Table 2.
Characteristics of 14 variants identified in 11 patients with intellectual disability/developmental delay
| Pt | G | Age | Gene | Inh | Reference | CDS | Protein | Or | N/R | Pat | AF | GERP | CADD | SI | Po | MT | Co | PR | MC |
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| 1 | F | 16Y | EFNB1 | XL | NM_004429.4 | c.640C > T | p.(Gln214Ter) | d | N | LP | – | 5.2 | 38.0 | – | – | D | – | – | – |
| 2 | F | 1Y3M | MECP2 | XL | NM_004992.3 | c.808C > T | p.(Arg270Ter) | d | R | P | – | 3.8 | 36.0 | – | – | D | – | – | – |
| 3 | M | 17Y | ATRX | XL | NM_000489.3 | c.6257 T > C | p.(Leu2086Ser) | m | N | LP | – | 5.5 | 31.0 | – | D | D | – | D | D |
| 4 | M | 1Y7M | ATRX | XL | NM_000489.3 | c.6679G > T | p.(Asp2227Tyr) | d | N | LP | – | 5.7 | 33.0 | – | D | D | – | D | D |
| 5 | M | 1Y3M | NAA10 | XL | NM_003491.3 | c.248G > A | p.(Arg83His) | ma | N | LP | – | 5.0 | 34.0 | D | D | D | D | D | D |
| ANKRD11 | AD | NM_013275.5 | c.884G > A | p.(Ser295Asn) | d | N | VUS | – | 5.9 | 31.0 | D | D | D | D | N | T | |||
| 6 | F | 8Y4M | DHCR7 | AR | NM_001163817.1 | c.1376G > A | p.(Trp459Ter) | p | N | P | – | 5.1 | 42.0 | – | – | D | – | – | – |
| c.901C > A | p.(His301Asn) | m | N | LP | – | 3.6 | 25.7 | D | D | D | D | D | D | ||||||
| 7 | F | 9Y4M | LAMA1 | AR | NM_005559.3 | c.1711_1712del | p.(Ala571Pro fsTer8) | p | N | VUS | – | – | – | – | – | – | – | – | – |
| c.2755G > C | p.(Gly919Arg) | m | N | LP | 1.85e-3 | 5.5 | 29.2 | D | D | D | D | D | D | ||||||
| 8 | M | 4Y2M | NFIX | AD | NM_001271043.1 | c.613C > T | p.(Gln205Ter) | d | N | P | – | 4.6 | 39.0 | – | – | D | – | – | – |
| 9 | M | 3Y3M | UBE3A | AD | NM_000462.3 | c.403G > T | p.(Glu135Ter) | d | N | P | – | 5.8 | 37.0 | – | – | D | – | – | – |
| 10 | M | 1Y | ARID1B | AD | NM_001346813.1 | c.6212 T > A | p.(Ile2071Asn) | d | N | LP | – | 5.4 | 32.0 | D | D | D | D | D | D |
| 11 | F | 5Y5M | PTPRD | AD? | NM_002839.3 | c.5534 + 1G > A | p.(Ser1845Arg fsTer2) | d | N | – | – | −10.0 | – | – | – | D | – | – | – |
Note: Pt patient, G gender, Y years, M months, Inh inheritance pattern, XL X-linked, AD autosomal dominant, AR autosomal recessive, Or origin, m maternal, p paternal, d de novo, N novel, R reported, Pat pathogenicity, P pathogenic, LP likely pathogenic, VUS variant with uncertain significance, GERP GERP++RS score, D “probably damaging” in Polyphen2 or “deleterious” in other software, SI SIFT, Po PolyPhen2, MT MutationTaster, Co Condel, PR PROVEAN, MC M-CAP;a, the variant arose de novo in the patient’s mother