Entity Name Entity type Gene Symbol Sources(; separated) Level4 Level3 Level2 Model_Of_Inheritance Phenotypes Omim Orphanet HPO Publications Description Flagged GEL_Status UserRatings_Green_amber_red version ready Mode of pathogenicity EnsemblId(GRch37) EnsemblId(GRch38) HGNC Position Chromosome Position GRCh37 Start Position GRCh37 End Position GRCh38 Start Position GRCh38 End STR Repeated Sequence STR Normal Repeats STR Pathogenic Repeats Region Haploinsufficiency Score Region Triplosensitivity Score Region Required Overlap Percentage Region Variant Type Region Verbose Name AGMO gene AGMO Expert Review Amber;Literature;NHS GMS Severe microcephaly Neurology BIALLELIC, autosomal or pseudoautosomal Autosomal recessive primary microcephaly (MCPH); primary microcephaly, developmental delay, short stature and intellectual disability 27000257;31555905 False 2 50;50;0 8.43 False ENSG00000187546 ENSG00000187546 HGNC:33784 AKT3 gene AKT3 Expert list;Expert Review Amber Severe microcephaly Neurology MONOALLELIC, autosomal or pseudoautosomal, NOT imprinted Microcephaly 32827175;31929334;30853971;30053339;25424989 False 2 0;100;0 8.43 False ENSG00000117020 ENSG00000117020 HGNC:393 AP4B1 gene AP4B1 Expert list;Expert Review Amber Severe microcephaly Neurology BIALLELIC, autosomal or pseudoautosomal Spastic paraplegia 47, autosomal recessive, OMIM:614066;Hereditary spastic paraplegia 47, MONDO:0013551 21620353;29193663;30337681;32166732 False 2 100;0;0 8.43 False ENSG00000134262 ENSG00000134262 HGNC:572 AP4M1 gene AP4M1 Expert list;Expert Review Amber Severe microcephaly Neurology BIALLELIC, autosomal or pseudoautosomal Spastic paraplegia 50, autosomal recessive, OMIM:612936;Hereditary spastic paraplegia 50, MONDO:0013048 28464862;24700674 False 2 100;0;0 8.43 False ENSG00000221838 ENSG00000221838 HGNC:574 AP4S1 gene AP4S1 Expert list;Expert Review Amber Severe microcephaly Neurology BIALLELIC, autosomal or pseudoautosomal Spastic paraplegia 52, autosomal recessive, OMIM:614067;Hereditary spastic paraplegia 52, MONDO:0013552 21620353;25552650;27444738;32216065;32979048 False 2 100;0;0 8.43 False ENSG00000100478 ENSG00000100478 HGNC:575 ARCN1 gene ARCN1 Expert list;Expert Review Amber Severe microcephaly Neurology MONOALLELIC, autosomal or pseudoautosomal, NOT imprinted Short stature, rhizomelic, with microcephaly, micrognathia, and developmental delay, OMIM:617164 27476655;31075182;33154040 False 2 100;0;0 8.43 False ENSG00000095139 ENSG00000095139 HGNC:649 ATP9A gene ATP9A Expert Review Amber;Literature Severe microcephaly Neurology BIALLELIC, autosomal or pseudoautosomal Neurodevelopmental delay;Postnatal microcephaly;Failure to thrive;Gastrointestinal symptoms;Neurodevelopmental disorder with poor growth and behavioral abnormalities, OMIM:620242 34379057;34764295;27626380 False 2 0;100;0 8.43 False ENSG00000054793 ENSG00000054793 HGNC:13540 BRD4 gene BRD4 Expert list;Expert Review Amber Severe microcephaly Neurology MONOALLELIC, autosomal or pseudoautosomal, NOT imprinted Cornelia de Lange syndrome 6, OMIM:620568 29379197;30302754 False 2 0;100;0 8.43 False ENSG00000141867 ENSG00000141867 HGNC:13575 C7orf43 gene C7orf43 Expert Review Amber;Literature Severe microcephaly Neurology BIALLELIC, autosomal or pseudoautosomal Microcephaly 25, primary, autosomal recessive, OMIM:618351;Microcephaly 25, primary, autosomal recessive, MONDO:0032694 30715179 False 2 0;100;0 8.43 False ENSG00000146826 ENSG00000146826 HGNC:25604 COG3 gene COG3 Expert Review Amber;Literature Severe microcephaly Neurology BIALLELIC, autosomal or pseudoautosomal Congenital disorder of glycosylation, type IIbb, OMIM:620546 37711075 False 2 0;100;0 8.43 False ENSG00000136152 ENSG00000136152 HGNC:18619 COPB1 gene COPB1 Expert Review Amber;Literature Severe microcephaly Neurology BIALLELIC, autosomal or pseudoautosomal Baralle-Macken syndrome, OMIM:619255;Severe intellectual disability;Cataracts;Variable microcephaly 33632302 False 2 0;0;0 8.43 False ENSG00000129083 ENSG00000129083 HGNC:2231 CPSF3 gene CPSF3 Expert Review Amber;Literature Severe microcephaly Neurology BIALLELIC, autosomal or pseudoautosomal Neurodevelopmental disorder with microcephaly, hypotonia, nystagmus, and seizures, OMIM:619876 35121750 False 2 0;100;0 8.43 False ENSG00000119203 ENSG00000119203 HGNC:2326 CRIPT gene CRIPT Expert Review Amber;NHS GMS;Other Severe microcephaly Neurology BIALLELIC, autosomal or pseudoautosomal Short stature with microcephaly and distinctive facies, 615789 27250922 Leduc et al., 2016 describe a female with biallelic mutations in CRIPT, presenting with short stature, dysmorphic features, microcephaly and hypopigmented macules. They detect a c.8G>A (p.C3Y) missense variant inherited from the mother in exon 1, and a 1,331?bp deletion encompassing exon 1, inherited from the father;24389050 Shaheen et al., 2014 report 2 cases: they examined cases with Short stature with microcephaly and distinctive facies (OMIM:615789). In a 3 year old boy they identified homozygosity for a 2bp insertion (c.133_134insGG) predicted to cause premature termination (Ala45GlyfsTer87). They also analyzed DNA from the first-cousin parents of a deceased affected male Saudi Arabian infant. The patient was presumed homozygous for a loss of function variant based on the heterozygous status of the parents. False 2 0;100;0 8.43 False ENSG00000119878 ENSG00000119878 HGNC:14312 EIPR1 gene EIPR1 Expert Review Amber;Literature Severe microcephaly Neurology BIALLELIC, autosomal or pseudoautosomal neurodevelopmental disorder, MONDO:0700092 41058046 False 2 100;0;0 8.43 False ENSG00000032389 ENSG00000032389 HGNC:12383 ERCC5 gene ERCC5 Expert Review Amber;Literature;NHS GMS Severe microcephaly Neurology BIALLELIC, autosomal or pseudoautosomal Cerebrooculofacioskeletal syndrome 3, 616570 (Microcephaly); Xeroderma pigmentosum, group G/Cockayne syndrome, 278780 24700531;32052936;32557569;9096355 (Retracted) False 2 0;100;0 8.43 False ENSG00000134899 ENSG00000134899 HGNC:3437 EXOC7 gene EXOC7 Expert list;Expert Review Amber Severe microcephaly Neurology BIALLELIC, autosomal or pseudoautosomal brain atrophy;seizures;developmental delay;microcephaly 32103185 False 2 100;0;0 8.43 False ENSG00000182473 ENSG00000182473 HGNC:23214 FILIP1 gene FILIP1 Expert Review Amber;Literature Severe microcephaly Neurology BIALLELIC, autosomal or pseudoautosomal microcephaly, MONDO:0001149 36943452;37163662 False 2 0;100;0 8.43 False ENSG00000118407 ENSG00000118407 HGNC:21015 GPKOW gene GPKOW Expert Review Amber;PAGE Additional Gene List Severe microcephaly Neurology X-LINKED: hemizygous mutation in males, monoallelic mutations in females may cause disease (may be less severe, later onset than males) microcephaly with intrauterine growth restriction 28612833;40221893 False 2 50;50;0 8.43 False ENSG00000068394 ENSG00000068394 HGNC:30677 KBTBD2 gene KBTBD2 Expert Review Amber;Literature Severe microcephaly Neurology BIALLELIC, autosomal or pseudoautosomal Neurodevelopmental disorder, MONDO:0700092 39313616 False 2 0;100;0 8.43 False ENSG00000170852 ENSG00000170852 HGNC:21751 LHX2 gene LHX2 Expert Review Amber;Literature Severe microcephaly Neurology MONOALLELIC, autosomal or pseudoautosomal, imprinted status unknown neurodevelopmental disorder 37057675 False 2 0;100;0 8.43 False ENSG00000106689 ENSG00000106689 HGNC:6594 LRRC8C gene LRRC8C Expert Review Amber;Literature Severe microcephaly Neurology MONOALLELIC, autosomal or pseudoautosomal, NOT imprinted TIMES syndrome, OMIM:621056 39623139 False 2 0;100;0 8.43 False Loss-of-function variants (as defined in pop up message) DO NOT cause this phenotype - please provide details in the comments ENSG00000171488 ENSG00000171488 HGNC:25075 MCM7 gene MCM7 Expert Review Amber;Literature Severe microcephaly Neurology BIALLELIC, autosomal or pseudoautosomal Meier-Gorlin syndrome;Microcephaly;Intellectual disability 33654309;34059554 False 2 0;100;0 8.43 False ENSG00000166508 ENSG00000166508 HGNC:6950 MED11 gene MED11 Expert Review Amber;Literature Severe microcephaly Neurology BIALLELIC, autosomal or pseudoautosomal Neurodegeneration with developmental delay, early respiratory failure, myoclonic seizures, and brain abnormalities, OMIM:620327 36001086 False 2 0;100;0 8.43 False ENSG00000161920 ENSG00000161920 HGNC:32687 MED17 gene MED17 Expert list;Expert Review Amber Severe microcephaly Neurology BIALLELIC, autosomal or pseudoautosomal Microcephaly, postnatal progressive, with seizures and brain atrophy, OMIM:613668 20950787;30345598;26004231;33756211 False 2 100;0;0 8.43 False ENSG00000042429 ENSG00000042429 HGNC:2375 MIR17HG gene MIR17HG Expert Review;Expert Review Amber Severe microcephaly Neurology MONOALLELIC, autosomal or pseudoautosomal, imprinted status unknown Feingold syndrome 2, 614326;FS2;Brachydactyly with short stature and microcephaly;Intellectual disability 21892160;19344873;25391829;26360630 False 2 0;100;0 8.43 False ENSG00000215417 ENSG00000215417 HGNC:23564 MPLKIP gene MPLKIP Expert Review Amber;Literature Severe microcephaly Neurology BIALLELIC, autosomal or pseudoautosomal microcephaly (disease), MONDO:0001149 25655951;25290684;26518168;25606444;26880286;29421601;30580289;30598092;16977596;33043633;33729667 False 2 0;100;0 8.43 False ENSG00000168303 ENSG00000168303 HGNC:16002 MRE11 gene MRE11 Expert Review Amber;Literature;NHS GMS Severe microcephaly Neurology BIALLELIC, autosomal or pseudoautosomal Nijmegen breakage syndrome-like severe microcephaly 21227757 False 2 0;100;0 8.43 False ENSG00000020922 ENSG00000020922 HGNC:7230 NAA20 gene NAA20 Expert Review Amber;Literature Severe microcephaly Neurology BIALLELIC, autosomal or pseudoautosomal autosomal recessive developmental delay, intellectual disability, and microcephaly 34230638 False 2 0;100;0 8.43 False ENSG00000173418 ENSG00000173418 HGNC:15908 NRDC gene NRDC Expert Review Amber;Literature Severe microcephaly Neurology BIALLELIC, autosomal or pseudoautosomal microcephaly, MONDO:0001149;neurodevelopmental disorder, MONDO:0700092;Optic neuropathy, HP:0001138 41734767 False 2 100;0;0 8.43 False ENSG00000078618 ENSG00000078618 HGNC:7995 OLA1 gene OLA1 Expert Review Amber;Literature Severe microcephaly Neurology BIALLELIC, autosomal or pseudoautosomal Ehlers-Danlos syndrome, hypermobility type, MONDO:0007523;neurodevelopmental disorder,MONDO:0700092;microcephaly, MONDO:0001149 41887223 False 2 100;0;0 8.43 False ENSG00000138430 ENSG00000138430 HGNC:28833 PALB2 gene PALB2 Expert Review Amber;NHS GMS;Other Severe microcephaly Neurology BIALLELIC, autosomal or pseudoautosomal Fanconi anemia, complementation group N, 610832 (microcephaly) False 2 33;67;0 8.43 False ENSG00000083093 ENSG00000083093 HGNC:26144 PCDHGC4 gene PCDHGC4 Expert Review Amber;Literature Severe microcephaly Neurology BIALLELIC, autosomal or pseudoautosomal Neurodevelopmental disorder with poor growth and skeletal anomalies, OMIM:619880 34244665 False 2 0;100;0 8.43 False ENSG00000242419 ENSG00000242419 HGNC:8717 PDCD6IP gene PDCD6IP Expert list;Expert Review Amber Severe microcephaly Neurology BIALLELIC, autosomal or pseudoautosomal Primary microcephaly 32286682 False 2 0;100;0 8.43 False ENSG00000170248 ENSG00000170248 HGNC:8766 PPP1R15B gene PPP1R15B Expert Review Amber;NHS GMS;Other Severe microcephaly Neurology BIALLELIC, autosomal or pseudoautosomal Microcephaly, short stature, and impaired glucose metabolism 2, OMIM:616817 27640355;26159176;26307080 False 2 0;100;0 8.43 False ENSG00000158615 ENSG00000158615 HGNC:14951 PSMC3 gene PSMC3 Expert Review Amber;Literature Severe microcephaly Neurology MONOALLELIC, autosomal or pseudoautosomal, NOT imprinted neurodevelopmental disorder, MONDO:0700092;microcephaly, MONDO:0001149 37256937 False 2 0;100;0 8.43 False ENSG00000165916 ENSG00000165916 HGNC:9549 PTPMT1 gene PTPMT1 Expert Review Amber;Literature Severe microcephaly Neurology BIALLELIC, autosomal or pseudoautosomal neurodevelopmental disorder, MONDO:0700092 39279645 False 2 0;100;0 8.43 False ENSG00000110536 ENSG00000110536 HGNC:26965 QARS gene QARS Expert Review Amber;Literature;NHS GMS;Radboud University Medical Center, Nijmegen;UKGTN Severe microcephaly Neurology BIALLELIC, autosomal or pseudoautosomal Microcephaly, progressive, seizures, and cerebral and cerebellar atrophy 615760 24656866 False 2 0;100;0 8.43 False ENSG00000172053 ENSG00000172053 HGNC:9751 RAD51C gene RAD51C Expert Review Amber;NHS GMS;Other Severe microcephaly Neurology BIALLELIC, autosomal or pseudoautosomal Fanconi anemia, complementation group O, 613390 False 2 50;50;0 8.43 False ENSG00000108384 ENSG00000108384 HGNC:9820 RMI1 gene RMI1 Expert Review Amber;Literature;NHS GMS Severe microcephaly Neurology BIALLELIC, autosomal or pseudoautosomal Bloom Syndrome-like Disorder 30057030 False 2 0;100;0 8.43 False ENSG00000178966 ENSG00000178966 HGNC:25764 RRP7A gene RRP7A Expert Review Amber;Literature Severe microcephaly Neurology BIALLELIC, autosomal or pseudoautosomal Microcephaly 33199730 False 2 0;100;0 8.43 False ENSG00000189306 ENSG00000189306 HGNC:24286 SNAPIN gene SNAPIN Expert Review Amber;Literature Severe microcephaly Neurology BIALLELIC, autosomal or pseudoautosomal Neurodevelopmental disorder with structural brain abnormalities and craniofacial abnormalities, OMIM:621393 26539891;40930097 False 2 0;100;0 8.43 False ENSG00000143553 ENSG00000143553 HGNC:17145 TAF13 gene TAF13 Expert Review Amber;Literature;NHS GMS;Other Severe microcephaly Neurology BIALLELIC, autosomal or pseudoautosomal "Mental retardation, autosomal recessive 60 617432" 28257693 False 2 0;100;0 8.43 False ENSG00000197780 ENSG00000197780 HGNC:11546 TM2D3 gene TM2D3 Expert Review Amber;Literature Severe microcephaly Neurology BIALLELIC, autosomal or pseudoautosomal Neurocardiorenal malformation syndrome, OMIM:621379 40449487 False 2 100;0;0 8.43 False ENSG00000184277 ENSG00000184277 HGNC:24128 TRA2B gene TRA2B Expert Review Amber;Literature Severe microcephaly Neurology MONOALLELIC, autosomal or pseudoautosomal, NOT imprinted Ramond-Elliott neurodevelopmental syndrome, OMIM:621421 36549593 False 2 0;100;0 8.43 False ENSG00000136527 ENSG00000136527 HGNC:10781 TRIP13 gene TRIP13 Expert Review Amber;Literature Severe microcephaly Neurology BIALLELIC, autosomal or pseudoautosomal Mosaic variegated aneuploidy syndrome 3, OMIM:617598 28553959 False 2 0;100;0 8.43 False ENSG00000071539 ENSG00000071539 HGNC:12307 TYW1 gene TYW1 Expert Review Amber;Literature Severe microcephaly Neurology BIALLELIC, autosomal or pseudoautosomal cerebral palsy, MONDO:0006497;microcephaly, MONDO:0001149 34077496 False 2 0;100;0 8.43 False ENSG00000198874 ENSG00000198874 HGNC:25598 UBE3A gene UBE3A Expert list;Expert Review Amber Severe microcephaly Neurology MONOALLELIC, autosomal or pseudoautosomal, paternally imprinted (maternal allele expressed) Angelman syndrome, OMIM:105830 2012134;9182785;10861661;10861661 False 2 50;50;0 8.43 False ENSG00000114062 ENSG00000114062 HGNC:12496 UGGT1 gene UGGT1 Expert Review Amber;Literature Severe microcephaly Neurology BIALLELIC, autosomal or pseudoautosomal congenital disorder of glycosylation, MONDO:0015286 40267907 False 2 0;100;0 8.43 False ENSG00000136731 ENSG00000136731 HGNC:15663 VPS50 gene VPS50 Expert Review Amber;Literature Severe microcephaly Neurology BIALLELIC, autosomal or pseudoautosomal Neonatal cholestatic liver disease;Failure to thrive;Profound global developmental delay;Postnatal microcephaly;Seizures;Abnormality of the corpus callosum 34037727 False 2 0;100;0 8.43 False ENSG00000004766 ENSG00000004766 HGNC:25956 WDR47 gene WDR47 Expert Review Amber;Literature Severe microcephaly Neurology BIALLELIC, autosomal or pseudoautosomal neurodevelopmental disorder, MONDO:0700092;microcephaly, MONDO:0001149 39609633 False 2 0;100;0 8.43 False ENSG00000085433 ENSG00000085433 HGNC:29141 YIF1B gene YIF1B Expert list;Expert Review Amber Severe microcephaly Neurology BIALLELIC, autosomal or pseudoautosomal Kaya-Barakat-Masson syndrome, OMIM:619125 32006098;26077767 False 2 100;0;0 8.43 False ENSG00000167645 ENSG00000167645 HGNC:30511 ZNF668 gene ZNF668 Expert Review Amber;Literature Severe microcephaly Neurology BIALLELIC, autosomal or pseudoautosomal DNA damage repair defect;microcephaly;growth deficiency;severe global developmental delay;brain malformation;facial dysmorphism 34313816;26633546 False 2 0;100;0 8.43 False ENSG00000167394 ENSG00000167394 HGNC:25821 ISCA-46300-Loss region Expert Review Amber;ClinGen Severe microcephaly Neurology MONOALLELIC, autosomal or pseudoautosomal, imprinted status unknown Developmental delays/intellectual disability, brain anomalies, craniofacial abnormalities, hypermobile joints, digital findings, and other variable clinical features 27399968;22180641 False 2 0;100;0 8.43 False 15 75339446 75680568 3 60 cnv_loss 15q24 recurrent region (LCR C-LCR D) (includes SIN3A) Loss ISCA-46743-Loss region Expert Review Amber;ClinGen Severe microcephaly Neurology X-LINKED: hemizygous mutation in males, monoallelic mutations in females may cause disease (may be less severe, later onset than males) 30158690;33758131 False 2 0;100;0 8.43 False X 123900469 124102669 3 60 cnv_loss Xq25 region (includes STAG2) Loss