| 17-alpha-hydroxylase / 17,20-lyase deficiency | CYP17A1 |
| 17-beta hydroxysteroid dehydrogenase III deficiency | HSD17B3 |
| 2-methylbutyrylglycinuria | ACADSB |
| 3-beta-hydroxysteroid dehydrogenase deficiency (Adrenal hyperplasia, congenital) | HSD3B2 |
| 3-hydroxy-3-methylglutaryl-CoA lyase deficiency | HMGCL |
| 3-hydroxyacyl-CoA dehydrogenase deficiency | HADH |
| 3-Methylcrotonyl-CoA carboxylase 1 deficiency | MCCC1 |
| 3-Methylcrotonyl-CoA carboxylase 2 deficiency | MCCC2 |
| 3-methylglutaconic aciduria type III | OPA3 |
| 3-methylglutaconic aciduria with deafness, encephalopathy, and Leigh-like syndrome (MEGDEL) | SERAC1 |
| 46 XX sex reversal | NR5A1, SRY |
| 46 XY partial gonadal dysgenesis, with minifascicular neuropathy | DHH |
| 46 XY sex reversal | DHH, NR0B1, NR5A1, SRY, ZFPM2 |
| Aarskog-Scott syndrome | FGD1 |
| ABCD syndrome | EDNRB |
| Abetalipoproteinemia | MTTP |
| Achalasia-addisonianism-alacrimia syndrome | AAAS |
| Achondrogenesis, type IA | TRIP11 |
| Achondrogenesis, type IB | SLC26A2 |
| Achondrogenesis, type II | COL2A1 |
| Achondroplasia | FGFR3 |
| Achromatopsia | CNGB3 |
| Acro-dermato-ungual-lacrimal-tooth syndrome | TP63 |
| Acrocallosal syndrome | KIF7 |
| Acrodermatitis enteropathica, zink-deficiency type | SLC39A4 |
| Acromesomelic dysplasia, Hunter-Thompson type | GDF5 |
| Acromicric dysplasia | FBN1 |
| Adams-Oliver syndrome | NOTCH1 |
| Adenosine deaminase 2 deficiency (Vasculitis, autoinflammation, immunodeficiency, and hematologic defects syndrome) | CECR1 |
| Adenosine deaminase deficiency, severe combined immunodeficiency | ADA |
| Adrenal hyperplasia, congenital, due to steroid 11-beta-hydroxylase deficiency | CYP11B1 |
| Adrenal hypoplasia, congenital | NR0B1 |
| Adrenal insufficiency, congenital, with 46 XY sex reversal | CYP11A1 |
| Adrenocortical insufficiency | NR5A1 |
| Adrenoleukodystrophy | ABCD1 |
| Agammaglobulinemia | BTK |
| Agenesis of the corpus callosum with peripheral neuropathy | SLC12A6 |
| Aicardi-Goutieres syndrome | RNASEH2A, RNASEH2B, RNASEH2C, SAMHD1, TREX1 |
| Al-Awadi-Raas-Rothschild syndrome (Absence of ulna and fibula with severe limb deficiency) | WNT7A |
| Al-Gazali-Bakalinova syndrome | KIF7 |
| Alagille syndrome | JAG1 |
| Albinism, oculocutaneous type IA, IB | TYR |
| Albinism, oculocutaneous, type II | OCA2 |
| Albinism, oculocutaneous, type III | TYRP1 |
| Albinism, oculocutaneous, type IV | SLC45A2 |
| Alkaptonuria | HGD |
| Allan-Herndon-Dudley syndrome | SLC16A2 |
| Alopecia-intellectual disability syndrome | LSS |
| Alpha thalassemia X-linked intellectual disability syndrome | ATRX |
| Alpha-1-antitrypsin deficiency | SERPINA1 |
