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 CDON gene CDON Expert Review Green;Illumina TruGenome Clinical Sequencing Services;NHS GMS;Radboud University Medical Center, Nijmegen Holoprosencephaly - NOT chromosomal Neurology MONOALLELIC, autosomal or pseudoautosomal, imprinted status unknown Holoprosencephaly 11, 614226;Holoprosencephaly 21802063 False 3 0;100;0 5.11 False ENSG00000064309 ENSG00000064309 HGNC:17104 CNOT1 gene CNOT1 Expert Review Green;Literature;NHS GMS Holoprosencephaly - NOT chromosomal Neurology MONOALLELIC, autosomal or pseudoautosomal, imprinted status unknown Holoprosencephaly 12, with or without pancreatic agenesis, OMIM:618500;holoprosencephaly 12 with or without pancreatic agenesis, MONDO:0032787 31006513;31006510;35481434 False 3 100;0;0 5.11 False Other ENSG00000125107 ENSG00000125107 HGNC:7877 DHCR7 gene DHCR7 Expert list;Expert Review Green;NHS GMS Holoprosencephaly - NOT chromosomal Neurology BIALLELIC, autosomal or pseudoautosomal Smith-Lemli-Opitz syndrome, 270400;alobar holoprosencephaly (HPE) 11562938;28805615;20104611;17001700;15013448 False 3 0;100;0 5.11 False ENSG00000172893 ENSG00000172893 HGNC:2860 DISP1 gene DISP1 Expert list;Expert Review Green;NHS GMS Holoprosencephaly - NOT chromosomal Neurology BOTH monoallelic and biallelic, autosomal or pseudoautosomal Holoprosencephaly 10, OMIM:621143;holoprosencephaly 10, MONDO:0976262 19184110;23542665;26748417;27363716;38529886 False 3 33;67;0 5.11 False ENSG00000154309 ENSG00000154309 HGNC:19711 FGF8 gene FGF8 Expert list;Expert Review Green;NHS GMS Holoprosencephaly - NOT chromosomal Neurology MONOALLELIC, autosomal or pseudoautosomal, NOT imprinted Holoprosencephaly 27363716 False 3 0;100;0 5.11 False ENSG00000107831 ENSG00000107831 HGNC:3686 FGFR1 gene FGFR1 Expert Review;Expert Review Green;NHS GMS Holoprosencephaly - NOT chromosomal Neurology MONOALLELIC, autosomal or pseudoautosomal, NOT imprinted Hypogonadotropic hypogonadism 2 with or without anosmia, OMIM:147950;Hartsfield syndrome, OMIM:615465 19504604;27363716;23154428;23812909;25394172 False 3 67;33;0 5.11 False ENSG00000077782 ENSG00000077782 HGNC:3688 GLI2 gene GLI2 Expert Review Green;Illumina TruGenome Clinical Sequencing Services;NHS GMS;Other;Radboud University Medical Center, Nijmegen;UKGTN Holoprosencephaly - NOT chromosomal Neurology MONOALLELIC, autosomal or pseudoautosomal, imprinted status unknown Holoprosencephaly-9;Holoprosencephaly;Holoprosencephaly 9, 610829 False 3 100;0;0 5.11 False ENSG00000074047 ENSG00000074047 HGNC:4318 KMT2D gene KMT2D Expert Review Green;Literature Holoprosencephaly - NOT chromosomal Neurology MONOALLELIC, autosomal or pseudoautosomal, NOT imprinted Kabuki syndrome 1, OMIM:147920 31846209;31282990;32773771 False 3 100;0;0 5.11 False ENSG00000167548 ENSG00000167548 HGNC:7133 PTCH1 gene PTCH1 Expert Review Green;Illumina TruGenome Clinical Sequencing Services;NHS GMS;Other;Radboud University Medical Center, Nijmegen;UKGTN Holoprosencephaly - NOT chromosomal Neurology MONOALLELIC, autosomal or pseudoautosomal, imprinted status unknown Holoprosencephaly 7, OMIM:610828 False 3 100;0;0 5.11 False ENSG00000185920 ENSG00000185920 HGNC:9585 RAD21 gene RAD21 Expert Review Green;Literature Holoprosencephaly - NOT chromosomal Neurology MONOALLELIC, autosomal or pseudoautosomal, NOT imprinted Cornelia de Lange syndrome 4, OMIM:614701;Holoprosencephaly with or without CdLS features;Septo-optic dysplasia 31334757;32696056 False 3 100;0;0 5.11 False ENSG00000164754 ENSG00000164754 HGNC:9811 SHH gene SHH Expert Review Green;NHS GMS;Other;Radboud University Medical Center, Nijmegen;UKGTN Holoprosencephaly - NOT chromosomal Neurology MONOALLELIC, autosomal or pseudoautosomal, imprinted status unknown Holoprosencephaly-3;Holoprosencephaly;Holoprosencephaly 3, 142945 False 3 100;0;0 5.11 False ENSG00000164690 ENSG00000164690 HGNC:10848 SIX3 gene SIX3 Expert Review Green;NHS GMS;Other;Radboud University Medical Center, Nijmegen;UKGTN Holoprosencephaly - NOT chromosomal Neurology MONOALLELIC, autosomal or pseudoautosomal, imprinted status unknown Holoprosencephaly-2;Holoprosencephaly;Holoprosencephaly 2, 157170 False 3 100;0;0 5.11 False ENSG00000138083 ENSG00000138083 HGNC:10889 SMC1A gene SMC1A Expert Review Green;Other Holoprosencephaly - NOT chromosomal Neurology X-LINKED: hemizygous mutation in males, monoallelic mutations in females may cause disease (may be less severe, later onset than males) Developmental and epileptic encephalopathy 85, with midline brain defects, OMIM:301044;Developmental and epileptic encephalopathy, 85, with or without midline brain defects, MONDO:0026771 28166369;31334757 False 3 100;0;0 5.11 False ENSG00000072501 ENSG00000072501 HGNC:11111 STAG2 gene STAG2 Expert Review Green;Other Holoprosencephaly - NOT chromosomal Neurology X-LINKED: hemizygous mutation in males, monoallelic mutations in females may cause disease (may be less severe, later onset than males) Holoprosencephaly 13, X-linked OMIM:301043 PMID: 31334757 False 3 100;0;0 5.11 False ENSG00000101972 ENSG00000101972 HGNC:11355 TGIF1 gene TGIF1 Expert Review Green;Illumina TruGenome Clinical Sequencing Services;NHS GMS;Other;Radboud University Medical Center, Nijmegen;UKGTN Holoprosencephaly - NOT chromosomal Neurology MONOALLELIC, autosomal or pseudoautosomal, imprinted status unknown Holoprosencephaly-4;Holoprosencephaly;Holoprosencephaly 4, 142946 False 3 100;0;0 5.11 False ENSG00000177426 ENSG00000177426 HGNC:11776 ZIC2 gene ZIC2 Expert Review Green;NHS GMS;Other;Radboud University Medical Center, Nijmegen;UKGTN Holoprosencephaly - NOT chromosomal Neurology MONOALLELIC, autosomal or pseudoautosomal, imprinted status unknown Holoprosencephaly-5;Holoprosencephaly;Holoprosencephaly 5, 609637 False 3 100;0;0 5.11 False ENSG00000043355 ENSG00000043355 HGNC:12873 DLL1 gene DLL1 Expert Review Amber;Literature;NHS GMS Holoprosencephaly - NOT chromosomal Neurology MONOALLELIC, autosomal or pseudoautosomal, NOT imprinted 27363716;21196490;29771000 False 2 0;100;0 5.11 False ENSG00000198719 ENSG00000198719 HGNC:2908 HS2ST1 gene HS2ST1 Expert Review Amber;Literature Holoprosencephaly - NOT chromosomal Neurology BIALLELIC, autosomal or pseudoautosomal Intellectual disability;dysmorphic features;congenital anomalies 33159882 False 2 0;100;0 5.11 False ENSG00000153936 ENSG00000153936 HGNC:5193 PLCH1 gene PLCH1 Expert Review Amber;Literature Holoprosencephaly - NOT chromosomal Neurology BIALLELIC, autosomal or pseudoautosomal Severe developmental delay;Brain malformations;Holoprosencephaly spectrum 33820834 False 2 0;100;0 5.11 False ENSG00000114805 ENSG00000114805 HGNC:29185 PPP1R12A gene PPP1R12A Expert list;Expert Review Amber Holoprosencephaly - NOT chromosomal Neurology MONOALLELIC, autosomal or pseudoautosomal, NOT imprinted Genitourinary and/or/brain malformation syndrome, 618820 31883643 False 2 50;50;0 5.11 False ENSG00000058272 ENSG00000058272 HGNC:7618 SUFU gene SUFU Expert Review;Expert Review Amber;NHS GMS Holoprosencephaly - NOT chromosomal Neurology MONOALLELIC, autosomal or pseudoautosomal, NOT imprinted Basal cell nevus syndrome, OMIM:109400 27363716;29771000 False 2 0;100;0 5.11 False ENSG00000107882 ENSG00000107882 HGNC:16466 FOXH1 gene FOXH1 Expert Review Red;Illumina TruGenome Clinical Sequencing Services;NHS GMS Holoprosencephaly - NOT chromosomal Neurology MONOALLELIC, autosomal or pseudoautosomal, imprinted status unknown Holoprosencephaly 27363716 False 1 0;100;0 5.11 False ENSG00000160973 ENSG00000160973 HGNC:3814 GCM2 gene GCM2 Expert Review Red;NHS GMS;Other;UKGTN Holoprosencephaly - NOT chromosomal Neurology MONOALLELIC, autosomal or pseudoautosomal, imprinted status unknown Hypoparathyroidism, familial isolated (AD) False 1 0;0;100 5.11 False ENSG00000124827 ENSG00000124827 HGNC:4198 NODAL gene NODAL Expert Review Red;Illumina TruGenome Clinical Sequencing Services;NHS GMS Holoprosencephaly - NOT chromosomal Neurology MONOALLELIC, autosomal or pseudoautosomal, imprinted status unknown Holoprosencephaly 27363716 False 1 0;100;0 5.11 False ENSG00000156574 ENSG00000156574 HGNC:7865 SMAD2 gene SMAD2 Expert Review Red;NHS GMS;Radboud University Medical Center, Nijmegen Holoprosencephaly - NOT chromosomal Neurology Unknown Unknown (Roessler (2008) Am J Hum Genet 83,18) 18538293 False 1 0;0;100 5.11 False ENSG00000175387 ENSG00000175387 HGNC:6768 ISCA-46743-Loss region ClinGen;Expert Review Green Holoprosencephaly - NOT chromosomal 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 3 100;0;0 5.11 False X 123900469 124102669 3 60 cnv_loss Xq25 region (includes STAG2) Loss