Table 2.
Novel variants in ALMS1 identified in this study
| Number | Exon | Nucleotide change | Amino acid change | Variant Type | Source | ACMG |
|---|---|---|---|---|---|---|
| 1 | 4 | c.764 + 43 C > T | p.? | Splice site | NA | LP |
| 2 | 6 | c.1341G > C | p.Lys447Asn | Missense | F | LP |
| 3 | 8 | c.1688delA | p.Asp563Alafs*33 | Frameshift | F | LP |
| 4 | 8 | c.1995_1996insCT | p.Ser666Leufs*9 | Frameshift | F | P |
| 5 | 8 | c.2041 C > T | p.Arg681Ter | Nonsense | M | P |
| 6 | 8 | c.2064delT | p.Leu689Ter | Nonsense | F | P |
| 7 | 8 | c.2296_2299delTCAC | p.Ser766Lysfs*13 | Frameshift | M | P |
| 8 | 8 | c.2438 C > G | p.Ser813Ter | Nonsense | NA | LP |
| 9 | 8 | c.2675delC | p.Pro892Leufs*42 | Frameshift | M | LP |
| 10 | 8 | c.2888_2897delGTGTTTTCTA | p.Ser963Thrfs*15 | Frameshift | M | LP |
| 11 | 8 | c.3226_3232delAAAGTTT | p.Lys1076Glnfs*10 | Frameshift | M | P |
| 12 | 8 | c.3469 C > T | p.Gln1157Ter | Nonsense | M | P |
| 13 | 8 | c.3610 C > T | p.Gln1204Ter | Nonsense | M | P |
| 14 | 8 | c.3659 C > G | p.Ser1220Ter | Nonsense | F | P |
| 15 | 8 | c.4297delA | p.Thr1433Glnfs*40 | Frameshift | M | LP |
| 16 | 8 | c.4296_4299delCACA | p.His1432Glnfs*40 | Frameshift | F | P |
| 17 | 8 | c.4576 C > T | p.Gln1526Ter | Nonsense | F | P |
| 18 | 8 | c.4706_4707delinsCTCT | p.Thr1570Leufs*28 | Frameshift | NA | LP |
| 19 | 8 | c.4860_4873delACTTGGAGAGAAGC | p.Leu1621Hisfs*15 | Frameshift | F | LP |
| 20 | 8 | c.5385_5386delGA | p.Lys1796Aspfs*30 | Frameshift | F | P |
| 21 | 8 | c.5495delT | p.Leu1832Ter | Nonsense | M | P |
| 22 | 8 | c.5691delC | p.Ser1898Glnfs*22 | Frameshift | NA | LP |
| 23 | 8 | c.6109 C > T | p.Gln2037Ter | Nonsense | M | P |
| 24 | 8 | c.6161_6162insTA | p.Lys2054Asnfs*21 | Frameshift | M | LP |
| 25 | 8 | c.6164_6165insAT | p.Asn2056Serfs*19 | Frameshift | F | P |
| 26 | 8 | c.6760G > T | p.Glu2254Ter | Nonsense | NA | P |
| 27 | 8 | c.6784G > T | p.Glu2262Ter | Nonsense | M | P |
| 28 | 8 | c.7056_7057insC | p.Glu2353Argfs*4 | Frameshift | M | LP |
| 29 | 8 | c.7451delT | p.Val2484Glyfs*11 | Frameshift | M | LP |
| 30 | 8 | c.7499delinsTT | p.Leu2501Thrfs*25 | Frameshift | NA | LP |
| 31 | 8 | c.7505_7506delGA | p.Arg2502Lysfs*23 | Frameshift | NA | LP |
| 32 | 9 | c.7670T > A | p.Leu2557Ter | Nonsense | F | P |
| 33 | 9 | c.7680 + 8 A > G | p.? | Splice site | M | P |
| 34 | 10 | c.7797_7800delTAGA | p.Arg2600Thrfs*13 | Frameshift | M | LP |
| 35 | 10 | c.8082delA | p.Val2695Trpfs*15 | Frameshift | F | P |
| 36 | 10 | c.8242delG | p.Val2748Trpfs*39 | Frameshift | M | P |
| 37 | 10 | c.8301_8302delGA | p.Lys2768Asnfs*8 | Frameshift | M | LP |
| 38 | 10 | c.8329delA | p.Met2777Cysfs*10 | Frameshift | NA | P |
| 39 | 10 | c.8561delC | p.Leu2855Ter | Nonsense | F | LP |
| 40 | 10 | c.8653 C > T | p.Gln2885Ter | Nonsense | F | P |
| 41 | 10 | c.8959delC | p.Pro2987Profs*9 | Frameshift | F | LP |
| 42 | 10 | c.9149delinsTT | p.Thr3051Asnfs*12 | Frameshift | M | P |
| 43 | 10 | c.9150_9151delAA | p.Thr3051Serfs*11 | Frameshift | F | P |
| 44 | 10 | c.9222delT | p.Ala3075Leufs*6 | Frameshift | F | LP |
| 45 | 10 | c.9284 C > A | p.Ser3095Ter | Nonsense | NA | P |
| 46 | 10 | c.9445_9448delinsCAGACAGA | p.Asn3150Thrfs*3 | Frameshift | F | P |
| 47 | 10 | c.9448_9451delinsAATAAATA | p.Ser3151Lysfs*2 | Frameshift | M | LP |
| 48 | 10 | c.9460delG | p.Val3154Ter | Nonsense | NA | P |
| 49 | 11 | c.9636delG | p.Thr3213Profs*19 | Frameshift | F | P |
| 50 | 11 | c.9604delinsGG | p.Val3202Glyfs*17 | Frameshift | F | P |
| 51 | 16 | c.10390delT | p.Ser3464Profs*45 | Frameshift | F | LP |
| 52 | 16 | c.10618_10621delAAGA | p.Lys3540Glnfs*6 | Frameshift | F | P |
| 53 | 16 | c.10800_10803delTGAA | p.Glu3601Cysfs*60 | Frameshift | F | LP |
| 54 | 16 | c.11044delinsAA | p.Ser3682Lysfs*7 | Frameshift | M | P |
| 55 | 16 | c.11,140 C > T | p.Gln3714Ter | Nonsense | F | P |
| 56 | 16 | c.11367_11383delCCGGCTGATTCAAGCTT | p.Arg3790Trpfs*3 | Frameshift | M | LP |
| 57 | 16 | c.11,377 C > T | p.Gln3793Ter | Nonsense | De novo | P |
| 58 | 16 | c.11,460 C > A | p.Tyr3820Ter | Nonsense | M | LP |
| 59 | 17 | c.11619delT | p.Thr3874Leufs*11 | Frameshift | M | LP |
| 60 | 17 | c.11649delG | p.Met3883Ilefs*2 | Frameshift | F | LP |
| 61 | 18 | c.11686delG | p.Val3896Ter | Nonsense | F | P |
| 62 | 18 | c.11841_11844delAAAG | p.Arg3947Serfs*2 | Frameshift | F | P |
| 63 | 18 | c.11846_11847insA | p.Asn3952Leufs*10 | Frameshift | F | P |
| 64 | 19 | c.12034delC | p.Leu4012Trpfs*19 | Frameshift | F | P |
Note: M: Mother; F: Father; P: Pathogenic; LP: Likely Pathogenic; NA: Not Available