Table 3.
New variants (not described previously in literature)
| Gene | Patient | Inheritance | Type | Nomenclature | Classification ACMG |
|---|---|---|---|---|---|
| ACER3 | IDSPG75 | AR | Missense | NP_060837.3:p.(Gly211Cys) | Pathogenic |
| AMPD2 | IDSPG78 | AR | Frameshift deletion | NP_631895.1:p.(Ala62SerfsTer40) | Pathogenic |
| BCKDK | IDSPG47.0 | AR | Missense | NP_005872.2:p.(Arg327Trp) | Likely pathogenic |
| CAPN10 | IDSPG47.1 | AR | Splicing | NM_023083.3:c.1989 + 1G > A | Pathogenic |
| DLG4 | IDSPG107 | AD | Splicing | NM_001365.4:c.1721-1G > A | Pathogenic |
| ERBB4 | IDSPG38 | AD | Non-canonical splicing | NM_005235.2:c.2487 + 8_2487 + 11dell | VUS |
| FA2H | IDSPG10 | AR | Missense | NP_077282.3:p.(Lys262Thr) | Likely pathogenic |
| GFAP | IDSPG4 | AD | Missense | NP_001124491.1:p.(Gly18Val) | Pathogenic |
| IFIH1 | IDSPG3 | AD | Missense | NP_071451.2:p.(Leu320Phe) | VUS |
| KCNA1 | IDLNF52 | AR | Missense | NP_000208.2:p.(Val368Leu)) | Pathogenic |
| KIDINS220 | IDSPG118 | AD | Splicing | NM_020738.3:c.4054-1G > C | Likely pathogenic |
| KIF5A | IDSPG17 | AD | Missense | NP_004975.2:p.(Gly246Val) | Pathogenic |
| KMT2B | IDSPG114 | AD | Missense | NP_055542.1:p.(Ala1727Ser) | Likely pathogenic |
| LAMA1 | IDSPG56 | AR | Frameshift insertion | NP_005550.2:p.(Gly2899GlufsTer18) | Pathogenic |
| LAMA1 | IDSPG56 | AR | Non-canonical splicing | NM_005559.3:c.1423-12C > G | Pathogenic |
| LONP1 | IDSPG166 | AR | Splicing | NM_004793.3:c.2154 + 1G > C | Pathogenic |
| LONP1 | IDSPG166 | AR | Missense | NP_004784.2:p.(Leu306Trp) | Likely pathogenic |
| PCYT2 | IDSPG27 | AR | Missense, splicing | NP_001171846.1:p.(Lys319Asn) | Likely pathogenic |
| PI4KA | IDSPG16 | AR | Frameshift deletion | NP_477352.3:p.(Thr2053SerfsTer4) | Pathogenic |
| PI4KA | IDSPG16 | AR | Frameshift deletion | NP_477352.3:p.(Glu1820del) | Pathogenic |
| PI4KA | IDSPG149 | AR | Missense | NP_477352.3:p.(Val1556Met) | Pathogenic |
| PI4KA | IDSPG149 | AR | Missense | NP_477352.3:p.(Thr1720Ile) | Pathogenic |
| PNPLA6 | IDSPG13 | AR | Splicing | NM_006702.4:c.598-2A > C | Pathogenic |
| PNPLA6 | IDSPG13 | AR | Missense | NP_001159586.1:p.(Ser1138Cys) | Likely pathogenic |
| POLG | IDSPG113 | AR | Non-canonical splicing | NM_002693.2:c.2266-64C > T | VUS |
| POLR3B | IDSPG66 | AD | Missense | NP_060552.4:p.(Ala69Gly) | VUS |
| REEP1 | IDSPG12 | AD | Missense | NP_075063.1:p.(Leu59His) | Likely pathogenic |
| SARS1 | IDSPG64 | AD | Splicing | NM_006513.4:c.969 + 1_969 + 3del | Pathogenic |
| SHMT2 | IDSPG26 | AR | Missense | NP_005403.2:p.(Pro499Ala) | Likely pathogenic |
| SLC35B2 | IDLNF68 | AR | Frameshift deletion | NP_835361.1:p.Arg408SerfsTer18 | Pathogenic |
| SPG7 | IDSPG23 | AR | Non frameshift deletion | NP_003110.1:p.(Val311del) | Likely pathogenic |
| SPG7 | IDSPG30 | AR | Missense | NP_003110.1:p.(Met667Ile)) | Likely pathogenic |
| SPTBN2 | IDSPG125 | AD | Frameshift deletion | NP_008877.1:p.(Asp1861ThrfsTer59) | Pathogenic |
| SVBP | IDSPG8,IDSPG46 | AR | Missense | NP_955374.1:p.(Leu49Pro) | Likely pathogenic |
| TAF1 | IDSPG71 | XL | Missense | NP_001273003.1:p.(Ala1732Ser) | VUS |
| UBAP1 | IDSPG76 | AD | Frameshift deletion | NP_057609.2:p.(Phe159Ter) | Pathogenic |
AD autosomal dominant, AR autosomal recessive, SNV single-nucleotide variant, VUS variant of unknown significance
List with the 36 SNV/INDEL new variants identified in our cohort, classification according to ACMG criteria