Additional clinical features found in syndromic XLMR
| Characteristic | Gene |
| Microcephaly | ATRX, MECP2, PQBP1, SMCX |
| Cleft lip and palate | PQBP1 |
| Congenital heart disease | PQBP1 |
| Spastic paraplegia | SLC16A2, ATRX, SMCX, MECP2 |
| Seizures | AGTR2, SYN1, ATRX, SLC6A8, ARX, SMCX |
| Absent speech | ATRX, SLC16A2, SLC6A8 |
| Cerebellar hypoplasia | OPHN1 |
| Short stature | PQBP1, SMCX |
| Autistic behaviour | NLGN3, NLGN4, AGTR2, SLC6A8 |
| Dystonia | ARX |
| Hypertelorism | RSK2 |
| Scoliosis | RSK2, ATRX |
| Abnormal thyroid function | SLC16A2 |