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 CDCA8 gene CDCA8 Expert Review Green;Genomics England PanelApp Congenital hypothyroidism Thyroid disorders Endocrine disorders BOTH monoallelic and biallelic, autosomal or pseudoautosomal Congenital hypothyroidism, MONDO:0018612, CDCA8-related 28025328;29546359 False 3 100;0;0 0.43 True Other ENSG00000134690 ENSG00000134690 HGNC:14629 DUOX2 gene DUOX2 Expert Review Green;Genomics England PanelApp Congenital hypothyroidism Thyroid disorders Endocrine disorders BOTH monoallelic and biallelic (but BIALLELIC mutations cause a more SEVERE disease form), autosomal or pseudoautosomal Thyroid dyshormonogenesis 6, 607200 24423310;16134168;27525530 (Nicholas et al.,2016) identify a monogenic and digenic basis of disease;12110737;27166716 False 3 100;0;0 0.43 True ENSG00000140279 ENSG00000140279 HGNC:13273 DUOXA2 gene DUOXA2 Expert Review Green;Genomics England PanelApp Congenital hypothyroidism Thyroid disorders Endocrine disorders BOTH monoallelic and biallelic, autosomal or pseudoautosomal Thyroid dyshormonogenesis 5, 274900 27349010;21367925;28100324;26758695;18042646 False 3 100;0;0 0.43 True ENSG00000140274 ENSG00000140274 HGNC:32698 FOXE1 gene FOXE1 Expert Review Green;Genomics England PanelApp Congenital hypothyroidism Thyroid disorders Endocrine disorders BIALLELIC, autosomal or pseudoautosomal Bamforth Lazarus syndrome, MIM#241850 (hypothyroidism);Hypothyroidism, Thyroidal Or Athyroidal, With Spiky Hair And Cleft Palate, 241850 20484477;9697705;24219130 (gain-of-function mutation);9697704 (mouse model);28928994;28455095;12165566;16882747 False 3 100;0;0 0.43 True Other - please provide details in the comments ENSG00000178919 ENSG00000178919 HGNC:3806 GLIS3 gene GLIS3 Expert Review Green;Genomics England PanelApp Congenital hypothyroidism Thyroid disorders Endocrine disorders BIALLELIC, autosomal or pseudoautosomal Diabetes mellitus, neonatal, with congenital hypothyroidism, MIM# 610199 26259131;16715098;30555422;28253873 False 3 100;0;0 0.43 True ENSG00000107249 ENSG00000107249 HGNC:28510 GNAS gene GNAS Expert Review Green;Genomics England PanelApp Congenital hypothyroidism Thyroid disorders Endocrine disorders MONOALLELIC, autosomal or pseudoautosomal, paternally imprinted (maternal allele expressed) Pseudohypoparathyroidism Ia, MIM#103580 (Hypothyroidism) 27922245;17299070;23412865;27467896 False 3 100;0;0 0.43 True ENSG00000087460 ENSG00000087460 HGNC:4392 HESX1 gene HESX1 Expert Review Green;Genomics England PanelApp Congenital hypothyroidism Thyroid disorders Endocrine disorders BOTH monoallelic and biallelic (but BIALLELIC mutations cause a more SEVERE disease form), autosomal or pseudoautosomal Pituitary hormone deficiency, combined, 5, MIM# 182230 9620767;26416826 (2015 review);11136712 False 3 100;0;0 0.43 True ENSG00000163666 ENSG00000163666 HGNC:4877 IGSF1 gene IGSF1 Expert Review Green;Genomics England PanelApp Congenital hypothyroidism Thyroid disorders Endocrine disorders X-LINKED: hemizygous mutation in males, monoallelic mutations in females may cause disease (may be less severe, later onset than males) Hypothyroidism, central, and testicular enlargement, MIM# 300888 27310681;30086211;24108313 (reports that a subset of female carriers show central hypothyroidism).;26840047;27762734;23143598 False 3 100;0;0 0.43 True ENSG00000147255 ENSG00000147255 HGNC:5948 IRS4 gene IRS4 Expert Review Green;Genomics England PanelApp Congenital hypothyroidism Thyroid disorders Endocrine disorders X-LINKED: hemizygous mutation in males, biallelic mutations in females Hypothyroidism, congenital, nongoitrous, 9, MIM# 301035 30061370;10644546 False 3 100;0;0 0.43 True ENSG00000133124 ENSG00000133124 HGNC:6128 IYD gene IYD Expert Review Green;Genomics England PanelApp Congenital hypothyroidism Thyroid disorders Endocrine disorders BOTH monoallelic and biallelic, autosomal or pseudoautosomal childhood/adolescent onset hypothyroidism;Thyroid dyshormonogenesis 4, 274800;normal iodide organification;Congenital hypothyroidism;raised urinary MIT and DIT;goitre 24629858 (Review);18765512;PMID:18434651 (Moreno et al., 2008): 2 missense mutations and a 3bp deletion were identified in 4 patients with hypothryoidism from 3 unrelated families;PMID:22535972 (Burniat et al., 2012) identified a homozygous IYD mutation in a child born to first-cousins. A 4.5-yr-old unaffected sister was found homozygous for the mutation False 3 0;0;0 0.43 False ENSG00000009765 ENSG00000009765 HGNC:21071 KMT2D gene KMT2D Expert Review;Expert Review Green Congenital hypothyroidism Thyroid disorders Endocrine disorders MONOALLELIC, autosomal or pseudoautosomal, NOT imprinted Branchial arch abnormalities, choanal atresia, athelia, hearing loss, and hypothyroidism syndrome (BCAHH), MIM#620186 31949313;32083401 False 3 100;0;0 0.43 True ENSG00000167548 ENSG00000167548 HGNC:7133 LHX3 gene LHX3 Expert Review Green;Genomics England PanelApp Congenital hypothyroidism Thyroid disorders Endocrine disorders BIALLELIC, autosomal or pseudoautosomal "Pituitary hormone deficiency, combined, 3, 221750;sensorineural deafness;GH, TSH, LH, FSH, PRL deficiency;limited neck rotation;short cervical spine;anterior pituitary may be normal, hypoplastic or enlarged" 18407919;10835633;26416826 (2015 review);21249393 False 3 0;0;0 0.43 False ENSG00000107187 ENSG00000107187 HGNC:6595 LHX4 gene LHX4 Expert Review Green;Genomics England PanelApp Congenital hypothyroidism Thyroid disorders Endocrine disorders MONOALLELIC, autosomal or pseudoautosomal, NOT imprinted anterior pituitary hypoplasia;GH, TSH, ACTH, variable gonadotrophin deficiencies;etopic posterior pituitary;Pituitary hormone deficiency, combined, 4, 262700;cerebellar abnormalities 25955177;26416826 (2015 review);11567216 False 3 0;0;0 0.43 False ENSG00000121454 ENSG00000121454 HGNC:21734 NKX2-1 gene NKX2-1 Expert Review Green;Genomics England PanelApp Congenital hypothyroidism Thyroid disorders Endocrine disorders MONOALLELIC, autosomal or pseudoautosomal, NOT imprinted Choreoathetosis And Congenital Hypothyroidism With Or Without Pulmonary Dysfunction, 610978 11854319;24714694 False 3 0;0;0 0.43 True ENSG00000136352 ENSG00000136352 HGNC:11825 NKX2-5 gene NKX2-5 Expert Review Green;Genomics England PanelApp Congenital hypothyroidism Thyroid disorders Endocrine disorders MONOALLELIC, autosomal or pseudoautosomal, NOT imprinted Hypothyroidism, congenital nongoitrous, 5, 225250;thyrioid ectopy, thyroid agenesis, congenital heart disease 16418214 False 3 100;0;0 0.43 True Other - please provide details in the comments ENSG00000183072 ENSG00000183072 HGNC:2488 OTX2 gene OTX2 Expert Review Green;Genomics England PanelApp Congenital hypothyroidism Thyroid disorders Endocrine disorders MONOALLELIC, autosomal or pseudoautosomal, NOT imprinted Pituitary hormone deficiency, combined, 6, MIM# 613986 18628516;26416826;18728160;35320640;33950863 False 3 100;0;0 0.43 True ENSG00000165588 ENSG00000165588 HGNC:8522 PAX8 gene PAX8 Expert Review Green;Genomics England PanelApp Congenital hypothyroidism Thyroid disorders Endocrine disorders MONOALLELIC, autosomal or pseudoautosomal, NOT imprinted Hypothyroidism, Congenital, Nongoitrous, 2, 218700;thyroid dysgenesis;Congenital hypothyroidism;thyroid hypoplasia;Hypothyroidism, congenital, due to thyroid dysgenesis or hypoplasia, 218700;eutopic gland-in-situ;urogenital tract malformations PMID:23647375;PMID:9590296 False 3 100;0;0 0.43 False ENSG00000125618 ENSG00000125618 HGNC:8622 POU1F1 gene POU1F1 Expert Review Green;Genomics England PanelApp Congenital hypothyroidism Thyroid disorders Endocrine disorders BOTH monoallelic and biallelic, autosomal or pseudoautosomal congenital hypothyroidism;Pituitary hormone deficiency, combined, 1, 613038 (Hypopthyroidism) 16060904;11297581;26416826 False 3 0;0;0 0.43 False Other - please provide details in the comments ENSG00000064835 ENSG00000064835 HGNC:9210 PRKAR1A gene PRKAR1A Expert Review Green;Genomics England PanelApp Congenital hypothyroidism Thyroid disorders Endocrine disorders MONOALLELIC, autosomal or pseudoautosomal, NOT imprinted Acrodysostosis, mild hormone resistance (TSH, PTH, GPCR-cAMP signalling hormones;Acrodysostosis 1, with or without hormone resistance, 101800 22464250;21651393 False 3 0;0;0 0.43 False Other - please provide details in the comments ENSG00000108946 ENSG00000108946 HGNC:9388 PROP1 gene PROP1 Expert Review Green;Genomics England PanelApp Congenital hypothyroidism Thyroid disorders Endocrine disorders BIALLELIC, autosomal or pseudoautosomal Hypoplastic or normal anterior pituitary although there have been reports of an enlarged anterior pituitary at initial scanning in childhood with spontaneous involution over time;GH, TSH, LH, FSH, PRL deficiency with variable age of onset, evolving ACTH deficiency;Commonest cause of combined pituitary hormone deficit without extra pituitary manifestations;Pituitary hormone deficiency, combined, 2, 262600 15126542;16984240;9768691;15472175;26416826 (2015 review);23652424 False 3 0;0;0 0.43 False ENSG00000175325 ENSG00000175325 HGNC:9455 SECISBP2 gene SECISBP2 Expert Review Green;Genomics England PanelApp Congenital hypothyroidism Thyroid disorders Endocrine disorders BIALLELIC, autosomal or pseudoautosomal Thyroid hormone metabolism, abnormal, MIM# 609698 20501692;16228000;22247018;24629861;22986150;19602558;21084748 False 3 100;0;0 0.43 True ENSG00000187742 ENSG00000187742 HGNC:30972 SLC16A2 gene SLC16A2 Expert Review Green;Genomics England PanelApp Congenital hypothyroidism Thyroid disorders Endocrine disorders X-LINKED: hemizygous mutation in males, biallelic mutations in females "Allan-Herndon-Dudley syndrome, MIM# 300523" 24847459 False 3 0;0;0 0.43 True ENSG00000147100 ENSG00000147100 HGNC:10923 SLC26A4 gene SLC26A4 Expert Review Green;Genomics England PanelApp Congenital hypothyroidism Thyroid disorders Endocrine disorders BIALLELIC, autosomal or pseudoautosomal enlarged vestibular aqueduct;Sensorineural deafness;partial iodide organification defect;mild hypothyroidism;Pendred syndrome, 274600 (congenital deafness and thyroid goitre);goitre;Mondini defect 11932316;9398842 False 3 0;0;0 0.43 False ENSG00000091137 ENSG00000091137 HGNC:8818 SLC26A7 gene SLC26A7 Expert Review Green;Genomics England PanelApp Congenital hypothyroidism Thyroid disorders Endocrine disorders BIALLELIC, autosomal or pseudoautosomal Congenital hypothyroidism, MONDO:0018612, SLC26A7-related 30333321;29546359;34780050;32486989;31372509 False 3 100;0;0 0.43 True ENSG00000147606 ENSG00000147606 HGNC:14467 SLC5A5 gene SLC5A5 Expert Review Green;Genomics England PanelApp Congenital hypothyroidism Thyroid disorders Endocrine disorders BIALLELIC, autosomal or pseudoautosomal Apparent athyreosis on nuclear medicine scan;childhood onset hypothyroidism;goitre;Thyroid dyshormonogenesis 1, 274400;HYPOTHYROIDISM, CONGENITAL, DUE TO DYSHORMONOGENESIS, 1 9171822;16418213 False 3 0;0;0 0.43 False ENSG00000105641 ENSG00000105641 HGNC:11040 TBL1X gene TBL1X Expert Review Green;Genomics England PanelApp Congenital hypothyroidism Thyroid disorders Endocrine disorders X-LINKED: hemizygous mutation in males, monoallelic mutations in females may cause disease (may be less severe, later onset than males) isolated mild-moderate central hypothyroidism;Hypothyroidism, congenital, nongoitrous, 8, 301033 27603907;30591955 False 3 0;0;0 0.43 False ENSG00000101849 ENSG00000101849 HGNC:11585 TG gene TG Expert Review Green;Genomics England PanelApp Congenital hypothyroidism Thyroid disorders Endocrine disorders BIALLELIC, autosomal or pseudoautosomal Congenital hypothyroidism;Thyroid dyshormonogenesis 3, 274700;TDH3;low thyroglobulin, goitre 27525530 (Nicholas et al.,2016) identify a monogenic and polygenic basis of disease.;23164529 False 3 0;0;0 0.43 False ENSG00000042832 ENSG00000042832 HGNC:11764 THRA gene THRA Expert Review Green;Genomics England PanelApp Congenital hypothyroidism Thyroid disorders Endocrine disorders MONOALLELIC, autosomal or pseudoautosomal, NOT imprinted Congenital hypothyroidism or thyroid agenesis;delayed dentition;macrocephaly;Hypothyroidism, Congenital, Nongoitrous, 6, 614450;Hypothyroidism, congenital, nongoitrous, 6, 614450;neurodevelopmental delay;Resistance to thyroid hormone;constipation;skeletal dysplasia;growth retardation;macrocytic anaemia 27144938;22168587;27381958;2567082;24847459;23940126;22494134 False 3 0;0;0 0.43 False ENSG00000126351 ENSG00000126351 HGNC:11796 THRB gene THRB Expert Review Green;Genomics England PanelApp Congenital hypothyroidism Thyroid disorders Endocrine disorders BOTH monoallelic and biallelic, autosomal or pseudoautosomal HYPERTHYROIDISM, FAMILIAL, DUE TO INAPPROPRIATE THYROTROPIN SECRETION;THYROID HORMONE RESISTANCE, GENERALIZED, AUTOSOMAL RECESSIVE;THYROID HORMONE RESISTANCE, GENERALIZED, AUTOSOMAL DOMINANT;Thyroid hormone resistance, autosomal recessive, 274300;Thyroid Hormone Resistance, Selective Pituitary;Resistance to thyroid hormone (RTH);145650;PRTH;REFETOFF SYNDROME;THYROID HORMONE RESISTANCE, SELECTIVE PITUITARY;thyroid hormone unresponsiveness, generalized RTH, RTH beta;Thyroid Hormone Resistance (monoallelic);Thyroid hormone resistance, 188570;Thyroid hormone resistance, selective pituitary, 145650;THYROID HORMONE UNRESPONSIVENESS;THYROID HORMONE UNRESPONSIVENESS HYPERTHYROXINEMIA, FAMILIAL EUTHYROID, SECONDARY TO PITUITARY AND PERIPHERAL RESISTANCE TO THYROID HORMONES;Refetoff syndrome;GRTH 24847459 False 3 0;0;0 0.43 False ENSG00000151090 ENSG00000151090 HGNC:11799 TPO gene TPO Expert Review Green;Genomics England PanelApp Congenital hypothyroidism Thyroid disorders Endocrine disorders BIALLELIC, autosomal or pseudoautosomal Congenital hypothyroidism;Iodide organification defect;goitre;TDH2A;Thyroid dyshormonogenesis 2A, 274500 12938097;27166716;8964831;11061528;8027236;27525530 (Nicholas et al.,2016) identify a monogenic basis of disease False 3 0;0;0 0.43 False ENSG00000115705 ENSG00000115705 HGNC:12015 TRHR gene TRHR Expert Review Green;Genomics England PanelApp Congenital hypothyroidism Thyroid disorders Endocrine disorders BIALLELIC, autosomal or pseudoautosomal Hypothyroidism, congenital, nongoitrous, 7, MIM# 618573 PMID: 19213692;PMID: 9141550 False 3 100;0;0 0.43 True ENSG00000174417 ENSG00000174417 HGNC:12299 TSHB gene TSHB Expert Review Green;Genomics England PanelApp Congenital hypothyroidism Thyroid disorders Endocrine disorders BIALLELIC, autosomal or pseudoautosomal Congenital hypothyroidism;Hypothryoidism, congenital, nongoitrous 4, 275100;severe isolated central hypothyroidism 2792087;27362444 False 3 0;0;0 0.43 False ENSG00000134200 ENSG00000134200 HGNC:12372 TSHR gene TSHR Expert Review Green;Genomics England PanelApp Congenital hypothyroidism Thyroid disorders Endocrine disorders BOTH monoallelic and biallelic (but BIALLELIC mutations cause a more SEVERE disease form), autosomal or pseudoautosomal Hypothyroidism, congenital, nongoitrous, 1 275200;thyroid dysgenesis;Congenital hypothyroidism;thyroid hypoplasia;compensated hypothryoidism;subclinical hypothyroidism;Hypothyroidism, Congenital, Nongoitrous, 1, 275200;eutopic gland-in-situ;TSH resistance 16060907 (Camilot et al., 2005 report subclinical hypothyroid subjects with heterozygous substitutions;22876533;7528344;PMID:17526952 (Kanda et al., 2006) examine Japanese patients homozygous and heterozygous for the R450H mutation in the TSHR gene. Homozygous subjects displayed mild hypothyroidism/ Heterozygous patients also demonstrated hypothyroidism, but less severe than that of homozygous subjects.;27525530 (Nicholas et al.,2016) identify a monogenic basis of disease.;PMID:14725684 (Park et al. 2004) suggest that heterozygosity for an inactivating TSHR mutation may be associated with compensated hypothyroidism and thyroid hypoplasia False 3 0;0;0 0.43 False ENSG00000165409 ENSG00000165409 HGNC:12373 TUBB1 gene TUBB1 Expert Review Green;Genomics England PanelApp Congenital hypothyroidism Thyroid disorders Endocrine disorders BOTH monoallelic and biallelic, autosomal or pseudoautosomal Macrothrombocytopenia, autosomal dominant, TUBB1-related, OMIM # 613112;Primary congenital hypothyroidism, thyroid dysgenesis, macroplatelets 30446499;31642429 False 3 100;0;0 0.43 True ENSG00000101162 ENSG00000101162 HGNC:16257 DUOX1 gene DUOX1 Expert Review Amber;Literature Congenital hypothyroidism Thyroid disorders Endocrine disorders BOTH monoallelic and biallelic, autosomal or pseudoautosomal congenital hypothyroidism, No OMIM # PMID: 29650690 False 2 0;0;0 0.43 True ENSG00000137857 ENSG00000137857 HGNC:3062 DUOXA1 gene DUOXA1 Expert Review Amber;Literature Congenital hypothyroidism Thyroid disorders Endocrine disorders BOTH monoallelic and biallelic, autosomal or pseudoautosomal congenital hypothyroidism, No OMIM # PMID: 29650690 False 2 0;100;0 0.43 True ENSG00000140254 ENSG00000140254 HGNC:26507 GATA6 gene GATA6 Expert Review Amber;Literature Congenital hypothyroidism Thyroid disorders Endocrine disorders MONOALLELIC, autosomal or pseudoautosomal, NOT imprinted Pancreatic agenesis and congenital heart defects, OMIM# 600001 PMID: 31271559, 32207556 False 2 0;100;0 0.43 True ENSG00000141448 ENSG00000141448 HGNC:4174 TTF1 gene TTF1 Expert Review Amber;Literature Congenital hypothyroidism Thyroid disorders Endocrine disorders MONOALLELIC, autosomal or pseudoautosomal, NOT imprinted congenital hypothyroidism, thyroid dysgenesis, No OMIM # PMID: 30022773 False 2 0;100;0 0.43 True ENSG00000125482 ENSG00000125482 HGNC:12397