | None | 0.44 |
Novel (NC_000023.11:g.149498188_149498190delCAA) ClinVar accession SCV001450605 |
| 88 | c.667_683del17; p.Val223Thrfs | Small deletion | 5 | CD982702 | 0.44 | |
| 89 | c.687delC; p.His229Glnfs | Small deletion | 5 | None | 0.44 |
Novel (NC_000023.11:g.149498128delG) ClinVar accession SCV001450606 |
| 90 | c.715_721del7; p.Gln239Cysfs | Small deletion | 6 | None | 0.44 | Novel (NC_000023.11:g.149496504_149496510delACTTCTG) ClinVar accession SCV001450607 |
| 91 | c.782delC; p.Pro261Leufs | Small deletion | 6 | CD982703 | 0.44 | |
| 92 | c.800_801delGG; p.Trp267Tyrfs | Small deletion | 6 | None | 0.44 |
Novel (NC_000023.11:g.149496424_149496425delCC) ClinVar accession SCV001450611 |
| 93 | c.899_900delAC; p.Tyr300Phefs | Small deletion | 7 | None | 0.44 |
Novel (NC_000023.11:g.149490420_149490421delGT) ClinVar accession SCV001450614 |
| 94 | c.908_909delCT; p.Ser303Cysfs | Small deletion | 7 | CD1412401 | 0.44 | |
| 95 | c.1077delG; p.Ile360Tyrfs | Small deletion | 8 | CD146296 | 0.44 | |
| 96 | c.1129delC; p.Leu377Phefs | Small deletion | 8 | None | 0.44 |
Novel (NC_000023.11:g.149486976delG) ClinVar accession SCV001450618 |
| 97 | c.1191delC; p.Met398Trpfs | Small deletion | 9 | None | 0.44 |
Novel (NC_000023.11:g.149483208delG) ClinVar accession SCV001450620 |
| 98 | c.1214_1220del7; p.Ser405Phefs | Small deletion | 9 | None | 0.44 |
Novel (NC_000023.11:g.149483179_149483185delAAAAGAG) ClinVar accession SCV001450621 |
| 99 | c.1221delT; p.Ser409Argfs | Small deletion | 9 | None | 0.44 |
Novel (NC_000023.11:g.149483178delA) ClinVar accession SCV001450622 |
| 100 | c.1353_1357delGTACC; p.Tyr452Profs | Small deletion | 9 | None | 0.44 |
Novel (NC_000023.11:g. 149483042_149483046delGGTAC) ClinVar accession SCV001450626 |
| 101 | c.1426_1437 del12 p.476_479delAsnSerAspLys | Small deletion | 9 | None | 0.44 |
Novel (NC_000023.11:g.149482962_149482973delCTTGTCAGAATT) ClinVar accession SCV001450629 |
| 102 | c.1431delT; p.Asp478Thrfs | Small deletion | 9 | None | 0.44 |
Novel (NC_000023.11:g.149482968delA) ClinVar accession SCV001450628 |
| 103 | c.1438_1442delCCGAG;p.Pro480Phefs | Small deletion | 9 | None | 0.44 | Novel (NC_000023.11:g.149482957_149482961delCTCGG) ClinVar accession SCV001450630 |
| 104 | c.1466delG p.Val489Alafs | Small deletion | 9 | CD146297 | 0.44 | |
| 105 | c.776_777dupTA; p.Pro260Tyrfs | Small insertions/duplications | 6 | None | 0.44 |
Novel (NC_000023.11:g.149496448_149496449dupTA) ClinVar accession SCV001450608 |
| 106 | c.801_802insG; p.Met268Aspfs | Small insertions/duplications | 6 | None | 0.44 |
Novel (NC_000023.11:g.149496423_149496424insC) ClinVar accession SCV001450610 |
| 107 | c.1151_1152 insTGCGACCCTTT; p.Phe384Leufs | Small insertions/duplications | 8 | None | 0.44 |
Novel (NC_000023.11:g.149486954_149486955 insTGCGACCCTTT) ClinVar accession SCV001450619 |
| 108 | c.1239_c.1240insCT; p.Ala414Leufs | Small insertions/duplications | 9 | None | 0.44 |
Novel (NC_000023.11:g.149483159_149483160insAG) ClinVar accession SCV001450624 |
| 109 | c.1491_1492dupTA; p.Arg498Ileufs | Small insertions/duplications | 9 | None | 0.44 |
Novel (NC_000023.11:g.149482909_149482910dupTA) ClinVar accession SCV001450631 |
| 110 | c.104-1_104delGAinsT | Small indels | 2 | None | 0.44 | Novel (NC_000023.11:g.149504293_149504294delTCinsA) ClinVar accession SCV001450632 |
| 111 | c.240 +2_c.240+3insTCCCAGA | Small indels | Intron 2 | None | 0.44 | Novel (NC_000023.11:g.149504154_149504155insTCCCAGA) ClinVar accession SCV001450633 |
| 112 | c.786_787delGGinsC; p.Ala263Profs | Small indels | 6 | None | 0.44 | Novel (NC_000023.11:g.149496438_149496439delCCinsG) ClinVar accession SCV001450609 |
| 113 | gDNA level exons 1–3 deletion | Gross deletions | 0.88 | |||
| 114 | gDNA level exons 1–4 deletion | Gross deletions | 0.44 | |||
| 115 | gDNA level exons 1–7 deletion | Gross deletions | 0.44 | |||
| 116 | gDNA level exons 1–7 deletion | Gross deletions | 0.44 | |||
| 117 | gDNA level exon 4 deletion | Gross deletions | 0.44 | |||
| 118 | cDNA level del incl. ex 5–6 | Gross deletions | CG984375 | 0.44 | ||
| 119 | gDNA level exon 7 deletion | Gross deletions | 0.44 | |||
| 120 | Complete IDS del | Gross deletions | 3.5 | |||
| 121 | Recomb. between in. 7 and seq. distal of ex. 3 in IDS-2 without exons deletion | Complex rearrangements | CP973598 | 6.19 | ||
| 122 | Recomb. between in. 7 and seq. distal of ex. 3 in IDS-2 with 4–7 exons deletion | Complex rearrangements | 1.32 |