| Gene |
Chromosome |
Location |
Syndrome |
| AAAS | 12 | q13.13 | Microcephaly - other | |
| ABCD4 | 14 | q24.3 | Microcephaly - other | |
| ACADS | 12 | q24.31 | Short-chain acyl-CoA dehydrogenase (SCAD) deficiency | |
| ACSF3 | 16 | q24.3 | Combined malonic and methylmalonic aciduria (CMAMMA) | |
| ADSL | 22 | q13.1 | Microcephaly - other | |
| AFF4 | 5 | q31.1 | Microcephaly - other | |
| AKT3 | 1 | q44 | Microcephaly - other | |
| ALG12 | 22 | q13.33 | Microcephaly - other | |
| AMPD2 | 1 | p13.3 | Pontocerebellar hypoplasia | |
| ANKLE2 | 12 | q24 | Microcephaly - other | |
| ARFGEF2 | 20 | q13.13 | Periventricular heterotopia | |
| ARID1A | 1 | p36.11 | Microcephaly - other | |
| ARID1B | 6 | q25.3 | Microcephaly - other | |
| ASPM | 1 | q31 | Autosomal recessive primary microcephaly | |
| ATRX | 23 | q21.1 - al | Microcephaly - other | |
| ATRX | 23 | q21.1 | Microcephaly - other | |
| BRAT1 | 7 | p22.3 | Rigidity and multifocal seizure syndrome lethal neonatal (RMFSL) | |
| BRCA2 | 13 | q13.1 | Microcephaly - other | |
| BRIP1 | 17 | q23.2 | Microcephaly - other | |
| CASC5 | 15 | q14 | Microcephaly - other | |
| CASK | 23 | p11.4 | CASK-related intellectual disability | |
| CCBE1 | 18 | q21.32 | Microcephaly - other | |
| CDC6 | 17 | q21.3 | Meier-Gorlin syndrome | |
| CDK5RAP2 | 9 | q33.2 | Autosomal recessive primary microcephaly | |
| CDK6 | 7 | q21-q22 | Microcephaly 12 primary autosomal recessive (MCPH12) | |
| CDT1 | 16 | q24.3 | Meier-Gorlin syndrome | |
| CENPE | 4 | q24-q25 | Microcephaly 13 primary autosomal recessive (MCPH13) | |
| CENPJ | 13 | q12.12 | Autosomal recessive primary microcephaly | |
| CEP135 | 4 | q12 | Microcephaly 08 primary autosomal recessive (MCPH8) | |
| CEP152 | 15 | q21.1 | Autosomal recessive primary microcephaly | |
| CHMP1A | 16 | q24.3 | Pontocerebellar hypoplasia | |
| CHRNA1 | 2 | q31.1 | Microcephaly - other | |
| CHRND | 2 | q37.1 | Microcephaly - other | |
| CHRNG | 2 | q37.1 | Microcephaly - other | |
| CIT | 12 | q24 | Microcephaly - other | |
| CKAP2L | 2 | q14.1 | Microcephaly - other | |
| CLP1 | 11 | q12 | Pontocerebellar hypoplasia | |
| COG5 | 7 | q31 | Congenital disorder of glycosylation | |
| COL4A1 | 13 | q34 | Familial porencephaly | |
| CRIPT | 2 | p21 | Short stature with microcephaly and distinctive facies (SSMF) | |
| CTNND2 | 5 | p15.2 | Cri-du-chat (cat`s cry) syndrome | |
| CTSD | 11 | p15.5 | Congenital neuronal ceroid lipofuscinosis (NCL) | |
| CYB5R3 | 22 | q13.2 | Microcephaly - other | |
| DCX | 23 | q23 | Microcephaly - other | |
| DDX11 | 12 | p11 | Warsaw breakage syndrome | |
| DHCR7 | 11 | q13.4 | Microcephaly - other | |
| DISP1 | 1 | q41 | Microcephaly - other | |
| DPYD | 1 | p21.3 | Microcephaly - other | |
| EFTUD2 | 17 | q21.31 | Mandibulofacial dysostosis with microcephaly | |
| EHMT1 | 9 | q34.3 | Microcephaly - other | |
| EMG1 | 12 | p13.31 | Microcephaly - other | |
| ERCC6 | 10 | q11.23 | Cockayne syndrome | |
| ERCC8 | 5 | q12.1 | Cockayne syndrome | |
| ESCO2 | 8 | p21.1 | Microcephaly - other | |
| EXOSC3 | 9 | p11 | Pontocerebellar hypoplasia | |
| FANCA | 16 | q24.3 | Microcephaly - other | |
| FANCB | 23 | p22.2 | Microcephaly - other | |
| FANCC | 9 | q22.32 | Microcephaly - other | |
| FANCD2 | 3 | p25.3 | Microcephaly - other | |
| FANCE | 6 | p21.31 | Microcephaly - other | |
| FANCF | 11 | p14.3 | Microcephaly - other | |
| FANCG | 9 | p13.3 | Microcephaly - other | |
| FANCI | 15 | q26.1 | Microcephaly - other | |
| FANCL | 2 | p16.1 | Microcephaly - other | |
| FANCM | 14 | q21.2 | Microcephaly - other | |
| FAR1 | 11 | p15.3 | Microcephaly - other | |
| FAT4 | 4 | q28.1 | Microcephaly - other | |
| FGF8 | 10 | q24.32 | Microcephaly - other | |
| FH | 1 | q42.1 | Fumarase deficiency | |
| FLNA | 23 | q28 | Periventricular heterotopia | |
| FOXG1 | 14 | q12 | Microcephaly - other | |
| FOXH1 | 8 | q24.3 | Microcephaly - other | |
| FOXL2 | 3 | q22.3 | Microcephaly - other | |
| GJA1 | 6 | q22.31 | Oculodentodigital dysplasia | |
| GLI2 | 2 | q14.2 | Microcephaly - other | |
| GPHN | 14 | q22.3 | Molybdenum cofactor deficiency | |
| HBA1 | 16 | p13.3 | Alpha thalassemia | |
| HBA2 | 16 | p13.3 | Alpha thalassemia | |
| HCFC1 | 23 | q28 | Microcephaly - other | |
| HDAC8 | 23 | q13.1 | Microcephaly - other | |
| IER3IP1 | 18 | q12 | Microcephaly epilepsy and diabetes syndrome | |
| KAT6B | 10 | q22.2 | Microcephaly - other | |
| KCNT1 | 9 | q34.3 | Microcephaly - other | |
| KDM6A | 23 | p11.3 | Microcephaly - other | |
| KMT2D | 12 | q13.12 | Microcephaly - other | |
| KNL1 | 15 | q15.1 | Microcephaly - other | |
| LETM1 | 4 | p16.3 | Microcephaly - other | |
| LMBRD1 | 6 | q13 | Microcephaly - other | |
| MBD5 | 2 | q23.1 | Microcephaly - other | |
| MCPH1 | 8 | p23.1 | Autosomal recessive primary microcephaly | |
| MECP2 | 23 | q28.1 | Microcephaly - other | |
| MED17 | 11 | q14 | Microcephaly postnatal progressive with seizures and brain atrophy | |
| MFSD2A | 1 | p34.2 | Microcephaly - other | |
| MMACHC | 1 | P34.1 | Microcephaly - other | |
| MMSDHC | 2 | q23.2 | Microcephaly - other | |
| MOCS1 | 6 | p21.3 | Molybdenum cofactor deficiency | |
| MOCS2 | 5 | q11 | Molybdenum cofactor deficiency | |
| MSX1 | 4 | p16.2 | Microcephaly - other | |
| MT-ATP6 | 0 | 8527-9207 | Leigh syndrome | |
| MVK | 12 | q24.11 | Mevalonate kinase deficiency | |
| MYCN | 2 | p24.3 | Feingold syndrome | |
| NADK | 1 | p36.33 | Microcephaly - other | |
| NADK2 | 5 | p13.2 | Microcephaly - other | |
| NBN | 8 | q21 | Nijmegen breakage syndrome | |
| NDE1 | 16 | p13.11 | Microcephaly - other | |
| NIPBL | 5 | p13.2 | Microcephaly - other | |
| NODAL | 10 | q22.1 | Microcephaly - other | |
| NSD2 | 4 | p16.3 | Microcephaly - other | |
| OCA2 | 15 | q13.1 | Microcephaly - other | |
| ORC1 | 1 | p32 | Meier-Gorlin syndrome | |
| ORC4 | 2 | q22-23 | Meier-Gorlin syndrome | |
| ORC6 | 16 | q12 | Meier-Gorlin syndrome | |
| PAFAH1B1 | 17 | p13.3 | Microcephaly - other | |
| PAH | 12 | q23.2 | Microcephaly - other | |
| PALB2 | 16 | P12.2 | Microcephaly - other | |
| PCNT | 21 | q22.3 | Osteodysplastic primordial dwarfism type II | |
| PHC1 | 12 | q13 | Microcephaly 11 primary autosomal recessive (MCPH11) | |
| PHGDH | 1 | p12 | Phosphoglycerate dehydrogenase deficiency | |
| PLK4 | 4 | q28 | Microcephaly and chorioretinopathy autosomal recessive 2 (MCCRP2) | |
| PNKP | 19 | q13.3-13.4 | Microcephaly seizures and developmental delay (MCSZ) | |
| PPP1R15B | 1 | q32.1 | Microcephaly - other | |
| PPT1 | 1 | p32 | Infantile neuronal ceroid lipofuscinosis | |
| PQBP1 | 23 | p11.23 | Renpenning syndrome | |
| PTCH1 | 9 | q22.32 | Microcephaly - other | |
| PTRH2 | 17 | q23.1 | Microcephaly - other | |
| QARS | 3 | p21.31 | Microcephaly progressive with seizures cerebral/cerebellar atrophy (MSCCA) | |
| RAD21 | 8 | q24.11 | Microcephaly - other | |
| RAD51C | 17 | q22 | Microcephaly - other | |
| RAPSN | 11 | p11.2 | Microcephaly - other | |
| RARS2 | 6 | q16.1 | Pontocerebellar hypoplasia | |
| RNASEH2A | 19 | p13.13 | Microcephaly - other | |
| RNASEH2B | 13 | q14.3 | Microcephaly - other | |
| RNASEH2C | 11 | q13.1 | Microcephaly - other | |
| RNASET2 | 6 | q27 | Microcephaly - other | |
| RPL11 | 1 | p36.11 | Microcephaly - other | |
| RPL35A | 3 | q29 | Microcephaly - other | |
| RPL5 | 1 | p22.1 | Microcephaly - other | |
| RPS10 | 6 | p21.31 | Microcephaly - other | |
| RPS17 | 15 | q25.2 | Microcephaly - other | |
| RPS19 | 19 | q13.2 | Microcephaly - other | |
| RPS24 | 10 | q22.3 | Microcephaly - other | |
| RPS26 | 12 | q13.2 | Microcephaly - other | |
| RPS6KA3 | 23 | p22.1-.2 | Coffin-Lowry syndrome | |
| RPS7 | 2 | p25.3 | Microcephaly - other | |
| RRM2B | 8 | q22.3 | Microcephaly - other | |
| SAMHD1 | 20 | q11.23 | Microcephaly - other | |
| SASS6 | 1 | p21 | Microcephaly - other | |
| SCN1A | 2 | q24.3 | Microcephaly - other | |
| SEPSECS | 4 | p15.2 | Pontocerebellar hypoplasia | |
| SHH | 7 | q36.3 | Microcephaly - other | |
| SIX3 | 2 | p21 | Microcephaly - other | |
| SLC1A4 | 2 | p14 | Microcephaly - other | |
| SLC25A19 | 17 | q25.3 | Amish lethal microcephaly | |
| SLC2A1 | 1 | p34.2 | Microcephaly - other | |
| SLC6A8 | 23 | q28 | X-linked creatine deficiency | |
| SLC9A6 | 23 | q26.3 | Christianson syndrome | |
| SLX4 | 16 | p13.3 | Microcephaly - other | |
| SMARCA2 | 9 | p24.3 | Microcephaly - other | |
| SMARCA4 | 19 | p13.2 | Microcephaly - other | |
| SMARCB1 | 22 | q11.23 | Microcephaly - other | |
| SMARCE1 | 17 | q21.2 | Microcephaly - other | |
| SMC1A | 23 | p11.22 | Microcephaly - other | |
| SMC3 | 10 | q25.2 | Microcephaly - other | |
| SPR | 2 | p12-p14 | Sepiapterin reductase deficiency | |
| STAMBP | 2 | p13.1 | Microcephaly-capillary malformation syndrome | |
| STIL | 1 | p32 | Autosomal recessive primary microcephaly | |
| TBC1D24 | 16 | p13.3 | Microcephaly - other | |
| TCF4 | 18 | q21.2 | Microcephaly - other | |
| TDGF1 | 3 | p21.31 | Microcephaly - other | |
| TGIF1 | 18 | p11.31 | Microcephaly - other | |
| TREX1 | 3 | p21.31 | Microcephaly - other | |
| TRMT10A | 4 | q23 | Microcephaly short stature and impaired glucose metabolism | |
| TSEN2 | 3 | p25.2 | Pontocerebellar hypoplasia | |
| TSEN34 | 19 | q13.4 | Pontocerebellar hypoplasia | |
| TSEN54 | 17 | q25.1 | Pontocerebellar hypoplasia | |
| TUBA1A | 12 | q13.12 | Microcephaly - other | |
| TUBGCP4 | 15 | q15.3 | Microcephaly - other | |
| TUBGCP6 | 22 | q13.31-.33 | Microcephaly and chorioretinopathy autosomal recessive 1 (MCCRP1) | |
| UBE3A | 15 | q11.2 | Microcephaly - other | |
| UBE3B | 12 | q24.11 | Microcephaly - other | |
| UPB1 | 22 | q11.2 | Beta-ureidopropionase deficiency | |
| VPS13B | 8 | q22.2 | Cohen syndrome | |
| VRK1 | 14 | q32 | Pontocerebellar hypoplasia | |
| WDR62 | 19 | q13.12 | Autosomal recessive primary microcephaly | |
| XRCC4 | 5 | q14.2 | Microcephaly - other | |
| ZEB2 | 2 | q22.3 | Mowat-Wilson syndrome | |
| ZIC2 | 13 | q32.3 | Microcephaly - other | |
| ZNF335 | 20 | q13.12 | Microcephaly 10 primary autosomal recessive (MCPH10) | |